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; et al. (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2022)

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)

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; et al. (Nucleic Acids Res., 2021)

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; et al. (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; et al. (Nucleic Acids Res., 2020)

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; et al. (Database J. Biol. Databases Curation, 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)

SciApps: a cloud-based platform for reproducible bioinformatics workflows - Liya Wang; Zhenyuan Lu; Peter Van Buren; Doreen Ware (Bioinform., 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; et al. (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; et al. (Nucleic Acids Res., 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, PEARC 2018, Pittsburgh, PA, USA, July 22-26, 2018, 2018)

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)

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; et al. (Nucleic Acids Res., 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; et al. (Nat., 2017)

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; et al. (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2016)

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)

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; et al. (Nucleic Acids Res., 2015)

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; et al. (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2014)

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 (ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics. ACM-BCB 2013, Washington, DC, USA, September 22-25, 2013, 2013)

Building an open Genome Wide Association Study (GWAS) platform - Liya Wang; Doreen Ware; Nirav C. Merchant; Carol Lushbough (2013 IEEE International Conference on Cluster Computing, CLUSTER 2013, Indianapolis, IN, USA, September 23-27, 2013, 2013)

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)

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; et al. (Nucleic Acids Res., 2011)

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)

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; et al. (Database J. Biol. Databases Curation, 2009)

CMap 1.01: a comparative mapping application for the Internet - Ken Youens-Clark; Benjamin Faga; Immanuel Yap; Lincoln Stein; Doreen Ware (Bioinform., 2009)

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; et al. (Nucleic Acids Res., 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; et al. (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)

Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support - Payan Canaran; Lincoln Stein; Doreen Ware (Bioinform., 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; et al. (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2006)

Identifying MicroRNAs in Plant Genomes - Christopher Maher; Marja Timmermans; Lincoln Stein; Doreen Ware (3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2004, Stanford, CA, USA, August 16-19, 2004, 2004)

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)