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2020 – today
- 2023
[j55]Nina Petrovic
, Magbubah Essack, Ahmad Sami, George Perry, Takashi Gojobori, Esma R. Isenovic, Vladan P. Bajic:
MicroRNA networks linked with BRCA1/2, PTEN, and common genes for Alzheimer's disease and breast cancer share highly enriched pathways that may unravel targets for the AD/BC comorbidity treatment. Comput. Biol. Chem. 106: 107925 (2023)- [j54]Gengjie Jia, Yu Li, Xue Zhong, Kanix Wang, Milton Pividori, Rabab Alomairy, Aniello Esposito, Hatem Ltaief, Chikashi Terao, Masato Akiyama, Koichi Matsuda, David E. Keyes, Hae Kyung Im, Takashi Gojobori, Yoichiro Kamatani, Michiaki Kubo, Nancy J. Cox, James A. Evans, Xin Gao, Andrey Rzhetsky:
The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. Nat. Comput. Sci. 3(5): 403-417 (2023) - [j53]Gengjie Jia, Yu Li, Xue Zhong, Kanix Wang, Milton Pividori, Rabab Alomairy, Aniello Esposito, Hatem Ltaief, Chikashi Terao, Masato Akiyama, Koichi Matsuda, David E. Keyes, Hae Kyung Im, Takashi Gojobori, Yoichiro Kamatani, Michiaki Kubo, Nancy J. Cox, James A. Evans, Xin Gao, Andrey Rzhetsky:
Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci. Nat. Comput. Sci. 3(7): 658 (2023) - 2022
- [j52]Azza Althagafi, Lamia Alsubaie, Nagarajan Kathiresan, Katsuhiko Mineta, Taghrid Aloraini, Fuad Al Mutairi, Majid Alfadhel, Takashi Gojobori, Ahmad Alfares, Robert Hoehndorf:
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning. Bioinform. 38(6): 1677-1684 (2022) - 2021
- [j51]Farhat Khan, Aleksandar Radovanovic, Takashi Gojobori, Mandeep Kaur:
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease. Database J. Biol. Databases Curation 2021 (2021) - [j50]Seif Eldawlatly, Mohamed Abouelhoda, Omar Sultan Al-Kadi, Takashi Gojobori, Boris R. Jankovic, Mohamad Khalil, Ahsan H. Khandoker, Ahmed Morsy:
Biomedical computing in the Arab world: unlocking the potential of a growing research community. Commun. ACM 64(4): 108-113 (2021) - [j49]David Conchouso, Amani D. Alma'abadi, Hayedeh Behzad, Mohammed Alarawi, Masahito Hosokawa, Yohei Nishikawa, Haruko Takeyama, Katsuhiko Mineta, Takashi Gojobori:
Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start. Genom. Proteom. Bioinform. 19(3): 504-518 (2021) - [j48]Maha A. Thafar, Rawan S. Olayan, Somayah Albaradei, Vladimir B. Bajic, Takashi Gojobori, Magbubah Essack, Xin Gao:
DTi2Vec: Drug-target interaction prediction using network embedding and ensemble learning. J. Cheminformatics 13(1): 71 (2021) - 2020
- [j47]Maha A. Thafar, Rawan S. Olayan, Haitham Ashoor, Somayah Albaradei, Vladimir B. Bajic, Xin Gao, Takashi Gojobori, Magbubah Essack:
DTiGEMS+: drug-target interaction prediction using graph embedding, graph mining, and similarity-based techniques. J. Cheminformatics 12(1): 44 (2020) - [i1]Qiang Yang, Hind Alamro, Somayah Albaradei, Adil Salhi, Xiaoting Lv, Changsheng Ma, Manal Alshehri, Inji Jaber, Faroug Tifratene, Wei Wang, Takashi Gojobori, Carlos M. Duarte, Xin Gao, Xiangliang Zhang:
SenWave: Monitoring the Global Sentiments under the COVID-19 Pandemic. CoRR abs/2006.10842 (2020)
2010 – 2019
- 2019
