Updated on 2022/12/01

写真a

 
ABE Takashi
 
Organization
Academic Assembly Institute of Science and Technology JOUHOU DENSHI KOUGAKU KEIRETU Professor
Graduate School of Science and Technology Electrical and Information Engineering Professor
Faculty of Engineering Department of Engineering Professor
Title
Professor
External link

Degree

  • 博士(理学) ( 2004.3   総合研究大学院大学 )

Research Areas

  • Informatics / Life, health and medical informatics

  • Life Science / Genome biology

Research History (researchmap)

  • Niigata University   Faculty of Engineering Department of Engineering   Professor

    2020.10

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  • Niigata University   Graduate School of Science and Technology Specialized Course Electrical and Information Engineering   Professor

    2020.10

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  • Niigata University   Faculty of Engineering Department of Engineering   Associate Professor

    2017.4 - 2020.9

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  • Niigata University   Graduate School of Science and Technology Electrical and Information Engineering   Associate Professor

    2011.10 - 2020.9

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  • Niigata University   Faculty of Engineering Department of Information Engineering Computer Science   Associate Professor

    2011.10 - 2017.3

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  • Nagahama Institute of Bio-Science and Technology   Assistant Professor

    2007.4 - 2011.9

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  • National Institute of Genetics   Assistant Professor

    2004.4 - 2007.3

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  • The Graduate University for Advanced Studies   School of Life Science, Department of Genetics   Assistant Professor

    2004.4 - 2007.3

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  • Kyowa Hakko Co., Ltd.   Researcher

    2001.4 - 2004.3

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Research History

  • Niigata University   Faculty of Engineering Department of Engineering   Professor

    2020.10

  • Niigata University   Faculty of Engineering Department of Engineering   Associate Professor

    2017.4 - 2020.9

  • Niigata University   Graduate School of Science and Technology Electrical and Information Engineering   Associate Professor

    2011.10

  • Niigata University   Graduate School of Science and Technology Electrical and Information Engineering   Associate Professor

    2011.10

  • Niigata University   Abolition organization Computer Science   Associate Professor

    2011.10 - 2017.3

Professional Memberships

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Papers

  • Comparative genomic analysis of the human genome and six bat genomes using unsupervised machine learning: Mb-level CpG and TFBS islands Reviewed

    Yuki Iwasaki, Toshimichi Ikemura, Kennosuke Wada, Yoshiko Wada, Takashi Abe

    BMC Genomics   23 ( 1 )   2022.12

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    Authorship:Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    Abstract

    Background

    Emerging infectious disease-causing RNA viruses, such as the SARS-CoV-2 and Ebola viruses, are thought to rely on bats as natural reservoir hosts. Since these zoonotic viruses pose a great threat to humans, it is important to characterize the bat genome from multiple perspectives. Unsupervised machine learning methods for extracting novel information from big sequence data without prior knowledge or particular models are highly desirable for obtaining unexpected insights. We previously established a batch-learning self-organizing map (BLSOM) of the oligonucleotide composition that reveals novel genome characteristics from big sequence data.

    Results

    In this study, using the oligonucleotide BLSOM, we conducted a comparative genomic study of humans and six bat species. BLSOM is an explainable-type machine learning algorithm that reveals the diagnostic oligonucleotides contributing to sequence clustering (self-organization). When unsupervised machine learning reveals unexpected and/or characteristic features, these features can be studied in more detail via the much simpler and more direct standard distribution map method. Based on this combined strategy, we identified the Mb-level enrichment of CG dinucleotide (Mb-level CpG islands) around the termini of bat long-scaffold sequences. In addition, a class of CG-containing oligonucleotides were enriched in the centromeric and pericentromeric regions of human chromosomes. Oligonucleotides longer than tetranucleotides often represent binding motifs for a wide variety of proteins (e.g., transcription factor binding sequences (TFBSs)). By analyzing the penta- and hexanucleotide composition, we observed the evident enrichment of a wide range of hexanucleotide TFBSs in centromeric and pericentromeric heterochromatin regions on all human chromosomes.

    Conclusion

    Function of transcription factors (TFs) beyond their known regulation of gene expression (e.g., TF-mediated looping interactions between two different genomic regions) has received wide attention. The Mb-level TFBS and CpG islands are thought to be involved in the large-scale nuclear organization, such as centromere and telomere clustering. TFBSs, which are enriched in centromeric and pericentromeric heterochromatin regions, are thought to play an important role in the formation of nuclear 3D structures. Our machine learning-based analysis will help us to understand the differential features of nuclear 3D structures in the human and bat genomes.

    DOI: 10.1186/s12864-022-08664-9

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    Other Link: https://link.springer.com/article/10.1186/s12864-022-08664-9/fulltext.html

  • AI-based search for convergently expanding, advantageous mutations in SARS-CoV-2 by focusing on oligonucleotide frequencies Reviewed

    Toshimichi Ikemura, Yuki Iwasaki, Kennosuke Wada, Yoshiko Wada, Takashi Abe

    PLOS ONE   17 ( 8 )   e0273860 - e0273860   2022.8

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    Authorship:Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Public Library of Science (PLoS)  

    Among mutations that occur in SARS-CoV-2, efficient identification of mutations advantageous for viral replication and transmission is important to characterize and defeat this rampant virus. Mutations rapidly expanding frequency in a viral population are candidates for advantageous mutations, but neutral mutations hitchhiking with advantageous mutations are also likely to be included. To distinguish these, we focus on mutations that appear to occur independently in different lineages and expand in frequency in a convergent evolutionary manner. Batch-learning SOM (BLSOM) can separate SARS-CoV-2 genome sequences according by lineage from only providing the oligonucleotide composition. Focusing on remarkably expanding 20-mers, each of which is only represented by one copy in the viral genome, allows us to correlate the expanding 20-mers to mutations. Using visualization functions in BLSOM, we can efficiently identify mutations that have expanded remarkably both in the Omicron lineage, which is phylogenetically distinct from other lineages, and in other lineages. Most of these mutations involved changes in amino acids, but there were a few that did not, such as an intergenic mutation.

    DOI: 10.1371/journal.pone.0273860

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  • Unsupervised explainable AI for molecular evolutionary study of forty thousand SARS-CoV-2 genomes. Reviewed International journal

    Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura

    BMC microbiology   22 ( 1 )   73 - 73   2022.3

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    Language:English   Publishing type:Research paper (scientific journal)  

    BACKGROUND: Unsupervised AI (artificial intelligence) can obtain novel knowledge from big data without particular models or prior knowledge and is highly desirable for unveiling hidden features in big data. SARS-CoV-2 poses a serious threat to public health and one important issue in characterizing this fast-evolving virus is to elucidate various aspects of their genome sequence changes. We previously established unsupervised AI, a BLSOM (batch-learning SOM), which can analyze five million genomic sequences simultaneously. The present study applied the BLSOM to the oligonucleotide compositions of forty thousand SARS-CoV-2 genomes. RESULTS: While only the oligonucleotide composition was given, the obtained clusters of genomes corresponded primarily to known main clades and internal divisions in the main clades. Since the BLSOM is explainable AI, it reveals which features of the oligonucleotide composition are responsible for clade clustering. Additionally, BLSOM also provided information concerning the special genomic region possibly undergoing RNA modifications. CONCLUSIONS: The BLSOM has powerful image display capabilities and enables efficient knowledge discovery about viral evolutionary processes, and it can complement phylogenetic methods based on sequence alignment.

    DOI: 10.1186/s12866-022-02484-3

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  • Epidemiology and Genetic Analysis of SARS-CoV-2 in Myanmar during the Community Outbreaks in 2020. Reviewed International journal

    Wint Wint Phyu, Reiko Saito, Keita Wagatsuma, Takashi Abe, Htay Htay Tin, Eh Htoo Pe, Su Mon Kyaw Win, Nay Chi Win, Lasham Di Ja, Sekizuka Tsuyoshi, Kuroda Makoto, Yadanar Kyaw, Irina Chon, Shinji Watanabe, Hideki Hasegawa, Hisami Watanabe

    Viruses   14 ( 2 )   2022.1

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    We aimed to analyze the situation of the first two epidemic waves in Myanmar using the publicly available daily situation of COVID-19 and whole-genome sequencing data of SARS-CoV-2. From March 23 to December 31, 2020, there were 33,917 confirmed cases and 741 deaths in Myanmar (case fatality rate of 2.18%). The first wave in Myanmar from March to July was linked to overseas travel, and then a second wave started from Rakhine State, a western border state, leading to the second wave spreading countrywide in Myanmar from August to December 2020. The estimated effective reproductive number (Rt) nationwide reached 6-8 at the beginning of each wave and gradually decreased as the epidemic spread to the community. The whole-genome analysis of 10 Myanmar SARS-CoV-2 strains together with 31 previously registered strains showed that the first wave was caused by GISAID clade O or PANGOLIN lineage B.6 and the second wave was changed to clade GH or lineage B.1.36.16 with a close genetic relationship with other South Asian strains. Constant monitoring of epidemiological situations combined with SARS-CoV-2 genome analysis is important for adjusting public health measures to mitigate the community transmissions of COVID-19.

    DOI: 10.3390/v14020259

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  • AI for the collective analysis of a massive number of genome sequences: various examples from the small genome of pandemic SARS-CoV-2 to the human genome. Reviewed

    Toshimichi Ikemura, Yuki Iwasaki, Kennosuke Wada, Yoshiko Wada, Takashi Abe

    Genes & genetic systems   96 ( 4 )   165 - 176   2021.12

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    Authorship:Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    In genetics and related fields, huge amounts of data, such as genome sequences, are accumulating, and the use of artificial intelligence (AI) suitable for big data analysis has become increasingly important. Unsupervised AI that can reveal novel knowledge from big data without prior knowledge or particular models is highly desirable for analyses of genome sequences, particularly for obtaining unexpected insights. We have developed a batch-learning self-organizing map (BLSOM) for oligonucleotide compositions that can reveal various novel genome characteristics. Here, we explain the data mining by the BLSOM: an unsupervised AI. As a specific target, we first selected SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) because a large number of viral genome sequences have been accumulated via worldwide efforts. We analyzed more than 0.6 million sequences collected primarily in the first year of the pandemic. BLSOMs for short oligonucleotides (e.g., 4-6-mers) allowed separation into known clades, but longer oligonucleotides further increased the separation ability and revealed subgrouping within known clades. In the case of 15-mers, there is mostly one copy in the genome; thus, 15-mers that appeared after the epidemic started could be connected to mutations, and the BLSOM for 15-mers revealed the mutations that contributed to separation into known clades and their subgroups. After introducing the detailed methodological strategies, we explain BLSOMs for various topics, such as the tetranucleotide BLSOM for over 5 million 5-kb fragment sequences derived from almost all microorganisms currently available and its use in metagenome studies. We also explain BLSOMs for various eukaryotes, including fishes, frogs and Drosophila species, and found a high separation ability among closely related species. When analyzing the human genome, we found enrichments in transcription factor-binding sequences in centromeric and pericentromeric heterochromatin regions. The tDNAs (tRNA genes) could be separated according to their corresponding amino acid.

    DOI: 10.1266/ggs.21-00025

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  • Time-Series Trend of Pandemic SARS-CoV-2 Variants Visualized Using Batch-Learning Self-Organizing Map for Oligonucleotide Compositions Reviewed

    Takashi Abe, Ryuki Furukawa, Yuki Iwasaki, Toshimichi Ikemura

    Data Science Journal   20 ( 1 )   29 - 29   2021.9

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    Authorship:Lead author, Corresponding author   Publishing type:Research paper (scientific journal)   Publisher:Ubiquity Press, Ltd.  

    DOI: 10.5334/dsj-2021-029

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  • Human cell-dependent, directional, time-dependent changes in the mono- and oligonucleotide compositions of SARS-CoV-2 genomes. Reviewed International journal

    Yuki Iwasaki, Takashi Abe, Toshimichi Ikemura

    BMC microbiology   21 ( 1 )   89 - 89   2021.3

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    BACKGROUND: When a virus that has grown in a nonhuman host starts an epidemic in the human population, human cells may not provide growth conditions ideal for the virus. Therefore, the invasion of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is usually prevalent in the bat population, into the human population is thought to have necessitated changes in the viral genome for efficient growth in the new environment. In the present study, to understand host-dependent changes in coronavirus genomes, we focused on the mono- and oligonucleotide compositions of SARS-CoV-2 genomes and investigated how these compositions changed time-dependently in the human cellular environment. We also compared the oligonucleotide compositions of SARS-CoV-2 and other coronaviruses prevalent in humans or bats to investigate the causes of changes in the host environment. RESULTS: Time-series analyses of changes in the nucleotide compositions of SARS-CoV-2 genomes revealed a group of mono- and oligonucleotides whose compositions changed in a common direction for all clades, even though viruses belonging to different clades should evolve independently. Interestingly, the compositions of these oligonucleotides changed towards those of coronaviruses that have been prevalent in humans for a long period and away from those of bat coronaviruses. CONCLUSIONS: Clade-independent, time-dependent changes are thought to have biological significance and should relate to viral adaptation to a new host environment, providing important clues for understanding viral host adaptation mechanisms.

    DOI: 10.1186/s12866-021-02158-6

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  • An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. Reviewed International journal

    Hayato Harima, Yasuko Orba, Shiho Torii, Yongjin Qiu, Masahiro Kajihara, Yoshiki Eto, Naoya Matsuta, Bernard M Hang'ombe, Yuki Eshita, Kentaro Uemura, Keita Matsuno, Michihito Sasaki, Kentaro Yoshii, Ryo Nakao, William W Hall, Ayato Takada, Takashi Abe, Michael T Wolfinger, Martin Simuunza, Hirofumi Sawa

    Scientific reports   11 ( 1 )   4883 - 4883   2021.3

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    Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3'-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3'-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3'-UTR of flaviviruses.

    DOI: 10.1038/s41598-021-84365-9

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  • Genomic Epidemiology Reveals Multiple Introductions of Severe Acute Respiratory Syndrome Coronavirus 2 in Niigata City, Japan, Between February and May 2020. Reviewed International journal

    Keita Wagatsuma, Ryosuke Sato, Satoru Yamazaki, Masako Iwaya, Yoshiki Takahashi, Akiko Nojima, Mitsuru Oseki, Takashi Abe, Wint Wint Phyu, Tsutomu Tamura, Tsuyoshi Sekizuka, Makoto Kuroda, Haruki H Matsumoto, Reiko Saito

    Frontiers in microbiology   12   749149 - 749149   2021

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    The coronavirus disease 2019 (COVID-19) has caused a serious disease burden and poses a tremendous public health challenge worldwide. Here, we report a comprehensive epidemiological and genomic analysis of SARS-CoV-2 from 63 patients in Niigata City, a medium-sized Japanese city, during the early phase of the pandemic, between February and May 2020. Among the 63 patients, 32 (51%) were female, with a mean (±standard deviation) age of 47.9 ± 22.3 years. Fever (65%, 41/63), malaise (51%, 32/63), and cough (35%, 22/63) were the most common clinical symptoms. The median C t value after the onset of symptoms lowered within 9 days at 20.9 cycles (interquartile range, 17-26 cycles), but after 10 days, the median C t value exceeded 30 cycles (p < 0.001). Of the 63 cases, 27 were distributed in the first epidemic wave and 33 in the second, and between the two waves, three cases from abroad were identified. The first wave was epidemiologically characterized by a single cluster related to indoor sports activity spread in closed settings, which included mixing indoors with families, relatives, and colleagues. The second wave showed more epidemiologically diversified events, with most index cases not related to each other. Almost all secondary cases were infected by droplets or aerosols from closed indoor settings, but at least two cases in the first wave were suspected to be contact infections. Results of the genomic analysis identified two possible clusters in Niigata City, the first of which was attributed to clade S (19B by Nexstrain clade) with a monophyletic group derived from the Wuhan prototype strain but that of the second wave was polyphyletic suggesting multiple introductions, and the clade was changed to GR (20B), which mainly spread in Europe in early 2020. These findings depict characteristics of SARS-CoV-2 transmission in the early stages in local community settings during February to May 2020 in Japan, and this integrated approach of epidemiological and genomic analysis may provide valuable information for public health policy decision-making for successful containment of chains of infection.

    DOI: 10.3389/fmicb.2021.749149

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  • Batch-Learning Self-Organizing Map Identifies Horizontal Gene Transfer Candidates and Their Origins in Entire Genomes Reviewed International journal

    Takashi Abe, Yu Akazawa, Atsushi Toyoda, Hironori Niki, Tomoya Baba

    Frontiers in Microbiology   11   1486 - 1486   2020.7

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:Frontiers Media SA  

    Horizontal gene transfer (HGT) has been widely suggested to play a critical role in the environmental adaptation of microbes; however, the number and origin of the genes in microbial genomes obtained through HGT remain unknown as the frequency of detected HGT events is generally underestimated, particularly in the absence of information on donor sequences. As an alternative to phylogeny-based methods that rely on sequence alignments, we have developed an alignment-free clustering method on the basis of an unsupervised neural network "Batch-Learning Self-Organizing Map (BLSOM)" in which sequence fragments are clustered based solely on oligonucleotide similarity without taxonomical information, to detect HGT candidates and their origin in entire genomes. By mapping the microbial genomic sequences on large-scale BLSOMs constructed with nearly all prokaryotic genomes, HGT candidates can be identified, and their origin assigned comprehensively, even for microbial genomes that exhibit high novelty. By focusing on two types of Alphaproteobacteria, specifically psychrotolerant Sphingomonas strains from an Antarctic lake, we detected HGT candidates using BLSOM and found higher proportions of HGT candidates from organisms belonging to Betaproteobacteria in the genomes of these two Antarctic strains compared with those of continental strains. Further, an origin difference was noted in the HGT candidates found in the two Antarctic strains. Although their origins were highly diversified, gene functions related to the cell wall or membrane biogenesis were shared among the HGT candidates. Moreover, analyses of amino acid frequency suggested that housekeeping genes and some HGT candidates of the Antarctic strains exhibited different characteristics to other continental strains. Lys, Ser, Thr, and Val were the amino acids found to be increased in the Antarctic strains, whereas Ala, Arg, Glu, and Leu were decreased. Our findings strongly suggest a low-temperature adaptation process for microbes that may have arisen convergently as an independent evolutionary strategy in each Antarctic strain. Hence, BLSOM analysis could serve as a powerful tool in not only detecting HGT candidates and their origins in entire genomes, but also in providing novel perspectives into the environmental adaptations of microbes.

    DOI: 10.3389/fmicb.2020.01486

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  • Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens. Reviewed International journal

    Trieu-Duc Vu, Yuki Iwasaki, Shuji Shigenobu, Akiko Maruko, Kenshiro Oshima, Erica Iioka, Chao-Li Huang, Takashi Abe, Satoshi Tamaki, Yi-Wen Lin, Chih-Kuan Chen, Mei-Yeh Lu, Masaru Hojo, Hao-Ven Wang, Shun-Fen Tzeng, Hao-Jen Huang, Akio Kanai, Takashi Gojobori, Tzen-Yuh Chiang, H Sunny Sun, Wen-Hsiung Li, Norihiro Okada

    PLoS genetics   16 ( 6 )   e1008831   2020.6

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    Conspecific male animals fight for resources such as food and mating opportunities but typically stop fighting after assessing their relative fighting abilities to avoid serious injuries. Physiologically, how the fighting behavior is controlled remains unknown. Using the fighting fish Betta splendens, we studied behavioral and brain-transcriptomic changes during the fight between the two opponents. At the behavioral level, surface-breathing, and biting/striking occurred only during intervals between mouth-locking. Eventually, the behaviors of the two opponents became synchronized, with each pair showing a unique behavioral pattern. At the physiological level, we examined the expression patterns of 23,306 brain transcripts using RNA-sequencing data from brains of fighting pairs after a 20-min (D20) and a 60-min (D60) fight. The two opponents in each D60 fighting pair showed a strong gene expression correlation, whereas those in D20 fighting pairs showed a weak correlation. Moreover, each fighting pair in the D60 group showed pair-specific gene expression patterns in a grade of membership analysis (GoM) and were grouped as a pair in the heatmap clustering. The observed pair-specific individualization in brain-transcriptomic synchronization (PIBS) suggested that this synchronization provides a physiological basis for the behavioral synchronization. An analysis using the synchronized genes in fighting pairs of the D60 group found genes enriched for ion transport, synaptic function, and learning and memory. Brain-transcriptomic synchronization could be a general phenomenon and may provide a new cornerstone with which to investigate coordinating and sustaining social interactions between two interacting partners of vertebrates.

    DOI: 10.1371/journal.pgen.1008831

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  • A strategy for predicting gene functions from genome and metagenome sequences on the basis of oligopeptide frequency distance. Reviewed

    Takashi Abe, Ryo Ikarashi, Masaya Mizoguchi, Masashi Otake, Toshimichi Ikemura

    Genes & genetic systems   95 ( 1 )   11 - 19   2020.4

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    As a result of the extensive decoding of a massive amount of genomic and metagenomic sequence data, a large number of genes whose functions cannot be predicted by sequence similarity searches are accumulating, and such genes are of little use to science or industry. Current genome and metagenome sequencing largely depend on high-throughput and low-cost methods. In the case of genome sequencing for a single species, high-density sequencing can reduce sequencing errors. For metagenome sequences, however, high-density sequencing does not necessarily increase the sequence quality because multiple and unknown genomes, including those of closely related species, are likely to exist in the sample. Therefore, a function prediction method that is robust against sequence errors becomes an increased need. Here, we present a method for predicting protein gene function that does not depend on sequence similarity searches. Using an unsupervised machine learning method called BLSOM (batch-learning self-organizing map) for short oligopeptide frequencies, we previously developed a sequence alignment-free method for clustering bacterial protein genes according to clusters of orthologous groups of proteins (COGs), without using information from COGs during machine learning. This allows function-unknown proteins to cluster with function-known proteins, based solely on similarity with respect to oligopeptide frequency, although the method required high-performance supercomputers (HPCs). Based on a wide range of knowledge obtained with HPCs, we have now developed a strategy to correlate function-unknown proteins with COG categories, using only oligopeptide frequency distances (OPDs), which can be conducted with PC-level computers. The OPD strategy is suitable for predicting the functions of proteins with low sequence similarity and is applied here to predict the functions of a large number of gene candidates discovered using metagenome sequencing.

    DOI: 10.1266/ggs.19-00041

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  • The complete mitochondrial genome of Sarcoptes scabiei var. nyctereutis from the Japanese raccoon dog: Prediction and detection of two transfer RNAs (tRNA-A and tRNA-Y) Reviewed

    Takafumi Ueda, Hiroshi Tarui, Nobuhide Kido, Keitaro Imaizumi, Kenji Hikosaka, Takashi Abe, Daisuke Minegishi, Yoshifumi Tada, Masataka Nakagawa, Sohei Tanaka, Tomoko Omiya, Kouki Morikaku, Minori Kawahara, Takane Kikuchi-Ueda, Teruo Akuta, Yasuo Ono

    Genomics   111 ( 6 )   1183 - 1191   2019.12

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    Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.ygeno.2018.09.002

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  • Viral population analysis of the taiga tick, Ixodes persulcatus, by using Batch Learning Self-Organizing Maps and BLAST search. Reviewed

    Yongjin Qiu, Takashi Abe, Ryo Nakao, Kenro Satoh, Chihiro Sugimoto

    The Journal of veterinary medical science   81 ( 3 )   401 - 410   2019.3

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    Ticks transmit a wide range of viral, bacterial, and protozoal pathogens, which are often zoonotic. Several novel tick-borne viral pathogens have been reported during the past few years. The aim of this study was to investigate a diversity of tick viral populations, which may contain as-yet unidentified viruses, using a combination of high throughput pyrosequencing and Batch Learning Self-Organizing Map (BLSOM) program, which enables phylogenetic estimation based on the similarity of oligonucleotide frequencies. DNA/cDNA prepared from virus-enriched fractions obtained from Ixodes persulcatus ticks was pyrosequenced. After de novo assembly, contigs were cataloged by the BLSOM program. In total 41 different viral families and order including those previously associated with human and animal diseases such as Bunyavirales, Flaviviridae, and Reoviridae, were detected. Therefore, our strategy is applicable for viral population analysis of other arthropods of medical and veterinary importance, such as mosquitos and lice. The results lead to the contribution to the prediction of emerging tick-borne viral diseases. A sufficient understanding of tick viral populations will also empower to analyze and understand tick biology including vector competency and interactions with other pathogens.

