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Journal Articles
- 2023
[j18]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)- [j17]Alan M. Cleary, Andrew D. Farmer:
Genome Context Viewer (GCV) version 2: enhanced visual exploration of multiple annotated genomes. Nucleic Acids Res. 51(W1): 225-231 (2023) - 2022
- [j16]Éloi Durant, Mathieu Rouard, Eric W. Ganko, Cédric Muller, Alan M. Cleary, Andrew D. Farmer, Matthieu G. Conte, François Sabot:
Ten simple rules for developing visualization tools in genomics. PLoS Comput. Biol. 18(11): 1010622 (2022) - 2018
- [j15]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) - [j14]Alan M. Cleary, Andrew D. Farmer:
Genome Context Viewer: visual exploration of multiple annotated genomes using microsynteny. Bioinform. 34(9): 1562-1564 (2018) - 2016
- [j13]Yun Zheng, Vandana Hivrale, Xiaotuo Zhang, Babu Valliyodan, Christine Lelandais-Brière, Andrew D. Farmer, Gregory D. May, Martin Crespi, Henry T. Nguyen, Ramanjulu Sunkar:
Small RNA profiles in soybean primary root tips under water deficit. BMC Syst. Biol. 10(S-5): 1-10 (2016) - [j12]Sudhansu Dash, Jacqueline D. Campbell, Ethalinda K. S. Cannon, Alan M. Cleary, Wei Huang, Scott R. Kalberer, Vijay Karingula, Alex G. Rice, Jugpreet Singh, Pooja E. Umale, Nathan T. Weeks, Andrew P. Wilkey, Andrew D. Farmer, Steven B. Cannon:
Legume information system (LegumeInfo.org): a key component of a set of federated data resources for the legume family. Nucleic Acids Res. 44(Database-Issue): 1181-1188 (2016) - 2006
- [j11]Kamal Gajendran, Michael D. Gonzales, Andrew D. Farmer, Eric Archuleta, Joe Win, Mark E. Waugh, Sophien Kamoun:
Phytophthora functional genomics database (PFGD): functional genomics of phytophthora-plant interactions. Nucleic Acids Res. 34(Database-Issue): 465-470 (2006) - 2005
- [j10]Michael D. Gonzales, Eric Archuleta, Andrew D. Farmer, Kamal Gajendran, David M. Grant, Randy C. Shoemaker, William D. Beavis, Mark E. Waugh:
The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucleic Acids Res. 33(Database-Issue): 660-665 (2005) - 2001
- [j9]Adam C. Siepel, Andrew D. Farmer, Andrew N. Tolopko, Mingzhe Zhuang, Pedro Mendes, William D. Beavis, Bruno W. S. Sobral:
ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources. Bioinform. 17(1): 83-94 (2001) - [j8]Harry Mangalam, Jason E. Stewart, Jiaye Zhou, Karen Schlauch, Mark E. Waugh, Guanghong Chen, Andrew D. Farmer, Greg Colello, Jennifer W. Weller:
GeneX: An Open Source gene expression database and integrated tool set. IBM Syst. J. 40(2): 552-569 (2001) - [j7]Adam C. Siepel, Andrew N. Tolopko, Andrew D. Farmer, Peter A. Steadman, Faye D. Schilkey, B. Dawn Perry, William D. Beavis:
An integration platform for heterogeneous bioinformatics software components. IBM Syst. J. 40(2): 570-591 (2001) - [j6]Callum J. Bell, Richard A. Dixon, Andrew D. Farmer, H. Raul Flores, Jeff T. Inman, Robert A. Gonzales, Maria J. Harrison, Nancy L. Paiva, Angela D. Scott, Jennifer W. Weller, Gregory D. May:
The Medicago Genome Initiative: a model legume database. Nucleic Acids Res. 29(1): 114-117 (2001) - 2000
- [j5]Carol Harger, Guanghong Chen, Andrew D. Farmer, Wen Huang, Jeff T. Inman, Donald Kiphart, Faye D. Schilkey, M. P. Skupski, Jennifer W. Weller:
The Genome Sequence DataBase. Nucleic Acids Res. 28(1): 31-32 (2000) - 1999
- [j4]G. A. Seluja, Andrew D. Farmer, Mia McLeod, Carol Harger, Peter A. Schad:
Establishing a method of vector contamination identification in database sequences. Bioinform. 15(2): 106-110 (1999) - [j3]M. P. Skupski, M. Booker, Andrew D. Farmer, M. Harpold, Wen Huang, Jeff T. Inman, Donald Kiphart, C. Kodira, S. Root, Faye D. Schilkey, Jolene Schwertfeger, Adam C. Siepel, David Stamper, Nina Thayer, R. Thompson, Jennifer R. Wortman, J. J. Zhuang, Carol Harger:
The Genome Sequence DataBase: towards an integrated functional genomics resource. Nucleic Acids Res. 27(1): 35-38 (1999) - 1998
- [j2]Carol Harger, M. P. Skupski, J. Bingham, Andrew D. Farmer, S. Hoisie, Peter T. Hraber, Donald Kiphart, L. Krakowski, Mia McLeod, Jolene Schwertfeger, G. A. Seluja, Adam C. Siepel, Gautam Singh, David Stamper, Peter A. Steadman, Nina Thayer, R. Thompson, P. Wargo, Mark E. Waugh, J. J. Zhuang, Peter A. Schad:
The Genome Sequence DataBase (GSDB): improving data quality and data access. Nucleic Acids Res. 26(1): 21-26 (1998) - 1997
- [j1]Carol Harger, Marian Skupski, Ethan Allen, Christopher Clark, David Crowley, Emily Dickinson, David Easley, Ada Espinosa-Lujan, Andrew D. Farmer, Chris A. Fields, Leandrita Flores, Lynn Harris, Gifford Keen, Maurice Manning, Michael P. McLeod, John O'Neill, Maria Pumilia, Rhonda Reinert, David Rider, John Rohrlich, Yolanda Romero, Jolene Schwertfeger, Gustavo Seluja, Adam C. Siepel, Gautam Singh, Linda Smyth, David Stamper, Judy Stein, Randy Suggs, Rajini Takkallapalli, Nina Thayer, Gary Thompson, Colleen Walsh, Frederick Wedgeworth III, Peter A. Schad:
The Genome Sequence DataBase version 1.0 (GSDB): from low pass sequences to complete genomes. Nucleic Acids Res. 25(1): 18-23 (1997)
Informal and Other Publications
- 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)
Coauthor Index
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