A Quadruple Revolution: Deciphering Biological Complexity with Artificial Intelligence, Multiomics, Precision Medicine, and Planetary Health
Yi Cong, Toshinori Endo
OMICS: A Journal of Integrative Biology, 2024年06月01日
研究論文（学術雑誌）

Inference of selective forces on house mouse genomes during secondary contact in East Asia
Kazumichi Fujiwara, Shunpei Kubo, Toshinori Endo, Toyoyuki Takada, Toshihiko Shiroishi, Hitoshi Suzuki, Naoki Osada
Genome Research, 2024年03月20日
研究論文（学術雑誌）

Advancing Antibody-antigen Interface Analysis in Docking Scoring Functions for Precision Docking Analysis
Sangeetha Ratnayake, Axel Martinelli, Toshinori Endo, Naoki Osada
IPSJ Transactions on Bioinformatics, 17, 40, 47, Information Processing Society of Japan, 2024年
研究論文（学術雑誌）

Exploring The Interplay Between Scoring Functions and Physico-chemical Properties in Antibody-antigen Docking
Sangeetha Ratnayake, Axel Martinelli, Toshinori Endo, Naoki Osada
IPSJ Transactions on Bioinformatics, 17, 10, 17, Information Processing Society of Japan, 2024年
研究論文（学術雑誌）

Current trends in RNA virus detection through metatranscriptome sequencing data.
So Nakagawa, Shoichi Sakaguchi, Atsushi Ogura, Katsuhiko Mineta, Toshinori Endo, Yoshiyuki Suzuki, Takashi Gojobori
FEBS open bio, 13, 6, 992, 1000, 2023年05月10日, ［国際誌］
英語, 研究論文（学術雑誌）, With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.

Multi-Omics and Artificial Intelligence-Guided Drug Repositioning: Prospects, Challenges, and Lessons Learned from COVID-19
Yi Cong, Toshinori Endo
OMICS: A Journal of Integrative Biology, 26, 7, 361, 371, Mary Ann Liebert Inc, 2022年07月01日, ［査読有り］, ［招待有り］, ［最終著者, 責任著者］
研究論文（学術雑誌）

疾患特異的遺伝子発現データに対する機械学習と教師なしクラスタリングを用いた新しい2段階のドラッグリポジショニング予測法
CONG Yi, 新谷美咲, 今成楓河, 長田直樹, 遠藤俊徳
情報処理学会研究報告(Web), 26, 6, 339, 347, Mary Ann Liebert Inc, 2022年06月01日, ［査読有り］, ［最終著者, 責任著者］

Whole-Genome Sequencing of Vero E6 (VERO C1008) and Comparative Analysis of Four Vero Cell Sublines
Kazuhiro Konishi, Toshiyuki Yamaji, Chisato Sakuma, Fumio Kasai, Toshinori Endo, Arihiro Kohara, Kentaro Hanada, Naoki Osada
Frontiers in Genetics, 13, 1, 9, 2022年03月22日, ［査読有り］
英語, 研究論文（学術雑誌）

Predicting PRDM9 Binding Sites by a Convolutional Neural Network and Verification Using Genetic Recombination Map
Takahiro Nakamura, Toshinori Endo, Naoki Osada
IPSJ Transactions on Bioinformatics, 15, 9, 16, Information Processing Society of Japan, 2022年
研究論文（学術雑誌）

Identification of Characteristic Genomic Markers in Human Hepatoma HuH-7 and Huh7.5.1-8 Cell Lines
Masaki Kawamoto, Toshiyuki Yamaji, Kyoko Saito, Yoshitaka Shirasago, Kazuhiro Satomura, Toshinori Endo, Masayoshi Fukasawa, Kentaro Hanada, Naoki Osada
Frontiers in Genetics, 11, 546106, 546106, Frontiers Media SA, 2020年10月09日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, The human hepatoma-derived HuH-7 cell line and its derivatives (Huh7.5 and Huh7.5.1) have been widely used as a convenient experimental substitute for primary hepatocytes. In particular, these cell lines represent host cells suitable for propagating the hepatitis C virus (HCV) in vitro. The Huh7.5.1-8 cell line, a subline of Huh7.5.1, can propagate HCV more efficiently than its parental cells. To provide genomic information for cells' quality control, we performed whole-genome sequencing of HuH-7 and Huh7.5.1-8 and identified their characteristic genomic deletions, some of which are applicable to an in-house test for cell authentication. Among the genes related to HCV infection and replication, 53 genes were found to carry missense or loss-of-function mutations likely specific to the HuH-7 and/or Huh7.5.1-8. Eight genes, including DDX58 (RIG-I), BAX, EP300, and SPP1 (osteopontin), contained mutations observed only in Huh7.5.1-8 or mutations with higher frequency in Huh7.5.1-8. These mutations might be relevant to phenotypic differences between the two cell lines and may also serve as genetic markers to distinguish Huh7.5.1-8 cells from the ancestral HuH-7 cells.

Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes.
Hiro Takahashi, Shido Miyaki, Hitoshi Onouchi, Taichiro Motomura, Nobuo Idesako, Anna Takahashi, Masataka Murase, Shuichi Fukuyoshi, Toshinori Endo, Kenji Satou, Satoshi Naito, Motoyuki Itoh
Scientific reports, 10, 1, 16289, 16289, 2020年10月01日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, Upstream open reading frames (uORFs) are present in the 5'-untranslated regions of many eukaryotic mRNAs, and some peptides encoded by these regions play important regulatory roles in controlling main ORF (mORF) translation. We previously developed a novel pipeline, ESUCA, to comprehensively identify plant uORFs encoding functional peptides, based on genome-wide identification of uORFs with conserved peptide sequences (CPuORFs). Here, we applied ESUCA to diverse animal genomes, because animal CPuORFs have been identified only by comparing uORF sequences between a limited number of species, and how many previously identified CPuORFs encode regulatory peptides is unclear. By using ESUCA, 1517 (1373 novel and 144 known) CPuORFs were extracted from four evolutionarily divergent animal genomes. We examined the effects of 17 human CPuORFs on mORF translation using transient expression assays. Through these analyses, we identified seven novel regulatory CPuORFs that repressed mORF translation in a sequence-dependent manner, including one conserved only among Eutheria. We discovered a much higher number of animal CPuORFs than previously identified. Since most human CPuORFs identified in this study are conserved across a wide range of Eutheria or a wider taxonomic range, many CPuORFs encoding regulatory peptides are expected to be found in the identified CPuORFs.

Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA.
Hiro Takahashi, Noriya Hayashi, Yuta Hiragori, Shun Sasaki, Taichiro Motomura, Yui Yamashita, Satoshi Naito, Anna Takahashi, Kazuyuki Fuse, Kenji Satou, Toshinori Endo, Shoko Kojima, Hitoshi Onouchi
BMC genomics, 21, 1, 260, 260, 2020年03月30日, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, BACKGROUND: Upstream open reading frames (uORFs) in the 5'-untranslated regions (5'-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST between Arabidopsis and any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups. RESULTS: To efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 89 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved across wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides. CONCLUSIONS: This study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.

Computational Drug-repositioning Approach Identifying Sirolimus as a Potential Therapeutic Option for Inflammatory Dilated Cardiomyopathy.
Kyoko Shibata, Toshinori Endo, Yoshikazu Kuribayashi
Drug research, 69, 10, 565, 571, 2019年10月, ［査読有り］, ［国際誌］
英語, 研究論文（学術雑誌）, OBJECTIVE: The aim of this study was to determine promising treatment options for human inflammatory dilated cardiomyopathy using a computational drug-repositioning approach (repurposing established drug compounds for new therapeutic indications). BACKGROUND: If the myocardial tissue is detected to be infiltrated with inflammatory cells, primarily of lymphocytes, and if the virus is confirmed using genetic examination (PCR) or immunostaining, the infection is suspected. However, there is no specific treatment (i. e., an antiviral drug) even if the virus is identified; therefore, we used Connectivity Map to identify compounds showing inverse drug-disease signatures, indicating activity against inflammatory dilated cardiomyopathy. RESULTS: Potential drug-repositioning candidates for the treatment of inflammatory dilated cardiomyopathy were explored through a systematic comparison of the gene expression profiles induced by drugs using Gene Expression Omnibus and Connectivity Map databases. CONCLUSION: Using a computational drug-repositioning approach based on the integration of publicly available gene expression signatures of drugs and diseases, sirolimus was suggested as a novel therapeutic option for inflammatory dilated cardiomyopathy.

Achiasmy and sex chromosome evolution
Kazuhiro Satomura, Naoki Osada, Toshinori Endo
Ecological Genetics and Genomics, 13, 100045, 2019年09月, ［査読有り］, ［最終著者］
英語, 研究論文（学術雑誌）

Comprehensive phylogenomic analysis reveals a novel cluster of simian endogenous retroviral sequences in Colobinae monkeys
Masaki Ikeda, Kazuhiro Satomura, Tsuyoshi Sekizuka, Kentaro Hanada, Toshinori Endo, Naoki Osada
American Journal of Primatology, e22882, 2018年06月, ［査読有り］
英語, 研究論文（学術雑誌）

A Generalized Linear Model for Decomposing Cis-regulatory, Parent-of-Origin, and Maternal Effects on Allele-Specific Gene Expression
Yasuaki Takada, Ryutaro Miyagi, Aya Takahashi, Toshinori Endo, Naoki Osada
G3-GENES GENOMES GENETICS, 7, 7, 2227, 2234, GENETICS SOCIETY AMERICA, 2017年07月, ［査読有り］
英語, 研究論文（学術雑誌）, Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory (i.e., allelic genotype), genomic imprinting [i.e., parent-of-origin (PO)], and maternal [i.e., maternal genotype (MG)] effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the efficiency of method using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found little evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified dozens and hundreds of mouse genes with significant PO and MG effects, respectively. Interestingly, a similar number of genes with significant PO effect were detect in mouse TSCs and livers, whereas more genes with significant MG effect were observed in livers. Further application of this method will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.