    DOI: 10.1292/jvms.18-0483

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  • Phylogeographic analysis of human influenza A and B viruses in Myanmar, 2010-2015. Reviewed International journal

    Khin Thu Zar Htwe, Clyde Dapat, Yugo Shobugawa, Takashi Odagiri, Akinobu Hibino, Hiroki Kondo, Ren Yagami, Takehiko Saito, Nobuhiro Takemae, Tsutomu Tamura, Hisami Watanabe, Yadanar Kyaw, Nay Lin, Yi Yi Myint, Htay Htay Tin, Win Thein, Latt Latt Kyaw, Pan Ei Soe, Makoto Naito, Hassan Zaraket, Hiroshi Suzuki, Takashi Abe, Reiko Saito

    PloS one   14 ( 1 )   e0210550   2019

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    We investigated the circulation patterns of human influenza A and B viruses in Myanmar between 2010 and 2015 by analyzing full HA genes. Upper respiratory tract specimens were collected from patients with symptoms of influenza-like illness. A total of 2,860 respiratory samples were screened by influenza rapid diagnostic test, of which 1,577 (55.1%) and 810 (28.3%) were positive for influenza A and B, respectively. Of the 1,010 specimens that were positive for virus isolation, 370 (36.6%) were A(H1N1)pdm09, 327 (32.4%) were A(H3N2), 130 (12.9%) B(Victoria), and 183 (18.1%) were B(Yamagata) viruses. Our data showed that influenza epidemics mainly occurred during the rainy season in Myanmar. Our three study sites, Yangon, Pyinmana, and Pyin Oo Lwin had similar seasonality and circulating type and subtype of influenza in a given year. Moreover, viruses circulating in Myanmar during the study period were closely related genetically to those detected in Thailand, India, and China. Phylogeographic analysis showed that A(H1N1)pdm09 viruses in Myanmar originated from Europe and migrated to other countries via Japan. Similarly, A(H3N2) viruses in Myanmar originated from Europe, and disseminated to the various countries via Australia. In addition, Myanmar plays a key role in reseeding of influenza B viruses to Southeast Asia and East Asia as well as Europe and Africa. Thus, we concluded that influenza virus in Myanmar has a strong link to neighboring Asian countries, Europe and Oceania.

    DOI: 10.1371/journal.pone.0210550

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  • Complete Genome Sequence of Acidithiobacillus ferridurans JCM 18981. Reviewed

    Tomoko Miyauchi, Atsushi Kouzuma, Takashi Abe, Kazuya Watanabe

    Microbiology Resource Announcements   7   e01028018   2018.8

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    DOI: 10.1128/MRA.01028-18

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  • Discovery of Mwinilunga alphavirus: A novel alphavirus in Culex mosquitoes in Zambia. Reviewed International journal

    Shiho Torii, Yasuko Orba, Bernard M Hang'ombe, Aaron S Mweene, Yuji Wada, Paulina D Anindita, Wallaya Phongphaew, Yongjin Qiu, Masahiro Kajihara, Akina Mori-Kajihara, Yoshiki Eto, Hayato Harima, Michihito Sasaki, Michael Carr, William W Hall, Yuki Eshita, Takashi Abe, Hirofumi Sawa

    Virus research   250   31 - 36   2018.5

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    Mosquito-borne alphaviruses are disseminated globally and cause febrile illness in humans and animals. Since the prevalence and diversity of alphaviruses has not been previously investigated in Zambia, reverse transcription PCR was employed as a broad-spectrum approach for the detection of alphaviruses in mosquitoes. From 552 mosquito pools, a novel alphavirus, tentatively named Mwinilunga alphavirus (MWAV), was discovered from a single Culex quinquefasciatus mosquito pool. The full genome of MWAV was subsequently determined, and pairwise comparisons demonstrated that MWAV represented a new alphavirus species. Phylogenetic analyses and a linear discriminant analysis based on the dinucleotide ratios in various virus sequences indicated that MWAV is related to a mosquito-specific alphavirus distinct from other known mosquito-borne alphaviruses due to its inability to replicate in vertebrate cell lines. Further analyses of these novel alphaviruses will help to facilitate a greater understanding of the molecular determinants of host range restriction and the evolutionary relationships of alphaviruses.

    DOI: 10.1016/j.virusres.2018.04.005

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  • Methylomusa anaerophila gen. nov., sp. nov., an anaerobic methanol-utilizing bacterium isolated from a microbial fuel cell. Reviewed

    Nanako Amano, Ayaka Yamamuro, Morio Miyahara, Atsushi Kouzuma, Takashi Abe, Kazuya Watanabe

    International Journal of Systematic and Evolutionary Microbiology   68   1118 - 1122   2018.2

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  • IntroMap: a signal analysis based method for the detection of genomic introgressions Reviewed

    Daniel J. Shea, Motoki Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto, Keiichi Okazaki

    BMC GENETICS   18 ( 101 )   2017.12

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    Background: Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species. In this paper we present IntroMap, a bioinformatics pipeline for the screening of candidate plants through the application of signal processing techniques to NGS data, using alignment to a reference genome sequence (annotation is not required) that shares homology with the recurrent parental cultivar, and without the need for de novo assembly of the read data or variant calling.
    Results: We show the accurate identification of introgressed genomic regions using both in silico simulated genomes, and a hybridized cultivar data set using our pipeline. Additionally we show, through targeted marker-based assays, validation of the IntroMap predicted regions for the hybrid cultivar.
    Conclusions: This approach can be used to automate the screening of large populations, reducing the time and labor required, and can improve the accuracy of the detection of introgressed regions in comparison to a marker-based approach. In contrast to other approaches that generally rely upon a variant calling step, our method achieves accurate identification of introgressed regions without variant calling, relying solely upon alignment.

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  • Non-autotrophic methanogens dominate in anaerobic digesters Reviewed

    Atsushi Kouzuma, Maho Tsutsumi, Shun'ichi Ishii, Yoshiyuki Ueno, Takashi Abe, Kazuya Watanabe

    SCIENTIFIC REPORTS   7   1510   2017.5

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    Anaerobic digesters are man-made habitats for fermentative and methanogenic microbes, and are characterized by extremely high concentrations of organics. However, little is known about how microbes adapt to such habitats. In the present study, we report phylogenetic, metagenomic, and metatranscriptomic analyses of microbiomes in thermophilic packed-bed digesters fed acetate as the major substrate, and we have shown that acetoclastic and hydrogenotrophic methanogens that utilize acetate as a carbon source dominate there. Deep sequencing and precise binning of the metagenomes reconstructed complete genomes for two dominant methanogens affiliated with the genera Methanosarcina and Methanothermobacter, along with 37 draft genomes. The reconstructed Methanosarcina genome was almost identical to that of a thermophilic acetoclastic methanogen Methanosarcina thermophila TM-1, indicating its cosmopolitan distribution in thermophilic digesters. The reconstructed Methanothermobacter (designated as Met2) was closely related to Methanothermobacter tenebrarum, a non-autotrophic hydrogenotrophic methanogen that grows in the presence of acetate. Met2 lacks the Cdh complex required for CO2 fixation, suggesting that it requires organic molecules, such as acetate, as carbon sources. Although the metagenomic analysis also detected autotrophic methanogens, they were less than 1% in abundance of Met2. These results suggested that non-autotrophic methanogens preferentially grow in anaerobic digesters containing high concentrations of organics.

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  • An artificial intelligence approach fit for tRNA gene studies in the era of big sequence data Reviewed

    Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura

    Genes and Genetic Systems   92 ( 1 )   43 - 54   2017

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    Unsupervised data mining capable of extracting a wide range of knowledge from big data without prior knowledge or particular models is a timely application in the era of big sequence data accumulation in genome research. By handling oligonucleotide compositions as high-dimensional data, we have previously modified the conventional self-organizing map (SOM) for genome informatics and established BLSOM, which can analyze more than ten million sequences simultaneously. Here, we develop BLSOM specialized for tRNA genes (tDNAs) that can cluster (self-organize) more than one million microbial tDNAs according to their cognate amino acid solely depending on tetra- and pentanucleotide compositions. This unsupervised clustering can reveal combinatorial oligonucleotide motifs that are responsible for the amino acid-dependent clustering, as well as other functionally and structurally important consensus motifs, which have been evolutionarily conserved. BLSOM is also useful for identifying tDNAs as phylogenetic markers for special phylotypes. When we constructed BLSOM with ‘species-unknown’ tDNAs from metagenomic sequences plus ‘species-known’ microbial tDNAs, a large portion of metagenomic tDNAs self-organized with species-known tDNAs, yielding information on microbial communities in environmental samples. BLSOM can also enhance accuracy in the tDNA database obtained from big sequence data. This unsupervised data mining should become important for studying numerous functionally unclear RNAs obtained from a wide range of organisms.

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  • Genomic features of uncultured methylotrophs in activated-sludge microbiomes grown under different enrichment procedures Reviewed

    Kazuki Fujinawa, Yusuke Asai, Morio Miyahara, Atsushi Kouzuma, Takashi Abe, Kazuya Watanabe

    SCIENTIFIC REPORTS   6   26650   2016.5

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    Methylotrophs are organisms that are able to grow on C1 compounds as carbon and energy sources. They play important roles in the global carbon cycle and contribute largely to industrial wastewater treatment. To identify and characterize methylotrophs that are involved in methanol degradation in wastewater-treatment plants, methanol-fed activated-sludge (MAS) microbiomes were subjected to phylogenetic and metagenomic analyses, and genomic features of dominant methylotrophs in MAS were compared with those preferentially grown in laboratory enrichment cultures (LECs). These analyses consistently indicate that Hyphomicrobium plays important roles in MAS, while Methylophilus occurred predominantly in LECs. Comparative analyses of bin genomes reconstructed for the Hyphomicrobium and Methylophilus methylotrophs suggest that they have different C1-assimilation pathways. In addition, function-module analyses suggest that their cell-surface structures are different. Comparison of the MAS bin genome with genomes of closely related Hyphomicrobium isolates suggests that genes unnecessary in MAS (for instance, genes for anaerobic respiration) have been lost from the genome of the dominant methylotroph. We suggest that genomic features and coded functions in the MAS bin genome provide us with insights into how this methylotroph adapts to activated-sludge ecosystems.

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  • Understanding skin color variations as an adaptation by detecting gene-environment interactions Reviewed

    Sumiko Anno, Kazuhiko Ohshima, Takashi Abe

    Gene-Environment Interaction Analysis: Methods in Bioinformatics and Computational Biology   1 - 37   2016.4

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    Genetic and environmental factors influence the elaborate feedback mechanism that enables the human adaptive form to make internal adjustments in response to environmental stimuli. Human survival may ultimately depend on research elucidating the complex dynamics of the human genome, as well as an understanding of how environmental pressures affect the genome and influence human traits. This chapter reviews our present knowledge of the mechanisms by which haplotypes comprising multiple single-nucleotide polymorphisms (SNPs) can contribute to differences between human population groups. Herein, we describe current approaches to detecting natural selection in pigmentation candidate genes on the basis of haplotypes revealed by SNP analyses. This chapter also discusses methods for elucidating the selective genetic mechanisms that have operated to alter human skin pigmentation, which may be induced by ultraviolet radiation (UVR) in the birthplaces of human populations. Finally, we present our recommendation of spatial statistical methods for clarifying gene-environment interactions, as applicable to interactions with UVR levels. Spatial statistical approaches that apply environmental association rules can be used to extend our knowledge of human adaptation to the environment.

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  • Horizontally Transferred Genetic Elements in the Tsetse Fly Genome: An Alignment-Free Clustering Approach Using Batch Learning Self-Organising Map (BLSOM) Reviewed

    Ryo Nakao, Takashi Abe, Shunsuke Funayama, Chihiro Sugimoto

    BIOMED RESEARCH INTERNATIONAL   2016   3164624   2016

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    Tsetse flies (Glossina spp.) are the primary vectors of trypanosomes, which can cause human and animal African trypanosomiasis in Sub-Saharan African countries. The objective of this study was to explore the genome of Glossina morsitans morsitans for evidence of horizontal gene transfer (HGT) from microorganisms. We employed an alignment-free clustering method, that is, batch learning self-organising map (BLSOM), in which sequence fragments are clustered based on the similarity of oligonucleotide frequencies independently of sequence homology. After an initial scan of HGT events using BLSOM, we identified 3.8% of the tsetse fly genome as HGT candidates. The predicted donors of these HGT candidates included known symbionts, such as Wolbachia, as well as bacteria that have not previously been associated with the tsetse fly. We detected HGT candidates from diverse bacteria such as Bacillus and Flavobacteria, suggesting a past association between these taxa. Functional annotation revealed that the HGT candidates encoded loci in various functional pathways, such as metabolic and antibiotic biosynthesis pathways. These findings provide a basis for understanding the coevolutionary history of the tsetse fly and its microbes and establish the effectiveness of BLSOM for the detection of HGT events.

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  • CG-containing oligonucleotides and transcriptionfactor-binding motifs are enrichedin human pericentric regions Reviewed

    Yoshiko Wada, Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Ikuo Tooyama, Toshimichi Ikemura

    Genes and Genetic Systems   90 ( 1 )   43 - 53   2015.6

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    Unsupervised data mining capable of extracting a wide range of information from big sequence data without prior knowledge or particular models is highly desirable in an era of big data accumulation for research on genes, genomes and genetic systems. By handling oligonucleotide compositions in genomic sequences as high-dimensional data, we have previously modified the conventional SOM (self-organizing map) for genome informatics and established BLSOM for oligonucleotide composition, which can analyze more than ten million sequences simultaneously and is thus suitable for big data analyses. Oligonucleotides often represent motif sequences responsible for sequence-specific binding of proteins such as transcription factors. The distribution of such functionally important oligonucleotides is probably biased in genomic sequences, and may differ among genomic regions. When constructing BLSOMs to analyze pentanucleotide composition in 50-kb sequences derived from the human genome in this study, we found that BLSOMs did not classify human sequences according to chromosome but revealed several specific zones, which are enriched for a class of CG-containing pentanucleotides
    these zones are composed primarily of sequences derived from pericentric regions. The biological significance of enrichment of these pentanucleotides in pericentric regions is discussed in connection with cell type- and stage-dependent formation of the condensed heterochromatin in the chromocenter, which is formed through association of pericentric regions of multiple chromosomes.

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  • Multi-Pathway Cellular Analysis on Crude Natural Drugs/Herbs from Japanese Kampo Formulations Reviewed

    Shizuka Eshima, Satoru Yokoyama, Takashi Abe, Yoshihiro Hayakawa, Ikuo Saiki

    PLOS ONE   10 ( 6 )   e0128872   2015.6

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    Kampo formulations comprise a number of crude natural drugs/herbs as constituents. The crude drugs/herbs have been traditionally classified by their traditional classifications or efficacies in Kampo medicines; however, it has been difficult to establish the scientific link between experimental evidence and traditional classifications in Kampo medicine. To clarify such traditional conceptions, we tested 112 crude drugs/herbs that are major components of Kampo formulations, in the multi-pathway analysis of 10 well-studied transcriptional activities including CREB, ERSF, HIF-1 alpha, IRFs, MYC, NF-kappa B, p53, SMAD, SOX2, and TCF/LEF in A549 human lung cancer cells. By clustering the results of multi-pathway analysis with the Spearman rank-correlation coefficient and Ward linkage, three distinct traditional categories were significantly enriched in the major groupings, which are heat-clearing and dampness-drying herbs, acrid and warm exterior-resolving herbs, and acrid and cool exterior-resolving herbs. These results indicate that these crude drugs/herbs have similar effects on intracellular signaling and further imply that the traditional classifications of those enriched crude drugs/herbs can be supported by such experimental evidence. Collectively, our new in vitro multi-pathway analysis may be useful to clarify the mechanism of action of crude drugs/herbs and Kampo formulations.

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  • Potential Small Guide RNAs for tRNase Z(L) from Human Plasma, Peripheral Blood Mononuclear Cells, and Cultured Cell Lines Reviewed

    Sho Ninomiya, Mitsuoki Kawano, Takashi Abe, Tatsuya Ishikawa, Masayuki Takahashi, Masato Tamura, Yoshiaki Takahashi, Masayuki Nashimoto

    PLOS ONE   10 ( 3 )   e0118631   2015.3

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    Several pieces of evidence suggest that small RNA degradation products together with tRNase Z(L) appear to form another layer of the whole gene regulatory network. The degraded RNAsuch as a 5'-half-tRNA and an rRNA fragment function as small guide RNA (sgRNA) to guide the enzyme to target RNA. We were curious whether there exist RNAs in plasma that can function as sgRNAs for tRNase Z(L), whether these RNAs are working as signaling molecules between cells to fulfill physiological roles, and whether there are any differences in plasma sgRNA species and levels between normal and pathological conditions. Here, we analyzed small plasma RNAs from three healthy persons and three multiple myeloma patients for potential sgRNAs by deep sequencing. We also examined small RNAs from peripheral blood mononuclear cells (PBMC) of three healthy persons and three myeloma patients and from various cultured human cell lines for sgRNAs. We found that read-number distribution patterns of plasma and PBMC RNAs differ between persons in the range of 5-40 nt and that there are many RNA species that exist significantly more or less abundantly in the plasma or PBMC of the myeloma patients than those of the healthy persons. Furthermore, we found that there are many potential sgRNAs in the 5-40-nt RNAs and that, among them, a 31-nt RNA fragment derived from 94-nt Y4-RNA, which can function as a 50-half-tRNA-type sgRNA, is overwhelmingly abundant in the plasma of 2/3 of the examinees. These observations suggest that the gene regulatory network via tRNase Z(L) and sgRNA may be extended intercellularly.

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  • Development of Self-Compressing BLSOM for Comprehensive Analysis of Big Sequence Data Invited Reviewed

    Akihito Kikuchi, Toshimichi Ikemura, Takashi Abe

    BIOMED RESEARCH INTERNATIONAL   2015   506052   2015

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    With the remarkable increase in genomic sequence data from various organisms, novel tools are needed for comprehensive analyses of available big sequence data. We previously developed a Batch-Learning Self-Organizing Map (BLSOM), which can cluster genomic fragment sequences according to phylotype solely dependent on oligonucleotide composition and applied to genome and metagenomic studies. BLSOM is suitable for high-performance parallel-computing and can analyze big data simultaneously, but a large-scale BLSOM needs a large computational resource. We have developed Self-Compressing BLSOM (SC-BLSOM) for reduction of computation time, which allows us to carry out comprehensive analysis of big sequence data without the use of high-performance supercomputers. The strategy of SC-BLSOM is to hierarchically construct BLSOMs according to data class, such as phylotype. The first-layer BLSOM was constructed with each of the divided input data pieces that represents the data subclass, such as phylotype division, resulting in compression of the number of data pieces. The second BLSOM was constructed with a total of weight vectors obtained in the first-layer BLSOMs. We compared SC-BLSOM with the conventional BLSOM by analyzing bacterial genome sequences. SC-BLSOM could be constructed faster than BLSOM and cluster the sequences according to phylotype with high accuracy, showing the method's suitability for efficient knowledge discovery from big sequence data.

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  • Metagenomic approaches to identify potential pathogens in ticks Reviewed

    Ryo Nakao, Qiu Yongjin, Takashi Abe, Toshimichi Ikemura, Chihiro Sugimoto

    GENES & GENETIC SYSTEMS   89 ( 6 )   277 - 277   2014.12

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  • Evolutionary Changes in Vertebrate Genome Signatures with Special Focus on Coelacanth Reviewed

    Yuki Iwasaki, Takashi Abe, Norihiro Okada, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura

    DNA RESEARCH   21 ( 5 )   459 - 467   2014.10

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    With a remarkable increase in genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-organizingmap (SOM) is a powerful tool for clustering high-dimensional data on one plane. For oligonucleotide composition shandled as high-dimensional data, we have previously modified the conventional SOM for genome informatics: BLSOM. In the present study, we constructed BLSOMs for oligonucleotide compositions in fragment sequences (e.g. 100 kb) from a wide range of vertebrates, including coelacanth, and found that the sequences were clustered primarily according to species without species information. As one of the nearest living relatives of tetrapod ancestors, coelacanth is believed to provide access to the phenotypic and genomic transitions leading to the emergence of tetrapods. The characteristic oligonucleotide composition found for coelacanth was connected with the lowest dinucleotide CG occurrence (i.e. the highest CG suppression) among fishes, which was rather equivalent to that of tetrapods. This evident CG suppression in coelacanth should reflect molecular evolutionary processes of epigenetic systems including DNA methylation during vertebrate evolution. Sequence of a de novo DNA methylase (Dntm3a) of coelacanth was found to be more closely related to that of tetrapods than that of other fishes.

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  • Metagenomic Analyses Reveal the Involvement of Syntrophic Consortia in Methanol/Electricity Conversion in Microbial Fuel Cells Reviewed

    Ayaka Yamamuro, Atsushi Kouzuma, Takashi Abe, Kazuya Watanabe

    PLOS ONE   9 ( 5 )   e98425   2014.5

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    Methanol is widely used in industrial processes, and as such, is discharged in large quantities in wastewater. Microbial fuel cells (MFCs) have the potential to recover electric energy from organic pollutants in wastewater; however, the use of MFCs to generate electricity from methanol has not been reported. In the present study, we developed single-chamber MFCs that generated electricity from methanol at the maximum power density of 220 mW m(-2) (based on the projected area of the anode). In order to reveal how microbes generate electricity from methanol, pyrosequencing of 16S rRNA-gene amplicons and Illumina shotgun sequencing of metagenome were conducted. The pyrosequencing detected in abundance Dysgonomonas, Sporomusa, and Desulfovibrio in the electrolyte and anode and cathode biofilms, while Geobacter was detected only in the anode biofilm. Based on known physiological properties of these bacteria, it is considered that Sporomusa converts methanol into acetate, which is then utilized by Geobacter to generate electricity. This speculation is supported by results of shotgun metagenomics of the anode-biofilm microbes, which reconstructed relevant catabolic pathways in these bacteria. These results suggest that methanol is anaerobically catabolized by syntrophic bacterial consortia with electrodes as electron acceptors.

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  • TRNADB-CE: TRNA gene database well-timed in the era of big sequence data Reviewed

    Takashi Abe, Hachiro Inokuchi, Yuko Yamada, Akira Muto, Yuki Iwasaki, Toshimichi Ikemura

    Frontiers in Genetics   5 ( MAY )   114   2014

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    The tRNA gene data base curated by experts "tRNADB-CE" (http://trna.ie.niigata-u.ac.jp) was constructed by analyzing 1,966 complete and 5,272 draft genomes of prokaryotes, 171 viruses', 121 chloroplasts', and 12 eukaryotes' genomes plus fragment sequences obtained by metagenome studies of environmental samples. 595,115 tRNA genes in total, and thus two times of genes compiled previously, have been registered, for which sequence, clover-leaf structure, and results of sequence-similarity and oligonucleotide-pattern searches can be browsed. To provide collective knowledge with help from experts in tRNA researches, we added a column for enregistering comments to each tRNA. By grouping bacterial tRNAs with an identical sequence, we have found high phylogenetic preservation of tRNA sequences, especially at the phylum level. Since many species-unknown tRNAs from metagenomic sequences have sequences identical to those found in species-known prokaryotes, the identical sequence group (ISG) can provide phylogenetic markers to investigate the microbial community in an environmental ecosystem. This strategy can be applied to a huge amount of short sequences obtained from next-generation sequencers, as showing that tRNADB-CE is a well-timed database in the era of big sequence data. It is also discussed that batch-learning self-organizing-map with oligonucleotide composition is useful for efficient knowledge discovery from big sequence data. © 2014 Abe, Inokuchi, Yamada, Muto, Iwasaki and Ikemura.