- [j46]Zhang Zhang, Jun Yu, Frank Eisenhaber, Xin Gao, Takashi Gojobori:
In Memory of Vladimir B. Bajic (1952-2019). Genom. Proteom. Bioinform. 17(5): 473-474 (2019) - 2018
- [j45]Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo:
Maser: one-stop platform for NGS big data from analysis to visualization. Database J. Biol. Databases Curation 2018: bay027 (2018) - [j44]Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Bernhard O. Palsson, Nathan E. Lewis, Neema Jamshidi:
Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting. PLoS Comput. Biol. 14(1) (2018) - 2016
- [j43]Adil Salhi, Magbubah Essack, Aleksandar Radovanovic, Benoit Marchand, Salim Bougouffa, André Antunes, Marta Filipa Simões, Feras F. Lafi, Olaa A. Motwalli, Ameerah Bokhari, Tariq Malas, Soha Al Amoudi, Ghofran Othum, Intikhab Alam, Katsuhiko Mineta, Xin Gao, Robert Hoehndorf, John A. C. Archer, Takashi Gojobori, Vladimir B. Bajic:
DESM: portal for microbial knowledge exploration systems. Nucleic Acids Res. 44(Database-Issue): 624-633 (2016) - 2015
- [j42]Amani D. Alma'abadi, Takashi Gojobori, Katsuhiko Mineta:
Marine Metagenome as A Resource for Novel Enzymes. Genom. Proteom. Bioinform. 13(5): 290-295 (2015) - 2013
- [j41]Jun-ichi Takeda, Chisato Yamasaki, Katsuhiko Murakami, Yoko Nagai, Miho Sera, Yuichiro Hara, Nobuo Obi, Takuya Habara, Takashi Gojobori, Tadashi Imanishi:
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Res. 41(Database-Issue): 915-919 (2013) - 2012
- [j40]Yuichi Kodama, Jun Mashima, Eli Kaminuma, Takashi Gojobori, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura:
The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. Nucleic Acids Res. 40(Database-Issue): 38-42 (2012) - 2011
- [j39]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Database J. Biol. Databases Curation 2011 (2011) - [j38]Pascale Gaudet, Amos Bairoch, Dawn Field, Susanna-Assunta Sansone, Chris F. Taylor, Teresa K. Attwood, Alex Bateman, Judith A. Blake, Carol J. Bult, J. Michael Cherry, Rex L. Chisholm, Guy Cochrane, Charles E. Cook, Janan T. Eppig, Michael Y. Galperin, Robert Gentleman, Carole A. Goble, Takashi Gojobori, John M. Hancock, Douglas G. Howe, Tadashi Imanishi, Janet Kelso, David Landsman, Suzanna E. Lewis, Ilene Karsch-Mizrachi, Sandra E. Orchard, B. F. Francis Ouellette, Shoba Ranganathan, Lorna J. Richardson, Philippe Rocca-Serra, Paul N. Schofield, Damian Smedley, Christopher Southan, Tin Wee Tan, Tatiana A. Tatusova, Patricia L. Whetzel, Owen White, Chisato Yamasaki:
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res. 39(Database-Issue): 7-10 (2011) - [j37]Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura:
DDBJ progress report. Nucleic Acids Res. 39(Database-Issue): 22-27 (2011) - 2010
- [j36]Yoji Nakamura, Tomoyoshi Komiyama, Motoki Furue, Takashi Gojobori, Yasuto Akiyama:
CIG-DB: the database for human or mouse immunoglobulin and T cell receptor genes available for cancer studies. BMC Bioinform. 11: 398 (2010) - [j35]Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura:
DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res. 38(Database-Issue): 33-38 (2010) - [j34]Jun-ichi Takeda, Yutaka Suzuki, Ryuichi Sakate, Yoshiharu Sato, Takashi Gojobori, Tadashi Imanishi, Sumio Sugano:
H-DBAS: human-transcriptome database for alternative splicing: update 2010. Nucleic Acids Res. 38(Database-Issue): 86-90 (2010) - [j33]Chisato Yamasaki, Katsuhiko Murakami, Jun-ichi Takeda, Yoshiharu Sato, Akiko Ogura Noda, Ryuichi Sakate, Takuya Habara, Hajime Nakaoka, Fusano Todokoro, Akihiro Matsuya, Tadashi Imanishi, Takashi Gojobori:
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Nucleic Acids Res. 38(Database-Issue): 626-632 (2010)
2000 – 2009
- 2009
- [j32]Yoshihiro Kawahara, Ryuichi Sakate, Akihiro Matsuya, Katsuhiko Murakami, Yoshiharu Sato, Hao Zhang, Takashi Gojobori, Takeshi Itoh, Tadashi Imanishi:
G-compass: a web-based comparative genome browser between human and other vertebrate genomes. Bioinform. 25(24): 3321-3322 (2009) - [j31]José Carlos Clemente, Kazuho Ikeo, Gabriel Valiente, Takashi Gojobori:
Optimized ancestral state reconstruction using Sankoff parsimony. BMC Bioinform. 10 (2009) - [j30]Hideaki Sugawara, Kazuho Ikeo, Satoshi Fukuchi, Takashi Gojobori, Yoshio Tateno:
DDBJ dealing with mass data produced by the second generation sequencer. Nucleic Acids Res. 37(Database-Issue): 16-18 (2009) - [j29]Satoshi Fukuchi, Keiichi Homma, Shigetaka Sakamoto, Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori, Ken Nishikawa:
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. Nucleic Acids Res. 37(Database-Issue): 333-337 (2009) - [j28]Makoto K. Shimada, Ryuzou Matsumoto, Yosuke Hayakawa, Ryoko Sanbonmatsu, Craig Gough, Yumi Yamaguchi-Kabata, Chisato Yamasaki, Tadashi Imanishi, Takashi Gojobori:
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. Nucleic Acids Res. 37(Database-Issue): 810-815 (2009) - 2008
- [j27]Hideaki Sugawara, Osamu Ogasawara, Kousaku Okubo, Takashi Gojobori, Yoshio Tateno:
DDBJ with new system and face. Nucleic Acids Res. 36(Database-Issue): 22-24 (2008) - [j26]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 Ota, 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:
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Nucleic Acids Res. 36(Database-Issue): 787-792 (2008) - [c10]Hong-Woo Chun, Chisato Yamasaki, Naomi Saichi, Masayuki Tanaka, Teruyoshi Hishiki, Tadashi Imanishi, Takashi Gojobori, Jin-Dong Kim, Jun'ichi Tsujii, Toshihisa Takagi:
Prediction of Protein Sub-cellular Localization using Information from Texts and Sequences. BioNLP 2008: 90-91 - 2007
- [j25]Hideaki Sugawara, Takashi Abe, Takashi Gojobori, Yoshio Tateno:
DDBJ working on evaluation and classification of bacterial genes in INSDC. Nucleic Acids Res. 35(Database-Issue): 13-15 (2007) - [j24]Jun-ichi Takeda, Yutaka Suzuki, Mitsuteru Nakao, Tsuyoshi Kuroda, Sumio Sugano, Takashi Gojobori, Tadashi Imanishi:
H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Nucleic Acids Res. 35(Database-Issue): 104-109 (2007) - 2006
- [j23]Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori, Yoshio Tateno:
DDBJ in preparation for overview of research activities behind data submissions. Nucleic Acids Res. 34(Database-Issue): 6-9 (2006) - [j22]Hajime Ohyanagi, Tsuyoshi Tanaka, Hiroaki Sakai, Yasumasa Shigemoto, Kaori Yamaguchi, Takuya Habara, Yasuyuki Fujii, Baltazar A. Antonio, Yoshiaki Nagamura, Tadashi Imanishi, Kazuho Ikeo, Takeshi Itoh, Takashi Gojobori, Takuji Sasaki:
The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information. Nucleic Acids Res. 34(Database-Issue): 741-744 (2006) - [j21]Chisato Yamasaki, Hiroaki Kawashima, Fusano Todokoro, Yasuhiro Imamizu, Makoto Ogawa, Motohiko Tanino, Takeshi Itoh, Takashi Gojobori, Tadashi Imanishi:
TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB. Nucleic Acids Res. 34(Web-Server-Issue): 345-349 (2006) - 2005
- [j20]Maria Luisa Chiusano, Takashi Gojobori, Gerardo Toraldo:
A C++ computational environment for biomolecular sequence management. Comput. Manag. Sci. 2(3): 165-180 (2005) - [j19]Yoshio Tateno, Naruya Saitou, Kousaku Okubo, Hideaki Sugawara, Takashi Gojobori:
DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Res. 33(Database-Issue): 25-28 (2005) - [j18]Motohiko Tanino, Marie-Anne Debily, Takuro Tamura, Teruyoshi Hishiki, Osamu Ogasawara, Katsuji Murakawa, Shoko Kawamoto, Kouichi Itoh, Shinya Watanabe, Sandro José de Souza, Sandrine Imbeaud, Esther Graudens, Eric Eveno, Phillip Hilton, Yukio Sudo, Janet Kelso, Kazuho Ikeo, Tadashi Imanishi, Takashi Gojobori, Charles Auffray, Winston Hide, Kousaku Okubo:
The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. Nucleic Acids Res. 33(Database-Issue): 567-572 (2005) - 2004
- [j17]Satoru Miyazaki, Hideaki Sugawara, Kazuho Ikeo, Takashi Gojobori, Yoshio Tateno:
DBJ in the stream of various biological data. Nucleic Acids Res. 32(Database-Issue): 31-34 (2004) - 2003
- [j16]Satoru Miyazaki, Hideaki Sugawara, Takashi Gojobori, Yoshio Tateno:
DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res. 31(1): 13-16 (2003) - 2002
- [j15]Yoshio Tateno, Tadashi Imanishi, Satoru Miyazaki, Kaoru Fukami-Kobayashi, Naruya Saitou, Hideaki Sugawara, Takashi Gojobori:
DNA Data Bank of Japan (DDBJ) for genome scale research in life science. Nucleic Acids Res. 30(1): 27-30 (2002) - 2001
- [j14]Yoshiyuki Suzuki, Takashi Gojobori, Masatoshi Nei:
ADAPTSITE: detecting natural selection at single amino acid sites. Bioinform. 17(7): 660-661 (2001) - 2000
- [j13]Yoshio Tateno, Satoru Miyazaki, Motonori Ota, Hideaki Sugawara, Takashi Gojobori:
DNA Data Bank of Japan (DDBJ) in collaboration with mass sequencing teams. Nucleic Acids Res. 28(1): 24-26 (2000) - [j12]Yasukazu Nakamura, Takashi Gojobori, Toshimichi Ikemura:
Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28(1): 292 (2000) - [c9]Takashi Gojobori, T. Daniel Andrews, Takeshi Itoh:
Evolutionary features of genomes as disclosed by comparative analysis of complete genome sequences (abstract only). RECOMB 2000: 137
1990 – 1999
- 1999
- [j11]Hideaki Sugawara, Satoru Miyazaki, Takashi Gojobori, Yoshio Tateno:
DNA Data Bank of Japan dealing with large-scale data submission. Nucleic Acids Res. 27(1): 25-28 (1999) - [j10]Yasukazu Nakamura, Takashi Gojobori, Toshimichi Ikemura:
Codon usage tabulated from the international DNA sequence databases; its status 1999. Nucleic Acids Res. 27(1): 292 (1999) - [c8]Hiroshi Tanaka, Fengrong Ren, Toshitsugu Okayama, Takashi Gojobori:
