Tanya Z. Berardini

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 9

Top Topics

Protein Function

High Throughput

Preliminary Study

Top Venues

Database J. Biol. Databases Curation

J. Biomed. Semant.

Publications

Jennifer L. Clarke, Laurel D. Cooper, Monica F. Poelchau, Tanya Z. Berardini, Justin Elser, Andrew D. Farmer, Stephen P. Ficklin, Sunita Kumari, Marie-Angélique Laporte, Rex T. Nelson, Rie Sadohara, Peter Selby, Anne E. Thessen, Brandon Whitehead, Taner Z. Sen
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. Database J. Biol. Databases Curation 2023 (2023)
Jennifer L. Clarke, Laurel D. Cooper, Monica F. Poelchau, Tanya Z. Berardini, Justin Elser, Andrew D. Farmer, Stephen P. Ficklin, Sunita Kumari, Marie-Angélique Laporte, Rex T. Nelson, Rie Sadohara, Peter Selby, Anne E. Thessen, Brandon Whitehead, Taner Z. Sen
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the AgBioData Consortium. CoRR (2023)
Jolene Ramsey, Brenley K. McIntosh, Daniel P. Renfro, Suzanne A. Aleksander, Sandra A. LaBonte, Curtis Ross, Adrienne E. Zweifel, Nathan Liles, Shabnam Farrar, Jason J. Gill, Ivan Erill, Sarah Ades, Tanya Z. Berardini, Jennifer A. Bennett, Siobhan M. Brady, Robert Britton, Seth Carbon, Steven M. Caruso, Dave Clements, Ritu Dalia, Meredith Defelice, Erin L. Doyle, Iddo Friedberg, Susan M. R. Gurney, Lee Hughes, Allison Johnson, Jason M. Kowalski, Donghui Li, Ruth C. Lovering, Tamara L. Mans, Fiona McCarthy, Sean D. Moore, Rebecca Murphy, Timothy D. Paustian, Sarah Perdue, Celeste N. Peterson, Birgit M. Prüß, Margaret S. Saha, Robert R. Sheehy, John T. Tansey, Louise Temple, Alexander William Thorman, Saul Trevino, Amy Cheng Vollmer, Virginia Walbot, Joanne Willey, Deborah A. Siegele, James C. Hu
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PLoS Comput. Biol. 17 (10) (2021)
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 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) (2021)
Helen Attrill, Pascale Gaudet, Rachael P. Huntley, Ruth C. Lovering, Stacia R. Engel, Sylvain Poux, Kimberly M. Van Auken, George E. Georghiou, Marcus C. Chibucos, Tanya Z. Berardini, Valerie Wood, Harold J. Drabkin, Petra Fey, Penelope Garmiri, Midori A. Harris, Tony Sawford, Leonore Reiser, Rebecca Tauber, Sabrina Toro, The Gene Ontology Consortium
Annotation of gene product function from high-throughput studies using the Gene Ontology. Database J. Biol. Databases Curation 2019 (2019)
Lisa C. Harper, Jacqueline D. Campbell, Ethalinda K. S. Cannon, Sook Jung, Monica Poelchau, Ramona L. Walls, Carson M. Andorf, Elizabeth Arnaud, Tanya Z. Berardini, Clayton L. Birkett, Steven B. Cannon, James D. Carson, Bradford Condon, Laurel Cooper, Nathan A. Dunn, Christine G. Elsik, Andrew Farmer, Stephen P. Ficklin, David Grant, Emily S. Grau, Nic Herndon, Zhi-Liang Hu, Jodi L. Humann, Pankaj Jaiswal, Clément Jonquet, Marie-Angélique Laporte, Pierre Larmande, Gerard R. Lazo, Fiona McCarthy, Naama Menda, Christopher J. Mungall, Monica C. Munoz-Torres, Sushma Naithani, Rex T. Nelson, Daureen Nesdill, Carissa A. Park, James M. Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Z. Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak R. Unni, Liya Wang, Doreen Ware, Jill L. Wegrzyn, Jason Williams, Margaret Woodhouse, Jing Yu, Doreen Main
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database J. Biol. Databases Curation 2018 (2018)
Leonore Reiser, Tanya Z. Berardini, Donghui Li, Robert J. Muller, Emily M. Strait, Qian Li, Yarik Mezheritsky, Andrey Vetushko, Eva Huala