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  • Visualization of Genome Signatures of Eukaryote Genomes by Batch-Learning Self-Organizing Map with a Special Emphasis on Drosophila Genomes Reviewed

    Takashi Abe, Yuta Hamano, Toshimichi Ikemura

    BIOMED RESEARCH INTERNATIONAL   2014   985706   2014

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    A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

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  • A Novel Bioinformatics Strategy to Analyze Microbial Big Sequence Data for Efficient Knowledge Discovery: Batch-Learning Self-Organizing Map (BLSOM). Reviewed

    Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura

    Microorganisms   1 ( 1 )   137 - 157   2013.11

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  • Approaches to Detecting Gene-Environment Interactions in Human Variation Using Genetic Engineering, Remote Sensing and GIS. Reviewed

    Sumiko Anno, Kazuhiko Ohshima, Takashi Abe, Takeo Tadono, Aya Yamamoto, Tamotsu Igarashi

    Journal of Earth Science and Engineering   3   371 - 378   2013.11

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  • Comparative Metagenomics of Anode-Associated Microbiomes Developed in Rice Paddy-Field Microbial Fuel Cells Reviewed

    Atsushi Kouzuma, Takuya Kasai, Gen Nakagawa, Ayaka Yamamuro, Takashi Abe, Kazuya Watanabe

    PLOS ONE   8 ( 11 )   e77443   2013.11

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    In sediment-type microbial fuel cells (sMFCs) operating in rice paddy fields, rice-root exudates are converted to electricity by anode-associated rhizosphere microbes. Previous studies have shown that members of the family Geobacteraceae are enriched on the anodes of rhizosphere sMFCs. To deepen our understanding of rhizosphere microbes involved in electricity generation in sMFCs, here, we conducted comparative analyses of anode-associated microbiomes in three MFC systems: a rice paddy-field sMFC, and acetate-and glucose-fed MFCs in which pieces of graphite felt that had functioned as anodes in rice paddy-field sMFC were used as rhizosphere microbe-bearing anodes. After electric outputs became stable, microbiomes associated with the anodes of these MFC systems were analyzed by pyrotag sequencing of 16S rRNA gene amplicons and Illumina shotgun metagenomics. Pyrotag sequencing showed that Geobacteraceae bacteria were associated with the anodes of all three systems, but the dominant Geobacter species in each MFC were different. Specifically, species closely related to G. metallireducens comprised 90% of the anode Geobacteraceae in the acetate-fed MFC, but were only relatively minor components of the rhizosphere sMFC and glucose-fed MFC, whereas species closely related to G. psychrophilus were abundantly detected. This trend was confirmed by the phylogenetic assignments of predicted genes in shotgun metagenome sequences of the anode microbiomes. Our findings suggest that G. psychrophilus and its related species preferentially grow on the anodes of rhizosphere sMFCs and generate electricity through syntrophic interactions with organisms that excrete electron donors.

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  • Novel bioinformatics strategies for prediction of directional sequence changes in influenza virus genomes and for surveillance of potentially hazardous strains Reviewed

    Yuki Iwasaki, Takashi Abe, Yoshiko Wada, Kennosuke Wada, Toshimichi Ikemura

    BMC INFECTIOUS DISEASES   13   2013.8

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    Background: With the remarkable increase of microbial and viral sequence data obtained from high-throughput DNA sequencers, novel tools are needed for comprehensive analysis of the big sequence data. We have developed "Batch-Learning Self-Organizing Map (BLSOM)" which can characterize very many, even millions of, genomic sequences on one plane. Influenza virus is one of zoonotic viruses and shows clear host tropism. Important issues for bioinformatics studies of influenza viruses are prediction of genomic sequence changes in the near future and surveillance of potentially hazardous strains.
    Methods: To characterize sequence changes in influenza virus genomes after invasion into humans from other animal hosts, we applied BLSOMs to analyses of mono-, di-, tri-, and tetranucleotide compositions in all genome sequences of influenza A and B viruses and found clear host-dependent clustering (self-organization) of the sequences.
    Results: Viruses isolated from humans and birds differed in mononucleotide composition from each other. In addition, host-dependent oligonucleotide compositions that could not be explained with the host-dependent mononucleotide composition were revealed by oligonucleotide BLSOMs. Retrospective time-dependent directional changes of mono-and oligonucleotide compositions, which were visualized for human strains on BLSOMs, could provide predictive information about sequence changes in newly invaded viruses from other animal hosts (e. g. the swine-derived pandemic H1N1/09).
    Conclusions: Basing on the host-dependent oligonucleotide composition, we proposed a strategy for prediction of directional changes of virus sequences and for surveillance of potentially hazardous strains when introduced into human populations from non-human sources. Millions of genomic sequences from infectious microbes and viruses have become available because of their medical and social importance, and BLSOM can characterize the big data and support efficient knowledge discovery.

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  • Notable clustering of transcription-factor-binding motifs in human pericentric regions and its biological significance. Reviewed

    Yuki Iwasaki, Kennosuke Wada, Yoshiko Wada, Takashi Abe, Toshimichi Ikemura

    Chromosome Research   in press   2013.7

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  • Systematization of the Protein Sequence Diversity in Enzymes Related to Secondary Metabolic Pathways in Plants, in the Context of Big Data Biology Inspired by the KNApSAcK Motorcycle Database Reviewed

    Shun Ikeda, Takashi Abe, Yukiko Nakamura, Nelson Kibinge, Aki Hirai Morita, Atsushi Nakatani, Naoaki Ono, Toshimichi Ikemura, Kensuke Nakamura, Md. Altaf-Ul-Amin, Shigehiko Kanaya

    PLANT AND CELL PHYSIOLOGY   54 ( 5 )   711 - 727   2013.5

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    Biology is increasingly becoming a data-intensive science with the recent progress of the omics fields, e.g. genomics, transcriptomics, proteomics and metabolomics. The species-metabolite relationship database, KNApSAcK Core, has been widely utilized and cited in metabolomics research, and chronological analysis of that research work has helped to reveal recent trends in metabolomics research. To meet the needs of these trends, the KNApSAcK database has been extended by incorporating a secondary metabolic pathway database called Motorcycle DB. We examined the enzyme sequence diversity related to secondary metabolism by means of batch-learning self-organizing maps (BL-SOMs). Initially, we constructed a map by using a big data matrix consisting of the frequencies of all possible dipeptides in the protein sequence segments of plants and bacteria. The enzyme sequence diversity of the secondary metabolic pathways was examined by identifying clusters of segments associated with certain enzyme groups in the resulting map. The extent of diversity of 15 secondary metabolic enzyme groups is discussed. Data-intensive approaches such as BL-SOM applied to big data matrices are needed for systematizing protein sequences. Handling big data has become an inevitable part of biology.

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  • Whole-genome sequencing of Theileria parva strains provides insight into parasite migration and diversification in the African continent. Reviewed

    Kyoko Hayashida, Takashi Abe, William Weir, Ryo Nakao, Kimihito Ito, Kiichi Kajino, Yutaka Suzuki, Frans Jongejan, Dirk Geysen, Chihiro Sugimoto

    DNA Research   20 ( 3 )   209 - 220   2013.2

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  • Rice annotation project database (RAP-DB): An integrative and interactive database for rice genomics Reviewed

    Hiroaki Sakai, Sung Shin Lee, Tsuyoshi Tanaka, Hisataka Numa, Jungsok Kim, Yoshihiro Kawahara, Hironobu Wakimoto, Ching-Chia Yang, Masao Iwamoto, Takashi Abe, Yuko Yamada, Akira Muto, Hachiro Inokuchi, Toshimichi Ikemura, Takashi Matsumoto, Takuji Sasaki, Takeshi Itoh

    Plant and Cell Physiology   54 ( 2 )   e6 - 11   2013.2

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    The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/ ) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics. © 2013 The Author 2013. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved.

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  • A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks Reviewed

    Ryo Nakao, Takashi Abe, Ard M. Nijhof, Seigo Yamamoto, Frans Jongejan, Toshimichi Ikemura, Chihiro Sugimoto, co

    ISME Journal   7   1003 - 1015   2013.1

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  • Comparative Genome Analysis of Three Eukaryotic Parasites with Differing Abilities To Transform Leukocytes Reveals Key Mediators of Theileria-Induced Leukocyte Transformation Reviewed

    Kyoko Hayashida, Yuichiro Hara, Takashi Abe, Chisato Yamasaki, Atsushi Toyoda, Takehide Kosuge, Yutaka Suzuki, Yoshiharu Sato, Shuichi Kawashima, Toshiaki Katayama, Hiroyuki Wakaguri, Noboru Inoue, Keiichi Homma, Masahito Tada-Umezaki, Yukio Yagi, Yasuyuki Fujii, Takuya Habara, Minoru Kanehisa, Hidemi Watanabe, Kimihito Ito, Takashi Gojobori, Hideaki Sugawara, Tadashi Imanishi, William Weir, Malcolm Gardner, Arnab Pain, Brian Shiels, Masahira Hattori, Vishvanath Nene, Chihiro Sugimoto

    MBIO   3 ( 5 )   e00204-12   2012.9

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    We sequenced the genome of Theileria orientalis, a tick-borne apicomplexan protozoan parasite of cattle. The focus of this study was a comparative genome analysis of T. orientalis relative to other highly pathogenic Theileria species, T. parva and T. annulata. T. parva and T. annulata induce transformation of infected cells of lymphocyte or macrophage/monocyte lineages; in contrast, T. orientalis does not induce uncontrolled proliferation of infected leukocytes and multiplies predominantly within infected erythrocytes. While synteny across homologous chromosomes of the three Theileria species was found to be well conserved overall, subtelomeric structures were found to differ substantially, as T. orientalis lacks the large tandemly arrayed subtelomere-encoded variable secreted protein-encoding gene family. Moreover, expansion of particular gene families by gene duplication was found in the genomes of the two transforming Theileria species, most notably, the TashAT/TpHN and Tar/Tpr gene families. Gene families that are present only in T. parva and T. annulata and not in T. orientalis, Babesia bovis, or Plasmodium were also identified. Identification of differences between the genome sequences of Theileria species with different abilities to transform and immortalize bovine leukocytes will provide insight into proteins and mechanisms that have evolved to induce and regulate this process. The T. orientalis genome database is available at http://totdb.czc.hokudai.ac.jp/.
    IMPORTANCE Cancer-like growth of leukocytes infected with malignant Theileria parasites is a unique cellular event, as it involves the transformation and immortalization of one eukaryotic cell by another. In this study, we sequenced the whole genome of a nontransforming Theileria species, Theileria orientalis, and compared it to the published sequences representative of two malignant, transforming species, T. parva and T. annulata. The genome-wide comparison of these parasite species highlights significant genetic diversity that may be associated with evolution of the mechanism(s) deployed by an intracellular eukaryotic parasite to transform its host cell.

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  • Diverse RuBisCO genes responsible for CO2 fixation in an Antarctic moss pillar. Reviewed

    Ryosuke Nakai, Takashi Abe, Tomoya Baba, Satoshi Imura, Hiroshi Kagoshima, Hiroshi Kanda, Yuji Kohara, Akiko Koi, Hironori Niki, Katsuhiko Yanagihara, Takeshi Naganuma

    Polar Biology   35 ( 11 )   1641 - 1650   2012.6

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  • Eukaryotic phylotypes in aquatic moss pillars inhabiting a freshwater lake in East Antarctica, based on 18S rRNA gene analysis. Reviewed

    Ryosuke Nakai, Takashi Abe, Tomoya Baba, Satoshi Imura, Hiroshi Kagoshima, Hiroshi Kanda, Yuji Kohara, Akiko Koi, Hironori Niki, Katsuhiko Yanagihara, Takeshi Naganuma

    Polar Biology   35   1495 - 1504   2012.5

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  • Microflorae of aquatic moss pillars in a freshwater lake, East Antarctica, based on fatty acid and 16S rRNA gene analyses. Reviewed

    Ryosuke Nakai, Takashi Abe, Tomoya Baba, Satoshi Imura, Hiroshi Kagoshima, Hiroshi Kanda, Atsuko Kanekiyo, Yuji Kohara, Akiko Koi, Keiko Nakamura, Takanori Narita, Hironori Niki, Katsuhiko Yanagihara, Takeshi Naganuma

    Polar Biology   35   425 - 433   2012.1

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  • Metagenomic analysis of 0.2-μm-passable microorganisms in deep-sea hydrothermal fluid. Reviewed

    Ryosuke Nakai, Takashi Abe, Haruko Takeyama, Takeshi Naganuma

    Marine Biotechnology   13   900 - 908   2011.8

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  • The possibility of detecting natural selection in pigmentation candidate genes from haplotype structure as revealed by SNP analysis Reviewed

    Sumiko Anno, Kazuhiko Ohshima, Takashi Abe

    Japanese Journal of Physiological Anthropology   16 ( 2 )   99 - 102   2011.5

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    Detecting natural selection would provide valuable insight into the molecular mechanisms of pathogenesis and advanced knowledge about the history of human adaptations to local environments. This study tried to detect natural selection in pigmentation candidate genes from haplotype structure as revealed by SNP analyses. We estimated the frequencies of diplotypes (combinations of the haplotypes) expected from Hardy-Weinberg equilibrium to evaluate natural selection. We also tested for correlations between the haplotypes with a high frequency and melanin content. The results indicated the possible difference of the melanin contents among the haplotypes. We suggest the possibility of natural selection to a mutation linking to the SNPs in the haplotypes. This paper also discusses future approaches to detecting natural selection in pigmentation candidate genes from haplotype structure as revealed by SNP analyses.

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  • Prediction of Directional Changes of influenza A Virus Genome Sequences with Emphasis on Pandemic H1N1/09 as a Model Case Reviewed

    Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Masae Itoh, Toshimichi Ikemura

    DNA RESEARCH   18 ( 2 )   125 - 136   2011.4

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    Influenza virus poses a significant threat to public health, as exemplified by the recent introduction of the new pandemic strain H1N1/09 into human populations. Pandemics have been initiated by the occurrence of novel changes in animal sources that eventually adapt to human. One important issue in studies of viral genomes, particularly those of influenza virus, is to predict possible changes in genomic sequence that will become hazardous. We previously established a clustering method termed 'BLSOM' (batch-learning self-organizing map) that does not depend on sequence alignment and can characterize and compare even 1 million genomic sequences in one run. Strategies for comparing a vast number of genomic sequences simultaneously become increasingly important in genome studies because of remarkable progresses in nucleotide sequencing. In this study, we have constructed BLSOMs based on the oligonucleotide and codon composition of all influenza A viral strains available. Without prior information with regard to their hosts, sequences derived from strains isolated from avian or human sources were successfully clustered according to the hosts. Notably, the pandemic H1N1/09 strains have oligonucleotide and codon compositions that are clearly different from those of human seasonal influenza A strains. This enables us to infer future directional changes in the influenza A viral genome.

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  • tRNADB-CE 2011: tRNA gene database curated manually by experts Reviewed

    Takashi Abe, Toshimichi Ikemura, Junichi Sugahara, Akio Kanai, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi

    NUCLEIC ACIDS RESEARCH   39   D210 - D213   2011.1

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    We updated the tRNADB-CE by analyzing 939 complete and 1301 draft genomes of prokaryotes and eukaryotes, 171 complete virus genomes, 121 complete chloroplast genomes and approximately 230 million sequences obtained by metagenome analyses of 210 environmental samples. The 287 102 tRNA genes in total, and thus two times of the tRNA genes compiled previously, are compiled, in which sequence information, clover-leaf structure and results of sequence similarity and oligonucleotide-pattern search can be browsed. In order to pool collective knowledge with help from any experts in the tRNA research field, we included a column to which comments can be added on each tRNA gene. By compiling tRNAs of known prokaryotes with identical sequences, we found high phylogenetic preservation of tRNA sequences, especially at a phylum level. Furthermore, a large number of tRNAs obtained by metagenome analyses of environmental samples had sequences identical to those found in known prokaryotes. The identical sequence group, therefore, can be used as phylogenetic markers to clarify the microbial community structure of an ecosystem. The updated tRNADB-CE provided functions, with which users can obtain the phylotype-specific markers (e.g. genus-specific markers) by themselves and clarify microbial community structures of ecosystems in detail. tRNADB-CE can be accessed freely at http://trna.nagahama-i-bio.ac.jp.

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  • A Novel Bioinformatics Strategy to Predict Directional Changes of Influenza A Virus Genome Sequences Reviewed

    Yuki Iwasaki, Kennosuke Wada, Masae Itoh, Toshimichi Ikemura, Takashi Abe

    ADVANCES IN SELF-ORGANIZING MAPS, WSOM 2011   6731   198 - 206   2011

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    Influenza A viruses cause a significant threat to public health as highlighted by the recent introduction of the swine-derived H1N1 virus (pandemic H1N1/09) into human populations. Pandemics were primarily initiated by introduction from animal sources and successive adaptation among humans through human-to-human transmission. We established a sequence alignment-free clustering method "BLSOM", which can analyze and compare all influenza A virus genome sequences on one map. Separation according to host animal, subtype and epidemic year could be efficiently visualized. Notably, H1N1/09 strains have oligonucleotide and codon compositions clearly distinct from those of seasonal human flu strains. This enabled us to make inferences about directional changes of H1N1/09 sequences in the near future and to list codons and oligonucleotides with the potential of reduction in H1N1/09 sequences. The strong visualization power of BLSOM also provides surveillance strategies for efficiently detecting potential precursors to pandemic viruses.

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  • A novel bioinformatics strategy for searchingindustrially useful genome resources frommetagenomic sequence libraries Reviewed

    Hiroshi Uehara, Yuki Iwasaki, Chieko Wada, Toshimichi Ikemura, Takashi Abe

    Genes and Genetic Systems   86 ( 1 )   53 - 66   2011

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    Although remarkable progress in metagenomic sequencing of various environmental samples has been made, large numbers of fragment sequences have been registered in the international DNA databanks, primarily without information on gene function and phylotype, and thus with limited usefulness. Industrial useful biological activity is often carried out by a set of genes, such as those constituting an operon. In this connection, metagenomic approaches have a weakness because sets of the genes are usually split up, since the sequences obtained by metagenome analyses are fragmented into 1-kb or much shorter segments. Therefore, even when a set of genes responsible for an industrially useful function is found in one metagenome library, it is usually difficult to know whether a single genome harbors the entire gene set or whether different genomes have individual genes. By modifying Self-Organizing Map (SOM), we previously developed BLSOM for oligonucleotide composition, which allowed classification (self-organization) of sequence fragments according to genomes. Because BLSOM could reassociate genomic fragments according to genomes, BLSOM may ameliorate the abovementioned weakness of metagenome analyses. Here, we have developed a strategy for clustering of metagenomic sequences according to phylotypes and genomes, by testing a gene set contributing to environment preservation.

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  • Approaches to understanding adaptations of skin color variation by detecting gene-environment interactions Reviewed

    Sumiko Anno, Kazuhiko Ohshima, Takashi Abe

    EXPERT REVIEW OF MOLECULAR DIAGNOSTICS   10 ( 8 )   987 - 991   2010.11

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    Genetic and environmental factors are both part of an elaborate feedback mechanism whereby the human adaptive form reacts to environmental stimuli via internal adjustments. Human survival may ultimately depend on understanding two important components of future environmental adaptation. First, we must elucidate the dynamics of the human genome underpinning the complex human phenotype. Second, we must understand how the environment pressures and affects the genome, helping to determine human traits. This article reviews current approaches to detecting the natural selection of skin color variation in human populations. We include statistical methods for clarifying gene environment interactions applicable to the interactions with UV radiation levels. We recommend spatial data mining as an efficient approach that applies environmental association rules, extending our knowledge of adaptation to the environment.

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  • Sequences from Prokaryotic, Eukaryotic, and Viral Genomes Available Clustered According to Phylotype on a Self-Organizing Map Reviewed

    Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura

    Knowledge-Based Bioinformatics: From Analysis to Interpretation   233 - 249   2010.7

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    DOI: 10.1002/9780470669716.ch10

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  • Preliminary Evaluation of Batch-Learning Self-Organizing Map Algorithm on a Graphic Processor. Reviewed

    Akihiro Shitara, Yuri Nishikawa, Masato Yoshimi, Takashi Abe, Toshimichi Ikemura, Hideharu Amano

    Proceedings of Parallel and Distributed Computing and Networks   676 - 689   2010.2

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  • A Novel Bioinformatics Strategy for Function Prediction of Poorly-Characterized Protein Genes Obtained from Metagenome Analyses Reviewed

    Takashi Abe, Shigehiko Kanaya, Hiroshi Uehara, Toshimichi Ikemura

    DNA RESEARCH   16 ( 5 )   287 - 297   2009.10

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    As a result of remarkable progresses of DNA sequencing technology, vast quantities of genomic sequences have been decoded. Homology search for amino acid sequences, such as BLAST, has become a basic tool for assigning functions of genes/proteins when genomic sequences are decoded. Although the homology search has clearly been a powerful and irreplaceable method, the functions of only 50% or fewer of genes can be predicted when a novel genome is decoded. A prediction method independent of the homology search is urgently needed. By analyzing oligonucleotide compositions in genomic sequences, we previously developed a modified Self-organizing Map &apos;BLSOM&apos; that clustered genomic fragments according to phylotype with no advance knowledge of phylotype. Using BLSOM for di-, trii- and tetrapeptide compositions, we developed a system to enable separation (self-organization) of proteins by function. Analyzing oligopeptide frequencies in proteins previously classified into COGs (clusters of orthologous groups of proteins), BLSOMs could faithfully reproduce the COG classifications. This indicated that proteins, whose functions are unknown because of lack of significant sequence similarity with function-known proteins, can be related to function-known proteins based on similarity in oligopeptide composition. BLSOM was applied to predict functions of vast quantities of proteins derived from mixed genomes in environmental samples.

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  • Intra-Species Diversity between Seven Bifidobacterium adolescentis Strains Identified by Genome-Wide Tiling Array Analysis Reviewed

    Kazumasa Yasui, Mototsugu Tabata, Satoki Yamada, Takashi Abe, Toshimichi Ikemura, Ro Osawa, Tohru Suzuki

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   73 ( 6 )   1422 - 1424   2009.6

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    Six Bifidobacterium adolescentis strains, JCM1275, JCM1251, JCM7044, JCM7045, JCM7046, and 9-124, were analyzed using a tiling array designed according to the full genome sequence of ATCC15703. The results demonstrated deletion clusters along with single-gene mutations and deletions. Most deletions concerned genes involved in polysaccharide and cell-surface biogenesis. A dendrogram illustrating the deletions and mutations is presented and the evolution of B. adolescentis is discussed.

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  • Relationships between replication timing and GC content of cancer-related genes on human chromosomes 11q and 21q Reviewed

    Yoshihisa Watanabe, Takashi Abe, Toshimichi Ikemura, Masato Maekawa

    GENE   433 ( 1-2 )   26 - 31   2009.3

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    The human genome is composed of large-scale compartmentalized structures, including long G+C% (GC%) mosaic structures and replication-timing zones, which are related to chromosome band zones. Previously, we measured replication timing along the entire lengths of human chromosomes 11q and 21q at the sequence level, and it was suggested that the transition regions of replication timing from early to late S-phase coincided with "unstable" regions of the genome associated with increased DNA damage. In the present study, we measured replication timing of 15 known oncogenes and tumor suppressor genes on human chromosomes 11q and 21q using two human cell lines (THP-1 and Jurkat). We found unusual relationships between replication timing and the GC content of the genomic regions in which these cancer-related genes were located. Many of these genes showed similar replication timing between the two cell lines, and the majority replicated intermediately between early and late in both cell lines. On the other hand, more than half of these genes were located at very GC-rich (50-55 GC%) regions. In addition, we analyzed the exact relationships between early/late-switch regions of replication timing where cancer-related genes were located, and GC% transitions in and around five R/G-chromosomal band boundaries (each ca. 4 Mb) by using newly designed PCR primer sets. We found that the majority of cancer-related genes including oncogenes were located in GC-rich isochores close to GC% transitions within early/late-switch regions of replication timing. many of which replicated intermediately between the early and late S-phase. Unusual relationships between replication timing and GC content of the genomic regions in which cancer-related genes were located may be related to the molecular mechanisms of genomic instability associated with increased DNA damage. (C) 2008 Elsevier B.V. All rights reserved.

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  • tRNADB-CE: tRNA gene database curated manually by experts Reviewed

    Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Hiroshi Uehara, Makoto Kinouchi, Shigehiko Kanaya, Yuko Yamada, Akira Muto, Hachiro Inokuchi

    NUCLEIC ACIDS RESEARCH   37   D163 - D168   2009.1

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    We constructed a new large-scale database of tRNA genes by analyzing 534 complete genomes of prokaryotes and 394 draft genomes in WGS (Whole Genome Shotgun) division in DDBJ/EMBL/GenBank and approximately 6.2 million DNA fragment sequences obtained from metagenomic analyses. This exhaustive search for tRNA genes was performed by running three computer programs to enhance completeness and accuracy of the prediction. Discordances of assignment among three programs were found for similar to 4% of the total of tRNA gene candidates obtained from these prokaryote genomes analyzed. The discordant cases were manually checked by experts in the tRNA experimental field. In total, 144 061 tRNA genes were registered in the database &apos;tRNADB-CE&apos;, and the number of the genes was more than four times of that of the genes previously reported by the database from analyses of complete genomes with tRNAscan-SE program. The tRNADB-CE allows for browsing sequence information, cloverleaf structures and results of similarity searches among all tRNA genes. For each of the complete genomes, the number of tRNA genes for individual anticodons and the codon usage frequency in all protein genes and the positioning of individual tRNA genes in each genome can be browsed. tRNADB-CE can be accessed freely at http://trna.nagahamaibio.ac.jp.