Topology Selection in Unrooted Molecular Phylogenetic Tree By Minimum Model-Based Complexity Method. Pacific Symposium on Biocomputing 1999: 326-337 - 1998
- [j9]Toshitsugu Okayama, Takuro Tamura, Takashi Gojobori, Yoshio Tateno, Kazuho Ikeo, Satoru Miyazaki, Kaoru Fukami-Kobayashi, Hideaki Sugawara:
Formal design and implementation of an improved DDBJ DNA database with a new schema and object-oriented library. Bioinform. 14(6): 472-478 (1998) - [j8]Yoshio Tateno, Kaoru Fukami-Kobayashi, Satoru Miyazaki, Hideaki Sugawara, Takashi Gojobori:
DNA Data Bank of Japan at work on genome sequence data. Nucleic Acids Res. 26(1): 16-20 (1998) - [j7]Guy Perrière, Manolo Gouy, Takashi Gojobori:
The non-redundant Bacillus subtilis (NRSub) database: update 1998. Nucleic Acids Res. 26(1): 60-62 (1998) - [j6]Yasukazu Nakamura, Takashi Gojobori, Toshimichi Ikemura:
Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 26(1): 334 (1998) - [c7]Fengrong Ren, Hiroshi Tanaka, Toshitsugu Okayama, Takashi Gojobori:
The Application of Model-based Complexity Inference Method to Molecular Evolution Analysis. MedInfo 1998: 367-371 - 1997
- [j5]Yoshio Tateno, Takashi Gojobori:
DNA Data Bank of Japan in the age of information biology. Nucleic Acids Res. 25(1): 14-17 (1997) - [j4]Guy Perrière, Ivan Moszer, Takashi Gojobori:
The NRSub database: update 1997. Nucleic Acids Res. 25(1): 53-56 (1997) - [j3]Yasukazu Nakamura, Takashi Gojobori, Toshimichi Ikemura:
Codon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 25(1): 244-245 (1997) - [c6]Fengrong Ren, Hiroshi Tanaka, Toshitsugu Okayama, Takashi Gojobori:
Molecular Phylogenetic Trees are Inferred by Using Minimum Model-Based Complexity. BCEC 1997: 122-131 - [c5]Hiroshi Tanaka, Fengrong Ren, Toshitsugu Okayama, Takashi Gojobori:
Inference of Molecular Phylogenetic Tree Based on Minimum Model-Based Complexity Method. ISMB 1997: 319-328 - 1996
- [j2]Guy Perrière, Ivan Moszer, Takashi Gojobori:
NRSub: a non-redundant database for Bacillus subtilis. Nucleic Acids Res. 24(1): 41-45 (1996) - [j1]Yasukazu Nakamura, Ken-nosuke Wada, Yoshiko Wada, Hirofumi Doi, Shigehiko Kanaya, Takashi Gojobori, Toshimichi Ikemura:
Condon usage tabulated from the international DNA sequence databases. Nucleic Acids Res. 24(1): 214-215 (1996) - [c4]Hajime Kitakami, Yasuma Mori, Yoshio Tateno, Takashi Gojobori:
A Biological Taxonomy Database System an World-Wide Web. German Conference on Bioinformatics 1996: 244-246 - 1995
- [c3]Hajime Kitakami, Tadasu Shin-I, Kazuho Ikeo, Yoshihiro Ugawa, Naruya Saitou, Takashi Gojobori, Yoshio Tateno:
YAMATO and ASUKA: DNA database management system. HICSS (5) 1995: 72-80 - [c2]Fengrong Ren, Hiroshi Tanaka, Noria Fukuda, Takashi Gojobori:
Molecular evolutionary phylogenetic trees based on minimum description length principle. HICSS (5) 1995: 165-173 - 1994
- [c1]Hajime Kitakami, Yoshio Tateno, Takashi Gojobori:
Toward Unification of Taxonomy Databases in a Distributed Environment. ISMB 1994: 227-235
Coauthor Index
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