旧世界ザルにおけるサルレトロウイルスの内在化に関する進化系統解析
池田 昌輝, 遠藤 俊徳, 長田 直樹
霊長類研究 Supplement, 32, Supplement, 59, 59, 日本霊長類学会, 2016年
日本語,

旧世界ザルのゲノムには、サルレトロウイルス（SRV）と相同なDNA塩基配列を持つ内在性サルレトロウイルス（SERV）のDNA塩基配列が存在することが知られている。SERVの多くは挿入や欠損などを含んだ不完全な状態でゲノムに存在するが、一部は完全な状態を保っていることが報告されている。また、不完全なSERV配列が組換えを起こすことによって完全な状態になり感染性を再獲得する可能性がある。さらに、旧世界ザルの細胞は細胞製材として使用されているため、SERV感染の可能性は医学的にも非常に重要な問題であるが、SERVが旧世界ザルのゲノム中にどのように分布、進化したかは明らかになっていない。これらの問題に答えるために本研究では、アフリカミドリザル（Chlorocebus sabaeus）、アカゲザル（Macaca mulatta）、アヌビスヒヒ（Papio anubis）、ヒト（Homo sapiens）のゲノム配列に存在するSERV配列を網羅的に探索し、それらの配列を用いて分子系統学的解析を行った。解析は、系統樹作成や同義置換率と非同義置換率の計算を行った。マルチプルアライメントの結果から、旧世界ザルのゲノムに存在する一部のSERVは、全てのタンパク質をコードしている状態でゲノム上に存在していることがわかった。また、得られた系統樹から、SRVとSERVは2つのクラスターに分かれていることもわかった。さらに、探索して得られた塩基配列の非同義置換率と同義置換率を調べて機能的制約の有無を確認したところ、挿入や欠損を含まない塩基配列は機能的制約を受けていることがわかった。解析の結果から、旧世界ザルのゲノム上に完全な状態で存在する内在性サルレトロウイルスは、過去に感染したSRVが機能を失われないままの状態で残っている可能性が示唆された。

Guidelines for the Nomenclature of Genetic Elements in Tunicate Genomes
Stolfi, Alberto, Sasakura, Yasunori, Chalopin, Domitille, Satou, Yutaka, Christiaen, Lionel, Dantec, Christelle, Endo, Toshinori, Naville, Magali, Nishida, Hiroki, Swalla, Billie J, Volff, Jean-Nicolas, Voskoboynik, Ayelet, Dauga, Delphine, Lemaire, Patrick
GENESIS, 53, 1:::SI, 1, 14, WILEY-BLACKWELL, 2015年01月, ［査読有り］
英語, 研究論文（学術雑誌）

Sustained Heterozygosity Across a Self-Incompatibility Locus in an Inbred Ascidian
Satou, Yutaka, Hirayama, Kazuko, Mita, Kaoru, Fujie, Manabu, Chiba, Shota, Yoshida, Reiko, Endo, Toshinori, Sasakura, Yasunori, Inaba, Kazuo, Satoh, Nori
MOLECULAR BIOLOGY AND EVOLUTION, 32, 1, 81, 90, OXFORD UNIV PRESS, 2015年01月, ［査読有り］
英語, 研究論文（学術雑誌）, Because self-incompatibility loci are maintained heterozygous and recombination within self-incompatibility loci would be disadvantageous, self-incompatibility loci are thought to contribute to structural and functional differentiation of chromosomes. Although the hermaphrodite chordate, Ciona intestinalis, has two self-incompatibility genes, this incompatibility system is incomplete and self-fertilization occurs under laboratory conditions. Here, we established an inbred strain of C. intestinalis by repeated self-fertilization. Decoding genome sequences of sibling animals of this strain identified a 2.4-Mbheterozygous region on chromosome 7. A self-incompatibility gene, Themis-B, was encoded within this region. This observation implied that this self-incompatibility locus and the linkage disequilibrium of its flanking region contribute to the formation of the 2.4-Mb heterozygous region, probably through recombination suppression. We showed that different individuals in natural populations had different numbers and different combinations of Themis-B variants, and that the rate of self-fertilization varied among these animals. Our result explains why self-fertilization occurs under laboratory conditions. It also supports the concept that the Themis-B locus is preferentially retained heterozygous in the inbred line and contributes to the formation of the 2.4-Mb heterozygous region. High structural variations might suppress recombination, and this long heterozygous region might represent a preliminary stage of structural differentiation of chromosomes.

Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands
Keisuke Ueno, Katsuhiko Mineta, Kimihito Ito, Toshinori Endo
BMC STRUCTURAL BIOLOGY, 12, 5, BIOMED CENTRAL LTD, 2012年04月, ［査読有り］, ［最終著者, 責任著者］
英語, 研究論文（学術雑誌）, Background: Structural genomics approaches, particularly those solving the 3D structures of many proteins with unknown functions, have increased the desire for structure-based function predictions. However, prediction of enzyme function is difficult because one member of a superfamily may catalyze a different reaction than other members, whereas members of different superfamilies can catalyze the same reaction. In addition, conformational changes, mutations or the absence of a particular catalytic residue can prevent inference of the mechanism by which catalytic residues stabilize and promote the elementary reaction. A major hurdle for alignment-based methods for prediction of function is the absence (despite its importance) of a measure of similarity of the physicochemical properties of catalytic sites. To solve this problem, the physicochemical features radially distributed around catalytic sites should be considered in addition to structural and sequence similarities.
Results: We showed that radial distribution functions (RDFs), which are associated with the local structural and physicochemical properties of catalytic active sites, are capable of clustering oxidoreductases and transferases by function. The catalytic sites of these enzymes were also characterized using the RDFs. The RDFs provided a measure of the similarity among the catalytic sites, detecting conformational changes caused by mutation of catalytic residues. Furthermore, the RDFs reinforced the classification of enzyme functions based on conventional sequence and structural alignments.
Conclusions: Our results demonstrate that the application of RDFs provides advantages in the functional classification of enzymes by providing information about catalytic sites.

Proteomic Profiling Reveals Compartment-Specific, Novel Functions of Ascidian Sperm Proteins
Mia Nakachi, Ayako Nakajima, Mamoru Nomura, Kouki Yonezawa, Keisuke Ueno, Toshinori Endo, Kazuo Inaba
MOLECULAR REPRODUCTION AND DEVELOPMENT, 78, 7, 529, 549, WILEY-BLACKWELL, 2011年07月, ［査読有り］
英語, 研究論文（学術雑誌）, In this study, we performed extensive proteomic analysis of sperm from the ascidian Ciona intestinalis. Sperm were fractionated into heads and flagella, followed by further separation into Triton X-100-soluble and -insoluble fractions. Proteins from each fraction and whole sperm were separated by isoelectric focusing using two different pH ranges, followed by SDS-PAGE at two different polyacrylamide concentrations. In total, 1,294 protein spots representing 304 non-redundant proteins were identified by mass spectrometry (MALDI-TOF). On comparison of the proteins in each fraction, we were able to identify the proteins specific to different sperm compartments. Further comparison with the testis proteome allowed the pairing of proteins with sperm-specific functions. Together with information on gene expression in developing embryos and adult tissues, these results provide insight into novel cellular and functional aspects of sperm proteins, such as distinct localization of actin isoforms, novel Ca-2 vertical bar-binding proteins in axonemes, localization of testis-specific serine/threonine kinase, and the presence of G-protein coupled signaling and ubiquitin pathway in sperm flagella. Mol. Reprod. Dev. 78: 529-549, 2011. (C) 2011 Wiley-Liss, Inc.

Predicted expansion of the claudin multigene family
Katsuhiko Mineta, Yasuko Yamamoto, Yuji Yamazaki, Hiroo Tanaka, Yukiyo Tada, Kuniaki Saito, Atsushi Tamura, Michihiro Igarashi, Toshinori Endo, Kosei Takeuchi, Sachiko Tsukita
FEBS LETTERS, 585, 4, 606, 612, ELSEVIER SCIENCE BV, 2011年02月, ［査読有り］
英語, 研究論文（学術雑誌）, Claudins (Cldn) are essential membrane proteins of tight junctions (TJs), which form the paracellular permselective barrier. They are produced by a multi-gene family of 24 reported members in mouse and human. Based on a comprehensive search combined with phylogenetic analyses, we identified three novel claudins (claudin-25, -26, and -27). Quantitative RT-PCR revealed that the three novel claudins were expressed in a tissue- and/or developmental stage-dependent manner. Claudins-25 and -26, but not claudin-27, were immunofluorescently localized to TJs when exogenously expressed in cultured MDCK and Eph epithelial cell lines. These findings expand the claudin family to include at least 27 members.
Structured summary:
Claudin-25 and ZO-1 colocalize by fluorescence microscopy (View interaction)
ZO-1 and Claudin-26 colocalize by fluorescence microscopy (View interaction) (C) 2011 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments
Lixy Yamada, Mamoru Nomura, Michio Ogasawara, Junko Yaguchi, Hiroki Takahashi, Alu Konno, Ayako Nakajima, Sasakura Yasunori, Akiyasu Yoshizawa, Toshinori Endo, Hisaaki Taniguchi, Keisuke Ueno, Chisato Yamasaki, Kouki Yonezawa, Miho Sera, Katsuhiko Mineta, Tadashi Imanishi, Kazuo Inaba, Kohji Hotta, Mia Nakachi, Yutaka Satou
Nature Precedings, Springer Science and Business Media LLC, 2011年01月06日
研究論文（学術雑誌）, Abstract

CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata. Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans. Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data. The CIPRO database is aimed at not only collecting published data, but also presenting unique information, including the unpublished transcriptomic and proteomic data and human curated annotation, for the use by researchers in broad research fields of biology and bioinformatics.

CIPRO 2.5: Ciona intestinalis protein database, a unique integrated repository of large-scale omics data, bioinformatic analyses and curated annotation, with user rating and reviewing functionality
Toshinori Endo, Keisuke Ueno, Kouki Yonezawa, Katsuhiko Mineta, Kohji Hotta, Yutaka Satou, Lixy Yamada, Michio Ogasawara, Hiroki Takahashi, Ayako Nakajima, Mia Nakachi, Mamoru Nomura, Junko Yaguchi, Yasunori Sasakura, Chisato Yamasaki, Miho Sera, Akiyasu C. Yoshizawa, Tadashi Imanishi, Hisaaki Taniguchi, Kazuo Inaba
NUCLEIC ACIDS RESEARCH, 39, suppl, D807, D814, OXFORD UNIV PRESS, 2011年01月, ［筆頭著者, 責任著者］
英語, 研究論文（学術雑誌）, The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includes original large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite of developmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and gene expression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analyses at various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequences, but for higher usability it covers 89 683 all known and predicted proteins from all gene models for this species. Of these sequences, more than 10 000 proteins have been manually annotated. Furthermore, to establish a community-supported protein database, these annotations are open to evaluation by users through the CIPRO website. CIPRO 2.5 is freely accessible at http://cipro.ibio.jp/2.5.