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  • Novel bioinformatics for inter- and intraspecies comparison of genome signatures in plant genomes Reviewed

    Takashi Abe, Kennosuke Wada, Yuki Iwasaki, Toshimichi Ikemura

    PLANT BIOTECHNOLOGY   26 ( 5 )   469 - 477   2009

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    Novel tools are needed for comprehensive comparisons of the inter-and intraspecies characteristics of a large amounts of available genome sequences. An unsupervised neural network algorithm, Kohonen&apos;s Self-Organizing Map (SOM), is an effective tool for clustering and visualizing high-dimensional complex data on a single map. We modified the conventional SOM for genome informatics on the basis of Batch Learning SOM (BLSOM), making the resulting map independent of the order of data input. We generated BLSOMs for oligonucleotide frequencies in fragment sequences (e. g. 10-kb) from 13 plant genomes for which almost complete genome sequences are available. BLSOM recognized species-specific characteristics (key combinations of oligonucleotide frequencies) in most of the fragment sequences, permitting classification (self-organization) of sequences according to species without any information regarding the species during computation. To disclose sequence characteristics of a single genome independently of other genomes, we constructed BLSOMs for sequence fragments from one genome plus computer-generated random sequences. Genomic sequences were clearly separated from random sequences, revealing the oligonucleotides with characteristic occurrence levels in the genomic sequences. We discussed these oligonucleotides diagnostic for genomic sequences, in connection with genetic signal sequences. Because the classification and visualization power is very high, BLSOM is thought to be an efficient and powerful tool for extracting a wide range of genomic information.

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  • Batch-Learning Self-Organizing Map for Predicting Functions of Poorly-Characterized Proteins Massively Accumulated Reviewed

    Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura

    ADVANCES IN SELF-ORGANIZING MAPS, PROCEEDINGS   5629   1 - +   2009

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    As the result of the decoding of large numbers of genome sequences, numerous proteins whose functions cannot be identified by the homology search of amino acid sequences have accumulated and remain of no use to science and industry. Establishment of novel prediction methods for protein function is urgently needed. We previously developed Batch-Learning SOM (BL-SOM) for genome informatics; here, we developed BL-SOM to predict functions of proteins on the basis of similarity in oligopeptide composition of proteins. Oligopeptides are component parts of a protein and involved in formation of its functional motifs and structural parts. Concerning oligopeptide frequencies in 110,000 proteins classified into 2853 function-known COGS (clusters of orthologous groups), BL-SOM could faithfully reproduce the COG classifications, and therefore, proteins whose functions have been unidentified with homology searches could be related to function-known proteins. BL-SOM was applied to predict protein functions of large numbers of proteins obtained from metagenome analyses.

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  • A Large-Scale Genomics Studies Conducted with Batch-Learning SOM Utilizing High-Performance Supercomputers Reviewed

    Takashi Abe, Yuta Hamano, Shigehiko Kanaya, Kennosuke Wada, Toshimichi Ikemura

    BIO-INSPIRED SYSTEMS: COMPUTATIONAL AND AMBIENT INTELLIGENCE, PT 1   5517   829 - +   2009

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    Self-Organizing Map (SOM) developed by Kohonen's group is an effective tool for clustering and visualizing high-dimensional complex data on a two-dimensional map. We previously modified the conventional SOM to genome informatics, making the learning process and resulting map independent of the order of data input. This BLSOM developed on the basis of batch-learning SOM became Suitable for actualizing high-performance parallel-computing using high-performance supercomputers. This BLSOM revealed phylotype-specific characteristics of oligonucleotide frequencies occurred in their genome sequences and thus permitted clustering (self-organization) of genome fragments (e.g., 10 kb) according to phylotype without phylogenetic information during the BLSOM learning. Using a high-performance supercomputer "the Earth Simulator", almost all prokaryotic, eukaryotic and viral sequences currently available could be classified according to phylotypes on a single map. Using this large-scale BLSOM, phylotypes of a large lumber of genomic fragments obtained by metagenome analyses of environmental samples could be predicted.

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  • Construction of tRNA database curated by experts Reviewed

    Takashi Abe, Toshimichi Ikemura, Yasuo Ohara, Akira Muto, Yuko Yamada, Uehara Hiroshi, Makoto Kinouchi, Shigehiko Kanaya, Hachiro Inokuchi

    GENES & GENETIC SYSTEMS   83 ( 6 )   482 - 482   2008.12

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  • A novel bioinformatics strategy for unveiling microbial diversity of uncultured environmental microbe mixtures on the basis of Batch Learning Self-Organizing Map (BLSOM) Reviewed

    Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   83 ( 6 )   483 - 483   2008.12

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  • The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota. Reviewed International journal

    Tomoyuki Kosaka, Souichiro Kato, Takefumi Shimoyama, Shunichi Ishii, Takashi Abe, Kazuya Watanabe

    Genome research   18 ( 3 )   442 - 8   2008.3

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    The anaerobic biodegradation of organic matter is accomplished by sequential syntrophic catabolism by microbes in different niches. Pelotomaculum thermopropionicum is a representative syntrophic bacterium that catalyzes the intermediate bottleneck step in the anaerobic-biodegradation process, whereby volatile fatty acids (VFAs) and alcohols produced by upstream fermenting bacteria are converted to acetate, hydrogen, and carbon dioxide (substrates for downstream methanogenic archaea). To reveal genomic features that contribute to our understanding of the ecological niche and evolution of P. thermopropionicum, we sequenced its 3,025,375-bp genome and performed comparative analyses with genomes of other community members available in the databases. In the genome, 2920 coding sequences (CDSs) were identified. These CDSs showed a distinct distribution pattern in the functional categories of the Clusters of Orthologous Groups database, which is considered to reflect the niche of this organism. P. thermopropionicum has simple catabolic pathways, in which the propionate-oxidizing methylmalonyl-CoA pathway constitutes the backbone and is linked to several peripheral pathways. Genes for most of the important catabolic enzymes are physically linked to those for PAS-domain-containing regulators, suggesting that the catabolic pathways are regulated in response to environmental conditions and/or global cellular situations rather than specific substrates. Comparative analyses of codon usages revealed close evolutionary relationships between P. thermopropionicum and other niche members, while it was distant from phylogenetically related sugar-fermenting bacteria. These analyses suggest that P. thermopropionicum has evolved as a syntrophy specialist by interacting with niche-associated microbes.

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  • Interactions between SNP alleles at multiple loci contribute to skin color differences between Caucasoid and Mongoloid subjects Reviewed

    Sumiko Anno, Takashi Abe, Takushi Yamamoto

    INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES   4 ( 2 )   81 - 86   2008

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    This study aimed to identify single nucleotide polymorphism (SNP) alleles at multiple loci associated with racial differences in skin color using SNP genotyping. A total of 122 Caucasians in Toledo, Ohio and 100 Mongoloids in Japan were genotyped for 20 SNPs in 7 candidate genes, encoding the Agouti signaling protein (ASIP), tyrosinase-related protein 1 (TYRP1), tyrosinase (TYR), melanocortin 1 receptor (MC1R), oculocutaneous albinism II (OCA2), microphthalmia-associated transcription factor (MITF), and myosin VA (MYO5A). Data were used to analyze associations between the 20 SNP alleles using linkage disequilibrium (LD). Combinations of SNP alleles were jointly tested under LD for associations with racial groups by performing chi(2) test for independence. Results showed that SNP alleles at multiple loci can be considered the haplotype that contributes to significant differences between the two population groups and suggest a high probability of LD. Confirmation of these findings requires further study with other ethnic groups to analyze the associations between SNP alleles at multiple loci and skin color variation among races.

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  • A large-scale Batch-learning self-organizing map for function prediction of poorly-characterized proteins progressively accumulating in sequence databases Reviewed

    Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   82 ( 6 )   517 - 517   2007.12

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  • Characterization of Genetic Signal Sequences with Batch-Learning SOM. Reviewed

    Takashi Abe, Shun Ikeda, Shigehiko Kanaya, Kennosuke Wada, Toshimichi Ikemura

    Proceedings of the 6th International Workshop on Self-Organizing Maps   2007.9

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  • Interaction with SNP allele in multiple loci contributes to human skin color diversity Reviewed

    ANNO Sumiko, ABE Takashi, SAIRYO Koichi, KUDO Susumu, YAMAMOTO Takuji, OGATA Koretsugu, Goel Vijay K.

    Japanese Journal of Physiological Anthropology   12 ( 1 )   1 - 10   2007.2

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    Our study aims to clarify molecular basis of human skin color diversity and investigate environmental adaptability to ultraviolet irradiation in order to predict human health risk influenced by severe environments in the future. One hundred and twenty-two Caucasians living in Toledo, Ohio participated in this study. Their back and cheek were measured for melanin value for skin pigmentation index as a quantitative trait. Their buccal cells as samples were collected and used for DNA extraction. DNA was used for SNP genotyping with the technology of Masscode system that involves the two-step PCR amplification and comprises a platform chemistry of cleavable mass spectrometry tags. Our results of statistical analysis show that SNP allele in multiple loci are related and suggest high possibility of linkage disequilibrium. Our study plans to collect data on other ethic groups in order to analyze correlation between SNP allele in multiple loci and identify loci associated with human skin color diversity.

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  • Genome Information Broker for Viruses (GIB-V): database for comparative analysis of virus genomes Reviewed

    Masaki Hirahata, Takashi Abe, Naoto Tanaka, Yoshikazu Kuwana, Yasumasa Shigemoto, Satoru Miyazaki, Yoshiyuki Suzuki, Hideaki Sugawara

    NUCLEIC ACIDS RESEARCH   35   D339 - D342   2007.1

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    Genome Information Broker for Viruses (GIB-V) is a comprehensive virus genome/segment database. We extracted 18 418 complete virus genomes/segments from the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org/) by DNA Data Bank of Japan (DDBJ), EMBL and GenBank and stored them in our system. The list of registered viruses is arranged hierarchically according to taxonomy. Keyword searches can be performed for genome/segment data or biological features of any virus stored in GIB-V. GIB-V is equipped with a BLAST search function, and search results are displayed graphically or in list form. Moreover, the BLAST results can be used online with the ClustalW feature of the DDBJ. All available virus genome/segment data can be collected by the GIB-V download function. GIB-V can be accessed at no charge at http://gib-v.genes.nig.ac.jp/.

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  • DDBJ working on evaluation and classification of bacterial genes in INSDC Reviewed

    Hideaki Sugawara, Takashi Abe, Takashi Gojobori, Yoshio Tateno

    NUCLEIC ACIDS RESEARCH   35   D13 - D15   2007.1

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    DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) newly collected and released 12 927 184 entries or 13 787 688 598 bases in the period from July 2005 to June 2006. The released data contain honeybee expressed sequence tags (ESTs), re-examined and re-annotated complete genome data of Escherichia coli K-12 W3110, medaka WGS and human MGA. We also systematically evaluated and classified the genes in the complete bacterial genomes submitted to the International Nucleotide Sequence Database Collaboration (INSDC, http://insdc.org) that is composed of DDBJ, EMBL Bank and GenBank. The examination and classification selected 557 000 genes as reliable ones among all the bacterial genes predicted by us.

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  • Interactions Between SNP Alleles at Multiple Loci and Variation in Skin Pigmentation in 122 Caucasians Reviewed

    Sumiko Anno, Takashi Abe, Koichi Sairyo, Susumu Kudo, Takushi Yamamoto, Koretsugu Ogata, Vijay K. Goel

    EVOLUTIONARY BIOINFORMATICS   3   169 - 178   2007

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    This study was undertaken to clarify the molecular basis for human skin color variation and the environmental adaptability to ultraviolet irradiation, with the ultimate goal of predicting the impact of changes in future environments on human health risk. One hundred twenty-two Caucasians living in Toledo, Ohio participated. Back and cheek skin were assayed for melanin as a quantitative trait marker. Buccal cell samples were collected and used for DNA extraction. DNA was used for SNP genotyping using the Masscode (TM) system, which entails two-step PCR amplification and a platform chemistry which allows cleavable mass spectrometry tags. The results show gene-gene interaction between SNP alleles at multiple loci (not necessarily on the same chromosome) contributes to inter-individual skin color variation while suggesting a high probability of linkage disequilibrium. Confirmation of these findings requires further study with other ethic groups to analyze the associations between SNP alleles at multiple loci and human skin color variation. Our overarching goal is to use remote sensing data to clarify the interaction between atmospheric environments and SNP allelic frequency and investigate human adaptability to ultraviolet irradiation. Such information should greatly assist in the prediction of the health effects of future environmental changes such as ozone depletion and increased ultraviolet exposure. If such health effects are to some extent predictable, it might be possible to prepare for such changes in advance and thus reduce the extent of their impact.

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  • Studies of closely related genomes such as human and chimpanzee genomes using Self-Organizing Map Reviewed

    Takashi Abe, Hideaki Sugawara, Shigehiko Kanaya, Hijiri Maeno, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   81 ( 6 )   457 - 457   2006.12

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  • A novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from mixed genomes of uncultured environmental microbes. Reviewed

    Takashi Abe, Hideaki Sugawara, Shigehiko Kanaya, Toshimichi Ikemura

    Polar Bioscience   20   103 - 112   2006.12

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  • Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS) Reviewed

    Takehide Kosuge, Takashi Abe, Toshihisa Okido, Naoto Tanaka, Masaki Hirahata, Yutaka Maruyama, Jun Mashima, Aki Tomiki, Motoyoshi Kurokawa, Ryutaro Himeno, Satoshi Fukuchi, Satoru Miyazaki, Takashi Gojobori, Yoshio Tateno, Hideaki Sugawara

    DNA RESEARCH   13 ( 6 )   245 - 254   2006.12

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    A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB, http://gib.genes.nig.ae.jp/). However, when comparative genomics is carried out, researchers must be aware that there are protein-coding genes not confirmed by homology or motif search and that reliable protein-coding genes are missing. Therefore, we developed a protocol (Gene Trek in Prokaryote Space, GTPS) for finding possible protein-coding genes in bacterial genomes. GTPS assigns a degree of reliability to predicted protein-coding genes. We first systematically applied the protocol to the complete genomes of all 123 bacterial species and strains that were publicly available as of July 2003, and then to those of 183 species and strains available as of September 2004. We found a number of incorrect genes and several new ones in the genome data in question. We also found a way to estimate the total number of orthologous genes in the bacterial world.

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  • Sequences from almost all prokaryotic, eukaryotic, and viral genomes available could be classified according to genomes on a large-scale Self-Organizing Map constructed with the Earth Simulator. Reviewed

    Takashi Abe, Hideaki Sugawara, Shigehiko Kanaya, Toshimichi Ikemura

    Journal of the Earth Simulator   6   17 - 23   2006.10

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  • A useful bioinformatics suite for retrieving and analyzing microbial genome data (G-InforBIO). Reviewed

    Naoto Tanaka, Takashi Abe, Satoru Miyazaki, Hideaki Sugawara

    Journal of Computer Aided Chemistry   7   87 - 93   2006.9

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  • G-InforBIO: integrated system for microbial genomics Reviewed

    Naoto Tanaka, Takashi Abe, Satoru Miyazaki, Hideaki Sugawara

    BMC BIOINFORMATICS   7   368   2006.8

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    Background: Genome databases contain diverse kinds of information, including gene annotations and nucleotide and amino acid sequences. It is not easy to integrate such information for genomic study. There are few tools for integrated analyses of genomic data, therefore, we developed software that enables users to handle, manipulate, and analyze genome data with a variety of sequence analysis programs.
    Results: The G-InforBIO system is a novel tool for genome data management and sequence analysis. The system can import genome data encoded as eXtensible Markup Language documents as formatted text documents, including annotations and sequences, from DNA Data Bank of Japan and GenBank encoded as flat files. The genome database is constructed automatically after importing, and the database can be exported as documents formatted with eXtensible Markup Language or tab-deliminated text. Users can retrieve data from the database by keyword searches, edit annotation data of genes, and process data with G-InforBIO. In addition, information in the G-InforBIO database can be analyzed seamlessly with nine different software programs, including programs for clustering and homology analyses.
    Conclusion: The G-InforBIO system simplifies genome analyses by integrating several available software programs to allow efficient handling and manipulation of genome data. G-InforBIO is freely available from the download site.

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  • Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes Reviewed

    T Abe, H Sugawara, S Kanaya, M Kinouchi, T Ikemura

    GENE   365   27 - 34   2006.1

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    Novel tools are needed for comprehensive comparisons of interspecies characteristics of massive amounts of genomic sequences currently available. An unsupervised neural network algorithm, Self-Organizing Map (SOM), is an effective tool for clustering and visualizing high-dimensional complex data on a single map. We modified the conventional SOM, oil the basis of batch-learning SOM, for genome informatics making the learning process and resulting map independent of the order of data input. We generated the SOMs for tri- and tetranucleotide frequencies in 10- and 100-kb sequence fragments from 38 eukaryotes for which almost complete genome sequences are available. SOM recognized species-specific characteristics (key combinations of oligonucleotide frequencies) in the genomic sequences, permitting species-specific classification of the sequences without any information regarding the species. We also generated the SOM for tetranucleotide frequencies in 1-kb sequence fragments from the human genome and found sequences for four functional categories (5' and 3' UTRs, CDSs and introns) were classified primarily according to the categories. Because the classification and visualization power is very high, SOM is an efficient and powerful tool for extracting a wide range of genome information. (C) 2005 Elsevier B.V. All rights reserved.

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  • Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs): paternally methylated DMRs contain less CpGs than maternally methylated DMRs Reviewed

    H Kobayashi, C Suda, T Abe, Y Kohara, T Ikemura, H Sasaki

    CYTOGENETIC AND GENOME RESEARCH   113 ( 1-4 )   130 - 137   2006

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    Imprinted genes in mammals show monoallelic expression dependent on parental origin and are often associated with differentially methylated regions (DMRs). There are two classes of DMR: primary DMRs acquire gamete-specific methylation in either spermatogenesis or oogenesis and maintain the allelic methylation differences throughout development; secondary DMRs establish differential methylation patterns after fertilization. Targeted disruption of some primary DMRs showed that they dictate the allelic expression of nearby imprinted genes and the establishment of the allelic methylation of secondary DMRs. However, how primary DMRs are recognized by the imprinting machinery is unknown. As a step toward elucidating the sequence features of the primary DMRs, we have determined the extents and boundaries of 15 primary mouse DMRs (including 12 maternally methylated and three paternally methylated DMRs) in 12.5-dpc embryos by bisulfite sequencing. We found that the average size of the DMRs was 3.2 kb and that their average G+C content was 54%. Dinucleotide content analysis of the DMR sequences revealed that, although they are generally CpG rich, the paternally methylated DMRs contain less CpGs than the maternally methylated DMRs. Our findings provide a basis for the further characterization of DMRs. Copyright (c) 2006 S. Karger AG, Basel.

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  • Escherichia coli K-12: a cooperatively developed annotation snapshot - 2005 Reviewed

    M Riley, T Abe, MB Arnaud, MKB Berlyn, FR Blattner, RR Chaudhuri, JD Glasner, T Horiuchi, IM Keseler, T Kosuge, H Mori, NT Perna, G Plunkett, KE Rudd, MH Serres, GH Thomas, NR Thomson, D Wishart, BL Wanner

    NUCLEIC ACIDS RESEARCH   34 ( 1 )   1 - 9   2006

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    The goal of this group project has been to coordinate and bring up-to-date information on all genes of Escherichia coli K-12. Annotation of the genome of an organism entails identification of genes, the boundaries of genes in terms of precise start and end sites, and description of the gene products. Known and predicted functions were assigned to each gene product on the basis of experimental evidence or sequence analysis. Since both kinds of evidence are constantly expanding, no annotation is complete at any moment in time. This is a snapshot analysis based on the most recent genome sequences of two E.coli K-12 bacteria. An accurate and up-to-date description of E.coli K-12 genes is of particular importance to the scientific community because experimentally determined properties of its gene products provide fundamental information for annotation of innumerable genes of other organisms. Availability of the complete genome sequence of two K-12 strains allows comparison of their genotypes and mutant status of alleles.

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  • Characterization of transcriptional regulatory signals with novel bioinformatics tools Reviewed

    Takashi Abe, Hideaki Sugawara, Shigehiko Kanaya, Yoko Kosaka, Toshimichi Ikemura

    DNA STRUCTURE, CHROMATIN AND GENE EXPRESSION, 2006   1 - 16   2006

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    Novel tools are needed for comprehensive comparisons of the inter- and intraspecies characteristics of massive amounts of available genomic sequences. An unsupervised neural network algorithm, Kohonen's Self-Organizing Map (SOM), is an effective tool for clustering and visualizing high-dimensional complex data on a single map. We modified the conventional SOM for genome informatics, making the learning process and resulting map independent of the order of data input. We generated SOMs for tri-, tetra-, and pentanucleotide frequencies in 300,000 10-kb sequences derived from 13 eukaryote genomes for which almost complete sequences are available (a total of 3 Gb), using a high-performance supercomputer, the Earth Simulator. SOM recognized species-specific characteristics (key combinations of oligonucleotide frequencies) in most 10-kb sequences, permitting species-specific classification (self-organization) of sequences without any information regarding the species. Because the classification power is very high, SOM is thought to be an efficient andpowerful tool for extracting a wide range of genomic information. SOM was then constructed with oligonucleotide frequencies in 10-kb sequences from 2.8 Gb of human genome sequences, and the SOM identified oligonucleotides with ftequencies characteristically biased from random occurrence level. Furthermore, 1-kb sequences rich in the biased oligonucleotides were self-organized on the map. Because these oligonucleotides often corresponded to functional signal sequences (e.g. binding sites for transcription factors) or their constituent elements, we could categorize occurrence patterns and frequencies of such pentanucleotides in the human genome that are thought to regulate transcription.

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  • Biological Data Analysis using DDBJ Web services. Reviewed

    Hideaki Sugawara, Satoru Miyazaki, Takashi Abe, Yasumasa Shigemoto

    Proceedings of BIOINFO2005   379 - 382   2005.9

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  • A novel bioinformatics strategy for phylogenetic study of genomic sequence fragments: self-organizing map (SOM) of oligonucleotide frequencies. Reviewed

    Takashi Abe, Toshimichi Ikemura, Shigehiko Kanaya, Makoto Kinouchi, Hideaki Sugawara

    Proceedings of Workshop 2005 on Self-Organizing Maps   669 - 676   2005.9

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  • A large-scale Self-Organizing Map (SOM) constructed with the Earth Simulator unveils sequence characteristics of a wide range of eukaryotic genomes. Reviewed

    Takashi Abe, Hideaki Sugawara, Shigehiko Kanaya, Makoto Kinouchi, Yasaburo Matsuura, Heizo Tokutaka, Toshimichi Ikemura

    Proceedings of Workshop 2005 on Self-Organizing Maps   187 - 194   2005.9

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  • Direct cloning of genes encoding novel xylanases from the human gut Reviewed

    H Hayashi, T Abe, M Sakamoto, H Ohara, T Ikernura, K Sakka, Y Benno

    CANADIAN JOURNAL OF MICROBIOLOGY   51 ( 3 )   251 - 259   2005.3

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    The aim of this study was to identify a novel 1,4-beta-xylanase gene from the mixed genome DNA of human fecal bacteria without bacterial cultivation. Total DNA was isolated from a population of bacteria extracted from fecal microbiota. Using PCR, the gene fragments encoding 5 different family 10 xylanases (xyn10A, xyn10B, xyn10C, xyn10D, and xyn10E) were found. Amino acid sequences deduced from these genes were highly homologous with those of xylanases from anaerobic intestinal bacteria such as Bacteroides spp. and Prevotella spp. Self-organizing map (SOM) analysis revealed that xynA10 was classified into Bacteroidetes. To confirm that one of these genes encodes an active enzyme, a full-length xyn10A gene was obtained using nested primers specific to the internal fragments and random primers. The xyn10A gene encoding the xylanase Xyn10A consists of 1146 bp and encodes a protein of 382 amino acids and a molecular weight of 43 552. Xyn10A was a single module novel xylanase. Xyn10A was purified from a recombinant Escherichia coli strain and characterized. This enzyme was optimally active at 40 degrees C and stable up to 50 degrees C at pH 6.5 and over the pH range 4.0-11.0 at 25 degrees C. In addition, 2 ORFs (ORF1 and ORF2) were identified upstream of xyn10A. These results suggested that many unidentified xylanolytic bacteria exist in the human gut and may contribute to the breakdown of xylan which contains dietary fiber.

