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2020 – today
- 2021
[j73]Benjamin M. Good, Kimberly Van Auken, David P. Hill, Huaiyu Mi, Seth Carbon, James P. Balhoff, Laurent-Philippe Albou
, Paul D. Thomas, Christopher J. Mungall, Judith A. Blake, Peter D'Eustachio:
Reactome and the Gene Ontology: digital convergence of data resources. Bioinform. 37(19): 3343-3348 (2021)- [j72]Seth Carbon, Eric Douglass, Benjamin M. Good, Deepak R. Unni, Nomi L. Harris, Christopher J. Mungall, Siddartha Basu, Rex L. Chisholm, Robert J. Dodson, Eric Hartline, Petra Fey, Paul D. Thomas, Laurent-Philippe Albou, Dustin Ebert, Michael J. Kesling, Huaiyu Mi, Anushya Muruganujan, Xiaosong Huang, Tremayne Mushayahama, Sandra A. LaBonte, Deborah A. Siegele, Giulia Antonazzo, Helen Attrill, Nick H. Brown, Phani V. Garapati, Steven J. Marygold, Vitor Trovisco, Gilberto dos Santos, Kathleen Falls, Christopher J. Tabone, Pinglei Zhou, Joshua L. Goodman, Victor B. Strelets, Jim Thurmond, Penelope Garmiri, Rizwan Ishtiaq, Milagros Rodríguez-López, Marcio Luis Acencio, Martin Kuiper, Astrid Lægreid, Colin Logie, Ruth C. Lovering, Barbara Kramarz, Shirin C. C. Saverimuttu, Sandra M. Pinheiro, Heather Gunn, Renzhi Su, Katherine E. Thurlow, Marcus C. Chibucos, Michelle G. Giglio, Suvarna Nadendla, James B. Munro, Rebecca C. Jackson, Margaret J. Duesbury, Noemi del-Toro, Birgit H. M. Meldal, Kalpana Paneerselvam, Livia Perfetto, Pablo Porras, Sandra E. Orchard, Anjali Shrivastava, Hsin-Yu Chang, Robert D. Finn, Alex L. Mitchell, Neil D. Rawlings, Lorna J. Richardson, Amaia Sangrador-Vegas, Judith A. Blake, Karen R. Christie, Mary E. Dolan, Harold J. Drabkin, David P. Hill, Li Ni, Dmitry M. Sitnikov, Midori A. Harris, Stephen G. Oliver, Kim Rutherford, Valerie Wood, Jaqueline Hayles, Jürg Bähler, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, G. Thomas Hayman, Mary L. Kaldunski, Anne E. Kwitek, Stanley J. F. Laulederkind, Cody Plasterer, Marek Tutaj, Mahima Vedi, Shur-Jen Wang, Peter D'Eustachio, Lisa Matthews, James P. Balhoff, Suzi A. Aleksander, Michael J. Alexander, J. Michael Cherry, Stacia R. Engel, Felix Gondwe, Kalpana Karra, Stuart R. Miyasato, Robert S. Nash, Matt Simison, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, Marc Feuermann, Pascale Gaudet, Anne Morgat, Erica Bakker, Tanya Z. Berardini, Leonore Reiser, Shabari Subramaniam, Eva Huala, Cecilia N. Arighi, Andrea H. Auchincloss, Kristian B. Axelsen, Ghislaine Argoud-Puy, Alex Bateman, Marie-Claude Blatter, Emmanuel Boutet, Emily Bowler, Lionel Breuza, Alan J. Bridge, Ramona Britto, Hema Bye-A-Jee, Cristina Casals-Casas, Elisabeth Coudert, Paul Denny, Anne Estreicher, Maria Livia Famiglietti, George E. Georghiou, Arnaud Gos, Nadine Gruaz-Gumowski, Emma Hatton-Ellis, Chantal Hulo, Alexandr Ignatchenko, Florence Jungo, Kati Laiho, Philippe Le Mercier, Damien Lieberherr, Antonia Lock, Yvonne Lussi, Alistair MacDougall, Michele Magrane, Maria Jesus Martin, Patrick Masson, Darren A. Natale, Nevila Hyka-Nouspikel, Ivo Pedruzzi, Lucille Pourcel, Sylvain Poux, Sangya Pundir, Catherine Rivoire, Elena Speretta, Shyamala Sundaram, Nidhi Tyagi, Kate Warner, Rossana Zaru, Cathy H. Wu, Alexander D. Diehl, Juancarlos Chan, Christian A. Grove, Raymond Y. N. Lee, Hans-Michael Müller, Daniela Raciti, Kimberly Van Auken, Paul W. Sternberg, Matthew Berriman, Michael Paulini, Kevin L. Howe, Sibyl Gao, Adam Wright, Lincoln Stein, Douglas G. Howe, Sabrina Toro, Monte Westerfield, Pankaj Jaiswal, Laurel Cooper, Justin Elser:
