Doreen Ware

According to our database, Doreen Ware authored at least 37 papers between 2002 and 2022.

Collaborative distances:

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

2022

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Andrew D. Yates, James E. Allen, M. Ridwan Amode, Andrey G. Azov, Matthieu Barba, Andrés Becerra, Jyothish Bhai, Lahcen I. Campbell, Manuel Carbajo Martinez, Marc Chakiachvili, Kapeel Chougule, Mikkel B. Christensen, Bruno Contreras-Moreira, Alayne Cuzick, Luca Da Rin Fioretto, Paul Davis, Nishadi De Silva, Stavros Diamantakis, Sarah Dyer, Justin Elser, Carla V. Filippi, Astrid Gall, Dionysios Grigoriadis, Cristina Guijarro-Clarke, Parul Gupta, Kim E. Hammond-Kosack, Kevin L. Howe, Pankaj Jaiswal, Vinay Kaikala, Vivek Kumar, Sunita Kumari, Nick Langridge, Tuan Le, Manuel Luypaert, Gareth Maslen, Thomas Maurel, Benjamin Moore, Matthieu Muffato, Aleena Mushtaq, Guy Naamati, Sushma Naithani, Andrew Olson, Anne Parker, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Mark Quinton-Tulloch, Faye Rodgers, Marc Rosello, Magali Ruffier, James Seager, Vasily Sitnik, Michal Szpak, John G. Tate, Marcela K. Tello-Ruiz, Stephen J. Trevanion, Martin Urban, Doreen Ware, Sharon Wei, Gary Williams, Andrea Winterbottom, Magdalena Zarowiecki, Robert D. Finn, Paul Flicek

Nucleic Acids Res., 2022

Expression Atlas update: gene and protein expression in multiple species.

Pablo A. Moreno, Silvie Fexova, Nancy George, Jonathan R. Manning, Zhichao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer Fuentes, Anja Füllgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham, Andrey Solovyev, Lingyun Zhao, Ananth Prakash, David García-Seisdedos, Deepti Jaiswal Kundu, Shengbo Wang, Mathias Walzer, Laura Clarke, David Osumi-Sutherland, Marcela Karey Tello-Ruiz, Sunita Kumari, Doreen Ware, Jana Eliasova, Mark J. Arends, Martijn C. Nawijn, Kerstin B. Meyer, Tony Burdett, John C. Marioni, Sarah A. Teichmann, Juan Antonio Vizcaíno, Alvis Brazma, Irene Papatheodorou

Nucleic Acids Res., 2022

2021

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.

Marcela K. Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari, Vivek Kumar, Bruno Contreras-Moreira, Guy Naamati, Nancy George, Justin Cook, Dan M. Bolser, Peter D'Eustachio, Lincoln D. Stein, Amit Gupta, Weijia Xu, Jennifer Regala, Irene Papatheodorou, Paul J. Kersey, Paul Flicek, Crispin Taylor, Pankaj Jaiswal, Doreen Ware

Nucleic Acids Res., 2021

BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations.

Liya Wang, Zhenyuan Lu, Michael Regulski, Yinping Jiao, Junping Chen, Doreen Ware, Zhanguo Xin

Bioinform., 2021

Ranked choice voting for representative transcripts with TRaCE.

Andrew Olson, Doreen Ware

Bioinform., 2021

2020

Plant Reactome: a knowledgebase and resource for comparative pathway analysis.

Sushma Naithani, Parul Gupta, Justin Preece, Peter D'Eustachio, Justin Elser, Priyanka Garg, Daemon A. Dikeman, Jason Kiff, Justin Cook, Andrew Olson, Sharon Wei, Marcela K. Tello-Ruiz, Antonio Fabregat Mundo, Alfonso Muñoz-Pomer Fuentes, Suhaib Mohammed, Tiejun Cheng, Evan Bolton, Irene Papatheodorou, Lincoln Stein, Doreen Ware, Pankaj Jaiswal

Nucleic Acids Res., 2020

Ensembl Genomes 2020 - enabling non-vertebrate genomic research.