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  • Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes Reviewed

    T Uchiyama, T Abe, T Ikemura, K Watanabe

    NATURE BIOTECHNOLOGY   23 ( 1 )   88 - 93   2005.1

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    Recent awareness that most microorganisms in the environment are resistant to cultivation has prompted scientists to directly clone useful genes from environmental metagenomes(1). Two screening methods are currently available for the metagenome approach, namely, nucleotide sequence-based screening(2) and enzyme activity-based screening(3). Here we have introduced and optimized a third option for the isolation of novel catabolic operons, that is, substrate-induced gene expression screening (SIGEX). This method is based on the knowledge that catabolic-gene expression is generally induced by relevant substrates and, in many cases, controlled by regulatory elements situated proximate to catabolic genes. For SIGEX to be high throughput, we constructed an operon-trap gfp-expression vector available for shotgun cloning that allows for the selection of positive clones in liquid cultures by fluorescence-activated cell sorting. The utility of SIGEX was demonstrated by the cloning of aromatic hydrocarbon-induced genes from a groundwater metagenome library and subsequent genome-informatics analysis.

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  • Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples Reviewed

    Takashi Abe, Hideaki Sugawara, Makoto Kinouchi, Shigehiko Kanaya, Toshimichi Ikemura

    DNA Research   12 ( 5 )   281 - 290   2005

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    A self-organizing map (SOM) was developed as a novel bioinformatics strategy for phylogenetic classification of sequence fragments obtained from pooled genome samples of uncultured microbes in environmental and clinical samples. This phylogenetic classification was possible without either orthologous sequence sets or sequence alignments. We first constructed SOMs for tetranucleotide frequencies in 210 000 5 kb sequence fragments obtained from 1502 prokaryotes for which at least 10 kb of genomic sequence has been deposited in public DNA databases. The sequences could be classified primarily according to phylogenetic groups without information regarding the species. We used the SOM method to classify sequence fragments derived from environmental samples of the Sargasso Sea and of an acidophilic biofilm growing in acid mine drainage. Phylogenetic diversity of the environmental sequences was effectively visualized on a single map. Sequences that were derived from a single genome but cloned independently could be reassociated in silico. G + C% has been used for a long period as a fundamental parameter for phylogenetic classification of microbes, but the G + C% is apparently too simple a parameter to differentiate a wide variety of known species. Oligonucleotide frequency can be used to distinguish the species because oligonucleotide frequencies vary significantly among their genomes. © The Author 2006. Kazusa DNA Research Institute.

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  • Splicing Profile Based Protein Categorization between Human and Mouse Genomes by use of the DDBJ Web Services. Reviewed

    Johannes Vastermark, Yasumasa Shigemoto, Takashi Abe, Hideaki Sugawara

    Genome Informatics   15 ( 2 )   13 - 20   2004.12

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    In one scenario of gene evolution, exon shuffling plays a fundamental role in increasing gene diversity. This paper is an appraisal of the biological relevance of categorising proteins by their splicing profiles (exon-intron structures). The central question is whether protein function is more correlated with splicing profiles than sequence similarity, or not. To approach this question, a splicing profile similarity (SPS) index, which measures relative exon length discrepancy, was devised. Arbitrary human proteins were compared, in terms of SPS and amino acid sequence similarity, to their 1) mouse orthologues and 2) human paralogues, which epitomise functional equivalence and non-equivalence, respectively, to methodically elucidate the global relationship between a) biological function, b) splicing profile similarity, and c) sequence similarity. Protein function is more correlated with splicing profile similarity than sequence similarity as demonstrated by the fact that human-mouse orthologues (HMOs) display significantly higher splicing profile similarity than do human-human paralogues (HHPs), despite the mutual sequence similarity between these two categories. This finding indicates that splicing profile-based protein categorisation is biologically meaningful.

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  • Novel genome informatics for unveiling hidden signatures in genome sequences: self-organizing map (SOM) of oligonucleotide frequencies. Reviewed

    Takashi Abe, Toshimichi Ikemura, Shigehiko Kanaya, Makoto Kinouchi, Hideaki Sugawara

    Proceedings of 2004 Workshop on Information-Based Induction Sciences   94 - 99   2004.9

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  • Gene classification based on expression profile using BL-SOM: Suitability assessment of multivariate gene expression data to spherical and plain SOM by N-measure Reviewed

    H Nishio, M Altaf-Ul-Amin, Y Nakamura, K Kurokawa, Y Sinbo, T Abe, M Kinouchi, T Ikemura, K Kobayashi, N Ogasawara, S Kanaya

    8TH WORLD MULTI-CONFERENCE ON SYSTEMICS, CYBERNETICS AND INFORMATICS, VOL VII, PROCEEDINGS   189 - 192   2004

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    Expression profile data for all the genes in a genome can be obtained by transcriptome experiments such as GeneChip and cDNA array systems. Classification of genes in high resolution based on expression profiles may become a key to understand the integrated system in a cell. To attain this purpose, we conduct butch-learning self-organizing map (BL-SOM) for classifying genes based on expression profiles. In the present study, we consider two-types of SOMs based on configuration of units. One of them has planar representation space called "Plain SOM" and the other has spherical space called "Spherical SOM". In general, the profile vectors of gene expression are normalized to unity in length in order to focus not on the absolute quantity of expression but the similarity of the direction. In the present study, we propose a measure for the suitability of SOM to a given data set and confirm that the Spherical SOM is actually suitable for the data on gene expression. Then, we examine biological meanings of gene classification of Bacillus subtilis.

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  • A novel bioinformatics strategy for unveiling hidden characteristics in genome sequences and searching in silico for genetic signal sequences Reviewed

    T Abe, S Kanaya, M Kinouchi, Y Kosaka, T Ikemura

    8TH WORLD MULTI-CONFERENCE ON SYSTEMICS, CYBERNETICS AND INFORMATICS, VOL VII, PROCEEDINGS   105 - 112   2004

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    Novel bioinformatic tools are needed for comprehensive analyses of massive amounts of available genome DNA sequences. An unsupervised neural network algorithm, self-organizing map (SOM), is an effective tool for clustering and visualizing high-dimensional complex data on a single map. We generated SOMs for tri-, tetra-, and pentanucleotide frequencies in 300,000 10-kb sequences from 13 eukaryotes for which almost complete genomic sequences are available (a total of 3 Gb). SOM recognized in most 10-kb sequences species-specific characteristics (key combinations of oligonucleotide frequencies), permitting species-specific classification of sequences without any information regarding the species. Because the classification power is very high, SOM is an efficient and powerful tool for extracting a wide range of genomic information. SOM constructed with oligonucleotide frequencies in 10-kb sequences from 2.8 Gb of human sequences identified oligonucleotides occurring with frequencies characteristically biased from random occurrence predicted from the mononucleotide composition; 10-kb sequences rich in these oligonucleotides were self-organized on a map. Because these oligonucleotides often corresponded to genetic signals or their constituent elements, we propose an in silico method that should be useful for identification of genetic signal sequences in genomes for which large amounts of sequence data are available but additional experimental data are lacking.

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  • Self-organizing map reveals sequence characteristics of 90 prokaryotic and eukaryotic genomes on a single map. Reviewed

    Takashi Abe, Tokio Kozuki, Yoko Kosaka, Atsushi Fukushima, Satoshi Nakagawa, Toshimichi Ikemura

    Proceedings of Workshop 2003 on Self-Organizing Maps   95 - 100   2003.9

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  • Dinucleosome DNA of human K562 cells: Experimental and computational characterizations Reviewed

    M Kato, Y Onishi, Y Wada-Kiyama, T Abe, T Ikemura, S Kogan, A Bolshoy, EN Trifonov, R Kiyama

    JOURNAL OF MOLECULAR BIOLOGY   332 ( 1 )   111 - 125   2003.9

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    Dinucleosome formation is the first step in the organization of the higher order chromatin structure. With the ultimate aim of elucidating the dinucleosome structure, we constructed a library of human dinucleosome DNA. The library consists of PCR-amplifiable DNA fragments obtained by treatment of nuclei of erythroid K562 cells with micrococcal nuclease followed by extraction of DNA and adaptor ligation to the blunt-ended DNA fragments. The library was then cloned using a plasmid vector and the sequences of the clones were determined. The dominating clones containing the Alu elements were removed. A total of 1002 clones, which comprised a dinucleosome database, contained 84 and 918 clones from the clones before and after removing Alu elements, respectively. Approximately 70% of the clones were between 300 and 400 bp in size and they were distributed to various locations of all chromosomes except the Y chromosome. The clones containing A(2)N(8)A(2)N(8)A(2) or T2N8T2N8T2 sequences were classified into three types, Type I (N shape), Type II (V shape) and Type III (M shape) according to DNA curvature plots. The locations of experimentally determined curved DNA segments matched well with the calculated ones though the clones of Types I and Ill showed additional curved DNA segments as revealed by the curvature plots. The distributions of complementary dinucleotides in the nucleosome DNA, at the ends of the dinucleosome DNA clones, allowed us to predict the positions of the nucleosome dyad axis, and estimate the size of the nucleosome core DNA, 125 nt. The distributions of AA and TT dinucleotides, as well as other RR and YY dinucleotides, showed a periodicity with an average period of 10.4 bases, close to the values observed before. Mapping of nucleosome positions in the dinucleosome database based on the observed periodicity revealed that the nucleosomes were separated by a linker of 7.5+ similar to 10 X n nt. This indicates that the nucleosome-nucleosome orientations are, typically, halfway between parallel and antiparallel. Also an important finding is that the distributions of AA/TT and other RR/YY dinucleotides, apparently, reflect both DNA curvature and DNA bendability cooperatively contributing to the nucleosome formation. (C) 2003 Elsevier Ltd. All rights reserved.

    DOI: 10.1016/S0022-2836(03)00838-6

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  • Informatics for unveiling hidden genome signatures Reviewed

    T Abe, S Kanaya, M Kinouchi, Y Ichiba, T Kozuki, T Ikemura

    GENOME RESEARCH   13 ( 4 )   693 - 702   2003.4

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    With the increasing amount of available genome sequences, novel tools are needed for comprehensive analysis of species-specific sequence characteristics for a wide variety of genomes. We used an unsupervised neural network algorithm, a self-organizing map (SOM), to analyze di-, tri-, and tetranucleotide frequencies in a wide variety of prokaryotic and eukaryotic genomes. The SOM, which can cluster complex data efficiently, was shown to be an excellent tool for analyzing global characteristics of genome sequences and for revealing key combinations of oligonucleotides representing individual genomes. From analysis of 1- and 10-kb genomic sequences derived from 65 bacteria (a total of 170 Mb) and from 6 eukaryotes (460 Mb), clear species-specific separations of major portions of the sequences were obtained with the di-, tri-, and tetranucleotide SOMs. The unsupervised algorithm could recognize, in most 10-kb sequences, the species-specific characteristics (key combinations of oligonucleotide frequencies) that are signature features of each genome. We were able to classify DNA sequences within one and between many species into subgroups that corresponded generally to biological categories. Because the classification power is very high, the SOM is an efficient and fundamental bioinformatic strategy for extracting a wide range of genomic information from a vast amount of sequences.

    DOI: 10.1101/gr.634603

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  • A novel bioinformatic strategy for unveiling hidden genome signatures of eukaryotes: self-organizing map of oligonucleotide frequency. Reviewed

    Takashi Abe, Shigehiko Kanaya, Makoto Kinouchi, Yuta Ichiba, Tokio Kozuki, Toshimichi Ikemura

    Genome Informatics   13   12 - 20   2002.12

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    With the increasing amount of available genome sequences, novel tools are needed for comprehensive analysis of species-specific sequence characteristics for a wide variety of genomes. We used an unsupervised neural network algorithm, Kohonen's self-organizing map (SOM), to analyze diand trinucleotide frequencies in 9 eukaryotic genomes of known sequences (a total of 1.2 Gb); <I>S. cerevisiae, S. pombe, C. elegans, A. thaliana, D. melanogaster, Fugu</I>, and rice, as well as <I>P. falciparum</I> chromosomes 2 and 3, and human chromosomes 14, 20, 21, and 22, that have been almost completely sequenced. Each genomic sequence with different window sizes was encoded as a 16-and 64-dimensional vector giving relative frequencies of di- and trinucleotides, respectively. From analysis of a total of 120, 000 nonoverlapping 10-kb sequences and overlapping 100-kb sequences with a moving step size of 10 kb, derived from a total of the 1.2 Gb genomic sequences, clear species-specific separations of most sequences were obtained with the SOMs. The unsupervised algorithm could recognize, in most of the 120, 000 10-kb sequences, the species-specific characteristics (key combinations of oligonucleotide frequencies) that are signature representations of each genome. Because the classification power is very high, the SOMs can provide fundamental bioinformatic strategies for extracting a wide range of genomic information that could not otherwise be obtained.

    DOI: 10.11234/gi1990.13.12

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  • Analysis of codon usage diversity of bacterial genes with a self-organizing map (SOM): characterization of horizontally transferred genes with emphasis on the E. coli O157 genome Reviewed

    S Kanaya, M Kinouchi, T Abe, Y Kudo, Y Yamada, T Nishi, H Mori, T Ikemura

    GENE   276 ( 1-2 )   89 - 99   2001.10

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    With increases in the amounts of available DNA sequence data, it has become increasingly important to develop tools for comprehensive systematic analysis and comparison of species-specific characteristics of protein-coding sequences for a wide variety of genomes. In the present study, we used a novel neural-network algorithm, a self-organizing map (SOM), to efficiently and comprehensively analyze codon usage in approximately 60,000 genes from 29 bacterial species simultaneously. This SOM makes it possible to cluster and visualize genes of individual species separately at a much higher resolution than can be obtained with principal component analysis. The organization of the SOM can be explained by the genome G + C% and tRNA compositions of the individual species. We used SOM to examine codon usage heterogeneity in the E. coli O157 genome, which contains 'O157-unique segments' (O-islands), and showed that SOM is a powerful tool for characterization of horizontally transferred genes. (C) 2001 Elsevier Science B.V. All rights reserved.

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  • Self-organizing mapping in codon usage diversity of bacterial genes. Reviewed

    Makoto Kinouchi, Takashi Abe, Yoshihiro Kudo

    Proceedings of Joint Symposium on Bio-Sensing and Bio-Imaging   243 - 246   2001.8

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  • Gene classification method based on batch-learning SOM. Reviewed

    Takashi Abe, Shigehiko Kanaya, Makoto Kinouchi, Yoshihiro Kudo, Hirotada Mori, Hideo Matsuda, Carlos D. Carpio, Toshimichi Ikemura

    Genome Informatics   10   314 - 315   1999.12

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    DOI: 10.11234/gi1990.10.314

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  • Gene classification by self-organization mapping of codon usage in bacteria with completely sequenced genome. Reviewed

    Shigehiko Kanaya, Yoshihiro Kudo, Takashi Abe, Takanori Okazaki, Carlos D. Carpio, Toshimichi Ikemura

    Genome Informatics   9   369 - 371   1998.12

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    DOI: 10.11234/gi1990.9.369

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Books

  • バイオインフォマティクス入門

    日本バイオインフォマティクス学会編集( Role: Contributor ,  第3章 配列解析)

    慶応義塾大学出版会  2015.8  ( ISBN:9784766422511

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  • 生命のビッグデータ利用の最前線. 3.2 一括学習型自己組織化マップ(BLSOM)を用いた大量メタゲノム解析

    植田充美, 監修, 阿部貴志, 金谷重彦, 池村淑道( Role: Contributor)

    シーエムシー出版  2014.4  ( ISBN:9784781305370

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  • Advances in Viral Genomes Research; Novel bioinformatics method to analyze more than 10,000 influenza virus strains easily at once: Batch-Learning Self Organizing Map (BLSOM).

    Yuki Iwasaki, Toshimichi Ikemura, Kennosuke Wada, Yoshiko Wada, Takashi Abe( Role: Contributor)

    Nova Science Publishers, Inc.  2013.12 

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  • ベーシックマスター分子生物学; 16章 ゲノミクス

    東中川徹, 大山隆, 清水光弘共編, 池村淑道, 阿部貴志( Role: Contributor)

    オーム社  2013.10 

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  • Encyclopedia of Metagenomics; tRNADB-CE and use of tRNAs as phylogenetic markers for metagenomic sequences.

    Karen E. Nelson, Takashi Abe, Hachiro Inokuchi, Yuko Yamada, Akira Muto, Yuki Iwasaki, Toshimichi Ikemura( Role: Contributor)

    Springer  2013.3 

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  • Knowledge-Based Bioinformatics; 10 Sequences from prokaryotic, eukaryotic and viral genomes currently available clustered according to phylotype on a large-scale Self-Organizing Map.

    Gil Alterovitz, Marco Ramoni (Eds, Takashi Abe, Shigehiko Kanaya, Toshimichi Ikemura( Role: Contributor ,  233-249)

    Wiley & Sons, Ltd.  2010.9  ( ISBN:4781301142

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  • マリンメタゲノムの有効利用 第17章 環境由来大量DNA配列を利用した難培養性生物群の系統推定のための新規情報学手法

    松永是, 竹山春子, 阿部貴志, 上原啓史, 金谷重彦, 池村淑道( Role: Joint author ,  228-239)

    シーエムシー出版  2009.8  ( ISBN:4781301142

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  • Computational Biology: New Research; A Linkage Disequilibrium-based Statistical Approach to Discovering Interractions among SNP Alleles at Multiple Loci Contributing to Human Skin Pigmentation Variation.

    Alona S. Russe, Sumiko Anno, Takashi Abe( Role: Joint author ,  19-27)

    Nova Science Publishers  2008.10  ( ISBN:1606920405

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  • 自己組織化マップとその応用 第7章 SOMの医学・生物学からバイオ産業への応用まで;第8章 球面SOMによるゲノム解析

    徳高平蔵, 第, 章 阿部貴志, 池村淑道, 木ノ内誠, 中村由紀子, 前野聖, 金谷重彦, 第8章 松浦弥三郎, 阿部貴志, 池村淑道, 徳高平蔵, 大北正昭( Role: Joint author ,  87-103)

    シュプリンガー・ジャパン株式会社  2007.7  ( ISBN:4431723153

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  • DNAチップ活用テクノロジーと応用 第3章2節 自己組織化法のバイオインフォマティクスへの応用-メタボロームおよびトランスクリプトデータの統合解析に向けて

    久原哲, 編, 中村由紀子, 真保陽子, 矢野美弦, モハマド・アルタフル・アミン, 黒川顕, 阿部貴志, 木ノ内誠, 斉藤和季, 池村淑道, 金谷重彦( Role: Joint author ,  191-200)

    シーエムシー出版  2006.10  ( ISBN:4882315904

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  • DNA structure, Chromatin and Gene Expression; Characterization of transcriptional regulatory signals with novel bioinformatics tools.

    Ryoichi Kiyama, Misuhiro Shimizu (Eds, Takashi Abe, Hideaki Sugawara, Shigehiko Kanaya, Yoko Kosaka, Toshimichi Ikemura( Role: Joint author ,  1-16)

    Transworld Research Network.  2006.1  ( ISBN:8178952289

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  • 生物工学ハンドブック I編2.5.4〔4〕(d) コドン使用頻度と生産収量との関連

    日本生物工学会, 阿部貴志, 金谷重彦, 木ノ内誠, 池村淑道( Role: Joint author ,  131-132)

    コロナ社  2005.6  ( ISBN:4339067342

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  • DDBJの利用法 5.1章 マルチプルアラインメント、5.2章 進化系統解析

    五條堀孝, 菅原秀明, 編, 阿部貴志( Role: Joint author ,  107-127)

    共立出版  2005.5  ( ISBN:4320056299

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  • ゲノミクス・プロテオミクスの新展開 第3編第2章第4節 自己組織化マップ(SOM):比較ゲノムと生物多様性研究への新規な情報学的手法

    今中忠行, 阿部貴志, 金谷重彦, 木ノ内誠, 池村淑道( Role: Joint author ,  890-896)

    エヌ・ティ・エス  2004.4  ( ISBN:4860430492

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  • ゲノムからみた生物の多様性と進化 8. ゲノム配列にひそむ特徴的なサインからみた生物多様性

    五條堀孝, 金谷重彦, 阿部貴志, 木ノ内誠, 池村淑道( Role: Joint author ,  58-64)

    シュプリンガー・フェアラーク東京.  2003.6  ( ISBN:4431710221

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MISC

  • 一括学習型自己組織化マップに基づく水平伝播候補遺伝子の探索法の開発

    阿部貴志, 中尾亮, 杉本千尋

    日本生化学会大会(Web)   90th   ROMBUNNO.4AT27‐02(3P‐1460) (WEB ONLY)   2017

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  • マダニの共生関係に着目した水平伝播候補領域の検出

    松本光司, 菊池亮仁, 中尾亮, 杉本千尋, 池村淑道, 阿部貴志

    日本ゲノム微生物学会年会要旨集   11th   95   2017

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  • 超高速遺伝子解析技術によるマダニ保有微生物の探索

    中尾亮, 中尾亮, QIU Yongjin, 木下豪太, THU May June, 阿部貴志, 片倉賢, 杉本千尋

    日本寄生虫学会大会プログラム・抄録集   85th   83   2016.2

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  • 相対エントロピーによる水平伝播候補領域検出法の開発

    舩山俊介, 中尾亮, 杉本千尋, 阿部貴志

    日本ゲノム微生物学会年会要旨集   9th   81   2015

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  • Unsupervised data mining suitable for evolutionary and genomic studies in the era of big data

    Hiroki Iwasaki, Takashi Abe, Yoshiko Wada, Kennosuke Wada, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   89 ( 6 )   285 - 285   2014.12

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  • Allele-specific gene expression analysis by mouse inter-subspecific genome divergence

    Toyoyuki Takada, Shinji Kondo, Takashi Abe, Hidenori Kiyosawa, Atsushi Toyoda, Asao Fujiyama, Toshihiko Shiroishi

    GENES & GENETIC SYSTEMS   89 ( 6 )   327 - 327   2014.12

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  • 一括学習型自己組織化マップ(BLSOM)法を用いたマダニ保有ウイルス叢の網羅的解析

    KYU EISHIN, NAKAO RYO, ABE TAKASHI, SUGIMOTO CHIHIRO

    日本獣医学会学術集会講演要旨集   157th   406   2014.8

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  • A novel approach, based on BLSOMs (Batch Learning Self-Organizing Maps), to the microbiome analysis of ticks (vol 7, pg 1003, 2013)

    Ryo Nakao, Takashi Abe, Ard M. Nijhof, Seigo Yamamoto, Frans Jongejan, Toshimichi Ikemura, Chihiro Sugimoto

    ISME JOURNAL   8 ( 8 )   1752 - 1752   2014.8

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    Language:English   Publisher:NATURE PUBLISHING GROUP  

    DOI: 10.1038/ismej.2014.83

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  • 遺伝子工学・リモートセンシング・地理情報システムの技術を応用したヒトの環境適応能における遺伝‐環境の相互作用解明への新研究法

    安納住子, 大島一彦, 阿部貴志, 田殿武雄, 山本彩, 五十嵐保

    日本生理人類学会誌   19 ( 1 )   13 - 18   2014.2

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    Language:Japanese   Publisher:Japan Society of Physiological Anthropology  

    To gain a better understanding of the adaptive evolution of human skin pigmentation, we combined genetic engineering, remote sensing, and geographic information systems in a new approach for detecting gene-environment interactions. Previously, we detected natural selection on haplotypes of the OCA2 gene that had been revealed by SNP analyses. In this study, we analyzed ultraviolet radiation data obtained from satellite records. These results were subjected to a spatial statistical analysis technique for analyzing gene-environment interactions. The results suggested that skin color variations may be affected by mutations induced by ultraviolet radiation. These findings are consistent with the hypothesis that global variations in skin pigmentation may have resulted from localized adaptations to different ultraviolet radiation conditions via natural selection.

