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Tanya Z. Berardini
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2020 – today
- 2023
- [j20]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) - [i1]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 abs/2307.08958 (2023) - 2021
- [j19]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) - [j18]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)
2010 – 2019
- 2019
- [j17]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: baz007 (2019) - 2018
- [j16]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 D. Farmer, Stephen P. Ficklin
, David M. 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: bay088 (2018) - [p1]Ian Braun, James P. Balhoff, Tanya Z. Berardini, Laurel Cooper, Georgios V. Gkoutos, Lisa C. Harper, Eva Huala, Pankaj Jaiswal, Toni Kazic, Hilmar Lapp
, James A. Macklin, Chelsea D. Specht, Todd J. Vision, Ramona L. Walls, Carolyn J. Lawrence-Dill:
'Computable' Phenotypes Enable Comparative and Predictive Phenomics Among Plant Species and Across Domains of Life. Application of Semantic Technology in Biodiversity Science 2018: 187-205 - 2016
- [j15]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) - [j14]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) - [j13]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) - 2014
- [j12]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: 48 (2014) - 2013
- [j11]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: 20 (2013) - 2012
- [j10]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) - [j9]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) - [j8]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) - [j7]Donghui Li, Tanya Z. Berardini
, Robert J. Muller, Eva Huala
:
Building an efficient curation workflow for the Arabidopsis literature corpus. Database J. Biol. Databases Curation 2012 (2012) - [j6]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) - [j5]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): 1202-1210 (2012) - 2011
- [j4]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): 80-86 (2011)
2000 – 2009
- 2008
- [j3]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): 1009-1014 (2008) - 2005
- [j2]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): 262-266 (2005) - 2003
- [j1]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): 224-228 (2003)
Coauthor Index
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