Expression Atlas update: gene and protein expression in multiple species. - Moreno, Pablo A.; Fexova, Silvie; George, Nancy; Manning, Jonathan R.; Miao, Zhichao; Mohammed, Suhaib; Fuentes, Alfonso Muñoz-Pomer; Füllgrabe, Anja; Bi, Yalan; Bush, Natassja; Iqbal, Haider; Kumbham, Upendra; et al. (Nucleic Acids Res., 2022)

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. - Yates, Andrew D.; Allen, James E.; Amode, M. Ridwan; Azov, Andrey G.; Barba, Matthieu; Becerra, Andrés; Bhai, Jyothish; Campbell, Lahcen I.; Martinez, Manuel Carbajo; Chakiachvili, Marc; Chougule, Kapeel; Christensen, Mikkel B.; et al. (Nucleic Acids Res., 2022)

BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations. - Wang, Liya; Lu, Zhenyuan; Regulski, Michael; Jiao, Yinping; Chen, Junping; Ware, Doreen; Xin, Zhanguo (Bioinform., 2021)

Ranked choice voting for representative transcripts with TRaCE. - Olson, Andrew; Ware, Doreen (Bioinform., 2021)

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. - Tello-Ruiz, Marcela K.; Naithani, Sushma; Gupta, Parul; Olson, Andrew; Wei, Sharon; Preece, Justin; Jiao, Yinping; Wang, Bo; Chougule, Kapeel; Garg, Priyanka; Elser, Justin; Kumari, Sunita; et al. (Nucleic Acids Res., 2021)

Plant Reactome: a knowledgebase and resource for comparative pathway analysis. - Naithani, Sushma; Gupta, Parul; Preece, Justin; D'Eustachio, Peter; Elser, Justin; Garg, Priyanka; Dikeman, Daemon A.; Kiff, Jason; Cook, Justin; Olson, Andrew; Wei, Sharon; Tello-Ruiz, Marcela K.; et al. (Nucleic Acids Res., 2020)

Ensembl Genomes 2020 - enabling non-vertebrate genomic research. - Howe, Kevin L.; Contreras-Moreira, Bruno; Silva, Nishadi De; Maslen, Gareth; Akanni, Wasiu A.; Allen, James E.; Álvarez-Jarreta, Jorge; Barba, Matthieu; Bolser, Dan M.; Cambell, Lahcen; Carbajo, Manuel; Chakiachvili, Marc; et al. (Nucleic Acids Res., 2020)

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. - Harper, Lisa C.; Campbell, Jacqueline D.; Cannon, Ethalinda K. S.; Jung, Sook; Poelchau, Monica; Walls, Ramona L.; Andorf, Carson M.; Arnaud, Elizabeth; Berardini, Tanya Z.; Birkett, Clayton L.; Cannon, Steven B.; Carson, James D.; et al. (Database J. Biol. Databases Curation, 2018)

Predicting gene structure changes resulting from genetic variants via exon definition features. - Majoros, William H.; Holt, Carson; Campbell, Michael; Ware, Doreen; Yandell, Mark; Reddy, Timothy E. (Bioinform., 2018)

SciApps: a cloud-based platform for reproducible bioinformatics workflows. - Wang, Liya; Lu, Zhenyuan; Buren, Peter Van; Ware, Doreen (Bioinform., 2018)

Gramene 2018: unifying comparative genomics and pathway resources for plant research. - Tello-Ruiz, Marcela K.; Naithani, Sushma; Stein, Joshua C.; Gupta, Parul; Campbell, Michael; Olson, Andrew; Wei, Sharon; Preece, Justin; Geniza, Matthew J.; Jiao, Yinping; Lee, Young Koung; Wang, Bo; et al. (Nucleic Acids Res., 2018)

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. - Kersey, Paul Julian; Allen, James E.; Allot, Alexis; Barba, Matthieu; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel B.; Davis, Paul; Grabmueller, Christoph; Kumar, Navin; Liu, Zicheng; et al. (Nucleic Acids Res., 2018)

SciApps: a Bioinformatics Workflow Platform Powered by XSEDE and CyVerse. - Wang, Liya; Lu, Zhenyuan; Buren, Peter Van; Ware, Doreen (2018)

High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. - Majoros, William H.; Campbell, Michael; Holt, Carson; DeNardo, Erin K.; Ware, Doreen; Allen, Andrew S.; Yandell, Mark; Reddy, Timothy E. (Bioinform., 2017)

Plant Reactome: a resource for plant pathways and comparative analysis. - Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Wu, Guanming; Fabregat, Antonio; Elser, Justin; Weiser, Joel; Keays, Maria; Fuentes, Alfonso Muñoz-Pomer; et al. (Nucleic Acids Res., 2017)

Improved maize reference genome with single-molecule technologies. - Jiao, Yinping; Peluso, Paul; Shi, Jinghua; Liang, Tiffany Y.; Stitzer, Michelle C.; Wang, Bo; Campbell, Michael; Stein, Joshua C.; Wei, Xuehong; Chin, Chen-Shan; Guill, Katherine E.; Regulski, Michael; et al. (Nat., 2017)

Ensembl Genomes 2016: more genomes, more complexity. - Kersey, Paul Julian; Allen, James E.; Armean, Irina M.; Boddu, Sanjay; Bolt, Bruce J.; Carvalho-Silva, Denise; Christensen, Mikkel B.; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Humphrey, Jay C.; Kerhornou, Arnaud; et al. (Nucleic Acids Res., 2016)