    DOI: 10.20718/jjpa.19.1_13

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  • Evolutionary changes of vertebrate genome signatures with special focus on coelacanth

    Yuki Iwasaki, Norihiro Okada, Takashi Abe, Kennosuke Wada, Yoshiko Wada, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   88 ( 6 )   381 - 381   2013.12

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  • 遺伝子工学・リモートセンシング・地理情報システムの技術を応用したヒトの環境適応能における遺伝‐環境の相互作用解明への新研究法

    安納住子, 大島一彦, 阿部貴志

    日本生理人類学会誌   18   206 - 207   2013.6

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  • BLSOM解析を活用したマダニ媒介性病原体の検索

    NAKAO RYO, ABE TAKASHI, YAMAMOTO SEIGO, ARD NIJHOF, FRANS JONGEJAN, IKEMURA TOSHIMICHI, SUGIMOTO CHIHIRO

    日本ゲノム微生物学会年会要旨集   7th   57   2013

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  • PJ-002 メタノールを基質とする発電微生物群の集積とメタゲノム解析(ゲノミクス・メタゲノミクス,ポスター発表)

    山室 彩香, 高妻 篤史, 阿部 貴志, 渡邉 一哉

    日本微生物生態学会講演要旨集   ( 29 )   134 - 134   2013

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  • OJ-001 水田土壌を利用した微生物発電に関連する微生物群集の比較メタゲノム解析(ゲノミクス・メタゲノミクス,口頭発表)

    高妻 篤史, 阿部 貴志, 渡邉 一哉

    日本微生物生態学会講演要旨集   ( 29 )   92 - 92   2013

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  • PJ-003 酢酸微生物燃料電池中の微生物群集のメタゲノム解析(ゲノミクス・メタゲノミクス,ポスター発表)

    月田 匠二, 高妻 篤史, 阿部 貴志, 渡邉 一哉

    日本微生物生態学会講演要旨集   ( 29 )   134 - 134   2013

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  • 新規情報学的手法を用いたインフルエンザウイルスのゲノム塩基配列の変化の方向性の予測

    岩崎裕貴, 阿部貴志, 和田健之介, 池村淑道

    生物工学会誌   90 ( 12 )   769 - 772   2012.12

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  • メタゲノム解析による微生物群集構造の解明への 一括学習型自己組織化マップ(BLSOM)の活用

    阿部貴志, 中尾亮, 杉本千尋

    生物工学会誌   90 ( 12 )   765 - 768   2012.12

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  • 次世代ゲノム解析技術により明らかとなりつつあるマダニ保有微生物叢の多様性

    NAKAO RYO, SUGIMOTO CHIHIRO, ABE TAKASHI, YAMAMOTO SEIGO, ARD NIJHOF, FRANS JONGEJAN, IKEMURA TOSHIMICHI

    大原綜合病院年報   52   107   2012.12

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  • ヒトの環境適応能のメカニズムの解明および地球環境変動が及ぼす健康環境影響評価

    安納住子, SURENDRAN Sinnathamby Noble, RAMASAMY Ranjan, 阿部貴志, 大島一彦

    芝浦工業大学特別教育・研究報告集(CD-ROM)   2011   187 - 190   2012.12

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  • Vertebrate genome signatures and its causative factors unveiled by novel bioinformatics strategies

    Toshimichi Ikemura, Yuki Iwasaki, Takashi Abe, Kennosuke Wada

    GENES & GENETIC SYSTEMS   87 ( 6 )   383 - 383   2012.12

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  • Detection of viral segments with oligonucleotide compositions similar with host RNAs for studies of viral adaptation to host

    Yuki Iwasaki, Kennosuke Wada, Taiki Akiba, Ayumi Ogura, Takashi Abe, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   87 ( 6 )   428 - 428   2012.12

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  • インフルエンザウイルスゲノム配列の変化方向の予測

    岩崎裕貴, 和田健之介, 阿部貴志, 池村淑道

    アドバンスシミュレーション   12   56 - 57   2012.6

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  • メタゲノム解析によるマダニ保有微生物叢の検索

    中尾亮, 阿部貴志, 阿部貴志, 山本正悟, NIJHOF Ard, JONGEJAN Frans, 池村淑道, 杉本千尋

    日本獣医学会学術集会講演要旨集   153rd   239   2012.3

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  • マダニ保有微生物叢の解明へ向けたメタゲノム解析技術の応用

    中尾亮, 阿部貴志, 阿部貴志, 山本正悟, NIJHOF Ard, JONGEJAN Frans, 池村淑道, 杉本千尋

    日本寄生虫学会大会プログラム・抄録集   81st   85   2012.2

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  • A novel bioinformatics strategy to investigate characteristics of influenza virus genomes related with their host adaptation

    Yuki Iwasaki, Toshimichi Ikemura, Kennosuke Wada, Masae Itoh, Takashi Abe

    GENES & GENETIC SYSTEMS   86 ( 6 )   419 - 419   2011.12

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  • In Silico analyses of the constant bases of tRNA utilizing "tRNA Gene Database, tRNADB-CE 2011"

    Hachiro Inokuchi, Toshimichi Ikemura, Akira Muto, Yuko Yamada, Takashi Abe

    GENES & GENETIC SYSTEMS   86 ( 6 )   428 - 428   2011.12

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  • Prediction of directional changes of influenza virus genome sequences using by a novel bioinformatics strategy

    Yuki Iwasaki, Takashi Abe, Kennosuke Wada, Masae Itoh, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   85 ( 6 )   397 - 397   2010.12

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  • Phylotype prediction of metagenomic sequences using tRNA gene sequences compiled by tRNADB-CE

    Takashi Abe, Hachiro Inokuchi, Hiroshi Uehara, Yuko Yamada, Akira Muto, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   85 ( 6 )   411 - 411   2010.12

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  • A bioinformatics strategy to clarify microbial community structures by analyzing metagenomic sequences from an environmental sample

    Manabu Ohi, Yuki Iwasaki, Kennosuke Wada, Ikemura Toshimichi, Takashi Abe

    GENES & GENETIC SYSTEMS   85 ( 6 )   410 - 410   2010.12

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  • A novel bioinformatics strategy of searching for useful protein genes for environmental improvement from unexplored genome resources

    Hiroshi Uehara, Chieko Wada, Yuki Nakaizumi, Yuki Iwasaki, Toshimichi Ikemura, Takashi Abe

    GENES & GENETIC SYSTEMS   85 ( 6 )   411 - 411   2010.12

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  • ハプロタイプ構造に基づいたヒト皮膚色候補遺伝子の自然選択の検出

    安納住子, 大島一彦, 阿部貴志

    日本生理人類学会誌   15   70 - 71   2010.10

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  • The hunting Genes contributing to "Human Health" and "Sustainable World" as the educational program for undergraduate and high-school students

    Hiroshi Uehara, Takashi Abe, Yuki Nakaizumi, Chieko Wada, Hachiro Inokuchi, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   84 ( 6 )   482 - 482   2009.12

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  • A novel informatics and visualization method to analyze all influenza A virus genomes on one plane

    Yuki Iwasaki, Takashi Abe, Masae Itoh, Toshimichi Ikemura

    GENES & GENETIC SYSTEMS   84 ( 6 )   447 - 447   2009.12

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  • A novel informatics and visualization method to analyze all influenza A virus genomes on the basis of Batch-Learning Self-Organizing Map

    IWASAKI Yuki, IKEMURA Toshimichi, ITOH Masae, ABE Takashi

    2009 ( 5 )   1 - 6   2009.9

  • 遺伝分野の教育における高校と大学の連携の可能性

    上原啓史, 阿部貴志, 池村淑道

    遺伝   63 ( 1 )   92 - 96   2009.1

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  • 公的データベースからの有用遺伝子の発掘: 持続可能型社会への貢献遺伝子データベースの構築と世界最高水準スーパーコンピュータの利用

    池村淑道, 上原啓史, 棚橋佳世, 阿部貴志

    日本化学会情報化学部会誌   26 ( 2 )   40 - 44   2008.4

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    DOI: 10.11546/cicsj.26.40

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  • エキスパートがキュレートしたtRNAデータベース

    井口八郎, 小原康雄, 武藤あきら, 山田優子, 木ノ内誠, 前野聖, 金谷重彦, 池村淑道, 阿部貴志

    日本化学会情報化学部会誌   26 ( 1 )   11 - 16   2008.4

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    DOI: 10.11546/cicsj.26.11

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  • 持続可能型社会への貢献遺伝子データベース

    上原啓史, 棚橋佳世, 阿部貴志, 池村淑道

    日本化学会情報化学部会誌   26 ( 1 )   17 - 19   2008.4

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  • ゲノム配列情報からの効率的な知識発見のための情報学的手法の確立

    阿部貴志, 金谷重彦, 池村淑道

    日本化学会情報化学部会誌   26 ( 1 )   20 - 22   2008.4

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    DOI: 10.11546/cicsj.26.20

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  • データベースに蓄積の著しい機能未知のタンパク質類の機能推定のための自己組織化マップ法による新規情報学的手法の開発

    阿部貴志, 金谷重彦, 池村淑道

    日本化学会情報化学部会誌   26 ( 2 )   31 - 33   2008.4

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    DOI: 10.11546/cicsj.26.31

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  • Database for genes contributing sustainable world constructed by undergraduate students

    Uehara Hiroshi, Abe Takashi, Tanahashi Kayo, Nakahara Taku, Ohshima Kazuhiko, Ikemura Toshimichi

    GENES & GENETIC SYSTEMS   82 ( 6 )   553 - 553   2007.12

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  • 学部教育としての持続可能型社会への貢献遺伝子データベース構築

    上原啓史, 阿部貴志, 棚橋佳世, 中原拓, 中原拓, 大島一彦, 池村淑道

    情報化学討論会講演要旨集   30th   51 - 52   2007.11

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  • 学部教育としての持続可能型社会への貢献遺伝子データベース構築

    上原啓史, 阿部貴志, 棚橋佳世, 中原拓, 大島一彦, 池村淑道

    日本遺伝学会大会プログラム・予稿集   79th   86   2007.9

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  • 持続可能型社会への貢献遺伝子データベースの構築

    棚橋佳世, 上原啓史, 中原拓, 大島一彦, 阿部貴志, 池村淑道

    生化学   1P-1058   2007

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  • Encounter of Microbiology and data science in the phase of post-genome sequencing

    Sugawara Hideaki, Abe Takashi, Tanaka Naoto, Miyazaki Satoru

    Soil Microorganisms   58 ( 2 )   57 - 67   2004.5

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    DOI: 10.18946/jssm.58.2_57

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    Other Link: http://agriknowledge.affrc.go.jp/RN/2010701558

  • ゲノムDNA配列に潜んでいる生物種の個性を明らかにする新規な統計数理的手法

    阿部貴志, 金谷重彦, 木ノ内誠, 池村淑道

    統計数理   52 ( 1 )   207 - 215   2004.1

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Presentations

  • 微生物ゲノムとメタゲノムからの効率的な知識発見に向けて

    阿部 貴志

    木村資生記念 第2回進化学セミナー  2018.9 

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  • ウイルスゲノムの連続塩基組成を活用した効率的な知識発見 Invited

    阿部 貴志

    進化学会第20回大会  2018.8 

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  • ゲノムアノテーション

    阿部 貴志

    統合データベース講習会AJACS越後  2018.6 

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  • ビッグデータ時代のデータ分析の実践 ~統計分析や機械学習を上手く活用しよう~

    阿部 貴志

    新潟大学産学連携協力会IoT/ビッグデータ研修会  2017.11 

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  • ゲノムデータからの効率的な知識発見に向けた一括学習型自己組織化マップの活用 Invited

    阿部 貴志

    第27回日本数理生物学会年会  2017.10 

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  • シニア研究者の専門知識を活用したtRNA遺伝子データベースtRNADB-CEの運用

    阿部 貴志

    日本遺伝学会第89回大会  2017.9 

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  • 機械学習を活用したゲノムビッグデータからの知識発見

    阿部 貴志

    第1回新潟大学シーズプレゼンテーション  2017.4 

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  • 連続塩基組成に基づくウイルスゲノムの多様性の解明 Invited

    阿部 貴志

    第1回内在性ウイルス様エレメント研究会  2016.12 

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  • 「統計ソフトウェア「R」を活用したデータ分析コース」

    阿部 貴志

    平成28年度 新潟大学高度技術研修  2016.11 

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  • A bioinformatics analysis for efficient knowledge discovery from big sequence data with BLSOM Invited

    ABE Takashi

    2016.3 

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  • メタゲノム解析を活用した新規微生物群の効率的な探索 Invited

    阿部 貴志

    第157回日本獣医学会学術集会  2014.9 

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  • ゲノムアノテーション

    阿部 貴志

    統合データベース講習会:AJASC琉球  2013.7 

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  • Metagenomic analysis for unveiling of microbial diversities within tick guts Invited International conference

    ABE Takashi

    International Union of Microbiological Societies 2011 Congress  2011.9 

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  • 全地球レベルの環境微生物多様性を把握・俯瞰するための新規情報学的手法の開発 Invited

    阿部 貴志

    静岡大学GPLバイオサイエンスセミナー  2011.6 

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  • 学部教育における DDBJ の活用について

    阿部 貴志

    DDBJing講習会  2008.6 

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  • 自己組織化マップ(SOM)によるゲノムとタンパク質配列からの効率的な知識発見 Invited

    阿部 貴志

    化学と生物学を統合する情報学に関するシンポジウム  2007.12 

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Industrial property rights

  • レジオネラ属菌による汚染度の評価方法

    近藤 昭宏, 阿部 貴志

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    Application no:特願2018-030538  Date applied:2018.2

    Announcement no:特開2019-141005  Date announced:2019.8

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  • 「塩基配列の分類システムおよびオリゴヌクレオチド出現頻度の解析システム」

    池村淑道, 金谷重彦, 阿部貴志, 木ノ内誠, 中川智, 上月登喜男

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    Application no:特願2003-328845  Date applied:2003.9

    Announcement no:特開2005-92786  Date announced:2005.4

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Works

Awards

  • 2019年(第81巻)JVMS優秀論文賞

    2020.9   日本獣医学会   Viral population analysis of the taiga tick, Ixodes persulcatus, by using Batch Learning Self-Organizing Maps and BLAST search. The Journal of Veterinary Medical Science 81(3)401-410, 2019

    Yongjin Qiu, Takashi Abe, Ryo Nakao, Kenro Satoh, Chihiro Sugimoto

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  • 日本ゲノム微生物学会研究奨励賞

    2011.3   日本ゲノム微生物学会  

    阿部貴志

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    Award type:Award from Japanese society, conference, symposium, etc.  Country:Japan

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  • 日本生理人類学会優秀論文賞

    2008.6   日本生理人類学会  

    安納住子, 阿部貴志, 西良浩一, 工藤奨, 山本卓志, 緒方是嗣, Vijay K. Goel

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    Award type:Award from Japanese society, conference, symposium, etc.  Country:Japan

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  • 日本進化学会第5回大会最優秀ポスター賞

    2003.8   日本進化学会  

    阿部貴志

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  • 第22回情報科学討論会ポスター賞

    1999.11   社団法人日本化学会情報化学部会  

    阿部貴志, 金谷重彦, 工藤喜弘, 木ノ内誠, 大平賢

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Research Projects

  • Elucidation of the mechanism for auto-penetrating DNA aptamers and their application as post-antibody drugs

    Grant number:19H03512  2019.4 - 2022.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

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    Grant amount:\17290000 ( Direct Cost: \13300000 、 Indirect Cost:\3990000 )

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  • The integrated multi-omics analysis of nontuberculous mycobacteria using neural network algorithms to construct a predictive model of the pathological features

    Grant number:18KT0019  2018.7 - 2021.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

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    Grant type:Competitive

    Grant amount:\18460000 ( Direct Cost: \14200000 、 Indirect Cost:\4260000 )

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  • エキスパートがキュレートしたtRNA遺伝子データベース

    2017.4 - 2022.3

    日本学術振興会  科学研究費助成事業  研究成果公開促進費・データベース

    阿部 貴志

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  • 水平伝播遺伝子予測システムの開発と環境適応と共進化過程の解明

    Grant number:17K00401  2017.4 - 2020.3

    日本学術振興会  科学研究費助成事業 基盤研究(C)  基盤研究(C)

    阿部 貴志, 池村 淑道

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\4550000 ( Direct Cost: \3500000 、 Indirect Cost:\1050000 )

    生物の進化や環境適応には生物種間での遺伝子の水平伝播が大きな役割を果たしていると考えられている.しかしながら,従来の配列相同性検索では水平伝播遺伝子の検出は限界があり,ゲノム全体における水平伝播遺伝子の全容解明には新規解析手法の開発が求められている.
    今年度は,これまで開発してきた水平伝播予測手法のさらなる改良を行った.従来の連続塩基組成のみに着目してゲノム配列断片を生物種別に高精度に分類可能な一括学習型自己組織化マップ(BLSOM)による水平伝播の候補ゲノム領域の検出に加え,近縁種ゲノム間での保存遺伝子の双方向ベストヒット解析を組み合わせる手法を開発した.よりそのゲノムが持つ固有の機能に特化した水平伝播の候補遺伝子検出と由来生物系統の推定が可能となった.南極コケ坊主由来のSphingomonas属細菌2種で評価したところ,水平伝播の由来は大きく異なったが,膜タンパク質など獲得した遺伝子機能に共通性が示唆された.また,アミノ酸組成でも南極株と近縁の他の大陸由来株の遺伝子で差異が認められ,遺伝子の水平伝播に基づく南極細菌の種固有な低温適応戦略の一端を明らかにすることができた.
    さらに,真核生物の共生関係解明のための予測システムとして開発したBLSOMを高速化した自己圧縮型BLSOMを用いた予測システムを用いて,植物と微生物の共生関係下における水平伝播遺伝子の検出を行うべく,7種のモデル植物と微生物ゲノムを対象にした解析を行った.その結果,植物ゲノムと共生細菌である全既知微生物で明瞭な分離が見られたが,各植物ゲノムの1%前後のゲノム配列断片が原核生物由来の領域に分類されていた.
    今後,植物共生細菌などのさらなる実課題での解析を行い,開発手法の更なる改良と活用を目指す.

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  • Elucidation of the function of a novel mouse gene in the central nervous system

    Grant number:16H04686  2016.4 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    TAKADA Toyoyuki

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    Grant amount:\17810000 ( Direct Cost: \13700000 、 Indirect Cost:\4110000 )

    We have previously identified a novel gene, Aobs1 (Ankirin-repeat containing Obesity-associated Brain Stem 1), by QTL analysis using mouse inter-subspecific consomic strains. However, the function of Aobs1 has not been elucidated. In this study, we found that Aobs1 expression levels increased in feeding behavior-associated nerve nucleuses depend on fat content of foods. Aobs1 gene expression levels also linked some genes that control of food intake volume. Overall, our results suggest that the mouse Aobs1 is likely to function in the specific nerve nucleuses for transmission of nutritional signals, such as leptin for food feeding behavior. In addition, Aobs1 mutant mice can be applied experimental animals for the aim of obesity research.

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  • Fundamentals for innovative anaerobic digestion processes using electric syntrophy

    Grant number:15H01753  2015.4 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (A)  Grant-in-Aid for Scientific Research (A)

    Watanabe Kazuya, Kouzuma Atsushi

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    Grant type:Competitive

    Grant amount:\44850000 ( Direct Cost: \34500000 、 Indirect Cost:\10350000 )

    Methanogenic microbiomes were supplemented with conductive nanoparticles for examining their effects on electric syntrophy and methanogenesis. Stimulatory effects of iron-oxide (magnetite) nanoparticles were observed both under static and agitated conditions. Microbiome structures were analyzed under these two conditions, and it was found that Geobacter and Methanosarcina were increased in the presence of magnetite nanoparticles under static conditions, suggesting that electric syntrophy accelerated methanogenesis. On the other hand, only Methanosarcina over grew in the presence of magnetite nanoparticles under agitated conditions. Metagenomic analyses demonstrated acetoclastic methanogenesis was activated by magnetite nanoparticles.

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  • Indicator search for bacterial taxon in the horizontal gene transfer world

    Grant number:15K14595  2015.4 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research  Grant-in-Aid for Challenging Exploratory Research

    BABA Tomoya, ABE takashi

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    Grant amount:\3510000 ( Direct Cost: \2700000 、 Indirect Cost:\810000 )

    It has been suggested that there are existing horizontal gene transfer (HGT) world in the Antarctic lake environments where bacteria had obtained so much genes from other bacteria by their genome analyses. We tried to search some new indicators for bacterial taxon in the HGT world by using bioinformatics of comparative genomics. Our approach is the application of Batch-Learning Self-Organizing Map, BLSOM, that enable each DNA sequence fragments to be clustered with a high degree of accuracy on species of each organism. Our BLSOM analysis suggested that depending on bacterial strains they had obtained genes by HGT from different taxon, however, those gene has common functions. It would be new findings to be start-points of the indicators for bacterial taxon in the HGT world.

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  • Archiving of the symbionts of arthropods for controlling vector-borne diseases

    Grant number:15H05633  2015.4 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (A)  Grant-in-Aid for Young Scientists (A)

    Nakao Ryo, ABE takashi, TANAKA tetsuya

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    Grant amount:\23790000 ( Direct Cost: \18300000 、 Indirect Cost:\5490000 )

    Some of the arthropods such as ticks can carry pathogens to humans and animals. The present study was aimed to disclose the diverse microbiome in such vector arthropods. We found that some bacteria such as Coxiella and Rickettsia dominantly exist in ticks. Comparison between tick phylogeny and bacterial genotypes revealed that ticks have acquired the dominant bacteria via both vertical and horizontal transmission.

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  • The role of protozoa in the emergence of diseases

    Grant number:15K14850  2015.4 - 2018.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research  Grant-in-Aid for Challenging Exploratory Research

    Nakao Ryo, ABE TAKASHI

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    Grant amount:\3900000 ( Direct Cost: \3000000 、 Indirect Cost:\900000 )

    The purpose of this project was to understand the role of protozoa in the emergence of diseases by analyzing microbial diversity harbored by protozoan population in the environment. Water and soil samples were collected in Nakhon Nayok, Thailand and subjected to high-throughput sequencing analysis. More than 200 different bacterial genera were obtained in each sample. However, there was no pathogenic bacterial lineage detected in the analyzed samples. In the eukaryote diversity analysis based on 18S ribosomal RNA (rRNA) amplicons, we found that most of the reads obtained were from algae but not from protozoa. In order to reduce the reads from specific organisms in 18S rRNA PCR, we developed a blocking PCR method using a PNA (Peptide Nucleic Acids) specifically designed for target organisms. This method can be applied to future studies to analyze protozoan diversity in the samples from disease endemic areas.

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  • エキスパートがキュレートしたtRNA遺伝子データベース

    2015.4 - 2017.3

    日本学術振興会  科学研究費助成事業  研究成果公開促進費・データベース

    阿部 貴志

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    Authorship:Principal investigator  Grant type:Competitive

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  • シニア専門家との協働作業による遺伝学関係 データベースのアノテーションの高品質化

    2015.4 - 2016.3

    国立遺伝学研究所共同研究(A)  国立遺伝学研究所共同研究(A) 

    阿部 貴志

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    Authorship:Principal investigator  Grant type:Competitive

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  • Kampo Signal Panelの構築

    2015.4 - 2016.3

    富山大学和漢医薬学総合研究所(S)特定研究  富山大学和漢医薬学総合研究所(S)特定研究 

    阿部 貴志

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  • マダニ保有ウイルス叢の網羅的解明に向けた情報学的手法の開発

    2015.4 - 2016.3

    北海道大学 人獣共通感染症リサーチセンター 一般共同研究  北海道大学 人獣共通感染症リサーチセンター 一般共同研究 

    阿部 貴志

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    Authorship:Principal investigator  Grant type:Competitive

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  • Development of a novel bioinformatics method to analyze big genome sequence data for efficient knowledge discovery

    Grant number:26330327  2014.4 - 2017.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    Abe Takashi

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    Grant type:Competitive

    Grant amount:\4810000 ( Direct Cost: \3700000 、 Indirect Cost:\1110000 )

    As the result of extensive decoding of genome sequences, novel tools are needed for comprehensive analyses of available big sequence data. We previously developed a BLSOM, which can cluster genomic fragment sequences according to phylotype solely dependent on oligonucleotide composition. Howerver, a large-scale BLSOM needs a large computational resource.
    We have developed Self-Compressing BLSOM (SC-BLSOM) for reduction of computation time, which allows us comprehensive analysis of big sequence data. The strategy of SC-BLSOM is to hierarchically construct BLSOMs according to data class such as phylotype. SC-BLSOM could be constructed faster than BLSOM and cluster the sequences according to phylotype with high accuracy. We have also developed a new method to predict protein function on the basis of similarity in oligonucleotide composition. The proteins could be related to function-known proteins. These methods are useful to analyze big sequence data for efficient knowledge discovery.