CIPRO 2.5
Endo Toshinori, Ueno Keisuke, Yonezawa Kouki, Mineta Katsuhiko, Hotta Kohji, Satou Yutaka, Yamada Lixy, Ogasawara Michio, Takahashi Hiroki, Nakajima Ayako, Nakachi Mia, Nomura Mamoru, Yaguchi Junko, Sasakura Yasunori, Yamasaki Chisato, Sera Miho, Yoshizawa Akiyasu C, Imanishi Tadashi, Taniguchi Hisaaki, Inaba Kazuo
Nucleic Acids Research, 39, SUPPL. 1, 2011年01月
英語, <p>The Ciona intestinalis protein database (CIPRO) is an integrated protein database for the tunicate species C. intestinalis. The database is unique in two respects: first, because of its phylogenetic position, Ciona is suitable model for understanding vertebrate evolution; and second, the database includesoriginal large-scale transcriptomic and proteomic data. Ciona intestinalis has also been a favorite ofdevelopmental biologists. Therefore, large amounts of data exist on its development and morphology, along with a recent genome sequence and geneexpression data. The CIPRO database is aimed at collecting those published data as well as providing unique information from unpublished experimental data, such as 3D expression profiling, 2D-PAGE and mass spectrometry-based large-scale analysesat various developmental stages, curated annotation data and various bioinformatic data, to facilitate research in diverse areas, including developmental, comparative and evolutionary biology. For medical and evolutionary research, homologs in humans and major model organisms are intentionally included. The current database is based on a recently developed KH model containing 36 034 unique sequenc

CIPRO 2.5: Ciona intestinalis Protein Database - a unique integrated repository of large-scale omics data, bioinformatic analyses, and curated annotation, with ability for user rating and comments
Endo, Toshinori, Ueno, Keisuke, Yonezawa, Kouki, Mineta, Katsuhiko, Hotta, Kohji, Satou, Yutaka, Yamada, Lixy, Ogasawara, Michio, Takahashi, Hiroki, Nakajima, Ayako, Nakachi, Mia, Nomura, Mamoru, Yaguchi, Junko, Konno, Alu, Sasakura, Yasunori, Yoshizawa, Akiyasu C, Taniguchi, Hisaaki, Yamasaki, Chisato, Sera, Miho, Imanishi, Tadashi, Inaba, Kazuo
GENOME BIOLOGY, 11, Suppl. 1, 0, 0, BIOMED CENTRAL LTD, 2010年01月, ［査読有り］
英語, 研究論文（学術雑誌）

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
Chisato Yamasaki, Katsuhiko Murakami, Yasuyuki Fujii, Yoshiharu Sato, Erimi Harada, Jun-Ichi Takeda, Takayuki Taniya, Ryuichi Sakate, Shingo Kikugawa, Makoto Shimada, Motohiko Tanino, Kanako O. Koyanagi, Roberto A. Barrero, Craig Gough, Hong-Woo Chun, Takuya Habara, Hideki Hanaoka, Yosuke Hayakawa, Phillip B. Hilton, Yayoi Kaneko, Masako Kanno, Yoshihiro Kawahara, Toshiyuki Kawamura, Akihiro Matsuya, Naoki Nagata, Kensaku Nishikata, Akiko Ogura Noda, Shin Nurimoto, Naomi Saichi, Hiroaki Sakai, Ryoko Sanbonmatsu, Rie Shiba, Mami Suzuki, Kazuhiko Takabayashi, Aiko Takahashi, Takuro Tamura, Masayuki Tanaka, Susumu Tanaka, Fusano Todokoro, Kaori Yamaguchi, Naoyuki Yamamoto, Toshihisa Okido, Jun Mashima, Aki Hashizume, Lihua Jin, Kyung-Bum Lee, Yi-Chueh Lin, Asami Nozaki, Katsunaga Sakai, Masahito Tada, Satoru Miyazaki, Takashi Makino, Hajime Ohyanagi, Naoki Osato, Nobuhiko Tanaka, Yoshiyuki Suzuki, Kazuho Ikeo, Naruya Saitou, Hideaki Sugawara, Claire O'Donovan, Tamara Kulikova, Eleanor Whitfield, Brian Halligan, Mary Shimoyama, Simon Twigger, Kei Yura, Kouichi Kimura, Tomohiro Yasuda, Tetsuo Nishikawa, Yutaka Akiyama, Chie Motono, Yuri Mukai, Hideki Nagasaki, Makiko Suwa, Paul Horton, Reiko Kikuno, Osamu Ohara, Doron Lancet, Eric Eveno, Esther Graudens, Sandrine Imbeaud, Marie Anne Debily, Yoshihide Hayashizaki, Clara Amid, Michael Han, Andreas Osanger, Toshinori Endo, Michael A. Thomas, Mika Hirakawa, Wojciech Makalowski, Mitsuteru Nakao, Nam-Soon Kim, Hyang-Sook Yoo, Sandro J. De Souza, Maria de Fatima Bonaldo, Yoshihito Niimura, Vladimir Kuryshev, Ingo Schupp, Stefan Wiemann, Matthew Bellgard, Masafumi Shionyu, Libin Jia, Danielle Thierry-Mieg, Jean Thierry-Mieg, Lukas Wagner, Qinghua Zhang, Mitiko Go, Shinsei Minoshima, Masafumi Ohtsubo, Kousuke Hanada, Peter Tonellato, Takao Isogai, Ji Zhang, Boris Lenhard, Sangsoo Kim, Zhu Chen, Ursula Hinz, Anne Estreicher, Kenta Nakai, Izabela Makalowska, Winston Hide, Nicola Tiffin, Laurens Wilming, Ranajit Chakraborty, Marcelo Bento Soares, Maria Luisa Chiusano, Yutaka Suzuki, Charles Auffray, Yumi Yamaguchi-Kabata, Takeshi Itoh, Teruyoshi Hishiki, Satoshi Fukuchi, Ken Nishikawa, Sumio Sugano, Nobuo Nomura, Yoshio Tateno, Tadashi Imanishi, Takashi Gojobori
NUCLEIC ACIDS RESEARCH, 36, D, D793, D799, OXFORD UNIV PRESS, 2008年01月
英語, 研究論文（学術雑誌）, Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, proteinprotein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees
Akihiro Matsuya, Ryuichi Sakate, Yoshihiro Kawahara, Kanako O. Koyanagi, Yoshiharu Sato, Yasuyuki Fujii, Chisato Yamasaki, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Kaori Yamaguchi, Toshinori Endo, Satoshi Oota, Wojciech Makalowski, Kazuho Ikeo, Yoshiyuki Suzuki, Kousuke Hanada, Katsuyuki Hashimoto, Momoki Hirai, Hisakazu Iwama, Naruya Saitou, Aiko T. Hiraki, Lihua Jin, Yayoi Kaneko, Masako Kanno, Katsuhiko Murakami, Akiko Ogura Noda, Naomi Saichi, Ryoko Sanbonmatsu, Mami Suzuki, Jun-Ichi Takeda, Masayuki Tanaka, Takashi Gojobori, Tadashi Imanishi, Takeshi Itoh
NUCLEIC ACIDS RESEARCH, 36, Database-Issue, D787, D792, OXFORD UNIV PRESS, 2008年01月, ［査読有り］
英語, 研究論文（学術雑誌）, Orthologs are genes in different species that evolved from a common ancestral gene by speciation. Currently, with the rapid growth of transcriptome data of various species, more reliable orthology information is prerequisite for further studies. However, detection of orthologs could be erroneous if pairwise distance-based methods, such as reciprocal BLAST searches, are utilized. Thus, as a sub-database of H-InvDB, an integrated database of annotated human genes (http://h-invitational.jp/), we constructed a fully curated database of evolutionary features of human genes, called Evola. In the process of the ortholog detection, computational analysis based on conserved genome synteny and transcript sequence similarity was followed by manual curation by researchers examining phylogenetic trees. In total, 18 968 human genes have orthologs among 11 vertebrates (chimpanzee, mouse, cow, chicken, zebrafish, etc.), either computationally detected or manually curated orthologs. Evola provides amino acid sequence alignments and phylogenetic trees of orthologs and homologs. In 'd(N)/d(S) view', natural selection on genes can be analyzed between human and other species. In 'Locus maps', all transcript variants and their exon/intron structures can be compared among orthologous gene loci. We expect the Evola to serve as a comprehensive and reliable database to be utilized in comparative analyses for obtaining new knowledge about human genes. Evola is available at http://www.h-invitational.jp/evola/.

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.
Satou Y, Mineta K, Ogasawara M, Sasakura Y, Shoguchi E, Ueno K, Yamada L, Matsumoto J, Wasserscheid J, Dewar K, Wiley GB, Macmil SL, Roe BA, Zeller RW, Hastings KE, Lemaire P, Lindquist E, Endo T, Hotta K, Inaba K
Genome biology, 9, 10, R152, BIOMED CENTRAL LTD, 2008年, ［査読有り］
英語, 研究論文（学術雑誌）, Background: The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene prediction programs and in part to the fragmented nature of the assembly.
Results: We have prepared a less-fragmented assembly on the basis of scaffold-joining guided by paired-end EST and bacterial artificial chromosome (BAC) sequences, and BAC chromosomal in situ hybridization data. The new assembly (115.2 Mb) is similar in length to the initial assembly (116.7 Mb) but contains 1,272 (approximately 50%) fewer scaffolds. The largest scaffold in the new assembly incorporates 95 initial-assembly scaffolds. In conjunction with the new assembly, we have prepared a greatly improved global gene model set strictly correlated with the extensive currently available EST data. The total gene number (15,254) is similar to that of the initial set (15,582), but the new set includes 3,330 models at genomic sites where none were present in the initial set, and 1,779 models that represent fusions of multiple previously incomplete models. In approximately half, 5'-ends were precisely mapped using 5'-full-length ESTs, an important refinement even in otherwise unchanged models.
Conclusion: Using these new resources, we identify a population of non-canonical (non-GT-AG) introns and also find that approximately 20% of Ciona genes reside in operons and that operons contain a high proportion of single-exon genes. Thus, the present dataset provides an opportunity to analyze the Ciona genome much more precisely than ever.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones
T Imanishi, T Itoh, Y Suzuki, C O'Donovan, S Fukuchi, KO Koyanagi, RA Barrero, T Tamura, Y Yamaguchi-Kabata, M Tanino, K Yura, S Miyazaki, K Ikeo, K Homma, A Kasprzyk, T Nishikawa, M Hirakawa, J Thierry-Mieg, D Thierry-Mieg, J Ashurst, LB Jia, M Nakao, MA Thomas, N Mulder, Y Karavidopoulou, LH Jin, S Kim, T Yasuda, B Lenhard, E Eveno, Y Suzuki, C Yamasaki, J Takeda, C Gough, P Hilton, Y Fujii, H Sakai, S Tanaka, C Amid, M Bellgard, MD Bonaldo, H Bono, SK Bromberg, AJ Brookes, E Bruford, P Carninci, C Chelala, C Couillault, SJ de Souza, MA Debily, MD Devignes, Dubchak, I, T Endo, A Estreicher, E Eyras, K Fukami-Kobayash, GR Gopinath, E Graudens, Y Hahn, M Han, ZG Han, K Hanada, H Hanaoka, E Harada, K Hashimoto, U Hinz, M Hirai, T Hishiki, Hopkinson, I, S Imbeaud, H Inoko, A Kanapin, Y Kaneko, T Kasukawa, J Kelso, P Kersey, R Kikuno, K Kimura, B Korn, Kuryshev, V, Makalowska, I, T Makino, S Mano, R Mariage-Samson, J Mashima, H Matsuda, HW Mewes, S Minoshima, K Nagai, H Nagasaki, N Nagata, R Nigam, O Ogasawara, O Ohara, M Ohtsubo, N Okada, T Okido, S Oota, M Ota, T Ota, T Otsuki, D Piatier-Tonneau, A Poustka, SX Ren, N Saitou, K Sakai, S Sakamoto, R Sakate, Schupp, I, F Servant, S Sherry, R Shiba, N Shimizu, M Shimoyama, AJ Simpson, B Soares, C Steward, M Suwa, M Suzuki, A Takahashi, G Tamiya, H Tanaka, T Taylor, JD Terwilliger, P Unneberg, Veeramachaneni, V, S Watanabe, L Wilming, N Yasuda, HS Yoo, M Stodolsky, W Makalowski, M Go, K Nakai, T Takagi, M Kanehisa, Y Sakaki, J Quackenbush, Y Okazaki, Y Hayashizaki, W Hide, R Chakraborty, K Nishikawa, H Sugawara, Y Tateno, Z Chen, M Oishi, P Tonellato, R Apweiler, K Okubo, L Wagner, S Wiemann, RL Strausberg, T Isogai, C Auffray, N Nomura, T Gojobori, S Sugano
PLOS BIOLOGY, 2, 6, 856, 875, PUBLIC LIBRARY SCIENCE, 2004年06月, ［査読有り］
英語, 研究論文（学術雑誌）, The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for nonprotein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.