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49(Database-Issue): D325-D334 (2021) - [j71]Judith A. Blake, Richard M. Baldarelli, James A. Kadin, Joel E. Richardson, Cynthia L. Smith, Carol J. Bult, Anna V. Anagnostopoulos, Jon S. Beal, Susan M. Bello, Olin Blodgett, Nancy E. Butler, Jeff Campbell, Karen R. Christie, Lori E. Corbani, Mary E. Dolan, Harold J. Drabkin, María Flores, Susan L. Giannatto, Angelina Guerra, Paul Hale, David P. Hill, Jonathan Judd, Meiyee Law, Monica McAndrews, Dave Miers, Cailey Mitchell, Howie Motenko, Li Ni, Hiroaki Onda, Janice Ormsby, Michelle Perry, Jill M. Recla, David R. Shaw, Dmitry Sitnikov, Monika Tomczuk, Laurens G. Wilming, Yunxia Sophia Zhu:
Mouse Genome Database (MGD): Knowledgebase for mouse-human comparative biology. Nucleic Acids Res. 49(Database-Issue): D981-D987 (2021) - 2020
- [j70]Xiangying Jiang, Pengyuan Li, James A. Kadin, Judith A. Blake, Martin Ringwald, Hagit Shatkay:
Integrating image caption information into biomedical document classification in support of biocuration. Database J. Biol. Databases Curation 2020 (2020) - [j69]Xiangying Jiang, Martin Ringwald, Judith A. Blake, Hagit Shatkay:
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). Database J. Biol. Databases Curation 2020 (2020) - [j68]Julie Agapite, Laurent-Philippe Albou, Suzi A. Aleksander, Joanna Argasinska, Valerio Arnaboldi, Helen Attrill, Susan M. Bello, Judith A. Blake, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jae-Hyoung Cho, Karen R. Christie, Madeline A. Crosby, Jeff de Pons, Mary E. Dolan, Gilberto dos Santos, Barbara Dunn, Nathan A. Dunn, Anne E. Eagle, Dustin Ebert, Stacia R. Engel, David Fashena, Ken Frazer, Sibyl Gao, Felix Gondwe, Joshua L. Goodman, L. Sian Gramates, Christian A. Grove, Todd W. Harris, Marie-Claire Harrison, Douglas G. Howe, Kevin L. Howe, Sagar Jha, James A. Kadin, Thomas C. Kaufman, Patrick Kalita, Kalpana Karra, Ranjana Kishore, Stanley J. F. Laulederkind, Raymond Y. N. Lee, Kevin A. MacPherson, Steven J. Marygold, Beverley Matthews, Gillian H. Millburn, Stuart R. Miyasato, Sierra A. T. Moxon, Hans-Michael Müller, Christopher J. Mungall, Anushya Muruganujan, Tremayne Mushayahama, Robert S. Nash, Patrick Ng, Michael Paulini, Norbert Perrimon, Christian Pich, Daniela Raciti, Joel E. Richardson, Matthew Russell, Susan Russo Gelbart, Leyla Ruzicka, Kevin Schaper, Mary Shimoyama, Matt Simison, Cynthia L. Smith, David R. Shaw, Ajay Shrivatsav, Marek S. Skrzypek, Jennifer R. Smith, Paul W. Sternberg, Christopher J. Tabone, Paul D. Thomas, Jyothi Thota, Sabrina Toro, Monika Tomczuk, Marek Tutaj, Monika Tutaj, Jose-Maria Urbano, Kimberly Van Auken, Ceri E. Van Slyke, Shur-Jen Wang, Shuai Weng, Monte Westerfield, Gary Williams, Edith D. Wong, Adam Wright, Karen Yook:
Alliance of Genome Resources Portal: unified model organism research platform. Nucleic Acids Res. 48(Database-Issue): D650-D658 (2020)
2010 – 2019
- 2019
- [j67]Jason A. Bubier, David P. Hill, Gaurab Mukherjee, Timothy Reynolds, Erich J. Baker, Alexander Berger, Jake Emerson, Judith A. Blake, Elissa J. Chesler:
Curating gene sets: challenges and opportunities for integrative analysis. Database J. Biol. Databases Curation 2019: baz036 (2019) - [j66]Xiangying Jiang, Martin Ringwald, Judith A. Blake, Cecilia N. Arighi, Gongbo Zhang, Hagit Shatkay:
An effective biomedical document classification scheme in support of biocuration: addressing class imbalance. Database J. Biol. Databases Curation 2019: baz045 (2019) - [j65]Carol J. Bult, Judith A. Blake, Cynthia L. Smith, James A. Kadin, Joel E. Richardson, The Mouse Genome Database Group:
Mouse Genome Database (MGD) 2019. Nucleic Acids Res. 47(Database-Issue): D801-D806 (2019) - 2018
- [j64]Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan W. Sousa da Silva, Adrian M. Altenhoff, Jaime Huerta-Cepas, Matthieu Muffato, Mateus Patricio, Klaas Vandepoele, Ingo Ebersberger, Judith A. Blake, Jesualdo Tomás Fernández-Breis, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis:
Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinform. 34(2): 323-329 (2018) - [j63]Cynthia L. Smith, Judith A. Blake, James A. Kadin, Joel E. Richardson, Carol J. Bult, The Mouse Genome Database Group:
Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse. Nucleic Acids Res. 46(Database-Issue): D836-D842 (2018) - 2017
- [j62]Xiangying Jiang, Martin Ringwald, Judith A. Blake, Hagit Shatkay:
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). Database J. Biol. Databases Curation 2017: bax017 (2017) - [j61]Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan P. Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Qinghua Wang, Jian Zhang, Abdelrahman Elsayed, Cathy H. Wu:
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities. Nucleic Acids Res. 45(Database-Issue): D339-D346 (2017) - [j60]Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Cynthia L. Smith, Carol J. Bult, The Mouse Genome Database Group:
Mouse Genome Database (MGD)-2017: community knowledge resource for the laboratory mouse. Nucleic Acids Res. 45(Database-Issue): D723-D729 (2017) - 2016
- [j59]David P. Hill, Peter D'Eustachio, Tanya Z. Berardini, Christopher J. Mungall, Nikolai Renedo, Judith A. Blake:
Modeling biochemical pathways in the gene ontology. Database J. Biol. Databases Curation 2016 (2016) - [j58]Sushil Tripathi, Steven Vercruysse, Konika Chawla, Karen R. Christie, Judith A. Blake, Rachael P. Huntley, Sandra E. Orchard, Henning Hermjakob, Liv Thommesen, Astrid Lægreid, Martin Kuiper:
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database J. Biol. Databases Curation 2016 (2016) - [j57]Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan:
The Non-Coding RNA Ontology (NCRO): a comprehensive resource for the unification of non-coding RNA biology. J. Biomed. Semant. 7: 24 (2016) - [j56]Jingshan Huang, Fernando Gutierrez, Harrison J. Strachan, Dejing Dou, Weili Huang, Barry Smith, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Yu Lin, Bin Wu, Nisansa de Silva, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan, Alan Ruttenberg:
OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. J. Biomed. Semant. 7: 25 (2016) - [j55]Alexander D. Diehl, Terrence F. Meehan, Yvonne M. Bradford, Matthew H. Brush, Wasila M. Dahdul, David S. Dougall, Yongqun He, David Osumi-Sutherland, Alan Ruttenberg, Sirarat Sarntivijai, Ceri E. Van Slyke, Nicole A. Vasilevsky, Melissa A. Haendel, Judith A. Blake, Christopher J. Mungall:
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability. J. Biomed. Semant. 7: 44 (2016) - [j54]Jingshan Huang, Karen Eilbeck, Barry Smith, Judith A. Blake, Dejing Dou, Weili Huang, Darren A. Natale, Alan Ruttenberg, Jun Huan, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Harrison J. Strachan, Nisansa de Silva, Mohan Vamsi Kasukurthi, Vikash Kumar Jha, Yongqun He, Shaojie Zhang, Xiaowei Wang, Zixing Liu, Glen M. Borchert, Ming Tan:
The development of non-coding RNA ontology. Int. J. Data Min. Bioinform. 15(3): 214-232 (2016) - [j53]Carol J. Bult, Janan T. Eppig, Judith A. Blake, James A. Kadin, Joel E. Richardson:
Mouse genome database 2016. Nucleic Acids Res. 44(Database-Issue): 840-847 (2016) - 2015
- [j52]Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease. Nucleic Acids Res. 43(Database-Issue): 726-736 (2015) - [c19]Jingshan Huang, Karen Eilbeck, Judith A. Blake, Dejing Dou, Darren A. Natale, Alan Ruttenberg, Barry Smith, Michael T. Zimmermann, Guoqian Jiang, Yu Lin, Bin Wu, Yongqun He, Shaojie Zhang, Xiaowei Wang, He Zhang, Zixing Liu, Ming Tan:
A domain ontology for the Non-Coding RNA field. BIBM 2015: 621-624 - [c18]Jingshan Huang, Fernando Gutierrez, Dejing Dou, Judith A. Blake, Karen Eilbeck, Darren A. Natale, Barry Smith, Yu Lin, Xiaowei Wang, Zixing Liu, Ming Tan, Alan Ruttenberg:
A semantic approach for knowledge capture of MIcroRNA-Target gene interactions. BIBM 2015: 975-982 - 2014
- [j51]Marcus C. Chibucos, Christopher J. Mungall, Rama Balakrishnan, Karen R. Christie, Rachael P. Huntley, Owen White, Judith A. Blake, Suzanna E. Lewis, Michelle G. Giglio:
Standardized description of scientific evidence using the Evidence Ontology (ECO). Database J. Biol. Databases Curation 2014 (2014) - [j50]Melissa A. Haendel, James P. Balhoff, Frederic B. Bastian, David C. Blackburn, Judith A. Blake, Yvonne M. Bradford, Aurélie Comte, Wasila M. Dahdul, Thomas Dececchi, Robert E. Druzinsky, Terry F. Hayamizu, Nizar Ibrahim, Suzanna E. Lewis, Paula M. Mabee, Anne Niknejad, Marc Robinson-Rechavi, Paul C. Sereno, Christopher J. Mungall:
Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J. Biomed. Semant. 5: 21 (2014) - [j49]Heather C. Wick, Harold J. Drabkin, Huy Ngu, Michael Sackman, Craig Fournier, Jessica Haggett, Judith A. Blake, Diana W. Bianchi, Donna K. Slonim:
DFLAT: functional annotation for human development. BMC Bioinform. 15: 45 (2014) - [j48]Rachael P. Huntley, Midori A. Harris, Yasmin Alam-Faruque, Judith A. Blake, Seth Carbon, Heiko Dietze, Emily C. Dimmer, Rebecca E. Foulger, David P. Hill, Varsha K. Khodiyar, Antonia Lock, Jane Lomax, Ruth C. Lovering, Prudence Mutowo-Meullenet, Tony Sawford, Kimberly Van Auken, Valerie Wood, Christopher J. Mungall:
A method for increasing expressivity of Gene Ontology annotations using a compositional approach. BMC Bioinform. 15: 155 (2014) - [j47]Joao A. Ascensao, Mary E. Dolan, David P. Hill, Judith A. Blake:
Methodology for the inference of gene function from phenotype data. BMC Bioinform. 15: 405 (2014) - [j46]Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Carol J. Bult, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, Olivia Helfer, Hongzhan Huang, Anna Maria Masci, Jia Ren, Natalia V. Roberts, Karen Ross, Alan Ruttenberg, Veronica Shamovsky, Barry Smith, Meher Shruti Yerramalla, Jian Zhang, Aisha AlJanahi, Irem Çelen, Cynthia Gan, Mengxi Lv, Emily Schuster-Lezell, Cathy H. Wu:
Protein Ontology: a controlled structured network of protein entities. Nucleic Acids Res. 42(Database-Issue): 415-421 (2014) - [j45]Judith A. Blake, Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse. Nucleic Acids Res. 42(Database-Issue): 810-817 (2014) - [j44]The Fantom Consortium, RIKEN PMII, RIKEN CLST (DGT), Alistair R. R. Forrest, Hideya Kawaji, Michael Rehli, J. Kenneth Baillie, Michiel J. L. de Hoon, Vanja Haberle, Timo Lassmann, Ivan V. Kulakovskiy, Marina Lizio, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki:
A promoter-level mammalian expression atlas. Nat. 507(7493): 462-470 (2014) - 2013
- [j43]Sushil Tripathi, Karen R. Christie, Rama Balakrishnan, Rachael P. Huntley, David P. Hill, Liv Thommesen, Judith A. Blake, Martin Kuiper, Astrid Lægreid:
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database J. Biol. Databases Curation 2013 (2013) - [j42]Terrence F. Meehan, Nicole A. Vasilevsky, Christopher J. Mungall, David S. Dougall, Melissa A. Haendel, Judith A. Blake, Alexander D. Diehl:
Ontology based molecular signatures for immune cell types via gene expression analysis. BMC Bioinform. 14: 263 (2013) - [j41]Carol J. Bult, Janan T. Eppig, Judith A. Blake, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database: Genotypes, Phenotypes, and Models of Human Disease. Nucleic Acids Res. 41(Database-Issue): 885-891 (2013) - [j40]Judith A. Blake:
Ten Quick Tips for Using the Gene Ontology. PLoS Comput. Biol. 9(11) (2013) - 2012
- [j39]Susan M. Bello, Joel E. Richardson, Allan Peter Davis, Thomas C. Wiegers, Carolyn J. Mattingly, Mary E. Dolan, Cynthia L. Smith, Judith A. Blake, Janan T. Eppig:
Disease model curation improvements at Mouse Genome Informatics. Database J. Biol. Databases Curation 2012 (2012) - [j38]Harold J. Drabkin, Judith A. Blake:
Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. Database J. Biol. Databases Curation 2012 (2012) - [j37]Pascale Gaudet, Cecilia N. Arighi, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, Raja Mazumder:
Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. Database J. Biol. Databases Curation 2012 (2012) - [j36]Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A. Baumgartner Jr., K. Bretonnel Cohen, Karin Verspoor, Judith A. Blake, Lawrence E. Hunter:
Concept annotation in the CRAFT corpus. BMC Bioinform. 13: 161 (2012) - [j35]Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res. 40(Database-Issue): 881-886 (2012) - [j34]Paul D. Thomas, Valerie Wood, Christopher J. Mungall, Suzanna E. Lewis, Judith A. Blake:
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput. Biol. 8(2) (2012) - [c17]Jingshan Huang, Xingyu Lu, Dejing Dou, William T. Gerthoffer, Jiangbo Dang, Judith A. Blake, Ming Tan:
An ontology-based MicroRNA knowledge sharing and acquisition framework. BIBM Workshops 2012: 740-747 - [c16]Li Ni, Carol J. Bult, James A. Kadin, Joel E. Richardson, Martin Ringwald, Janan T. Eppig, Judith A. Blake:
Using Biomedical Ontologies for Data Representation and Management in the Mouse Genome Informatics (MGI) System. ICBO 2012 - 2011