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  • 水平伝播遺伝子から探る節足動物内での異種共生関係の解明

    2014.4 - 2015.3

    北海道大学 人獣共通感染症リサーチセンター 一般共同研究  北海道大学 人獣共通感染症リサーチセンター 一般共同研究 

    阿部 貴志

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    Authorship:Principal investigator  Grant type:Competitive

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  • シニア専門家との協働作業による遺伝学関係 データベースのアノテーションの高品質化

    2014.4 - 2015.3

    国立遺伝学研究所  国立遺伝学研究所共同研究(A) 

    阿部 貴志

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    Authorship:Principal investigator  Grant type:Competitive

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  • Kampo Signal Panelの構築

    2014.4 - 2015.3

    富山大学和漢医薬学総合研究所(S)特定研究  富山大学和漢医薬学総合研究所(S)特定研究 

    阿部 貴志

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  • Comparative analysis of RNA editing sites in the mouse using intersubspecific consomic strains

    Grant number:25430097  2013.4 - 2016.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    TAKADA TOYOYUKI, ABE TAKASHI, YASAKA TAKU

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    Grant amount:\5200000 ( Direct Cost: \4000000 、 Indirect Cost:\1200000 )

    Japanese wild mice-derived inbred strain MSM/Ms belongs to the Mus musculus molossinus subspecies. It shows highly extent of phenotypic variations in many complex traits and vast amount of genome diversity for the most commonly used inbred strain B6J, genome of which is predominantly derived from west European subspecies M m domesticus. Using B6, MSM and a number of consomic (chromosome substitution) strains, we intend to survey the intersubspecific differences of the RNA editing sites that controlling the energy metabolism-associated phenotypes by the RNA-seq analysis of liver samples. We have used the suitable genome sequences of B6 and MSM allele to generate a list of RNA editing in this tissue. We observed variation in the number of preliminary predicted editing sites with 1,439 in B6 strain and 1,302 in MSM strain being called. Currently, we are exploring causative RNA editing sites that responsible for the energy metabolism associated phenotypic differences between these strains.

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  • メタゲノム解析による新興病原細菌の網羅的探索

    2013.4 - 2014.3

    北海道大学 人獣共通感染症リサーチセンター 一般共同研究  北海道大学 人獣共通感染症リサーチセンター 一般共同研究 

    阿部 貴志

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    Authorship:Principal investigator  Grant type:Competitive

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  • Genome analysis of biosphere of Moss-pillar in an east Antarctic lake

    Grant number:24310150  2012.4 - 2017.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    Baba Tomoya, IMURA Satoshi, TOYODA Atsushi, NAGANUMA Takeshi

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    Grant amount:\20540000 ( Direct Cost: \15800000 、 Indirect Cost:\4740000 )

    All of living organisms have been adapted to global environmental changes on the Earth. It is meaning that they have been rewriting their own genomic information again and again for their survivals, so it would be the first-step to analyze their genomes for the elucidation of adaptation strategies to their living environment. However, it is remaining unsettled of the genomic evaluation for environmental adaptations and evolutionary relationships among related species on the both polar regions and other continents. In order to address the challenge, we have isolated some of bacteria species from the biosphere of a moss pillar in East Antarctica and analyzed the genomes for focusing comparison with ones of related species from other continents. Consequently it was revealed that a lot of genes showed the feature of transferred ones from other species, crossing the species barriers, “horizontal gene transfer (HGT)” in technical terms of evolutionary biology.

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  • 東南極の湖沼におけるコケ坊主生物圏のゲノム解析

    2012.4 - 2016.3

    日本学術振興会  科学研究費助成事業  基盤研究(B)

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  • 次世代シーケンサを活用した病原因子探索、ならびに、病原性獲得機構解明のための情報学的手法の開発

    2012.4 - 2013.3

    北海道大学 人獣共通感染症リサーチセンター 一般共同研究  北海道大学 人獣共通感染症リサーチセンター 一般共同研究 

    阿部 貴志

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  • メタゲノム配列を活用した全地球レベルでの微生物生態系の全体把握のための情報学的手法の開発

    2012.4 - 2013.3

    民間財団等  内田エネルギー科学振興財団試験研究費 

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  • Genomic sequence studies of zoonotic disease viruses including influenza viruses with a novel bioinformatics method

    Grant number:23500371  2011.4 - 2015.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    IKEMURA Toshimichi, ABE Takashi

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    Grant amount:\5330000 ( Direct Cost: \4100000 、 Indirect Cost:\1230000 )

    Influenza virus presents significant threat to public health, and its pandemics has often been initiate by introduction of this virus from animal sources. Prediction of genomic sequence changes and surveillance of potentially hazardous strains that will cause new pandemics are important issues. We analyzed genome sequences with oligonucleotide BLSOMs and found the composition to differ between avian and human strains. Oligonucleotide composition of the pandemic H1N1/09 was different from that of human seasonal strains, and directional changes in composition in the pandemic strains toward seasonal human strains were observed even within the first pandemic year. This study developed new strategies for surveilling potentially hazardous strains that will cause new pandemics among humans.
    By similarly analyzing all ebolavirus genome sequences available, we have also found the time-dependent directional changes in oligonucleotide composition during the recent pandemic in West Africa.

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  • 新規情報学的手法によるインフルエンザを含む人獣共通感染症ウイルスゲノム配列の解析

    2011.4 - 2014.3

    日本学術振興会  科学研究費助成事業  基盤研究(C)

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    我々が開発した「一括学習型自己組織化マップ法BLSOM」を用いて、世界各地で採取された全てのA型インフルエンザ株について、各株の塩基配列の特徴を指標に一枚のマップ上で分類・可視化を可能にする。インフルエンザウィルスの塩基配列は速い速度で変化しているが、BLSOMを用いた予備的な解析は、新型インフルエンザの塩基配列が変化して行く方向が、一部ではあるが予測可能なことを示している。変化方向を予測出来れば、事前準備や予防措置に関して貴重な情報を提供できる。更には、ヒトで流行を起こす可能性のある高病原性の鳥インフルエンザ株について、地球規模での危険地域予測にも貴重な情報を提供できる。多様な宿主から分離されるウィルス株の多量な配列情報の全体を対象に、申請者らが開発したゲノム情報解析手法を用い、宿主との適合性に関しての新規視点での解析を行い、宿主を変えたことで起きるウィルスのゲノム配列の変化方向の予測法を確立する。

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  • メタゲノム資源からの新規微生物探索とその代謝経路予測による環境浄化システムの解明

    2011.4 - 2014.3

    日本学術振興会  科学研究費助成事業  若手研究(B)

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    Grant type:Competitive

    Grant amount:\3400000 ( Direct Cost: \2380000 、 Indirect Cost:\1020000 )

    環境メタゲノム資源から、地球環境改善に役立つ新規微生物ゲノムや、それらが持つ環境浄化システムに関与する有用遺伝子候補の探索手法を開発する。新規性の高いゲノム断片配列を微生物ゲノム別に再構成するためのアノテーション手法が開発できれば、環境が保有する環境浄化システムを構成する微生物や代謝遺伝子セットの全体像が把握できる。既知微生物による浄化に関与する酵素群をカタログ化することによって、様々な微生物が持つ環境浄化システムの全体像把握に向けた情報学的スクリーニング法としての活用も期待できる。

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  • 網羅的な比較ゲノム解析による病原体の生態と病原性獲得機構の解明

    2011.4 - 2012.3

    北海道大学 人獣共通感染症リサーチセンター 一般共同研究  北海道大学 人獣共通感染症リサーチセンター 一般共同研究 

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    Grant type:Competitive

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  • 次世代シークエンス技術導入によるアフリカを中心としたダニ媒介性感染症研究の新展開

    Grant number:23255016  2011 - 2014

    日本学術振興会  科学研究費助成事業 基盤研究(A)  基盤研究(A)

    杉本 千尋, 梶野 喜一, 中村 一郎, 阿部 貴志, 桜井 達也

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    Grant type:Competitive

    Grant amount:\12870000 ( Direct Cost: \9900000 、 Indirect Cost:\2970000 )

    国内(宮崎県、北海道)、オランダ、ガンビアでマダニ7種を採取し、メタゲノム解析を実施した。手法は、虫体を洗浄、破砕後、界面活性剤処理し、2種の孔径のフィルターでろ過し、細菌を濃縮した画分をDNA分解酵素処理して、宿主ゲノムDNAを除去した。その画分からDNAを精製し、全ゲノム増幅後、次世代シークエンサー(454FLX)で塩基配列を決定した。そのうち、300bp以上の断片を自己組織化マップ(BLSOM)法により分析し、DNA断片が由来する細菌の分類群の同定を行った。その結果、50%以上の配列が細菌由来と同定され、属レベルまでの帰属を明らかにすることができた。これと並行して、マダニホモジネートから精製したDNAを用いて細菌16Sリボソーム遺伝子の一部をPCRで増幅し、その産物を次世代シークエンサーで解析し、細菌16Sリボソーム遺伝子データベースに対してBLAST検索し、種同定を行った。
    いずれの解析結果においても、保有細菌叢が1)種間、2)同一種の雌雄間、3)採取地域で差があることが明らかとなった。また、BLSOM解析で人に対して病原性を有すると考えられる種を含む細菌属(Rickettsia, Chlamydia, Francilella, Leptospira等)が検出された。今後、どのような病原体が含まれるのか種レベルまで同定する必要がある。
    また、ザンビア、マレーシアの動物血液ならびにマダニDNAを用いてQ熱病原体(Coxiella burnettii)の保有状況を調査した結果、高率に本病原体の遺伝子が検出できた。その他のマダニ媒介性病原体のスクリーニングでは、人獣共通感染症の病原体となる種は検出できていない。

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  • A bioinformatics strategy for revealing microbial community structures and metabolic pathways by reconstructing multiple genomes from metagenomic sequences.

    Grant number:23710242  2011 - 2013

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)  Grant-in-Aid for Young Scientists (B)

    ABE Takashi

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    Grant amount:\4420000 ( Direct Cost: \3400000 、 Indirect Cost:\1020000 )

    Metagenomics studies of uncultivable microorganisms in clinical and environmental samples should allow extensive surveys of genes useful in medical and industrial applications. BLSOM is the most suitable for phylogenetic assignment of metagenomic sequences because fragmental sequences can be clustered according to phylotypes, solely depending on oligonucleotide composition.
    We constructed oligonucleotide-BLSOMs for all available sequences from species-known genomes, and by mapping metagenomic sequences on this large-scale BLSOMs, we could predict phylotypes of individual metagenomic sequences, revealing a microbial community structure of uncultured microorganisms including viruses. This software will be freely available at our website. We also developed another BLSOM strategy for clustering metagenomic sequences according to genome, and for function prediction of poorly-characterized protein genes obtained from metagenome analysis.

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  • 高性能スーパーコンピュータによるタンパク質の機能推定と一般利用のための公開

    2008.4 - 2011.3

    日本学術振興会  科学研究費助成事業  基盤研究(C)

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    Grant type:Competitive

    ゲノムが解読された際のタンパク質遺伝子の機能を推定する際には、配列相同性検索が重要な技術となるが、この方法で機能が推定できるタンパク質遺伝子は半数程度にとどまる。我々が開発した一括学習型自己組織化マップ法(BLSOM)を、オリゴペプチドの使用頻度に適用したところ、タンパク質が機能により分離(自己組織化)する傾向を示した。2?4連アミノ酸の頻度パターンの類似度を基礎にした機能推定法であり、多次元ベクトル空間の大量情報解析で、高性能なスーパーコンピュータの使用が重要となる。前年度までは、第一世代の地球シミュレータ(ES1)を用いたBLSOM解析を行い、20のアミノ酸を物理化学的な性質の類似度で、11ヘグループ化した3連アミノ酸頻度解析が機能を反映した高い分離(自己組織化)能を与えること、さらには、200アミノ酸のwindowを設けて50アミノ酸のstepで移動させることで、大型タンパク質の機能推定も可能なことを見出し、2009年度に論文として発表した(DNA Res.

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  • 環境由来塩基配列による微生物群集ゲノムシステム解明に向けた新規情報学的手法の開発

    2008.4 - 2011.3

    日本学術振興会  科学研究費助成事業  若手研究(B)

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    メタゲノム解析によって取得された塩基配列は、非常に新規性の高い微生物種を多く含み、これまで解読されてきたゲノムとは異なった特徴を有する場合が多い。新規性の高い生物種由来のゲノム断片配列を連続塩基頻度の特徴のみで生物種ゲノムごとに再構築するための解析手法の開発を行った。ヒト腸内細菌由来の混合メタゲノム解析由来配列を対象に、メタゲノム解析由来配列の塩基組成を反映させたランダム配列を数倍量混在させたBLSOMを作成したところ、同一生物種由来のゲノム配列ごとに分類でき、ゲノム再構築が可能であった。本手法の確立により、構成するゲノムの種数を明らかにでき、生物種別の代謝経路の概要を理解可能となる。様々な環境に対するメタゲノム解析由来配列を対象に検証を実施し、断片化サイズや連続塩基頻度などの最適な解析条件の検討を実施している。

    メタゲノム解析由来配列には、新規性の高い微生物種のみならず、ウイルスゲノムも豊富に

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  • 有用環境ゲノム資源発掘のシステム開発

    2008.4 - 2009.3

    JST  JSTシーズ発掘試験研究 

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    Grant type:Competitive

    未利用な環境ゲノム資源を対象に、大量なゲノム断片の配列決定を行うメタゲノム解析として、産業的に有用な遺伝子を発掘する技術が開発されたが、大半の遺伝子情報は既存の情報学手法での機能推定が困難であった。異なった原理での遺伝子機能推定法の確立が急務である。我々が開発した一括学習型自己組織化マップ(BLSOM)法を技術の核に、「環境由来微生物ゲノムからの有用遺伝子発掘システム」の確立と製品化を目指す。

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  • Function prediction of poorly-characterized protein genes found in genome sequences with high-performance supercomputers and its publication

    Grant number:20510194  2008 - 2010

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    IKEMURA Toshimichi, ABE Takashi

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    Grant amount:\4810000 ( Direct Cost: \3700000 、 Indirect Cost:\1110000 )

    Using Batch-Learning Self-Organizing Map"BLSOM"for di-, tri-and tetrapeptide compositions, we developed a system to enable separation(self-organization) of proteins by function. Analyzing oligopeptide frequencies in proteins previously classified into COGs(clusters of orthologous groups of proteins), BLSOMs could faithfully reproduce the COG classifications. This indicated that proteins, whose functions are unknown because of lack of significant sequence homology with function-known proteins, can be related to function-known proteins based on similarity in oligopeptide composition. BLSOM was applied to predict functions of vast quantities of proteins derived from mixed genomes in environmental samples.

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  • A bioinformatics strategy to clarify microbial community structures by analyzing metagenomic sequences on the basis of Batch-Learning Self-Organizing Map

    Grant number:20700273  2008 - 2010

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)  Grant-in-Aid for Young Scientists (B)

    ABE Takashi

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    Grant amount:\4160000 ( Direct Cost: \3200000 、 Indirect Cost:\960000 )

    Metagenomic approach, which is the genome analysis on a mixture of uncultured microorganisms, has been recently developed to search for novel and industrially useful genes and to study microbial diversity in a wide variety of environments. We have previously developed a Batch-Learning SOM (BLSOM) for genome informatics, which does not depend on the order of data input. Here we used BLSOM as a novel bioinformatics strategy to unveil and visualize microbial community structures and relative abundance of microorganisms within an environmental sample. The present method is also useful for surveys of microorganisms in extremity environment samples and novel pathogenetic microorganisms in clinical samples.

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  • 全ゲノム情報に基づいた病原微生物と常在菌の多様性と病原遺伝子に関する情報学的研究

    2006.4 - 2008.3

    文部科学省  科学研究費助成事業  特定領域研究

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    Grant type:Competitive

    少なくとも10kb以上の断片ゲノム配列がテータベースに存在する2000種を超える既知原核生物種に加えて、約1100種類のウイルス、配列解析の進んでいる約50種類の真核生物、約700種類のオルガネラ配列の全体を5kbに断片化し、地球シミュレータを用いて、4連塩基頻度に関するBLSOM解析を行った。真核と原核生物については96%の高精度で分離していた。オルガネラとウイルス相互や、これらと核ゲノムとの分離も80%レベルと高い。2000種を超える既知原核生物種に関して、25の系統群への分離の度合いを調べると、85%レベルで正しい系統群を反映して分離していた。体内環境や共生生物系を含む環境由来の大半のゲノム断片の系統推定を可能にできた。原核生物で系統群を間違えて分離した15%の配列上には、水平伝播をした外来性的な配列が多く見出され、病原性と関係する遺伝子群が濃縮されている可能性が高い。これらのカタログ化を行った。

    ヒトやマウスの腸内試料を対象にしたメタゲノ

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  • 環境由来DNA配列を用いた難培養性微生物類の多様性解明と系統推定法の確立

    2006.4 - 2008.3

    日本学術振興会  科学研究費助成事業  若手研究(B)

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    Grant type:Competitive

    今年度は、我々が開発してきた一括学習型自己組織化地図マップ法(Batch-Learning Self-Organizing Map, BLSOM)によるオリゴヌクレオチド組成を用いたゲノム断片配列の高精度な生物系統分類法を、実際のメタゲノム解析により取得された環境由来DNA断片配列に適用した。培養が困難な微生物混合試料に由来する配列を対象にした系統分類、異なる環境間での微生物群集の比較解析を可能にするためのワークフローを構築し、ワークフローを実施するためのソフトウェアのプロトタイプの開発を実施した。開発したソフトウェアでは、原核生物・ウイルス・オルガネラ・プラスミドの全配列を用いた大規模なBLSOM上へ、環境由来のゲノム断片配列類をマップし、次に各生物系統群で作成したBLSOMへ、最後は系統群内の微生物種ごとのBLSOM上ヘマップするといった、大分類から逐次的に絞込みを行うことにより、より高精度な微生物種の系統推定が可能となり、合わせて新規性の高いゲノム配列の探索も可

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  • 配列相同性検索に依存しない生物系統と機能推定法の確立と分子進化学への応用

    2006.4 - 2008.3

    日本学術振興会  科学研究費助成事業  基盤研究(C)

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    Grant type:Competitive

    塩基やアミノ酸配列の相同性検索は解読されたゲノムの、生物系統や遺伝子機能推定に不可欠の技術として利用されゲノム解析の基本手法となった。しかしながら、新規性の高いゲノムが解読された際には、配列相同性検索でタンパク質の機能が推定できない遺伝子は半数近くに及ぶ。タンパク質の機能については機能部品類の3次元上での配置が重要であり、同一ないしは類似の機能を持つタンパク質間でも1次元配列上での有意な相同性を見付けられない例が見られる。異なった原理に基づくタンパク質の機能推定法の確立が急務と言える。タンパク質の連続アミノ酸頻度を対象にしたBLSOM法を開発した。機能カテゴリー別のデータベースであるCOGに収録されたタンパク質を解析に用いた。2連アミノ酸頻度、アミノ酸を物理化学的な類似性で11のカテゴリーに集約した上での3連アミノ酸頻度、ならびに6カテゴリーに集約した上での4連アミノ酸頻度に着目したBLSOMを行った。地球シミュレー

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  • 地球温暖化による人類の生存環境および環境適応能に関する研究

    2006.4 - 2008.3

    科学研究費助成事業  萌芽研究

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    Grant type:Competitive

    本研究は,人類の"環境適応能"を明らかにすることにより、地球温暖化やオゾン層破壊による紫外線照射量の増加等の地球環境変動が及ぼすヒトへの健康リスク評価および予測モデルの構築を行うことを目的とし、また、アメリカ・オハイオ州に居住する白人122名を対象に実施した『大気環境の物理化学的要因がヒトの"環境適応能"に及ぼす影響について』(文部科学省科学研究費補助今基盤研究(B))の研究をさらに発展させる研究でもある。

    この人類の環境適応の本態解明に向けて、2局面のアプローチから行う。第1は、リモートセンシング(以下RS)の技術によって人工衛星が収集する大気、植生、水等に関するRSデータを解析することにより、自然生態系の物理的・化学的・生物的資源の特性と機能を明らかにする。第2は、ヒトの環境への適応結果の1つである多様化した皮膚色の形成に関する分子基盤について調べるため、SNP解析を行う。

    日本人100名を対象にデータ収集および試料採取、DNA

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  • 地球温暖化による人類の生存環境および環境適応能に関する研究

    Grant number:18657083  2006 - 2007

    日本学術振興会  科学研究費助成事業 萌芽研究  萌芽研究

    安納 住子, 緒方 是嗣, 阿部 貴志

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    Grant amount:\3300000 ( Direct Cost: \3300000 )

    本研究は,人類の"環境適応能"を明らかにすることにより、地球温暖化やオゾン層破壊による紫外線照射量の増加等の地球環境変動が及ぼすヒトへの健康リスク評価および予測モデルの構築を行うことを目的とし、また、アメリカ・オハイオ州に居住する白人122名を対象に実施した『大気環境の物理化学的要因がヒトの"環境適応能"に及ぼす影響について』(文部科学省科学研究費補助今基盤研究(B))の研究をさらに発展させる研究でもある。
    この人類の環境適応の本態解明に向けて、2局面のアプローチから行う。第1は、リモートセンシング(以下RS)の技術によって人工衛星が収集する大気、植生、水等に関するRSデータを解析することにより、自然生態系の物理的・化学的・生物的資源の特性と機能を明らかにする。第2は、ヒトの環境への適応結果の1つである多様化した皮膚色の形成に関する分子基盤について調べるため、SNP解析を行う。
    日本人100名を対象にデータ収集および試料採取、DNA抽出、PCR、SNP解析を行った。前述の白色人種のSNP解析結果および今回の黄色人種のSNP解析結果を用い、連鎖不平衡解析を行った結果、皮膚色の人種差に影響を及ぼすハプロタイプを発見した。
    ヒトに影響を及ぼす外的要因には、NASA Goddard Space Flight Center提供の単波長の紫外線放射に関する大気リモートセンシングデータを用いることとし、それらのデータの加工を行っている。
    上記のデータおよび解析結果を用い、自然界の動態とヒトの環境適応の結果に代表される皮膚色の形態的・機能的多様性との関係を地球科学的および分子生物学的の2つアプローチから人類の"環境適応能"を解明することにより、地球温暖化やオゾン層破壊による紫外線照射量の増加等の地球環境変動が及ぼすヒトへの健康リスク評価および予測モデルの構築を行う。

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  • 全ゲノム情報に基づいた病原微生物と常在菌の多様性と病原遺伝子に関する情報学的研究

    Grant number:18018015  2006 - 2007

    日本学術振興会  科学研究費助成事業 特定領域研究  特定領域研究

    池村 淑道, 阿部 貴志, 洞田 慎一

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    Grant amount:\3900000 ( Direct Cost: \3900000 )

    少なくとも10kb以上の断片ゲノム配列がテータベースに存在する2000種を超える既知原核生物種に加えて、約1100種類のウイルス、配列解析の進んでいる約50種類の真核生物、約700種類のオルガネラ配列の全体を5kbに断片化し、地球シミュレータを用いて、4連塩基頻度に関するBLSOM解析を行った。真核と原核生物については96%の高精度で分離していた。オルガネラとウイルス相互や、これらと核ゲノムとの分離も80%レベルと高い。2000種を超える既知原核生物種に関して、25の系統群への分離の度合いを調べると、85%レベルで正しい系統群を反映して分離していた。体内環境や共生生物系を含む環境由来の大半のゲノム断片の系統推定を可能にできた。原核生物で系統群を間違えて分離した15%の配列上には、水平伝播をした外来性的な配列が多く見出され、病原性と関係する遺伝子群が濃縮されている可能性が高い。これらのカタログ化を行った。
    ヒトやマウスの腸内試料を対象にしたメタゲノム解析が進行しており、データベースに登録された配列は1Gb分に達している。これらの大量断片配列についてのBLSOM解析を行なっているが、ヒトやマウスの腸内試料で見出された生物多様性は、サルガッソ海を代表とする海洋試料やミネソタの土壌試料に比べれば遥かに低かったが、個体差とその特徴が特定できた。BLSOMを用いると比較的少量しか存在しない生物種由来のゲノム配列についてもゲノム別での再集合が可能になる。
    機能未知タンパク質類の機能推定法を確立する目的で、機能が特定された2853種類のCOGカテゴリーへ分類がなされている、微生物ゲノム由来の約11万個のタンパク質類のアミノ酸配列をテストデータとして用いた。2〜4連アミノ酸頻度を対象に地球シミュレータを用いて大規模BLSOMを作成し、精度高くCOGへの分類を再現する計算条件を見出した。