Standardized phylogenetic tree: A reference to discover functional evolution
T Endo, S Ogishima, H Tanaka
JOURNAL OF MOLECULAR EVOLUTION, 57, S174, S181, SPRINGER, 2003年, ［査読有り］
英語, 研究論文（学術雑誌）, Functional evolution is often driven by positive natural selection. Although it is thought to be rare in evolution at the molecular level, its effects may be observed as the accelerated evolutionary rates. Therefore one of the effective ways to identify functional evolution is to identify accelerated evolution. Many methods have been developed to test the statistical significance of the accelerated evolutionary rate by comparison with the appropriate reference rate. The rates of synonymous substitution are one of the most useful and popular references, especially for large-scale analyses. On the other hand, these rates are applicable only to a limited evolutionary time period because they saturate quickly-i.e., multiple substitutions happen frequently because of the lower functional constraint. The relative rate test is an alternative method. This technique has an advantage in terms of the saturation effect but is not sufficiently powerful when the evolutionary rate differs considerably among phylogenetic lineages. For the aim to provide a universal reference tree, we propose a method to construct a standardized tree which serves as the reference for accelerated evolutionary rate. The method is based upon multiple molecular phylogenies of single genes with the aim of providing higher reliability. The tree has averaged and normalized branch lengths with standard deviations for statistical neutrality limits. The standard deviation also suggests the reliability level of the branch order. The resulting tree serves as a reference tree for the reliability level of the branch order and the test of evolutionary rate acceleration even when some of the species lineages show an accelerated evolutionary rate for most of their genes due to bottlenecking and other effects.

The genome sequence and structure of rice chromosome 1
T Sasaki, T Matsumoto, K Yamamoto, K Sakata, T Baba, Y Katayose, JZ Wu, Y Niimura, ZK Cheng, Y Nagamura, BA Antonio, H Kanamori, S Hosokawa, M Masukawa, K Arikawa, Y Chiden, M Hayashi, M Okamoto, T Ando, H Aoki, K Arita, M Hamada, C Harada, S Hijishita, M Honda, Y Ichikawa, A Idonuma, M Iijima, M Ikeno, S Ito, T Ito, Y Ito, Y Ito, A Iwabuchi, K Kamiya, W Karasawa, S Katagiri, A Kikuta, N Kobayashi, Kono, I, K Machita, T Maehara, H Mizuno, T Mizubayashi, Y Mukai, H Nagasaki, M Nakashima, Y Nakama, Y Nakamichi, M Nakamura, N Namiki, M Negishi, Ohta, I, N Ono, S Saji, K Sakai, M Shibata, T Shimokawa, A Shomura, JY Song, Y Takazaki, K Terasawa, K Tsuji, K Waki, H Yamagata, H Yamane, S Yoshiki, R Yoshihara, K Yukawa, HS Zhong, H Iwama, T Endo, H Ito, JH Hahn, HI Kim, MY Eun, M Yano, JM Jiang, T Gojohori
NATURE, 420, 6913, 312, 316, NATURE PUBLISHING GROUP, 2002年11月, ［査読有り］
英語, 研究論文（学術雑誌）, The rice species Oryza sativa is considered to be a model plant because of its small genome size, extensive genetic map, relative ease of transformation and synteny with other cereal crops(1-4). Here we report the essentially complete sequence of chromosome 1, the longest chromosome in the rice genome. We summarize characteristics of the chromosome structure and the biological insight gained from the sequence. The analysis of 43.3 megabases (Mb) of non-overlapping sequence reveals 6,756 protein coding genes, of which 3,161 show homology to proteins of Arabidopsis thaliana, another model plant. About 30% ( 2,073) of the genes have been functionally categorized. Rice chromosome 1 is (G + C)-rich, especially in its coding regions, and is characterized by several gene families that are dispersed or arranged in tandem repeats. Comparison with a draft sequence(5) indicates the importance of a high-quality finished sequence.

Do introns favor or avoid regions of amino acid conservation?
T Endo, A Fedorov, SJ de Souza, W Gilbert
MOLECULAR BIOLOGY AND EVOLUTION, 19, 4, 521, 525, SOC MOLECULAR BIOLOGY EVOLUTION, 2002年04月, ［査読有り］
英語, 研究論文（学術雑誌）, Are intron positions correlated with regions of high amino acid conservation? For a set of ancient conserved proteins, with intronless prokaryotic but intron-containing eukaryotic homologs, multiple sequence alignments identified residues invariant throughout evolution. Intron positions between codons show no preferences. However, introns lying after the first base of a codon prefer conserved regions, markedly in glycines. Because glycines are in excess in conserved regions, this behavior could reflect phase-one introns entering glycine residues randomly in the ancestral sequences. Examination of intron positions within codons of evolutionarily invariable amino acids showed that roughly 50% of these introns are bordered by guanines at both 5'- and 3'-ends, 25% have a G only before the intron, and 5% have a G only after the intron, whereas about 20% are bordered by nonguanine bases.

Protein-protein interaction panel using mouse full-length cDNAs
Harukazu Suzuki, Yoshifumi Fukunishi, Ikuko Kagawa, Rintaro Saito, Hiroshi Oda, Toshinori Endo, Shinji Kondo, Hidemasa Bono, Yasushi Okazaki, Yoshihide Hayashizaki
Genome Research, 11, 10, 1758, 1765, 2001年, ［査読有り］
英語, 研究論文（学術雑誌）, We have developed a novel assay system for systematic analysis of protein-protein interactions (PPIs) that is characteristic of a PCR-mediated rapid sample preparation and a high-throughput assay system based on the mammalian two-hybrid method. Using gene-specific primers, we successfully constructed the assay samples by two rounds of PCR with up to 3.6 kb from the first-round PCR fragments. In the assay system, we designed all the steps to be performed by adding only samples, reagents, and cells into 384-well assay plates using two types of semiautomatic multiple dispensers. The system enabled us examine more than 20,000 assay wells per day. We detected 145 interactions in our pilot study using 3500 samples derived from mouse full-length enriched cDNAs. Analysis of the interaction data showed both several significant interaction clusters and predicted functions of a few uncharacterized proteins. In combination with our comprehensive mouse full-length cDNA clone bank covering a large part of the whole genes, our high-throughput assay system will discover many interactions to facilitate understanding of the function of uncharacterized proteins and the molecular mechanism of crucial biological processes, and also enable completion of a rough draft of the entire PPI panel in certain cell types or tissues of mouse within a short time.

Comparative evaluation of 5 '-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries
Y Sugahara, P Carninci, M Itoh, K Shibata, H Konno, T Endo, M Muramatsu, Y Hayashizaki
GENE, 263, 1-2, 93, 102, ELSEVIER SCIENCE BV, 2001年01月, ［査読有り］
英語, 研究論文（学術雑誌）, To enhance the usefulness of the laboratory mouse and to facilitate the rapid assay of gene functions we have been collecting the entire set of mouse full-length cDNA by one-pass sequencing. To collect full-length cDNA clones efficiently, it is critical to construct high-quality cDNA libraries. In recent years, we have been developing a way to construct full-length cDNA libraries by using biotinylation of the cap structure (the 'CAP-trapper' method) coupled with treatment to increase reverse transcriptase efficiency at high temperature by the addition of trehalose. In this paper we report our evaluation of the quality of CAP trapper and a number of other full-length cDNA libraries, including the results of 5' end analysis of clones in CAP trapper and the other Libraries. We used a procedure that compared the 5'-ends of cDNA clones with those of genes in the public databases. Our analysis showed that 63% of cDNA clones in CAP trapper libraries had sequences that were either the same length as those of equivalent genes in the public database or 5'-extended, and that 90% of these clones maintained their coding sequences. These results indicate that the CAP trapper Library is a promising tool for collecting full-length cDNA in large-scale projects. Comparison of the quality of CAP trapper with that of other full-length-cDNA libraries confirmed the value of these libraries. (C) 2001 Elsevier Science B.V. All rights reserved.

Construction and Application of Mouse Full-length cDNA Database
Konno Hideaki, Fukunishi Yoshifumi, Endo Toshinori, Hayashizaki Yoshihide
Genome Informatics, 10, 288, 289, Japanese Society for Bioinformatics, 1999年
英語

Systematic analysis on mouse genome encyclopedia
Endo Toshinori, Yamanaka Itaru, Konno Hideki, Fukunishi Yoshifumi, Kawai Jun, Suzuki Harukazu, Ozawa Yasuhiro, Shibata Kazuhiro, Yoshino Masayasu, Itoh Masayoshi, Carninci Piero, Okazaki Yasushi, Hayashizaki Yoshihide
Genome Informatics, 10, 338, 339, Japanese Society for Bioinformatics, 1999年, ［査読有り］
英語, 研究論文（国際会議プロシーディングス）

Identification of regions in which positive selection may operate in S-RNase of Rosaceae: Implication for S-allele-specific recognition sites in S-RNase
Takeshi Ishimizu, Toshinori Endo, Yumi Yamaguchi-Kabata, Kazuo T. Nakamura, Fumio Sakiyama, Shigemi Norioka
FEBS Letters, 440, 3, 337, 342, 1998年12月04日, ［査読有り］
英語, 研究論文（学術雑誌）, A stylar S-RNase is associated with gametophytic self-incompatibility in the Rosaceae, Solanaceae, and Scrophulariaceae. This S-RNase is responsible for S-allele-specific recognition in the self-incompatible reaction, but how it functions in specific discrimination is not clear. Window analysis of the numbers of synonymous (d(S)) and non-synonymous (d(N)) substitutions in rosaceous S-RNases detected four regions with an excess of d(N) over d(S) in which positive selection may operate (PS regions). The topology of the secondary structure of the S-RNases predicted by the PHD method is very similar to that of fungal RNase Rh whose tertiary structure is known. When the sequences of S-RNases are aligned with the sequence of RNase Rh based on the predicted secondary structures, the four PS regions correspond to two surface sites on the tertiary structure of RNase Rh. These findings suggest that in S-RNases the PS regions also form two sites and are candidates for the recognition sites for S-allele-specific discrimination. Copyright (C) 1998 Federation of European Biochemical Societies.

