Jeff de Pons

According to our database, Jeff de Pons authored at least 21 papers between 2009 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

A roadmap for the functional annotation of protein families: a community perspective.

Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu

Database J. Biol. Databases Curation, 2022

2021

The Gene Ontology resource: enriching a GOld mine.

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

Nucleic Acids Res., 2021

2020

The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform.

Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Stanley J. F. Laulederkind, Matthew J. Hoffman, Mary L. Kaldunski, Monika Tutaj, Jyothi Thota, Harika S. Nalabolu, Santoshi L. R. Ellanki, Marek Tutaj, Jeffrey DePons, Anne E. Kwitek, Melinda R. Dwinell, Mary Shimoyama

Nucleic Acids Res., 2020

Alliance of Genome Resources Portal: unified model organism research platform.

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

Nucleic Acids Res., 2020

2019

Integrated curation and data mining for disease and phenotype models at the Rat Genome Database.

Shur-Jen Wang, Stanley J. F. Laulederkind, Yiqing Zhao, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Jyothi Thota, Marek Tutaj, Matthew J. Hoffman, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2019

2018

Adapting Disease Vocabularies for Curation at the Rat Genome Database.

Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Elizabeth R. Bolton, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Mary Shimoyama, Melinda R. Dwinell

Proceedings of the 9th International Conference on Biological Ontology (ICBO 2018), 2018

2017

The SmartAPI Ecosystem for Making Web APIs FAIR.

Shima Dastgheib, Trish Whetzel, Amrapali Zaveri, Cyrus Afrasiabi, Pedro Assis, Paul Avillach, Kathleen M. Jagodnik, Gabor Korodi, Marcin Pilarczyk, Jeff de Pons, Stephan C. Schürer, Raymond Terryn, Ruben Verborgh, Chunlei Wu, Michel Dumontier

Proceedings of the ISWC 2017 Posters & Demonstrations and Industry Tracks co-located with 16th International Semantic Web Conference (ISWC 2017), Vienna, Austria, October 23rd - to, 2017

2016

The Chinchilla Research Resource Database: resource for an otolaryngology disease model.

Mary Shimoyama, Jennifer R. Smith, Jeff de Pons, Marek Tutaj, Pawjai Khampang, Wenzhou Hong, Christy B. Erbe, Garth D. Ehrlich, Lauren O. Bakaletz, Joseph E. Kerschner

Database J. Biol. Databases Curation, 2016

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

G. Thomas Hayman, Stanley J. F. Laulederkind, Jennifer R. Smith, Shur-Jen Wang, Victoria Petri, Rajni Nigam, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2016

Disease Connections at RGD.

Mary Shimoyama, Stanley J. F. Laulederkind, Jeff de Pons, Marek Tutaj, Victoria Petri, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jyothi Thota, Omid Ghiasvand, Melinda R. Dwinell

Proceedings of the AMIA 2016, 2016

2015

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease.

Mary Shimoyama, Jeff de Pons, G. Thomas Hayman, Stanley J. F. Laulederkind, Weisong Liu, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Marek Tutaj, Shur-Jen Wang, Elizabeth A. Worthey, Melinda R. Dwinell, Howard J. Jacob

Nucleic Acids Res., 2015

Improved rat genome gene prediction by integration of ESTs with RNA-Seq information.

Liping Li, Enguo Chen, Chun Yang, Jun Zhu, Pushkala Jayaraman, Jeff de Pons, Catherine C. Kaczorowski, Howard J. Jacob, Andrew S. Greene, Matthew R. Hodges, Allen W. Cowley Jr., Mingyu Liang, Haiming Xu, Pengyuan Liu, Yan Lu

Bioinform., 2015

OntoMate: a text-mining tool aiding curation at the Rat Genome Database.

Weisong Liu, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2015

2014

The pathway ontology - updates and applications.

Victoria Petri, Pushkala Jayaraman, Marek Tutaj, G. Thomas Hayman, Jennifer R. Smith, Jeff de Pons, Stanley J. F. Laulederkind, Timothy Lowry, Rajni Nigam, Shur-Jen Wang, Mary Shimoyama, Melinda R. Dwinell, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob

J. Biomed. Semant., 2014

2013

The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications.

Jennifer R. Smith, Carissa A. Park, Rajni Nigam, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Timothy Lowry, Victoria Petri, Jeff de Pons, Marek Tutaj, Weisong Liu, Elizabeth A. Worthey, Mary Shimoyama, Melinda R. Dwinell

J. Biomed. Semant., 2013

PhenoMiner: quantitative phenotype curation at the rat genome database.

Stanley J. F. Laulederkind, Weisong Liu, Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Victoria Petri, Timothy Lowry, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama

Database J. Biol. Databases Curation, 2013

The Rat Genome Database 2013 - data, tools and users.

Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Jennifer R. Smith, Timothy Lowry, Rajni Nigam, Victoria Petri, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama, Diane H. Munzenmaier, Elizabeth A. Worthey, Howard J. Jacob

Briefings Bioinform., 2013

2012

Ontology searching and browsing at the Rat Genome Database.

Stanley J. F. Laulederkind, Marek Tutaj, Mary Shimoyama, G. Thomas Hayman, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, Melinda R. Dwinell, Howard J. Jacob

Database J. Biol. Databases Curation, 2012

2011

The Rat Genome Database Pathway Portal.

Victoria Petri, Mary Shimoyama, G. Thomas Hayman, Jennifer R. Smith, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Diane H. Munzenmaier, Simon N. Twigger, Howard J. Jacob

Database J. Biol. Databases Curation, 2011

The Rat Genome Database curation tool suite: a set of optimized software tools enabling efficient acquisition, organization, and presentation of biological data.

Stanley J. F. Laulederkind, Mary Shimoyama, G. Thomas Hayman, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, George Kowalski, Weisong Liu, Wes Rood, Diane H. Munzenmaier, Melinda R. Dwinell, Simon N. Twigger, Howard J. Jacob

Database J. Biol. Databases Curation, 2011

2009

The Rat Genome Database 2009: variation, ontologies and pathways.

Melinda R. Dwinell, Elizabeth A. Worthey, Mary Shimoyama, Burcu Bakir-Gungor, Jeffrey DePons, Stanley J. F. Laulederkind, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Alexander Stoddard, Simon N. Twigger, Howard J. Jacob

Nucleic Acids Res., 2009