Kevin L. Howe, Bruno Contreras-Moreira, Nishadi De Silva, Gareth Maslen, Wasiu A. Akanni, James E. Allen, Jorge Álvarez-Jarreta, Matthieu Barba, Dan M. Bolser, Lahcen Cambell, Manuel Carbajo, Marc Chakiachvili, Mikkel B. Christensen, Carla A. Cummins, Alayne Cuzick, Paul Davis, Silvie Fexova, Astrid Gall, Nancy George, Laurent Gil, Parul Gupta, Kim E. Hammond-Kosack, Erin Haskell, Sarah E. Hunt, Pankaj Jaiswal, Sophie H. Janacek, Paul J. Kersey, Nick Langridge, Uma Maheswari, Thomas Maurel, Mark D. McDowall, Benjamin Moore, Matthieu Muffato, Guy Naamati, Sushma Naithani, Andrew Olson, Irene Papatheodorou, Mateus Patricio, Michael Paulini, Helder Pedro, Emily Perry, Justin Preece, Marc Rosello, Matthew Russell, Vasily Sitnik, Daniel M. Staines, Joshua C. Stein, Marcela K. Tello-Ruiz, Stephen J. Trevanion, Martin Urban, Sharon Wei, Doreen Ware, Gary Williams, Andrew D. Yates, Paul Flicek

Nucleic Acids Res., 2020

2018

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Marcela K. Tello-Ruiz, Sushma Naithani, Joshua C. Stein, Parul Gupta, Michael Campbell, Andrew Olson, Sharon Wei, Justin Preece, Matthew J. Geniza, Yinping Jiao, Young Koung Lee, Bo Wang, Joseph Mulvaney, Kapeel Chougule, Justin Elser, Noor Al-Bader, Sunita Kumari, James Thomason, Vivek Kumar, Daniel M. Bolser, Guy Naamati, Electra Tapanari, Nuno A. Fonseca, Laura Huerta, Haider Iqbal, Maria Keays, Alfonso Muñoz-Pomer Fuentes, Y. Amy Tang, Antonio Fabregat, Peter D'Eustachio, Joel Weiser, Lincoln D. Stein, Robert Petryszak, Irene Papatheodorou, Paul J. Kersey, Patti Lockhart, Crispin Taylor, Pankaj Jaiswal, Doreen Ware

Nucleic Acids Res., 2018

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

Paul Julian Kersey, James E. Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu, Thomas Maurel, Benjamin Moore, Mark D. McDowall, Uma Maheswari, Guy Naamati, Victoria Newman, Chuang Kee Ong, Michael Paulini, Helder Pedro, Emily Perry, Matthew Russell, Helen Sparrow, Electra Tapanari, Kieron R. Taylor, Alessandro Vullo, Gareth Williams, Amonida Zadissa, Andrew Olson, Joshua C. Stein, Sharon Wei, Marcela K. Tello-Ruiz, Doreen Ware, Aurelien Luciani, Simon C. Potter, Robert D. Finn, Martin Urban, Kim E. Hammond-Kosack, Dan M. Bolser, Nishadi De Silva, Kevin L. Howe, Nicholas Langridge, Gareth Maslen, Daniel Michael Staines, Andrew D. Yates

Nucleic Acids Res., 2018

SciApps: a cloud-based platform for reproducible bioinformatics workflows.

Liya Wang, Zhenyuan Lu, Peter Van Buren, Doreen Ware

Bioinform., 2018

Predicting gene structure changes resulting from genetic variants via exon definition features.

William H. Majoros, Carson Holt, Michael Campbell, Doreen Ware, Mark Yandell, Timothy E. Reddy

Bioinform., 2018

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.

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

Database J. Biol. Databases Curation, 2018

SciApps: a Bioinformatics Workflow Platform Powered by XSEDE and CyVerse.

Liya Wang, Zhenyuan Lu, Peter Van Buren, Doreen Ware

Proceedings of the Practice and Experience on Advanced Research Computing, 2018

2017

Improved maize reference genome with single-molecule technologies.