Evolutionary significance of intra-genome duplications on human chromosomes (vol 205, pg 19, 1997)
T Endo, T Imanishi, T Gojobori, H Inoko
GENE, 210, 2, 351, +, ELSEVIER SCIENCE BV, 1998年04月, ［査読有り］
英語, 研究論文（学術雑誌）

Evolutionary significance of intra-genome duplications on human chromosomes.
Toshinori Endo, Tadashi Imanishi, Takashi Gojobori, Hidetoshi Inoko
GENE, 205, 1/2, 19, 27, 1997年12月, ［査読有り］
英語, 研究論文（学術雑誌）

Evolutionary motif and its biological and structural significance
Y Tateno, K Ikeo, T Imanishi, H Watanabe, T Endo, Y Yamaguchi, Y Suzuki, K Takahashi, K Tsunoyama, M Kawai, Y Kawanishi, K Naitou, T Gojobori
JOURNAL OF MOLECULAR EVOLUTION, 44, S38, S43, SPRINGER VERLAG, 1997年, ［査読有り］
英語, 研究論文（学術雑誌）, We developed a method for multiple alignment of protein sequences. The main feature of this method is that it takes the evolutionary relationships of the proteins in question into account repeatedly for execution, until the relationships and alignment results are in agreement. We then applied this method to the data of the international DNA sequence databases, which are the most comprehensive and updated DNA databases in the world, in order to estimate the ''evolutionary motif'' by extensive use of a supercomputer. Though a few problems needed to be solved, we could estimate the length of the motifs in the range of 20 to 200 amino acids, with about 60 the most frequent length. We then discussed their biological and structural significance. We believe that we are now in a position to analyze DNA and protein not only in vivo and in vitro but also in silico.

Monophyletic origin and unique dispersal patterns of domestic fowls
A Fumihito, T Miyake, M Takada, R Shingu, T Endo, T Gojobori, N Kondo, S Ohno
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 93, 13, 6792, 6795, NATL ACAD SCIENCES, 1996年06月, ［査読有り］
英語, 研究論文（学術雑誌）, With the aim of elucidating in greater detail the genealogical origin of the present domestic fowls of the world, we have determined mtDNA sequences of the D-loop regions for a total of 21 birds, of which 12 samples belong to red junglefowl (Gallus gallus) comprising three subspecies (six Gallus gallus gallus, three Gallus gallus spadiceus, and three Gallus gallus bankiva) and nine represent diverse domestic breeds (Gallus gallus domesticus). We also sequenced four green junglefowl (Gallus varius), two Lafayette's Junglefowl (Gallus lafayettei), and one grey junglefowl (Gallus sonneratii), We then constructed a phylogenetic tree for these birds by the use of nucleotide sequences, choosing the Japanese quail (Coturnix coturnix japonica) as an outgroup, We found that a continental population of G. g. gallus was the real matriarchic origin of all the domestic poultries examined in this study, It is also of particular interest that there were no discernible differences among G. gallus subspecies; G. g. bankiva was a notable exception, This was because G. g. spadiceus and a continental population of G. g. gallus formed a single cluster in the phylogenetic tree, G. g. bankiva, on the other hand, was a distinct entity, thus deserving its subspecies status, It implies that a continental population of G. g. gallus sufficed as the monophyletic ancestor of all domestic breeds, We also discussed a possible significance of the initial dispersal pattern of the present domestic fowls, using the phylogenetic tree.

Large-scale search for genes on which positive selection may operate
T Endo, K Ikeo, T Gojobori
MOLECULAR BIOLOGY AND EVOLUTION, 13, 5, 685, 690, SOC MOLECULAR BIOLOGY EVOLUTION, 1996年05月, ［査読有り］
英語, 研究論文（学術雑誌）, We conducted a systematic search for the candidate genes on which positive selection may operate, on the premise that for such genes the number of nonsynonymous substitution is expected to be larger than that of synonymous substitutions when the nucleotide sequences of the genes under investigation are compared with each other. By obtaining 3,595 groups of homologous sequences from the DDBJ, EMBL, and GenBank DNA sequence databases, we found that 17 gene groups can be the candidates for the genes on which positive selection may operate. Thus, such genes are found to occupy only about 0.5% of the vast number of gene groups so far available. Interestingly enough, 9 out of the 17 gene groups were the surface antigens of parasites or viruses.

Large-scale search for genes on which positive selection may operate.　　　　　　　　　　　　　　　
Toshinori Endo
Dessertation. Graduate School for Advanced Studies, 1995年, ［査読有り］
英語, 学位論文（博士）

Domain evolution of serine protease and its inhibitor genes
T Gojobori, T Endo, K Ikeo
TRACING BIOLOGICAL EVOLUTION IN PROTEIN AND GENE STRUCTURES, 249, 260, ELSEVIER SCIENCE PUBL B V, 1995年, ［査読有り］
英語, 研究論文（国際会議プロシーディングス）

CLONING AND CHARACTERIZATION OF THE MOUSE FRA-2 GENE
VC FOLETTA, MH SONOBE, T SUZUKI, T ENDO, H IBA, DR COHEN
ONCOGENE, 9, 11, 3305, 3311, STOCKTON PRESS, 1994年11月, ［査読有り］
英語, 研究論文（学術雑誌）, Transcription factor AP-1 is comprised of multiple protein complexes that include members of a family of genes related to the proto-oncogene c-fos. In this report, we have extended the analysis of one member of this family, fos-related antigen-2 (fra-2), by isolating and characterising genomic and cDNA clones encoding:the mouse fra-2 homolog. The overall gene structure (number and positions of introns) was similar to that of both the chicken fra-2 gene and other members of the fos family, and the relative positions of putative enhancers in the 5' regulatory region were well conserved between the mouse and chicken fra-2 genes. High levels of fra-2 mRNA were detected in ovary, stomach, small and large intestine, brain, lung and heart. The mouse Fra-2 protein showed 94% and 87.5% conservation with human and chicken Fra-2, respectively, and mouse Fra-2, like the chicken homolog, induced transformation of chicken embryo fibroblasts. The characterisation of the mouse fra-2 gene provides a basis for analysis of Fra-2 function in the whole animal.

JUND MUTANTS WITH SPONTANEOUSLY ACQUIRED TRANSFORMING POTENTIAL HAVE ENHANCED TRANSACTIVATING ACTIVITY IN COMBINATION WITH FRA-2
T KAMEDA, A AKAHORI, MH SONOBE, T SUZUKI, T ENDO, H IBA
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 90, 20, 9369, 9373, NATL ACAD SCIENCES, 1993年10月, ［査読有り］
英語, 研究論文（学術雑誌）, Although a replication-competent retrovirus that carries junD has no transforming activity in chicken embryo fibroblasts, we have isolated mutant viruses that have spontaneously acquired transforming activity. The molecularly cloned junD genes of three such mutant viruses (T1, T2, and T3) were shown to be responsible for the cellular transformation. DNA sequence analysis indicated that a specific polynucleotide in the junD sequence was tandemly multiplied three times or five times in T1 and T2, respectively. The repeated polynucleotide encodes 16 amino acid residues that are located in a highly conserved region among Jun family proteins. The junD mutation in T3 involved an inversion, a translocation, and nucleotide substitutions that caused drastic amino acid exchanges in another well-conserved region among Jun family proteins. The transcriptional activity of these mutants was analyzed by means of transient expression experiments in F9 cells using a reporter gene containing a single AP-1 binding site. Compared with the wild-type JunD, none of them showed enhanced transactivating activity in the forms of homodimers or of heterodimers with c-Fos or Fra-1. However, they did exhibit much higher transactivating activity than the wild type when they formed heterodimers with Fra-2, indicating that the mutated regions function as transactivation domains in a partner-specific manner. Since we have previously reported that there is a basal level of Fra-2 expression in chicken embryo fibroblasts, the results may indicate that protein complexes between JunD mutants and Fra-2 play a crucial role in the cellular transforming activity.

DIFFERENCE IN TRANSCRIPTIONAL REGULATORY FUNCTION BETWEEN C-FOS AND FRA-2
T SUZUKI, H OKUNO, T YOSHIDA, T ENDO, H NISHINA, H IBA
NUCLEIC ACIDS RESEARCH, 19, 20, 5537, 5542, OXFORD UNIV PRESS UNITED KINGDOM, 1991年10月, ［査読有り］
英語, 研究論文（学術雑誌）, Fra-2, one of the Fos-related antigens, is promptly expressed after the growth stimulation of fibroblasts, but its induction peak is later than that of c-Fos. In this report, we examined biochemical properties of Fra-2 and compared them with those of two other Fos family proteins, c-Fos and Fra-1. Like c-Fos and Fra-1, Fra-2 formed stable heterodimers with c-Jun, JunB or JunD in vitro and all these complexes had specific DNA-binding activity to AP-1-binding sites (AP-1 sites) or related sequences. When transiently introduced into a mouse embryonic carcinoma cell line, F9, with reporter genes containing the AP-1 site from the collagenase gene, fra-2 plus c-jun suppressed the transactivation by c-jun alone. This property of Fra-2 is in clear contrast to that of c-Fos, which stimulates the transcriptional activity of c-Jun by forming a stable heterodimer. Analysis of chimeric proteins between c-Fos and Fra-2 indicated that this difference is mainly attributable to their C terminal-half regions. Interestingly, this suppressive effect of Fra-2 was not observed in the combination with JunD: fra-2 plus junD, like c-fos plus junD, had higher transcriptional activity than junD alone. Fra-1 showed essentially the same transcriptional regulatory properties as Fra-2. These differential properties greatly expand the potential range of regulatory functions of the Fos family proteins.