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  • 環境由来DNA配列を用いた難培養性微生物類の多様性解明と系統推定法の確立

    Grant number:18710176  2006 - 2007

    日本学術振興会  科学研究費助成事業 若手研究(B)  若手研究(B)

    阿部 貴志

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    Grant amount:\3500000 ( Direct Cost: \3500000 )

    今年度は、我々が開発してきた一括学習型自己組織化地図マップ法(Batch-Learning Self-Organizing Map, BLSOM)によるオリゴヌクレオチド組成を用いたゲノム断片配列の高精度な生物系統分類法を、実際のメタゲノム解析により取得された環境由来DNA断片配列に適用した。培養が困難な微生物混合試料に由来する配列を対象にした系統分類、異なる環境間での微生物群集の比較解析を可能にするためのワークフローを構築し、ワークフローを実施するためのソフトウェアのプロトタイプの開発を実施した。開発したソフトウェアでは、原核生物・ウイルス・オルガネラ・プラスミドの全配列を用いた大規模なBLSOM上へ、環境由来のゲノム断片配列類をマップし、次に各生物系統群で作成したBLSOMへ、最後は系統群内の微生物種ごとのBLSOM上ヘマップするといった、大分類から逐次的に絞込みを行うことにより、より高精度な微生物種の系統推定が可能となり、合わせて新規性の高いゲノム配列の探索も可能にした。プロトタイプを用いて詳細な条件検討を行った後に、公開を予定している。
    また、環境由来ゲノム断片配列を対象に、共通の手法で遺伝子を探索し、機能等のアノテーション情報の付与を行うための情報基盤の作成を目的に、ゲノム配列の系統分類用に開発したBLSOMをオリゴペプチド頻度に適用し、その頻度パターンの類似度を基にした遺伝子機能の推定法の開発を実施した。機能既知なタンパク質を対象に解析を実施したところ、タンパク質の機能を反映したクラスタリングが可能であり、相同性検索に依存しないタンパク質の機能推定法として確立できる可能性が示された。メタゲノム解析で得られた機能未知タンパク質遺伝子候補類に適用し、メタゲノム解析で得られた多数のタンパク質の大規模な機能推定を行い、公開する予定である。

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  • Sequence alignment-free method for phylogenetic and functional prediction and its application to molecular evolutionary studies

    Grant number:18570216  2006 - 2007

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    IKEMURA Toshimichi, ABE Takashi

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    Grant amount:\4020000 ( Direct Cost: \3600000 、 Indirect Cost:\420000 )

    The homology search of base and amino acid sequences has become a basic tool in the bioinformatics field, which is essential not only for analyzing the evolution and phylogeny of genes and proteins but also for estimating the function of each protein gene in sequenced genomes. While sequence homology search is obviously useful, this method cannot estimate protein functions for almost half of genes in newly sequenced genomes, especially of novel species. To complement the sequence homology search, it is urgently required to establish methods for estimating protein functions based on different principles. By applying the BLSOM (Batch-learning SOM) method to amino-acid sequences of proteins, we established a function estimation method that utilizes clustering based on the similarity of oligopeptides frequencies. The BL-SOM for oligonucleotide frequencies could recognize genome-specific characteristics of oligonucleotide frequencies in individual genomes, permitting classification (self-organization) of genomic fragment sequences according to species without the need for species information during the calculation. We applied the BLSOMs to phylogenetic and functional prediction of a massive amount of environmental genomic sequences obtained by metagenomic analyses.

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  • Theileria orientalisゲノム完全解読と機能分子の比較解析

    2005.4 - 2008.3

    日本学術振興会  科学研究費助成事業  基盤研究(A)

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    Grant type:Competitive

    牛小型ピロプラズマ原虫、Theileria orientalisの全ゲノムを解読する目的で研究を行った。Whole Genome Shotgun Analysisにより111,954リードのゲノムDNA断片情報を得て、これを整列させ、最終的に80のコンティグとした。さらにギャップクロージングの結果、4本の染色体の完全解読に至った。ゲノムサイズ全長は8,983,596bp(染色体1:2,746,313bp,染色体2:2,216,979bp,染色体3:2,19,511bp,染色体4:2,0,793bp)であった。また、ピロプラズマステージに発現するmRNAについてOligo-capping法、V-Trapper法により完全長cDNAライブラリーを作製、解析し、27,478リードのEST情報を得た。さらに、ESTをゲノム上にマッピングし、3種類の遺伝子予測ソフトで染色体上に存在する遺伝子を予測、それに基づいたオートアノテーションとマニュアルでの校正を実施した。その結果、約3,900の遺伝子領域を確定させた。またゲノム構造比較ソフトによりTheileria parva,T.annulataとのゲノム構造の比較を行った結果、前2者で複数遺伝子コピーが存在する遺伝

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  • 全ゲノム情報に基づいた病原微生物と常在菌の多様性と病原遺伝子に関する情報学的研究

    2005.4 - 2006.3

    文部科学省  科学研究費助成事業  特定領域研究

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    Grant type:Competitive

    難培養性の常在ならびに病原微生物類の多様性と系統推定のための、既知の全ゲノム配列を対象にしたSOMの作成。広範囲の病原微生物類ならびに常在微生物を対象として考えているので原核生物にとどまらず、カビや原虫等の下等真核生物に加えて高等動植物、オルガネラやウイルスやプラスミド等の大量な既知配列を対象にした大規模SOMの作成を行なった。現時点で10kb以上の断片配列が存在する約1500種の原核生物に加えて、約1100種類のウイルス、配列解析の進んでいる約50種類の真核生物、約650種類のミトコンドリア、約50種類の葉緑体の塩基配列の全体を、地球シミュレータを用いて一括して解析した。真核生物と原核生物については96%の高精度で分離されている。オルガネラとウイルス相互や、これらと核ゲノムとの分離も80%レベルと高い。1500の既知原核生物に関して、25の系統群への分離の度合いを調べると、85%レベルで正しい系統群を反映した領域に分離(自己組織化)していた。

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  • Genome analysis of Theileria orientalis and its functional genomics

    Grant number:17208026  2005 - 2007

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (A)  Grant-in-Aid for Scientific Research (A)

    SUGIMOTO Chihiro, INOUE Noboru, HATTORI Masahira, SUGAWARA Hideaki, ABE Takashi, WATANABE Junichi

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    Grant amount:\48750000 ( Direct Cost: \37500000 、 Indirect Cost:\11250000 )

    The complete genome sequence of Theileria orientalis, the causal agent of bovine theileriosis in Japan, was determined. Total genome size is 8,983,596 bp consisting of four chromosomes. Two full-length cDNA libraries from intraerythrocytic piroplasm were constructed by using oligo-capping and vector-trapper methods and conventional cDNA library stage. A total of 27,478 ESTs were mapped on the genome sequence. By using two gene prediction soft-wares, Glimmer 2 and Genewise, about 3,900 genes were predicted, which were subsequently automatically and manually annotated. By comparison of T. orientalis genome with those of T. parva and T. annulata revealed significant structural differences. Among all, T. orientalis contains single copies of genes which are found as tandem-repeated multiple copy gene families in T. parva/annulata, and structures at subtelomeric ends of each chromosome are different.
    By synteny analysis, orthologues of T. parva/annulata schizont and spolozoite proteins were identified. Furthermore, orthologue of T. orientalis band 3 binding protein (TpSCOP) was found and its actin-binding activity and possible role in host cell resistance apoptosis were determined.

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  • 全ゲノム情報に基づいた病原微生物と常在菌の多様性と病原遺伝子に関する情報学的研究

    Grant number:17019018  2005

    日本学術振興会  科学研究費助成事業 特定領域研究  特定領域研究

    池村 淑道, 洞田 慎一, 阿部 貴志

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    Grant amount:\1300000 ( Direct Cost: \1300000 )

    難培養性の常在ならびに病原微生物類の多様性と系統推定のための、既知の全ゲノム配列を対象にしたSOMの作成。広範囲の病原微生物類ならびに常在微生物を対象として考えているので原核生物にとどまらず、カビや原虫等の下等真核生物に加えて高等動植物、オルガネラやウイルスやプラスミド等の大量な既知配列を対象にした大規模SOMの作成を行なった。現時点で10kb以上の断片配列が存在する約1500種の原核生物に加えて、約1100種類のウイルス、配列解析の進んでいる約50種類の真核生物、約650種類のミトコンドリア、約50種類の葉緑体の塩基配列の全体を、地球シミュレータを用いて一括して解析した。真核生物と原核生物については96%の高精度で分離されている。オルガネラとウイルス相互や、これらと核ゲノムとの分離も80%レベルと高い。1500の既知原核生物に関して、25の系統群への分離の度合いを調べると、85%レベルで正しい系統群を反映した領域に分離(自己組織化)していた。このSOM上へ、難培養性の混合ゲノム試料由来の断片配列をマップすることで、どの生物系統に属する配列類がどのような量比で混在していたのかを推定できる。従来の系統推定法とは異なって、オルソロガスな配列セットやそれらとの配列アラインメントが不必要である。従来からの研究の進んでいない生物種に由来する、新規性の高い遺伝子配列類にも適用が可能である。Venterらが報告している、Sargasso海由来の約100万本の断片配列をマップしたところ、86%が原核生物、8%が真核生物、1%がミトコンドリア,1.5%が葉緑体,3.5%がウィルスの領域へ帰属した。原核生物に帰属した配列のうち75%は新規性の高いゲノム由来の配列と推定され、残りの配列ついては、96の属へ帰属できている(DNA Res.,2006)。

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  • 大気環境の物理化学的要因がヒトの環境適応能に及ぼす影響について

    2004.4 - 2007.3

    日本学術振興会  科学研究費助成事業  基盤研究(B)

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    Grant type:Competitive

    本研究では、大気環境中にあるUV等の物理化学的諸要因による環境の違いに対し、反応・適応等を経て表れるヒトの形質(肌色)およびそれに関わる遺伝子多型の違いがどのように関連しているかについて明らかにするために、異なる環境下にあるヒトの遺伝情報、ヒトの適応能に関わる身体的形態および機能に関するデータ、文化的要因に関するデータ、大気リモートセンシングデータの解析結果を収集し、これらすべてのデータを統合・データベースを構築し、特定の時空間における大気環境の物理化学的諸要因とヒトの遺伝的・形態的・機能的多型性との関係について解明することを目的とする。

    白色人種に関するデータとして、アメリカ・オハイオ州在住の白人122名を対象に、遺伝的に支配される生来の皮膚色として背部のメラニン値を、また、環境により修飾される皮膚色として頬中央下部のメラニン値を測定、試料採取、DNA抽出、全ゲノム増幅を行い、メラニン色素が合成・沈着

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  • ゲノム塩基配列に潜む生物種の個性の情報学的探索と生物進化多様性の研究

    2004.4 - 2006.3

    日本学術振興会  科学研究費助成事業  基盤研究(C)

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    Grant type:Competitive

    教師なしニューラルネットワークアルゴリズムの自己組織化マップ(SOM)は大量情報の全体像と部分情報の両方を効率的に把握し、2次元上に可視化できる。ゲノム配列の解読の進んだ真核生物種、ならびにゲノム配列の完全に解読された原核生物の総計約300種のゲノム由来の10と100kbの断片化配列全体に関して、3~5連塩基頻度のSOM解析を行い、各ゲノムを特徴付ける連文字配列の出現パターンを明らかにした。4連や5連塩基頻度のSOM解析には長時間を必要とするが、地球シュミレータを使用できるようになったことで、大規模SOMが可能になった。1kb程度のヒトやマウスの断片配列をSOM解析すると、単一のゲノム内においても、遺伝子上流の転写制御領域、5'と3'UTR、CDS、イントロン領域の相互間で明瞭に分離する傾向を示した。また、これらの各グループ内でも複数のクラスターに分離する傾向を示した。機能と関係するシグナル配列類の候補を探索する新規な情報学的な手段を提供できた。

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  • ゲノムに潜むシグナル・モチーフ部品の網羅的探索のための自己組織化地図

    2004.4 - 2005.3

    文部科学省  科学研究費助成事業  特定領域研究

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    Grant type:Competitive

    ゲノム配列が解読された真核生物種を対象に、4~8連塩基頻度のSOMマップを作成した。高次元ベクトルの大量情報を対象にするので、地球シミュレータを用いた大規模計算を行った。8連塩基については回文型配列にのみ着目した。各生物種で特徴的な出現頻度を持つオリゴヌクレオチドを網羅的に探索することを可能にした。マウスの完全長cDNAをSOM解析したところ、protein-codingとnoncoding cDNA(ncRNA)で分離する傾向にあった。前者については5'と3'UTR、CDSの3領域に分割し、ncRNAを含めた4カテゴリーについてSOMを行ったところ、カテゴリーによる分離が起きており、SOMが各機能領域の配列上の特徴を識別すること判明し、各機能領域を特徴付けるシグナル配列類を抽出できた。

    SOM解析で得られた特徴的な連文字配列の生物学的な意味を知るためには、各連文字配列について、実験的な研究を報告した文献類を組織的に参照することが重要になる。この文献検索の過程で蓄積する検索情報を「GenomeWo

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  • The impact of the physical and chemical factors of atmospheric environment on men's environmental adaptabilities

    Grant number:16370108  2004 - 2006

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)  Grant-in-Aid for Scientific Research (B)

    ANNO Sumiko, OKI Kazuo, OGATA Koretsugu, ABE Takashi

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    Grant amount:\14700000 ( Direct Cost: \14700000 )

    The study aims to clarify molecular basis of human skin color diversity and investigate environmental adaptability to ultraviolet irradiation in order to predict human health risk influenced by severe environments in the future.
    Two approaches to this research are considered as the research method. The one is to identify and measure physical/chemical factors of atmospheric environment (i.e., an ultraviolet ray and infrared rays like the solar radiation energy), which affects men with the technologies of remote sensing (RS). The other is to clarify the process of men's morphological/functional diversity appearance through a reaction, adaptation, etc. to the environment by the combination of those factors or one factor at a molecule, a gene, a cell, and an individual level.
    One hundred and twenty-two Caucasians living in Toledo, Ohio participated in this study. Their back and cheek were measured for melanin value for skin pigmentation index as a quantitative trait. Their buccal cells as samples were collected and used for DNA extraction. DNA was used for SNP genotyping with the technology of Masscode^<TM> system that involves the two-step PCR amplification and comprises a platform chemistry of cleavable mass spectrometry tags.
    Genotype and allele frequencies for 20 SNPs in 122 Caucasians were calculated with the data obtained from the SNP genotyping. To examine the contribution of non-random associations of SNP alleles at multiple loci (not necessarily on the same chromosome) to skin color variation (ie, low/high melanin content), linkage disequilibrium (LD) coefficients (D) were calculated between 20 SNPs. Linkage disequilibrium was analyzed by application of a _X^2 test ; statistical significance was set at 0.05. Combinations of SNP alleles at multiple loci under LD were jointly tested for association with low/high melanin by performing a x2 test of independence. Only data under the assumption of Hardy-Weinberg equilibrium were used in the analysis.
    Our results show that SNP alleles at multiple loci associated with low and high melanin are not independent and indicate a high possibility of LD structure--despite the fact that the alleles are not on the same chromosome. Similar investigations must be performed with samples from non-Caucasians in order to confirm the association of LD with melanin content.
    Our overarching goal is to use remote sensing data to clarify interactions between atmospheric environments and SNP allele frequency and to investigate environmental adaptability to UV irradiation. The resulting data would help in predicting the impact of environmental changes such high UV exposure secondary to ozone depletion on health risk.

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  • Bioinformatics strategy for unveiling hidden genome signatures and biodiversity

    Grant number:16570190  2004 - 2005

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)  Grant-in-Aid for Scientific Research (C)

    IKEMURA Toshimichi, HORATA Shinichi, ABE Takashi, FUKAGAWA Tasuo

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    Grant amount:\3600000 ( Direct Cost: \3600000 )

    Novel tools are needed for comprehensive comparisons of interspecies characteristics of massive amounts of genomic sequences currently available. An unsupervised neural network algorithm, Self-Organizing Map (SOM), is an effective tool for clustering and visualizing high-dimensional complex data on a single map. We modified the conventional SOM, on the basis of batch-learning SOM, for genome informatics making the learning process and resulting map independent of the order of data input. We generated the SOMs for tri-and tetranucleotide frequencies in 10-and 100-kb sequence fragments from 38 eukaryotes for which almost complete genome sequences are available. SOM recognized species-specific characteristics (key combinations of oligonucleotide frequencies) in the genomic sequences, permitting species-specific classification of the sequences without any information regarding the species. We also generated the SOM for tetranucleotide frequencies in 1-kb sequence fragments from the human genome and found sequences for four functional categories (5' and 3' UTRs, CDSs and introns) were classified primarily according to the categories. Because the classification and visualization power is very high, SOM is an efficient and powerful tool for extracting a wide range of genome information.
    SOM that was constructed with oligonucleotide frequencies in 10-kb sequences from human genome sequences identified oligonucleotides with frequencies characteristically biased from random occurrence level, and 10-kb sequences rich in these biased oligonucleotides were self-organized on the map. Because these oligonucleotides often corresponded to functional signal sequences (e.g. binding sites for transcription factors) or their constituent elements, we categorized occurrence patterns and frequencies of such pentanucleotides in the human genome that are thought to regulate transcription. SOM analysis is dependent only on oligonucleotide frequencies and thus applicable even for the sequenced genomes with little additional experimental data. In order to know TSS, experimental data were required, but to know start sites of protein-coding sequences, such data were not required in most cases. When known signal sequences of various species with enough experimental data are characterized systematically, we can develop an in silico method of signal sequence prediction for a wide range of species. Recently, we have developed a novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from uncultured microorganism mixtures in environmental and clinical samples

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  • ゲノムに潜むシグナル・モチーフ部品の網羅的探索のための自己組織化地図

    Grant number:16014225  2004

    日本学術振興会  科学研究費助成事業 特定領域研究  特定領域研究

    池村 淑道, 高野 敏行, 阿部 貴志

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    Grant amount:\3600000 ( Direct Cost: \3600000 )

    ゲノム配列が解読された真核生物種を対象に、4〜8連塩基頻度のSOMマップを作成した。高次元ベクトルの大量情報を対象にするので、地球シミュレータを用いた大規模計算を行った。8連塩基については回文型配列にのみ着目した。各生物種で特徴的な出現頻度を持つオリゴヌクレオチドを網羅的に探索することを可能にした。マウスの完全長cDNAをSOM解析したところ、protein-codingとnoncoding cDNA(ncRNA)で分離する傾向にあった。前者については5'と3'UTR、CDSの3領域に分割し、ncRNAを含めた4カテゴリーについてSOMを行ったところ、カテゴリーによる分離が起きており、SOMが各機能領域の配列上の特徴を識別すること判明し、各機能領域を特徴付けるシグナル配列類を抽出できた。
    SOM解析で得られた特徴的な連文字配列の生物学的な意味を知るためには、各連文字配列について、実験的な研究を報告した文献類を組織的に参照することが重要になる。この文献検索の過程で蓄積する検索情報を「GenomeWordDictionary」と呼ぶ新規なデータベースとして構築した。4連続塩基は完成し、5連続塩基を編纂中である。
    Venterらはバーミューダ沖の海中微生物群の混合ゲノムDNAを回収し、80万本の断片配列を決定し約120万の遺伝子の候補を推定した。SOMは新規性の高い配列類の系統分類に最適な方法である。10kb以上の配列がデータベースに収録されている約1500種の既知原核生物種の総計1Gbの配列を5kbに断片化し、4連続塩基頻度のSOMを行い25の系統群への分類を解析したところ、約85%の配列が正しい系統を反映して分離していた。Venterらの環境由来の大量な断片配列を、そのSOM上へマップすることで、約12,000の新規配列を92の属へ帰属できた。

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Teaching Experience (researchmap)

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Teaching Experience

  • 論文輪講

    2022
    Institution name:新潟大学

  • 人工知能特論

    2021
    Institution name:新潟大学

  • データ工学

    2020
    Institution name:新潟大学

  • 知能情報システム概論

    2020
    Institution name:新潟大学

  • 情報工学演習

    2020
    -
    2021
    Institution name:新潟大学

  • 情報工学実験II

    2020
    -
    2021
    Institution name:新潟大学

  • 情報工学実験I

    2020
    -
    2021
    Institution name:新潟大学

  • 工学リテラシー入門(情報電子分野)

    2019
    Institution name:新潟大学

  • 情報システム基礎実習

    2018
    Institution name:新潟大学

  • プログラミング基礎Ⅱ

    2017
    Institution name:新潟大学

  • プログラミング基礎Ⅰ

    2017
    Institution name:新潟大学

  • プログラミング基礎実習

    2016
    Institution name:新潟大学

  • 形式言語とオートマトン

    2015
    Institution name:新潟大学

  • 情報数理演習III

    2015
    Institution name:新潟大学

  • 自然科学総論Ⅲ

    2014
    -
    2020
    Institution name:新潟大学

  • 情報工学研究発表(外部発表)

    2014
    -
    2015
    Institution name:新潟大学

  • 情報工学セミナーⅡ

    2014
    -
    2015
    Institution name:新潟大学

  • 情報工学特定研究Ⅱ

    2014
    -
    2015
    Institution name:新潟大学

  • 情報工学文献詳読Ⅱ

    2014
    Institution name:新潟大学

  • ゲノム情報解析特論

    2013
    Institution name:新潟大学

  • ゲノム情報解析概論

    2013
    Institution name:新潟大学

  • 情報工学基礎実習II

    2013
    -
    2021
    Institution name:新潟大学

  • プログラミング実習II

    2013
    -
    2018
    Institution name:新潟大学

  • バイオインフォマティクス入門

    2013
    -
    2018
    Institution name:新潟大学

  • プログラミングII

    2013
    -
    2018
    Institution name:新潟大学

  • 情報工学基礎実習I

    2013
    -
    2017
    Institution name:新潟大学

  • 情報工学文献詳読Ⅰ

    2013
    -
    2015
    Institution name:新潟大学

  • 情報工学セミナーⅠ

    2013
    -
    2015
    Institution name:新潟大学

  • 情報工学発表演習(中間発表)

    2013
    -
    2015
    Institution name:新潟大学

  • 情報工学特定研究Ⅰ

    2013
    -
    2015
    Institution name:新潟大学

  • バイオインフォマティクス概論

    2012
    Institution name:新潟大学

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Social Activities

  • 電子情報通信学会信越支部主催 100周年記念フォーラム

    Role(s): Planner, Organizing member

    電子情報通信学会信越支部  2017.9

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    Audience: General, Company, Governmental agency

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  • JSTイノベーションジャパン

    Role(s): Demonstrator

    2017.8

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    Audience: General, Company

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  • 出前講義(新潟明訓高等学校)

    Role(s): Lecturer

    2017.6

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    Audience: High school students

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  • 日本寄生虫学会主催 サイエンスカフェ「観て, 触って, 知ろう 身近な微生物 と その研究者!」

    Role(s): Demonstrator

    日本寄生虫学会  2017.5

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    Audience: Junior students, High school students, College students, General

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  • 第1回新潟大学シーズプレゼンテーション

    Role(s): Lecturer

    新潟大学  2017.4

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    Audience: General, Company

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  • 平成28年度 新潟大学高度技術研修 「統計ソフトウェア「R」を活用したデータ分析コース」

    Role(s): Lecturer

    新潟大学  2016.11

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    Audience: General

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  • 名古屋大学大学院医学系研究科 非常勤講師

    Role(s): Lecturer

    2016.11

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    Audience: Graduate students, Researchesrs

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  • 出前講義(福島県立白河高等学校)

    Role(s): Lecturer

    2016.9

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    Audience: High school students

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Academic Activities

  • 文部科学省 科学技術・学術政策研究所 NISTEP専門調査員

    Role(s): Planning/Implementing academic research

    2019.4

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    Type:Academic research 

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