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database J. Biol. Databases Curation 2016 (2016)
Tanya Z. Berardini, Ron Daniel Jr., Michael Lauruhn, Leonore Reiser
Preliminary Study on the Impact of Literature Curation in a Model Organism Database on Article Citation Rates. D Lib Mag. 22 (9/10) (2016)
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)
Heiko Dietze, Tanya Z. Berardini, Rebecca E. Foulger, David P. Hill, Jane Lomax, David Osumi-Sutherland, Paola Roncaglia, Christopher J. Mungall
TermGenie - A web application for pattern-based ontology class generation. J. Biomed. Semant. 5 (2014)
Paola Roncaglia, Maryann E. Martone, David P. Hill, Tanya Z. Berardini, Rebecca E. Foulger, Fahim T. Imam, Harold J. Drabkin, Christopher J. Mungall, Jane Lomax
The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments. J. Biomed. Semant. 4 (2013)
Kimberly Van Auken, Petra Fey, Tanya Z. Berardini, Robert J. Dodson, Laurel Cooper, Donghui Li, Juancarlos Chan, Yuling Li, Siddhartha Basu, Hans-Michael Müller, Rex L. Chisholm, Eva Huala, Paul W. Sternberg
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. Database J. Biol. Databases Curation 2012 (2012)
Tanya Z. Berardini, Donghui Li, Robert J. Muller, Raymond Chetty, Larry Ploetz, Shanker Singh, April Wensel, Eva Huala
Assessment of community-submitted ontology annotations from a novel database-journal partnership. Database J. Biol. Databases Curation 2012 (2012)
Donghui Li, Tanya Z. Berardini, Robert J. Muller, Eva Huala
literature corpus. Database J. Biol. Databases Curation 2012 (2012)
Sarah W. Burge, Teresa K. Attwood, Alex Bateman, Tanya Z. Berardini, J. Michael Cherry, Claire O'Donovan, Ioannis Xenarios, Pascale Gaudet
Biocurators and Biocuration: surveying the 21st century challenges. Database J. Biol. Databases Curation 2012 (2012)
Philippe Lamesch, Tanya Z. Berardini, Donghui Li, David Swarbreck, Christopher Wilks, Rajkumar Sasidharan, Robert J. Muller, Kate Dreher, Debbie L. Alexander, Margarita Garcia-Hernandez, Athikkattuvalasu S. Karthikeyan, Cynthia H. Lee, William D. Nelson, Larry Ploetz, Shanker Singh, April Wensel, Eva Huala
The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 40 (Database-Issue) (2012)
Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. Database J. Biol. Databases Curation 2012 (2012)
Christopher J. Mungall, Michael Bada, Tanya Z. Berardini, Jennifer I. Deegan, Amelia Ireland, Midori A. Harris, David P. Hill, Jane Lomax
Cross-product extensions of the Gene Ontology. J. Biomed. Informatics 44 (1) (2011)
David Swarbreck, Christopher Wilks, Philippe Lamesch, Tanya Z. Berardini, Margarita Garcia-Hernandez, Hartmut Foerster, Donghui Li, Tom Meyer, Robert J. Muller, Larry Ploetz, Amie Radenbaugh, Shanker Singh, Vanessa Swing, Christophe Tissier, Peifen Zhang, Eva Huala
The Arabidopsis Information Resource (TAIR): gene structure and function annotation. Nucleic Acids Res. 36 (Database-Issue) (2008)
Thomas Yan, Danny Yoo, Tanya Z. Berardini, Lukas A. Mueller, Dan C. Weems, Shuai Weng, J. Michael Cherry, Seung Yon Rhee
PatMatch: a program for finding patterns in peptide and nucleotide sequences. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Seung Yon Rhee, William D. Beavis, Tanya Z. Berardini, Guanghong Chen, David A. Dixon, Aisling Doyle, Margarita Garcia-Hernandez, Eva Huala, Gabriel Lander, Mary Montoya, Neil Miller, Lukas A. Mueller, Suparna Mundodi, Leonore Reiser, Julie Tacklind, Dan C. Weems, Yihe Wu, Iris Xu, Daniel Yoo, Jungwon Yoon, Peifen Zhang
The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 31 (1) (2003)