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藤原一道, 久保俊平, 遠藤俊徳, 高田豊行, 城石俊彦, 鈴木仁, 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 25th, 2023年

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疾患特異的遺伝子発現データによるドラッグリポジショニング予測
CONG Yi, 長田直樹, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 46th, 2023年

メンデル生誕200年記念 6 日本における遺伝学の発展
遠藤俊徳, 生物の科学 遺伝, 76, 4, 286, 289, 2022年
東京 : エヌ・ティー・エス, 日本語

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渡部大, 長田直樹, 湯浅浩史, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 94th (CD-ROM), 2022年

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有村親之介, 長田直樹, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 94th (CD-ROM), 2022年

神経変性疾患におけるlncRNA機能解明の試み
御手洗碩, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 94th (CD-ROM), 2022年

日本産野生ハツカネズミにおける適応進化にかかわるゲノム領域の探索
久保俊平, 藤原一道, 遠藤俊徳, 鈴木仁, 長田直樹, 日本遺伝学会大会プログラム・予稿集, 94th (CD-ROM), 2022年

データマイニングによるドラッグリポジショニング
塩崎朋也, 叢怡, 長田長樹, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 94th (CD-ROM), 2022年

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ソウ イ, 新谷美咲, 今成楓河, 長田直樹, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 94th (CD-ROM), 2022年

ニホンザルの分岐年代推定および過去の集団サイズ減少がゲノムに与えた影響の考察
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久保俊平, 藤原一道, 遠藤俊徳, 鈴木仁, 長田直樹, 日本分子生物学会年会プログラム・要旨集(Web), 45th, 2022年

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YI Cong, 新谷美咲, 今成楓河, 長田直樹, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 44th, 2021年

栽培植物アワおよびキビの系統化の歴史
里村和浩, 長田直樹, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 92nd, 2020年

膜翅目の多様性に影響を与えた遺伝子重複進化の解析
津田康太朗, 里村和浩, 長田直樹, 遠藤俊徳, 情報処理学会研究報告(Web), 2020, BIO-64, 2020年

深層学習を用いた酵素機能予測法の開発
川崎悠二, 里村和弘, 長田直樹, 遠藤俊徳, 情報処理学会研究報告(Web), 2020, BIO-64, 2020年

組織特異的な遺伝子発現に影響を与えた転移因子の同定
島野桂伍, 里村和浩, 長田直樹, 遠藤俊徳, 情報処理学会研究報告(Web), 2020, BIO-64, 2020年

マウスのアレル特異的遺伝子発現における遺伝的・後成遺伝的効果に関する推定とその検証
滝澤紘樹, 里村和浩, 遠藤俊徳, 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 22nd, 2020年

組織特異的な遺伝子発現に影響を与える転移因子の同定
島野桂伍, 里村和弘, 長田直樹, 遠藤俊徳, 日本進化学会大会プログラム・講演要旨集(Web), 22nd, 2020年

全ゲノム配列を用いたVero細胞系列の系統比較
小西一弘, 里村和浩, 遠藤俊徳, 花田賢太郎, 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 22nd, 2020年

栽培植物アワの系統化の歴史
里村和浩, 長田直樹, 遠藤俊徳, 日本進化学会大会プログラム・講演要旨集(Web), 22nd, 2020年

深層学習を用いた酵素機能予測法の開発
川崎悠二, 里村和弘, 長田直樹, 遠藤俊徳, 日本進化学会大会プログラム・講演要旨集(Web), 22nd, 2020年

膜翅目の多様性に影響を与えた遺伝子重複進化のビッグデータ解析
津田康太朗, 里村和浩, 長田直樹, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 43rd, 2020年

遺伝学用語の歴史的変遷-dominantとrecessiveの場合
澤村京一, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 91st, 2019年

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里村和浩, 長田直樹, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 91st, 2019年

ヒョウタンゲノムからみる古代の植物栽培伝播
渡部大, 里村和浩, 長田直樹, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 91st, 2019年

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藤原一道, 里村和浩, 遠藤俊徳, 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 21st, 2019年

転移因子の転移とゲノム進化の関係
島野桂伍, 里村和浩, 長田直樹, 遠藤俊徳, 日本進化学会大会プログラム・講演要旨集(Web), 21st, 2019年

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滝澤紘樹, 遠藤俊徳, 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 21st, 2019年

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弓至, 數藤由美子, 遠藤俊徳, 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 21st, 2019年

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里村和浩, 長田直樹, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 90th, 2018年

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遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 90th, 2018年

旧世界ザルゲノムに存在する内在性サルレトロウィルス(SERV)配列の探索と分子系統解析
池田昌輝, 里村和浩, 関塚剛史, 花田賢太郎, 遠藤俊徳, 長田直樹, 日本遺伝学会大会プログラム・予稿集, 90th, 2018年

ミツバチ上科におけるタンパク質の相同性に基づくゲノムの比較と進化の推定
小松玉麻果, 長田直樹, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 90th, 2018年

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池田昌輝, 遠藤俊徳, 長田直樹, 情報処理学会研究報告(Web), 2017, BIO-51, 2017年

遺伝学用語集”遺伝単”の刊行
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Revisiting the Relationship between Evolutionary Conservation and Disease Causality: A Case Study of Beta Globin Gene
Sangeetha Udani Ratnayake, Toshinori Endo, Naoki Osada, GENES & GENETIC SYSTEMS, 91, 6, 345, 345, 2016年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

The cause of gene expression changes in reciprocal crosses of Drosophila melanogaster by measuring allele-specific gene expression
Yasuaki Takada, Aya Takahashi, Ryutaro Miyagi, Toshinori Endo, Naoki Osada, GENES & GENETIC SYSTEMS, 91, 6, 372, 372, 2016年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

アリル特異的遺伝子発現の定量による,キイロショウジョウバエ(Drosophila melanogaster)の逆交雑における遺伝子発現変化の原因究明
高田恭彰, 高橋文, 宮城竜太郎, 遠藤俊徳, 長田直樹, 日本遺伝学会大会プログラム・予稿集, 88th, 2016年

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渡部大, 湯浅浩史, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 88th, 2016年

系統分類の各レベルに共通する遺伝子の抽出と比較解析
遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 88th, 2016年

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櫻井聡一, 遠藤俊徳, 長田直樹, 日本進化学会大会プログラム・講演要旨集(Web), 18th, 2016年

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遠藤俊徳, 小柳亮, 新里宙也, 佐藤矩行, 日本遺伝学会大会プログラム・予稿集, 87th, 2015年

C型肝炎由来の肝細胞癌において特徴的発現挙動を示す遺伝子の同定とドライバー遺伝子の探索
矢座寛人, 遠藤俊徳, 情報処理学会研究報告(Web), 2015, BIO-41, 1, 2, 2015年
一般社団法人情報処理学会, 日本語

miRNAと転写因子に注目したSCOT遺伝子の肝臓特異的発現抑制機構の解析
田中美早, 遠藤俊徳, 情報処理学会研究報告(Web), 2015, BIO-41, 1, 2, 2015年
一般社団法人情報処理学会, 日本語

肝炎慢性化に関わるHLAとHCVの相互作用の解析
三浦直人, 遠藤俊徳, 情報処理学会研究報告(Web), 2015, BIO-41, 1, 2, 2015年
一般社団法人情報処理学会, 日本語

Bombesin receptor subtype-3(BRS3)のリガンド予測
宮澤元基, 遠藤俊徳, 情報処理学会研究報告(Web), 2015, BIO-41, 1, 2, 2015年
一般社団法人情報処理学会, 日本語

生物進化を引き起こした遺伝子スペクトルの進化的変化
遠藤俊徳, 化学工学会秋季大会研究発表講演要旨集(CD-ROM), 47th, 2015年

次世代シーケンシング・ゲノムワイド関連解析を用いたC型肝炎治療に伴う肝病態進展軽快,肝発癌に関わる宿主因子の解析 NS5Aの構造およびHCV耐性へのHLA型の効果解析
遠藤俊徳, 山崎和思, 須田剛生, 次世代シーケンシング・ゲノムワイド関連解析を用いたC型肝炎治療に伴う肝病態進展軽快、肝発癌に関わる宿主因子の解析 平成26年度 総括・分担研究報告書 1/2冊, 2015年

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佐藤ゆたか, 平山和子, 三田薫, 藤江学, 千葉章太, 吉田麗子, 遠藤俊徳, 笹倉靖徳, 稲葉一男, 佐藤矩行, 日本動物学会大会予稿集, 85th, 2014年

分子系統解析によるアメリカ・アジアのヒョウタンの伝播経路の推定
渡部大, 安冨祖仁, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 37th, 2014年

miRNAと転写因子に注目したSCOT遺伝子の肝臓特異的発現抑制機構の解明
田中美早, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 37th, 2014年

次世代シーケンシング・ゲノムワイド関連解析を用いたC型肝炎治療に伴う肝病態進展軽快,肝発癌に関わる宿主因子の解析 HCVタンパク質NS5Aの分子動力学的手法による構造・機能解析
遠藤俊徳, 山崎和思, 次世代シーケンシング・ゲノムワイド関連解析を用いたC型肝炎治療に伴う肝病態進展軽快、肝発癌に関わる宿主因子の解析 平成25年度 総括・分担研究報告書 1/2冊, 2014年

グラフを用いたタンパク質のモーション表現法の提案
安富祖仁, 峯田克彦, 遠藤俊徳, 研究報告バイオ情報学（BIO）, 2013, 7, 1, 7, 2013年12月04日
本研究では、分子動力学法 （Molecular Dynamics, MD） を用いたシミュレーションによって得られるタンパク質の時系列座標データ （トラジェクトリ） からの非線形モーション抽出手法を提案した。従来、トラジェクトリからのモーション抽出には主成分分析 （Principal Component Analysis, PCA） を利用した Essential Dynamics Analysis などの手法が用いられてきたが、線形手法に基づく方法ではタンパク質の非線形モーションの扱いが難しいという問題があった。そこで本研究では、タンパク質構造のクラスタリングと構造間の時間的隣接関係を利用して、トラジェクトリ内の構造遷移を表現する有向グラフ （構造遷移グラフ） を構築し、構成されたグラフ内の各辺に対応する構造変化を可視化することで、タンパク質の非線形モーションを抽出する手法を提案した。提案手法を Villin headpiece subdomain （HP-35 NleNle） のトラジェクトリに対して適用した結果、タンパク質の折り畳み過程において生じている部分的回転という非線形モーションの抽出が可能であることが示された。また、構造遷移グラフの形状が従来研究の結果に対応していることも確認された。, 一般社団法人情報処理学会, 日本語

グラフを用いたタンパク質のモーション表現法の提案
安富祖仁, 峯田克彦, 遠藤俊徳, 研究報告数理モデル化と問題解決（MPS）, 2013, 7, 1, 7, 2013年12月04日
本研究では、分子動力学法 （Molecular Dynamics, MD） を用いたシミュレーションによって得られるタンパク質の時系列座標データ （トラジェクトリ） からの非線形モーション抽出手法を提案した。従来、トラジェクトリからのモーション抽出には主成分分析 （Principal Component Analysis, PCA） を利用した Essential Dynamics Analysis などの手法が用いられてきたが、線形手法に基づく方法ではタンパク質の非線形モーションの扱いが難しいという問題があった。そこで本研究では、タンパク質構造のクラスタリングと構造間の時間的隣接関係を利用して、トラジェクトリ内の構造遷移を表現する有向グラフ （構造遷移グラフ） を構築し、構成されたグラフ内の各辺に対応する構造変化を可視化することで、タンパク質の非線形モーションを抽出する手法を提案した。提案手法を Villin headpiece subdomain （HP-35 NleNle） のトラジェクトリに対して適用した結果、タンパク質の折り畳み過程において生じている部分的回転という非線形モーションの抽出が可能であることが示された。また、構造遷移グラフの形状が従来研究の結果に対応していることも確認された。, 一般社団法人情報処理学会, 日本語