Yinping Jiao, Paul Peluso, Jinghua Shi, Tiffany Y. Liang, Michelle C. Stitzer, Bo Wang, Michael Campbell, Joshua C. Stein, Xuehong Wei, Chen-Shan Chin, Katherine E. Guill, Michael Regulski, Sunita Kumari, Andrew Olson, Jonathan Gent, Kevin L. Schneider, Thomas K. Wolfgruber, Michael R. May, Nathan M. Springer, Eric Antoniou, W. Richard McCombie, Gernot G. Presting, Michael D. McMullen, Jeffrey Ross-Ibarra, R. Kelly Dawe, Alex Hastie, David R. Rank, Doreen Ware

Nat., 2017

Plant Reactome: a resource for plant pathways and comparative analysis.

Sushma Naithani, Justin Preece, Peter D'Eustachio, Parul Gupta, Vindhya Amarasinghe, Palitha Dharmawardhana, Guanming Wu, Antonio Fabregat, Justin Elser, Joel Weiser, Maria Keays, Alfonso Muñoz-Pomer Fuentes, Robert Petryszak, Lincoln D. Stein, Doreen Ware, Pankaj Jaiswal

Nucleic Acids Res., 2017

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE.

William H. Majoros, Michael Campbell, Carson Holt, Erin K. DeNardo, Doreen Ware, Andrew S. Allen, Mark Yandell, Timothy E. Reddy

Bioinform., 2017

2016

Gramene 2016: comparative plant genomics and pathway resources.

Marcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Justin Preece, Andrew Olson, Sushma Naithani, Vindhya Amarasinghe, Palitha Dharmawardhana, Yinping Jiao, Joseph Mulvaney, Sunita Kumari, Kapeel Chougule, Justin Elser, Bo Wang, James Thomason, Daniel M. Bolser, Arnaud Kerhornou, Brandon Walts, Nuno A. Fonseca, Laura Huerta, Maria Keays, Y. Amy Tang, Helen E. Parkinson, Antonio Fabregat, Sheldon J. McKay, Joel Weiser, Peter D'Eustachio, Lincoln Stein, Robert Petryszak, Paul J. Kersey, Pankaj Jaiswal, Doreen Ware

Nucleic Acids Res., 2016

Ensembl Genomes 2016: more genomes, more complexity.

Paul Julian Kersey, James E. Allen, Irina M. Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Jay C. Humphrey, Arnaud Kerhornou, Julia Khobova, Naveen K. Aranganathan, Nicholas Langridge, Ernesto Lowy-Gallego, Mark D. McDowall, Uma Maheswari, Michael Nuhn, Chuang Kee Ong, Bert Overduin, Michael Paulini, Helder Pedro, Emily Perry, Giulietta Spudich, Electra Tapanari, Brandon Walts, Gareth Williams, Marcela K. Tello-Ruiz, Joshua C. Stein, Sharon Wei, Doreen Ware, Daniel M. Bolser, Kevin L. Howe, Eugene Kulesha, Daniel Lawson, Gareth Maslen, Daniel M. Staines

Nucleic Acids Res., 2016

2015

The BioMart community portal: an innovative alternative to large, centralized data repositories.

Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, James E. Allen, Olivier Arnaiz, Mohammad Hamza Awedh, Richard A. Baldock, Giulia Barbiera, Philippe Bardou, Tim Beck, Andrew Blake, Merideth Bonierbale, Anthony J. Brookes, Gabriele Bucci, Iwan Buetti, Sarah W. Burge, Cédric Cabau, Joseph W. Carlson, Claude Chelala, Charalambos Chrysostomou, Davide Cittaro, Olivier Collin, Raul Cordova, Rosalind J. Cutts, Erik Dassi, Alex Di Génova, Anis Djari, Anthony Esposito, Heather Estrella, Eduardo Eyras, Julio Fernandez-Banet, Simon A. Forbes, Robert C. Free, Takatomo Fujisawa, Emanuela Gadaleta, Jose M. Garcia-Manteiga, David M. Goodstein, Kristian A. Gray, José Afonso Guerra-Assunção, Bernard Haggarty, Dongjin Han, Byungwoo Han, Todd W. Harris, Jayson Harshbarger, Robert K. Hastings, Richard D. Hayes, Claire Hoede, Shen Hu, Zhi-Liang Hu, Lucie N. Hutchins, Zhengyan Kan, Hideya Kawaji, Aminah-Olivia Keliet, Arnaud Kerhornou, Sunghoon Kim, Rhoda Kinsella, Christophe Klopp, Lei Kong, Daniel Lawson, Dejan Lazarevic, Ji-Hyun Lee, Thomas Letellier, Chuan-Yun Li, Pietro Liò, Chu-Jun Liu, Jie Luo, Alejandro Maass, Jérôme Mariette, Thomas Maurel, Stefania Merella, Azza Mostafa Mohamed, François Moreews, Nabihoudine Ibouniyamine, Nelson Ndegwa, Céline Noirot, Christian Perez-Llamas, Michael Primig, Alessandro Quattrone, Hadi Quesneville, Davide Rambaldi, James M. Reecy, Michela Riba, Steven Rosanoff, Amna Ali Saddiq, Elisa Salas, Olivier Sallou, Rebecca Shepherd, Reinhard Simon, Linda Sperling, William Spooner, Daniel M. Staines, Delphine Steinbach, Kevin R. Stone, Elia Stupka, Jon W. Teague, Abu Z. Dayem Ullah, Jun Wang, Doreen Ware, Marie Wong-Erasmus, Ken Youens-Clark, Amonida Zadissa, Shi-Jian Zhang, Arek Kasprzyk

Nucleic Acids Res., 2015

A genome-wide association study platform built on iPlant cyber-infrastructure.

Liya Wang, Doreen Ware, Carol Lushbough, Nirav C. Merchant, Lincoln Stein

Concurr. Comput. Pract. Exp., 2015

2014

Gramene 2013: comparative plant genomics resources.

Marcela K. Monaco, Joshua C. Stein, Sushma Naithani, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson, Yinping Jiao, Zhenyuan Lu, Daniel M. Bolser, Arnaud Kerhornou, Daniel M. Staines, Brandon Walts, Guanming Wu, Peter D'Eustachio, Robin Haw, David Croft, Paul J. Kersey, Lincoln Stein, Pankaj Jaiswal, Doreen Ware

Nucleic Acids Res., 2014

Ensembl Genomes 2013: scaling up access to genome-wide data.

Paul Julian Kersey, James E. Allen, Mikkel B. Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Daniel Seth Toney Hughes, Jay C. Humphrey, Arnaud Kerhornou, Julia Khobova, Nicholas Langridge, Mark D. McDowall, Uma Maheswari, Gareth Maslen, Michael Nuhn, Chuang Kee Ong, Michael Paulini, Helder Pedro, Iliana Toneva, Mary Ann Tuli, Brandon Walts, Gareth Williams, Derek Wilson, Ken Youens-Clark, Marcela K. Monaco, Joshua C. Stein, Xuehong Wei, Doreen Ware, Daniel M. Bolser, Kevin Lee Howe, Eugene Kulesha, Daniel Lawson, Daniel Michael Staines

Nucleic Acids Res., 2014

2013

Building an open Genome Wide Association Study (GWAS) platform.

Liya Wang, Doreen Ware, Nirav C. Merchant, Carol Lushbough

Proceedings of the 2013 IEEE International Conference on Cluster Computing, 2013

Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar.

Daifeng Wang, Eric Pan, Gang Fang, Sunita Kumari, Fei He, Doreen Ware, Sergei Maslov, Mark Gerstein

Proceedings of the ACM Conference on Bioinformatics, 2013

2012

GrameneMart: the BioMart data portal for the Gramene project.

William Spooner, Ken Youens-Clark, Daniel M. Staines, Doreen Ware

Database J. Biol. Databases Curation, 2012

2011

Gramene database in 2010: updates and extensions.