Gramene 2016: comparative plant genomics and pathway resources. - Tello-Ruiz, Marcela K.; Stein, Joshua C.; Wei, Sharon; Preece, Justin; Olson, Andrew; Naithani, Sushma; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Jiao, Yinping; Mulvaney, Joseph; Kumari, Sunita; Chougule, Kapeel; et al. (Nucleic Acids Res., 2016)

A genome-wide association study platform built on iPlant cyber-infrastructure. - Wang, Liya; Ware, Doreen; Lushbough, Carol; Merchant, Nirav C.; Stein, Lincoln (Concurr. Comput. Pract. Exp., 2015)

The BioMart community portal: an innovative alternative to large, centralized data repositories. - Smedley, Damian; Haider, Syed; Durinck, Steffen; Pandini, Luca; Provero, Paolo; Allen, James E.; Arnaiz, Olivier; Awedh, Mohammad Hamza; Baldock, Richard A.; Barbiera, Giulia; Bardou, Philippe; Beck, Tim; et al. (Nucleic Acids Res., 2015)

Ensembl Genomes 2013: scaling up access to genome-wide data. - Kersey, Paul Julian; Allen, James E.; Christensen, Mikkel B.; Davis, Paul; Falin, Lee J.; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay C.; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D.; et al. (Nucleic Acids Res., 2014)

Gramene 2013: comparative plant genomics resources. - Monaco, Marcela K.; Stein, Joshua C.; Naithani, Sushma; Wei, Sharon; Dharmawardhana, Palitha; Kumari, Sunita; Amarasinghe, Vindhya; Youens-Clark, Ken; Thomason, James; Preece, Justin; Pasternak, Shiran; Olson, Andrew; 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. - Wang, Daifeng; Pan, Eric; Fang, Gang; Kumari, Sunita; He, Fei; Ware, Doreen; Maslov, Sergei; Gerstein, Mark (2013)

Building an open Genome Wide Association Study (GWAS) platform. - Wang, Liya; Ware, Doreen; Merchant, Nirav C.; Lushbough, Carol (2013)

GrameneMart: the BioMart data portal for the Gramene project. - Spooner, William; Youens-Clark, Ken; Staines, Daniel M.; Ware, Doreen (Database J. Biol. Databases Curation, 2012)

Gramene database in 2010: updates and extensions. - Youens-Clark, Ken; Buckler, Edward S.; Casstevens, Terry M.; Chen, Charles; DeClerck, Genevieve; Derwent, Paul S.; Dharmawardhana, Palitha; Jaiswal, Pankaj; Kersey, Paul J.; Karthikeyan, A. S.; Lu, Jerry; McCouch, Susan; 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. - Nelson, Rex T.; Avraham, Shulamit; Shoemaker, Randy C.; May, Gregory D.; Ware, Doreen; Gessler, Damian (BioData Min., 2010)

Gramene QTL database: development, content and applications. - Ni, Junjian; Pujar, Anuradha; Youens-Clark, Ken; Yap, Immanuel; Jaiswal, Pankaj; Tecle, Isaak Y.; Tung, Chih-Wei; Ren, Liya; Spooner, William; Wei, Xuehong; Avraham, Shuly; Ware, Doreen; et al. (Database J. Biol. Databases Curation, 2009)

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

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations. - Avraham, Shulamit; Tung, Chih-Wei; Ilic, Katica; Jaiswal, Pankaj; Kellogg, Elizabeth A.; McCouch, Susan; Pujar, Anuradha; Reiser, Leonore; Rhee, Seung Yon; Sachs, Martin M.; Schaeffer, Mary L.; Stein, Lincoln; et al. (Nucleic Acids Res., 2008)

Gramene: a growing plant comparative genomics resource. - Liang, Chengzhi; Jaiswal, Pankaj; Hebbard, Claire; Avraham, Shuly; Buckler, Edward S.; Casstevens, Terry M.; Hurwitz, Bonnie L.; McCouch, Susan; Ni, Junjian; Pujar, Anuradha; Ravenscroft, Dean; Ren, Liya; et al. (Nucleic Acids Res., 2008)

Panzea: an update on new content and features. - Canaran, Payan; Buckler, Edward S.; Glaubitz, Jeffrey; Stein, Lincoln; Sun, Qi; Zhao, Wei; Ware, Doreen (Nucleic Acids Res., 2008)

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

Gramene: a bird's eye view of cereal genomes. - Jaiswal, Pankaj; Ni, Junjian; Yap, Immanuel; Ware, Doreen; Spooner, William; Youens-Clark, Ken; Ren, Liya; Liang, Chengzhi; Zhao, Wei; Ratnapu, Kiran; Faga, Benjamin; Canaran, Payan; et al. (Nucleic Acids Res., 2006)

Panzea: a database and resource for molecular and functional diversity in the maize genome. - Zhao, Wei; Canaran, Payan; Jurkuta, Rebecca; Fulton, Theresa; Glaubitz, Jeffrey; Buckler, Edward S.; Doebley, John; Gaut, Brandon S.; Goodman, Major; Holland, Jim; Kresovich, Stephen; McMullen, Michael D.; et al. (Nucleic Acids Res., 2006)

Identifying MicroRNAs in Plant Genomes. - Maher, Christopher; Timmermans, Marja; Stein, Lincoln; Ware, Doreen (2004)

Gramene: a resource for comparative grass genomics. - Ware, Doreen; Jaiswal, Pankaj; Ni, Junjian; Pan, Xiaokang; Chang, Kuan Y.; Clark, Kenneth; Teytelman, Leonid; Schmidt, Steven; Zhao, Wei; Cartinhour, Samuel; McCouch, Susan; Stein, Lincoln (Nucleic Acids Res., 2002)