Development of an efficient multiple sequence alignment method using GPGPU
Liu Zheng, Katsuhiko Mineta, Toshinori Endo, GENES & GENETIC SYSTEMS, 88, 6, 380, 380, 2013年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

発癌及び発癌抑制機構に関わるmicroRNAの標的遺伝子解析
久保研斗, 遠藤俊徳, 峯田克彦, 日本分子生物学会年会プログラム・要旨集(Web), 36th, 2013年

標準化系統樹を用いたモリクテス綱の細菌の進化解析
中西聡, 峯田克彦, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 36th, 2013年

Selective Constraint on Flanking Regions of Fish Genes
Du Peng, Katsuhiko Mineta, Toshinori Endo, GENES & GENETIC SYSTEMS, 87, 6, 435, 435, 2012年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

遺伝学用語と遺伝教育
池内達郎, 桝屋啓志, 遠藤俊徳, 布山喜章, 山本博章, 池内達郎, 桝屋啓志, 遠藤俊徳, 布山喜章, 山本博章, 日本遺伝学会大会プログラム・予稿集, 84th, 2012年

微細藻類由来のバイオ燃料開発のためのバイオインフォマティクス解析
石割晋作, 峯田克彦, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 2012年

分子系統解析によるヒョウタンの起源と伝搬経路の推定
渡部大, 遠藤俊徳, 湯浅浩史, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 2012年

代謝経路比較による寄生生物の経路進化
浅田浩郁, 遠藤俊徳, 峯田克彦, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 2012年

関節リウマチ患者に対するインフリキシマブの薬効予測に必要な遺伝子セットの探索
奥村慶太郎, 峯田克彦, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 2012年

OncomiRの発癌機構の解明に向けた統計的手法による標的遺伝子解析
久保研斗, 峯田克彦, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 2012年

刺胞動物TRPチャネルに注目したTRPチャネルファミリーの進化
黛恭英, 峯田克彦, 遠藤俊徳, 日本分子生物学会年会プログラム・要旨集(Web), 35th, 2012年

遺伝学用語集の編纂に向けて: オンライン編集システムの公開
桝屋啓志, 遠藤俊徳, 池内達郎, 布山喜章, 山本博章, 桝屋啓志, 遠藤俊徳, 布山喜章, 山本博章, 日本遺伝学会大会プログラム・予稿集, 83rd, 2011年

近交系カタユウレイボヤの作出
三田薫, 笹倉靖徳, 平山和子, 住吉範子, 藤江学, 吉田学, 赤坂甲治, 遠藤俊徳, 佐藤矩行, 佐藤ゆたか, 稲葉一男, 日本分子生物学会年会プログラム・要旨集(Web), 34th, 2011年

Developing a fast multiple sequence alignment on GPU toward high efficiency analysis of biological information
Hitoshi Orito, Katsuhiko Mineta, Toshinori Endo, GENES & GENETIC SYSTEMS, 85, 6, 429, 429, 2010年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

Molecular evolutionary study of the nonsyndromic deafness genes in mammals
Koya Kato, Toshinori Endo, Katsuhiko Mineta, GENES & GENETIC SYSTEMS, 85, 6, 401, 401, 2010年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

A Method for Construction of Protein-protein Interaction Network between Hepatitis B Virus and Human
Zhang Wenjuan, Liu Zhi-ping, Katsuhiko Mineta, Toshinori Endo, GENES & GENETIC SYSTEMS, 85, 6, 429, 429, 2010年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

Function Prediction for the Orphan GPCR based on Machine Learning
Takashi Tamura, Fuyuto Abe, Katsuhiko Mineta, Toshinori Endo, GENES & GENETIC SYSTEMS, 85, 6, 428, 428, 2010年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

Evolutionary divergence of the auditory system in mammals
Koya Kato, Toshinori Endo, Katsuhiko Mineta, GENES & GENETIC SYSTEMS, 85, 6, 455, 455, 2010年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

A new approach to estimate protein functions by Hidden Markov Model for enzyme classifications
Fuyuto Abe, Katsuhiko Mineta, Toshinori Endo, GENES & GENETIC SYSTEMS, 85, 6, 416, 416, 2010年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

Genetic polymorphisms of T1R family and the diversity of umami/sweet perception in human populations
Rie Watanabe, Toshinori Endo, Katsuhiko Mineta, GENES & GENETIC SYSTEMS, 85, 6, 439, 439, 2010年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

Development for a prediction method of drug therapy efficacy with support vector machine based on the personal gene expression patterns
Hiroki Yoshida, Katsuhiko Mineta, Toshinori Endo, GENES & GENETIC SYSTEMS, 85, 6, 429, 429, 2010年12月
GENETICS SOC JAPAN, 英語, 研究発表ペーパー・要旨（国際会議）

酵素の階層機能分類に基づくタンパク質機能予測
阿部布由人, 峯田克彦, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 82nd, 103, 2010年09月07日
日本語

機械学習を用いたオーファンGPCRの機能予測
田村崇, 阿部布由人, 峯田克彦, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 82nd, 118, 2010年09月07日
日本語

聴覚の多様性—聴覚に注目した哺乳動物の適応戦略—
加藤耕也, 遠藤俊徳, 峯田克彦, 日本遺伝学会大会プログラム・予稿集, 82nd, 74, 2010年09月07日
日本語

うま昧・甘昧受容体T1Rファミリー分子群の集団間多型と味覚多様性
渡邉理恵, 遠藤俊徳, 峯田克彦, 日本遺伝学会大会プログラム・予稿集, 82nd, 123, 2010年09月07日
日本語

遺伝子発現情報の機械学習に基づく投薬効果予測法の開発
吉田寛輝, 峯田克彦, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 82nd, 119, 2010年09月07日
日本語

GPGPU応用によるマルチプルシーケンスアラインメントの高速化
折戸仁志, 峯田克彦, 遠藤俊徳, 日本遺伝学会大会プログラム・予稿集, 82nd, 118, 2010年09月07日
日本語

哺乳動物における非症候性難聴にかかわる遺伝子群の分子進化
加藤耕也, 遠藤俊徳, 峯田克彦, 日本遺伝学会大会プログラム・予稿集, 82nd, 2010年

脊椎動物の聴覚多様性に関わる遺伝的要因
加藤耕也, 遠藤俊徳, 峯田克彦, 生化学, 2010年

新規クローディン候補遺伝子群の予測と機能推定
峯田克彦, 山本康子, 山本康子, 田中啓雄, 山崎裕自, 斎藤邦明, 田村淳, 武内恒成, 遠藤俊徳, 月田早智子, 生化学, 2010年

リウマチ患者における抗TNF-α抗体の薬効メカニズムの解析
吉田寛輝, 峯田克彦, 遠藤俊徳, 生化学, 2010年

G-008 遺伝子発現情報の機械学習に基づく投薬効果予測(生体情報科学,一般論文)
吉田 寛輝, 峯田 克彦, 遠藤 俊徳, 情報科学技術フォーラム講演論文集, 8, 2, 585, 586, 2009年08月20日
FIT(電子情報通信学会・情報処理学会)運営委員会, 日本語

1ZC-2 機械学習に基づく嗅覚受容体のリガンド予測(バイオ情報学と医用画像,学生セッション,コンピュータと人間社会)
小坂 宏四郎, 上野 恵介, 峯田 克彦, 遠藤 俊徳, 全国大会講演論文集, 71, 4, "4, 667"-"4-668", 2009年03月10日
一般社団法人情報処理学会, 日本語

豚の家畜化過程における人為淘汰の痕跡の探索
渡部大, 峯田克彦, 遠藤俊徳, 日本分子生物学会年会講演要旨集, 32nd, Late-Breaking Abstracts, 2009年

比較解析による脊椎動物の顎と獲得免疫の進化的特徴に関する研究
石崎誠志, 峯田克彦, 遠藤俊徳, 日本分子生物学会年会講演要旨集, 32nd, Vol.4, 2009年

タンデム質量分析実験によるタンパク質同定における閾値決定手法について (「生命情報からの知識発見」及び一般)
米澤 弘毅, 峯田 克彦, 遠藤 俊徳, 人工知能基本問題研究会, 68, 0, 27, 32, 2008年01月16日
人工知能学会, 日本語

文献データのメタアナリシスによる統合失調症候補遺伝子の疾患寄与度再評価
片岡翼, 遠藤俊徳, 峯田克彦, 生化学, 2008年

脳3次元モデルによる生命情報の可視化とデータ統合への展望
峯田克彦, 池尾一穂, 遠藤俊徳, 五條堀孝, 解剖学雑誌, 83, Supplement, 2008年

脳・神経系発現遺伝子群の種間比較に基いた生物種間での脳・神経系の機能的特徴の探索
菊井隆彦, 峯田克彦, 遠藤俊徳, 生化学, 2008年

肥満小児の身体組成におよぼす加圧トレーニングの効果
遠藤 明, 加藤 俊徳, 板橋 家頭夫, 日本小児栄養消化器肝臓学会雑誌 = Japanese journal of pediatric gastroenterology, hepatology and nutrition, 21, 1, 32, 35, 2007年07月20日
日本語

魚類・哺乳類のT1Rファミリーの分子進化学的解析による甘味・うま味受容部位の予測
菅野三奈子, 峯田克彦, 遠藤俊徳, 生化学, 2007年

Evola:系統樹解析にもとづくH‐InvDBヒト遺伝子のオルソログデータベース
松矢明宏, 松矢明宏, 坂手龍一, 坂手龍一, 川原善浩, 川原善浩, 佐藤慶治, 佐藤慶治, 藤井康之, 藤井康之, 武田淳一, 武田淳一, 最知直美, 最知直美, 三本松良子, 三本松良子, 鈴木満美, 鈴木満美, 田中政之, 田中政之, 村上勝彦, 村上勝彦, 野田彰子, 野田彰子, 山崎千里, 山崎千里, 小柳香奈子, 太田聡史, 遠藤俊徳, 今西規, 五條堀孝, 五條堀孝, 伊藤剛, 伊藤剛, 生化学, 1P-1063, 2007年
日本語

肥満男児の体脂肪分布とLDL粒子サイズの関係
遠藤 明, 加藤 俊徳, 板橋 家頭夫, 肥満研究 = Journal of Japan Society for the Study of Obesity : 日本肥満学会誌, 12, 1, 31, 34, 2006年
大阪 : 日本肥満学会, 日本語

P1-028 遺伝的多型を基盤とした立体構造解析からの薬物代謝酵素チトクロームP450の機能部位推定方法の開発(急性毒性)
徳光 綾子, 峯田 克彦, 遠藤 俊徳, 日本環境変異原学会大会プログラム・要旨集, 0, 33, 149, 149, 2004年11月30日
日本環境変異原学会, 日本語