Ken Youens-Clark, Edward S. Buckler, Terry M. Casstevens, Charles Chen, Genevieve DeClerck, Paul S. Derwent, Palitha Dharmawardhana, Pankaj Jaiswal, Paul J. Kersey, A. S. Karthikeyan, Jerry Lu, Susan McCouch, Liya Ren, William Spooner, Joshua C. Stein, Jim Thomason, Sharon Wei, Doreen Ware

Nucleic Acids Res., 2011

2010

Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration.

Rex T. Nelson, Shulamit Avraham, Randy C. Shoemaker, Gregory D. May, Doreen Ware, Damian Gessler

BioData Min., 2010

2009

CMap 1.01: a comparative mapping application for the Internet.

Ken Youens-Clark, Benjamin Faga, Immanuel Yap, Lincoln Stein, Doreen Ware

Bioinform., 2009

Gramene QTL database: development, content and applications.

Junjian Ni, Anuradha Pujar, Ken Youens-Clark, Immanuel Yap, Pankaj Jaiswal, Isaak Y. Tecle, Chih-Wei Tung, Liya Ren, William Spooner, Xuehong Wei, Shuly Avraham, Doreen Ware, Lincoln Stein, Susan McCouch

Database J. Biol. Databases Curation, 2009

2008

Gramene: a growing plant comparative genomics resource.

Chengzhi Liang, Pankaj Jaiswal, Claire Hebbard, Shuly Avraham, Edward S. Buckler, Terry M. Casstevens, Bonnie L. Hurwitz, Susan McCouch, Junjian Ni, Anuradha Pujar, Dean Ravenscroft, Liya Ren, William Spooner, Isaak Y. Tecle, Jim Thomason, Chih-Wei Tung, Xuehong Wei, Immanuel Yap, Ken Youens-Clark, Doreen Ware, Lincoln Stein

Nucleic Acids Res., 2008

Panzea: an update on new content and features.

Payan Canaran, Edward S. Buckler, Jeffrey Glaubitz, Lincoln Stein, Qi Sun, Wei Zhao, Doreen Ware

Nucleic Acids Res., 2008

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations.

Shulamit Avraham, Chih-Wei Tung, Katica Ilic, Pankaj Jaiswal, Elizabeth A. Kellogg, Susan McCouch, Anuradha Pujar, Leonore Reiser, Seung Yon Rhee, Martin M. Sachs, Mary L. Schaeffer, Lincoln Stein, Peter F. Stevens, Leszek Vincent, Felipe Zapata, Doreen Ware

Nucleic Acids Res., 2008

2006

Panzea: a database and resource for molecular and functional diversity in the maize genome.

Wei Zhao, Payan Canaran, Rebecca Jurkuta, Theresa Fulton, Jeffrey Glaubitz, Edward S. Buckler, John Doebley, Brandon S. Gaut, Major Goodman, Jim Holland, Stephen Kresovich, Michael D. McMullen, Lincoln Stein, Doreen Ware

Nucleic Acids Res., 2006

Gramene: a bird's eye view of cereal genomes.

Pankaj Jaiswal, Junjian Ni, Immanuel Yap, Doreen Ware, William Spooner, Ken Youens-Clark, Liya Ren, Chengzhi Liang, Wei Zhao, Kiran Ratnapu, Benjamin Faga, Payan Canaran, Molly Fogleman, Claire Hebbard, Shuly Avraham, Steven Schmidt, Terry M. Casstevens, Edward S. Buckler, Lincoln Stein, Susan McCouch

Nucleic Acids Res., 2006

Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support.

Payan Canaran, Lincoln Stein, Doreen Ware

Bioinform., 2006

2004

Identifying MicroRNAs in Plant Genomes.

Christopher Maher, Marja Timmermans, Lincoln Stein, Doreen Ware

Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004

2002

Gramene: a resource for comparative grass genomics.

Doreen Ware, Pankaj Jaiswal, Junjian Ni, Xiaokang Pan, Kuan Y. Chang, Kenneth Clark, Leonid Teytelman, Steven Schmidt, Wei Zhao, Samuel Cartinhour, Susan McCouch, Lincoln Stein

Nucleic Acids Res., 2002