- [j33]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) - [j32]Terrence F. Meehan, Anna Maria Masci, Amina Abdulla, Lindsay G. Cowell, Judith A. Blake, Christopher J. Mungall, Alexander D. Diehl:
Logical Development of the Cell Ontology. BMC Bioinform. 12: 6 (2011) - [j31]Carol J. Bult, Harold J. Drabkin, Alexei V. Evsikov, Darren A. Natale, Cecilia N. Arighi, Natalia V. Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A. Blake, Cathy H. Wu:
The Representation of Protein Complexes in the Protein Ontology (PRO). BMC Bioinform. 12: 371 (2011) - [j30]Alexander D. Diehl, Alison Deckhut Augustine, Judith A. Blake, Lindsay G. Cowell, Elizabeth S. Gold, Timothy A. Gondré-Lewis, Anna Maria Masci, Terrence F. Meehan, Penelope A. Morel, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard H. Scheuermann, Q. Alison Yao, Martin S. Zand, Christopher J. Mungall:
Hematopoietic cell types: Prototype for a revised cell ontology. J. Biomed. Informatics 44(1): 75-79 (2011) - [j29]Terrence F. Meehan, Christopher J. Carr, Jeremy J. Jay, Carol J. Bult, Elissa J. Chesler, Judith A. Blake:
Autism candidate genes via mouse phenomics. J. Biomed. Informatics 44(Supplement-1): S5-S11 (2011) - [j28]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) - [j27]Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D'Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang, Cathy H. Wu:
The Protein Ontology: a structured representation of protein forms and complexes. Nucleic Acids Res. 39(Database-Issue): 539-545 (2011) - [j26]Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson, Janan T. Eppig:
The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. 39(Database-Issue): 842-848 (2011) - [c15]Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei V. Evsikov, Hongzhan Huang, Natalia V. Roberts, Alan Ruttenberg, Barry Smith, Jian Zhang, Cathy H. Wu:
Protein-Centric Connection of Biomedical Knowledge: Protein Ontology (PRO) Research and Annotation Tools. ICBO 2011 - [c14]Susan M. Bello, Allan Peter Davis, Thomas C. Wiegers, Mary E. Dolan, Cynthia L. Smith, Joel E. Richardson, Judith A. Blake, Carolyn J. Mattingly, Janan T. Eppig:
Waiting for a Robust Disease Ontology: A Merger of OMIM and MeSH as a Practical Interim Solution. ICBO 2011 - [c13]Terrence F. Meehan, Christopher J. Mungall, Judith A. Blake, Alexander D. Diehl:
Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression Analysis. ICBO 2011 - [c12]Todd J. Vision, Judith A. Blake, Hilmar Lapp, Paula M. Mabee, Monte Westerfield:
Similarity Between Semantic Description Sets: Addressing Needs Beyond Data Integration. LISC 2011 - 2010
- [j25]Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake, Janan T. Eppig:
The Mouse Genome Database: enhancements and updates. Nucleic Acids Res. 38(Database-Issue): 586-592 (2010)
2000 – 2009
- 2009
- [j24]Mary E. Dolan, Judith A. Blake:
Using ontology visualization to facilitate access to knowledge about human disease genes. Appl. Ontology 4(1): 35-49 (2009) - [j23]Karen G. Dowell, Monica S. McAndrews-Hill, David P. Hill, Harold J. Drabkin, Judith A. Blake:
Integrating text mining into the MGI biocuration workflow. Database J. Biol. Databases Curation 2009 (2009) - [j22]Lee T. Sam, Eneida A. Mendonça, Jianrong Li, Judith A. Blake, Carol Friedman, Yves A. Lussier:
PhenoGO: an integrated resource for the multiscale mining of clinical and biological data. BMC Bioinform. 10(S-2) (2009) - [j21]Cecilia N. Arighi, Hongfang Liu, Darren A. Natale, Winona C. Barker, Harold J. Drabkin, Judith A. Blake, Barry Smith, Cathy H. Wu:
TGF-beta signaling proteins and the Protein Ontology. BMC Bioinform. 10(S-5) (2009) - [j20]Judith A. Blake, Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database genotypes: : phenotypes. Nucleic Acids Res. 37(Database-Issue): 712-719 (2009) - [c11]Gil Alterovitz, Judith A. Blake, Jonathan M. Dreyfuss, Drew Endy, Marco Ramoni:
Session Introduction. Pacific Symposium on Biocomputing 2009: 1-3 - 2008
- [j19]David P. Hill, Barry Smith, Monica S. McAndrews-Hill, Judith A. Blake:
Gene Ontology annotations: what they mean and where they come from. BMC Bioinform. 9(S-5) (2008) - [j18]Carol J. Bult, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Judith A. Blake:
The Mouse Genome Database (MGD): mouse biology and model systems. Nucleic Acids Res. 36(Database-Issue): 724-728 (2008) - [c10]Anna V. Anagnostopoulos, Judith A. Blake, Carol J. Bult, Martin Ringwald, Joel E. Richardson, James A. Kadin, Janan T. Eppig:
Using bio-ontologies as data annotation, integration & analytical tools at the Mouse Genome Informatics resource. BIBE 2008: 1-7 - [c9]Harold J. Drabkin, Cecilia N. Arighi, Cathy H. Wu, Judith A. Blake:
Functional Annotation of Protein Isoforms and Modified Forms. BIOCOMP 2008: 701-707 - 2007
- [j17]Alexander D. Diehl, Jamie A. Lee, Richard H. Scheuermann, Judith A. Blake:
Ontology development for biological systems: immunology. Bioinform. 23(7): 913-915 (2007) - [j16]Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Ti-Cheng Chang, Zhang-Zhi Hu, Hongfang Liu, Barry Smith, Cathy H. Wu:
Framework for a Protein Ontology. BMC Bioinform. 8(S-9) (2007) - [j15]Janan T. Eppig, Judith A. Blake, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The mouse genome database (MGD): new features facilitating a model system. Nucleic Acids Res. 35(Database-Issue): 630-637 (2007) - 2006
- [j14]Judith A. Blake, Carol J. Bult:
Beyond the data deluge: Data integration and bio-ontologies. J. Biomed. Informatics 39(3): 314-320 (2006) - [j13]Judith A. Blake, Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson:
The Mouse Genome Database (MGD): updates and enhancements. Nucleic Acids Res. 34(Database-Issue): 562-567 (2006) - [c8]Hua Xu, Debra M. Krupke, Judith A. Blake, Carol Friedman:
A Natural Language Processing (NLP) Tool to Assist in the Curation Of the Laboratory Mouse Tumor Biology Database. AMIA 2006 - [c7]Mary E. Dolan, Judith A. Blake:
Using Ontology Visualization to Coordinate Cross-species Functional Annotation for Human Disease Genes. CBMS 2006: 583-587 - [c6]Mary E. Dolan, Judith A. Blake:
Using Ontology Graphs to Understand Annotations and Reason about Them. KR-MED 2006 - 2005
- [j12]Harold J. Drabkin, Christopher Hollenbeck, David P. Hill, Judith A. Blake:
Ontological visualization of protein-protein interactions. BMC Bioinform. 6: 29 (2005) - [j11]Janan T. Eppig, Carol J. Bult, James A. Kadin, Joel E. Richardson, Judith A. Blake:
The Mouse Genome Database (MGD): from genes to mice - a community resource for mouse biology. Nucleic Acids Res. 33(Database-Issue): 471-475 (2005) - [c5]Donnie Qi, Judith A. Blake, James A. Kadin, Joel E. Richardson, Martin Ringwald, Janan T. Eppig, Carol J. Bult:
Data Integration in the Mouse Genome Informatics (MGI) Database. CSB Workshops 2005: 37-38 - [c4]Mary E. Dolan, Li Ni, Evelyn Camon, Judith A. Blake:
A procedure for assessing GO annotation consistency. ISMB (Supplement of Bioinformatics) 2005: 136-143 - 2004
- [j10]Carol J. Bult, Judith A. Blake, Joel E. Richardson, James A. Kadin, Janan T. Eppig:
The Mouse Genome Database (MGD): integrating biology with the genome. Nucleic Acids Res. 32(Database-Issue): 476-481 (2004) - [j9]David P. Hill, Dale A. Begley, Jacqueline H. Finger, Terry F. Hayamizu, Ingeborg J. McCright, Constance M. Smith, Jon S. Beal, Lori E. Corbani, Judith A. Blake, Janan T. Eppig, James A. Kadin, Joel E. Richardson, Martin Ringwald:
The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res. 32(Database-Issue): 568-571 (2004) - [j8]Michael Bada, Robert Stevens, Carole A. Goble, Yolanda Gil, Michael Ashburner, Judith A. Blake, J. Michael Cherry, Midori A. Harris, Suzanna Lewis:
A short study on the success of the Gene Ontology. J. Web Semant. 1(2): 235-240 (2004) - [c3]Joel E. Richardson, James A. Kadin, Judith A. Blake, Carol J. Bult, Janan T. Eppig, Martin Ringwald:
From Sipping on a Straw to Drinking from a Fire Hose: Data Integration in a Public Genome Database. ICDE 2004: 795-798 - [c2]Olivia Tuason, Lifeng Chen, Hongfang Liu, Judith A. Blake, Carol Friedman:
Biological Nomenclatures: A Source of Lexical Knowledge and Ambiguity. Pacific Symposium on Biocomputing 2004: 238-249 - 2003
- [j7]Judith A. Blake, Joel E. Richardson, Carol J. Bult, James A. Kadin, Janan T. Eppig:
MGD: the Mouse Genome Database. Nucleic Acids Res. 31(1): 193-195 (2003) - 2002
- [j6]Judith A. Blake, Joel E. Richardson, Carol J. Bult, James A. Kadin, Janan T. Eppig:
The Mouse Genome Database (MGD): the model organism database for the laboratory mouse. Nucleic Acids Res. 30(1): 113-115 (2002) - 2001
- [j5]Judith A. Blake, Janan T. Eppig, Joel E. Richardson, Carol J. Bult, James A. Kadin:
The Mouse Genome Database (MGD): integration nexus for the laboratory mouse. Nucleic Acids Res. 29(1): 91-94 (2001) - 2000
- [j4]Judith A. Blake, Janan T. Eppig, Joel E. Richardson, Muriel T. Davisson:
The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse. Nucleic Acids Res. 28(1): 108-111 (2000) - [c1]Carol J. Bult, Joel E. Richardson, Judith A. Blake, James A. Kadin, Martin Ringwald, Janan T. Eppig:
Mouse Genome Informatics in a New Age of Biological Inquiry. BIBE 2000: 29-32
1990 – 1999
- 1999
- [j3]Judith A. Blake, Joel E. Richardson, Muriel T. Davisson, Janan T. Eppig:
The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse. The Mouse Genome Database Group. Nucleic Acids Res. 27(1): 95-98 (1999) - 1998
- [j2]Judith A. Blake, Janan T. Eppig, Joel E. Richardson, Muriel T. Davisson:
The Mouse Genome Database (MGD): a community resource. Status and enhancements. The Mouse Genome Informatics Group. Nucleic Acids Res. 26(1): 130-137 (1998) - 1997
- [j1]Judith A. Blake, Joel E. Richardson, Muriel T. Davisson, Janan T. Eppig:
The Mouse Genome Database (MGD). A comprehensive public resource of genetic, phenotypic and genomic data. The Mouse Genome Informatics Group. Nucleic Acids Res. 25(1): 85-91 (1997)
Coauthor Index
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