Shoulder width stance squatとwide stance squatによる大腿筋への負荷の相違
遠藤 明, 加藤 俊徳, 堀川 浩之, 日本臨床スポーツ医学会誌 / 日本臨床スポーツ医学会編集委員会 編, 12, 2, 266, 271, 2004年
コレクション : 国立国会図書館デジタルコレクション > デジタル化資料 > 雑誌, 東京 : 日本臨床スポーツ医学会, 日本語

タンパク質立体構造における遺伝子多型の特定によるチトクロームP450の機能解析
徳光綾子, 峯田克彦, 遠藤俊徳, 日本分子生物学会年会プログラム・講演要旨集, 27th, 2004年

マルチプルアライメントを利用したヒトとマウスにおけるHuntingtin内の繰り返し塩基配列AluとB1の比較
肥田道彦, 荻島創一, 遠藤俊徳, 田中博, 日本分子生物学会年会プログラム・講演要旨集, 26th, 2003年

適応的進化の分子的実証の試み 2 祖先遺伝子の配列推定・合成・機能
青木誠志郎, 遠藤俊徳, 三島隆, 陶山明, 伊藤元己, 日本植物学会大会研究発表記録, 66th, 2002年

ネットワーク最前線 ゲノム・遺伝子解析とコンピュータネットワーク
遠藤俊徳, 医療とコンピュータ, 12, 9, 2001年

理研マウス完全長cDNAを用いたタンパク質相互作用網羅的解析法の開発
鈴木治和, 福西快文, 香川育子, 坊農秀雅, 斎藤輪太郎, 小田浩史, 遠藤俊徳, 近藤伸二, 林崎良英, 日本分子生物学会年会プログラム・講演要旨集, 23rd, 2000年

標準遺伝子系統樹の作成
遠藤俊徳, 荻島創一, 田中博, 日本分子生物学会年会プログラム・講演要旨集, 23rd, 2000年

マウス完全長cDNAの全長シーケンスプロジェクト
河合純, 福西快文, 吉野正康, 小沢泰裕, 柴田一浩, CARNINCI P, 今野英明, 遠藤俊徳, 林崎良英, 日本分子生物学会年会プログラム・講演要旨集, 22nd, 1999年

無細胞系を用いたタンパク質間相互作用を簡便かつ迅速に調べる手法の開発
鈴木治和, 小田浩史, 福西快文, 遠藤俊徳, 岡崎康司, 村松正実, 林崎良英, 日本分子生物学会年会プログラム・講演要旨集, 22nd, 1999年

米沢市における「在宅寝たきり者等訪問歯科診療」について (その1)
鈴木友一, 鈴木基, 遠藤浩, 平間和広, 林隆一, 笹生俊徳, 中条良文, みちのく齒學會雑誌, 30, 1/2, 1999年

ヒト遺伝子族データベースとヒト染色体重複領域データベースの開発
今西 規, 羽原 香織, 遠藤 俊徳, 大野 乾, 五條堀 孝, 日本分子生物学会年会プログラム・講演要旨集, 21, 261, 261, 1998年12月01日
日本語

ヒトゲノム中の重複遺伝子の分布と染色体の重複領域
今西規, 遠藤俊徳, 大野乾, 五条堀孝, 日本遺伝学会大会プログラム・予稿集, 70th, 1998年

ヒトゲノムにある大規模な重複領域の探索
今西規, 遠藤俊徳, 五条堀孝, 日本分子生物学会年会プログラム・講演要旨集, 20th, 1997年

HLA遺伝子群の進化と形成
猪子英俊, 椎名隆, 岡晃, 田宮元, 遠藤俊徳, 今西規, 池村淑道, 五条堀孝, 日本免疫学会総会・学術集会記録, 27, 1997年

ヒトゲノム中の大規模な重複領域の発見
今西規, 遠藤俊徳, 五条堀孝, 日本遺伝学会大会プログラム・予稿集, 69th, 1997年

日本におけるヒト・ゲノム研究の最前線 [1] ヒト 1. 物理地図からシークエンス地図へ 第6染色体HLA領域の遺伝子構成と第9染色体9q33-34領域との相同性
安藤麻子, 遠藤俊徳, 猪子英俊, 蛋白質 核酸 酵素, 42, 17, 2704, 2713, 1997年
東京 : 共立出版, 日本語

分子進化 (遺伝 創刊50周年記念企画--生物科学の現状と展望)
遠藤 俊徳, 五条堀 孝, 生物の科学「遺伝」別冊, 8, 139, 147, 1996年07月
裳華房, 日本語

正の自然淘汰の働く遺伝子内領域の推定とその機能の解析
遠藤俊徳, 五条堀孝, 日本分子生物学会年会プログラム・講演要旨集, 19th, 738, 1996年
日本語

コジュケイ属鳥類のmtDNAの解析: Eveは一人か複数か?
三宅哲雄, 秋篠宮文仁, 高田勝, 近藤典生, 遠藤俊徳, 五条堀孝, 大野乾, 日本分子生物学会年会プログラム・講演要旨集, 19th, 579, 1996年
日本語

正の淘汰を受ける遺伝子領域の特定と,その機能や構造の比較
遠藤俊徳, 池尾一穂, 五条堀孝, 日本遺伝学会大会プログラム・予稿集, 67th, 1995年

正の淘汰が働く可能性のある遺伝子内領域とその生物学的意義
遠藤俊徳, 池尾一穂, 五条堀孝, 日本分子生物学会年会プログラム・講演要旨集, 18th, 1995年

ドメイン構造からみたホメオドメイン遺伝子の分子進化
池尾一穂, 遠藤俊徳, 五条堀孝, 日本遺伝学会大会プログラム・予稿集, 67th, 1995年

正の自然淘汰を受けて進化する遺伝子の探索
遠藤俊徳, 池尾一穂, 五条堀孝, 日本分子生物学会年会プログラム・講演要旨集, 17th, 1994年

遺伝子間の分子進化学的関係に基づく配列モチーフの抽出
池尾一穂, 川西祐一, 河合正人, 内藤公敏, 遠藤俊徳, 山口由美, 今西規, 館野義男, 五条堀孝, 日本分子生物学会年会プログラム・講演要旨集, 17th, 1994年

大量の相同塩基配列情報に基づく同義・非同義塩基置換数の推定
遠藤俊徳, 池尾一穂, 五条堀孝, 日本遺伝学会大会プログラム・予稿集, 66th, 1994年

同義及び非同義塩基置換の大量解析とその分子進化学的意義
遠藤俊徳, 池尾一穂, 五条堀孝, 日本遺伝学会大会プログラム・予稿集, 65th, 1993年

染色体上の遺伝子の位置と進化速度の関係
遠藤俊徳, 五条堀孝, 日本分子生物学会年会プログラム・講演要旨集, 16th, 1993年

遺伝子に学ぶ 遺伝子と進化
遠藤俊徳, 五条堀孝, からだの科学, 173, p37, 41, 1993年
資料形態 : テキストデータ プレーンテキスト, 東京 : 日本評論社, 日本語

生物の科学 遺伝 Vol.76 No.4 特集:メンデル生誕200年記念
遠藤俊徳, 日本における遺伝学の発展
エヌ・ティー・エス, 2022年07月01日, 486043756X, 78, ［分担執筆］

遺伝学の百科事典 : 継承と多様性の源
日本遺伝学会
丸善出版, 2022年01月, 9784621306604, xvii, 668p, 日本語, ［共編者(共編著者)］

改訂 遺伝単 ―遺伝学用語集 対訳付き (『生物の科学 遺伝』別冊No.25)
日本遺伝学会・遺伝学教育用語検討委員会, 日本遺伝学会
エヌ・ティー・エス, 2021年03月15日, 4860437128, 456, 日本語, ［共編者(共編著者)］

遺伝単―遺伝学用語集 対訳付き (生物の科学 遺伝 別冊No.22)
日本遺伝学会
エヌ・ティー・エス, 2017年09月21日, 4860434994, 372, 日本語, ［共編者(共編著者)］

分子生物学のためのバイオインフォマティクス入門 : 生物情報解析の理論とアルゴリズム
Setubal, João Carlos, Meidanis, João, 遠藤, 俊徳, 五條堀, 孝
共立出版, 2001年12月, 4320055802, xiv, 268p, 日本語

すぐに使えるPerl/CGIモジュールサンプル集
遠藤, 俊徳
秀和システム, 2001年07月, 4798001600, 238p, 日本語

GNU C compiler : manual & reference
遠藤, 俊徳
秀和システム, 1999年04月, 4879668710, 215p, 日本語

GNU C compiler : Manual&reference
遠藤, 俊徳
秀和システム, 1998年05月, 487966782X, 191p, 日本語

はじめてのWindows95
遠藤, 俊徳
秀和システム, 1995年12月, 4879664952, 221p, 日本語

はじめてのロータス1-2-3 R5J : Windows版
遠藤, 俊徳
秀和システム, 1995年04月, 4879664308, 235p, 日本語

Tracing Biological Evolution in Protein and Gene Structures.　　　　　　　　　　　　　　　
Takashi Gojobori, Toshinori Endo, Kazuho Ikeo, Mitiko Go and Paul Schimmel eds. pp. 249-260
Elsevier Science B. V., Amsterdam., 1995年, ［共著］

はじめての98
遠藤, 俊徳
秀和システムトレーディング, 1994年11月, 4879663891, 245p, 日本語

はじめてのWindows3.1
遠藤, 俊徳
秀和システムトレーディング, 1994年01月, 4879663468, 251p, 日本語

はじめての9801
遠藤, 俊徳
秀和システムトレーディング, 1993年08月, 487966295X, 291p, 日本語

はじめてのWindows3
遠藤, 俊徳
秀和システムトレーディング, 1992年02月, 4879662623, 224p, 日本語

はじめてのパソコン通信
遠藤, 俊徳, 霜田, 靖
秀和システムトレーディング, 1991年05月, 4879662259, 329p, 日本語

はじめてのパソコン通信
遠藤, 俊徳, 霜田, 靖
秀和システムトレーディング, 1991年01月, 4879662259, 329p, 日本語

PC-9801のアソコが知りたい : PC-98常識アンサー
遠藤, 俊徳
秀和システムトレーディング, 1988年12月, 4879661589, 228p, 日本語

Evolutionary analysis of Mollicutes based on standardized phylogenetic tree　　　　　　　　　　　　　　　
遠藤 俊徳
2013年10月31日, 英語, シンポジウム・ワークショップパネル（指名）
［国際会議］

情報生物学特論　　　　　　　　　　　　　　　
北海道大学
2019年10月 - 現在

情報生命工学　　　　　　　　　　　　　　　
東京大学

情報学　　　　　　　　　　　　　　　
北海道大学

細胞生物学　　　　　　　　　　　　　　　
北海道大学工学部

生物学I　　　　　　　　　　　　　　　
北海道大学総合教育部

構造バイオインフォマティクス特論　　　　　　　　　　　　　　　
北海道大学大学院情報科学研究科

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北海道大学工学部

データ解析　　　　　　　　　　　　　　　
北海道大学工学部

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日本バイオインフォマティクス学会　　　　　　　　　　　　　　　

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日本遺伝学会