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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » People & Locations » Doreen Ware

Doreen Helen Ware
Plant, Soil and Nutrition Research
Computational Biologist

Phone: (516) 367-6979
Fax: (516) 367-6851

COLD SPRING HARBOR LABORATORY - 1 BUNGTOWN ROAD
COLD SPRING HARBOR, NY 11724
ITHACA , NY 14853
Projects
Computational and Genomic Resources to Support Plant Genome Function
Cooperative Agreement (A)
  Accession Number: 435146
Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement
In-House Appropriated (D)
  Accession Number: 434556
Standards Development for Phenotypes and Pathway Resource for Sorghum
Non-Assistance Cooperative Agreement (S)
  Accession Number: 434840
Impact of a Great Plains Production System on Sustainable Production of Grant Sorghum
Non-Assistance Cooperative Agreement (S)
  Accession Number: 435133
Development of Genomic and Computational Resources to Support Agriculture
Non-Assistance Cooperative Agreement (S)
  Accession Number: 433534

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Gapless assembly of maize chromosomes using long read technologies - (Peer Reviewed Journal)
Management, analyses, and distribution of the MaizeCODE Data on the Cloud Reprint Icon - (Peer Reviewed Journal)
Wang, L., Lu, Z., Delabastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Ware, D., Gingeras, T., Xu, X., Ramirez, C., Fernandez Marco, C., Williams, J., Dobin, A., Birnbaum, K., Jackson, D., Martienssen, R., Mccombie, R.W., Micklos, D., Schatz, M. 2020. Management, analyses, and distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science. 31. https://doi.org/10.3389/fpls.2020.00289.
Variant phasing and haplotypic expression from long-read sequencing in maize Reprint Icon - (Peer Reviewed Journal)
Wang, B., Tseng, E., Baybayan, P., Eng, K., Regulski, M., Jiao, Y., Wang, L., Olson, A., Chougule, K., Van Buren, P., Ware, D. 2020. Variant phasing and haplotypic expression from long-read sequencing in maize. Communications Biology. 3(78). https://doi.org/10.1038/s42003-020-0805-8.
A rhAmpSeq haplotype strategy targeting the collinear core genome improves marker transferability across a diverse genus - (Peer Reviewed Journal)
Zou, C., Karn, A., Reisch, B., Nguyen, A., Sun, Y., Bao, Y., Campbell, M.S., Church, D., Williams, S., Xu, X., Ledbetter, C.A., Patel, S., Fennell, A., Glaubitz, J., Clark, M., Ware, D., Londo, J.P., Sun, Q., Cadle Davidson, L.E. 2020. A rhAmpSeq haplotype strategy targeting the collinear core genome improves marker transferability across a diverse genus. Nature Biotechnology. 1.
Ngs-enabled fast gene discovery from sorghum pedigreed mutant library - (Abstract Only)
Xin, Z., Ware, D. 2020. Ngs-enabled fast gene discovery from sorghum pedigreed mutant library. Plant and Animal Genome Conference. PAG XXVIII W600.
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline Reprint Icon - (Peer Reviewed Journal)
Ou, S., Su, W., Liao, Y., Chougule, K.M., Agda, J.R., Hellinga, A.J., Lugo, C., Elliott, T.A., Ware, D., Peterson, T., Jiang, N., Hirsch, C.N., Hufford, M.B. 2019. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 20(1):275. https://doi.org/10.1186/s13059-019-1905-y.
Pedigreed mutant library as an efficient resource to discover targets for genome editing - (Abstract Only)
Xin, Z., Burow, G.B., Hayes, C.M., Emendack, Y., Chen, J., Ware, D. 2020. Pedigreed mutant library as an efficient resource to discover targets for genome editing. Plant and Animal Genome Conference. PE0768.
Plant Reactome: a knowledgebase and resource for comparative pathway analysis Reprint Icon - (Peer Reviewed Journal)
Naithani, S., Gupta, P., Preece, J., D'Eustachio, P., Elser, J.L., Garg, P., Dikeman, D.A., Kiff, J., Cook, J., Olson, A., Wei, S., Tello-Ruiz, M.K., Mundo, A.F., Munoz-Pomer, A., Mohammed, S., Cheng, T., Bolton, E., Papatheodorou, I., Stein, L., Ware, D., Jaiswal, P. 2020. Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Research. 48(D1):D1093-D1103. https://doi.org/10.1093/nar/gkz996.
Genetic and molecular analyses of nuclear male sterility loci in sorghum - (Abstract Only)
Chen, J., Echevarria Laza, H.J., Jiao, Y., Ware, D., Xin, Z. 2019. Genetic and molecular analyses of nuclear male sterility loci in sorghum. ASA-CSSA-SSSA Annual Meeting Abstracts. online.
Double triage to identify poorly annotated genes in maize: The missing link in community curation Reprint Icon - (Peer Reviewed Journal)
Tello-Ruiz, M.K., Marco, C.F., Hsu, F., Khangura, R.S., Qiao, P., Sapkota, S., Stiszer, M.C., Wasikowski, R., Wu, H., Junpeng, Z., Chougule, K., Barone, L.C., Ghiban, C., Muna, D., Olson, A.C., Wang, L.C., Ware, D., Micklos, D.A. 2019. Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS Computational Biology. 14(10). https://doi.org/10.1371/journal.pone.0224086.
A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits Reprint Icon - (Peer Reviewed Journal)
Knauer, S., Javell, M., Li, L., Li, X., Ma, X., Wimalanathan, K., Kumari, S., Johnston, R., Leiboff, S., Meeley, R., Schnable, P.S., Ware, D., Lawrence-Dill, C., Yu, J., Muehlbauer, G.J., Scanlon, M.J., Timmermans, M.C. 2019. A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits. Genome Research. 29(12):1962-1973. https://doi.org/10.1101/gr.250878.119.
Fertility of Pedicellate Spikelets in Sorghum is controlled by a Jasmonic Acid Regulatory Module Reprint Icon - (Peer Reviewed Journal)
Gladman, N.P., Jiao, Y., Lee, Y., Zhang, L., Chopra, R., Regulski, M., Burow, G.B., Hayes, C.M., Christensen, S.A., Dampanaboina, L., Chen, J., Burke, J.J., Ware, D., Xin, Z. 2019. Fertility of Pedicellate Spikelets in Sorghum is controlled by a Jasmonic Acid Regulatory Module. Nature Plants. 20(19). https://doi.org/10.3390/ijms20194951.
Ensembl Genomes 2020-enabling non-vertebrate genomic research Reprint Icon - (Peer Reviewed Journal)
Howe, K.L., Contreras-Moreira, B., De Silva, N., Maslen, G., Akanni, W., Allen, J., Alvarez-Jarreta, J., Barba, M., Bolser, D.M., Cambell, L., Carbajo, M., Chakiachvili, M., Christensen, M., Cummins, C., Cuzick, A., Davis, P., Fexova, S., Gall, A., George, N., Gil, L., Gupta, P., Hammond-Kosack, K.E., Haskell, E., Hunt, S.E., Jaiswal, P., Janacek, S.H., Kersey, P.J., Langridge, N., Maheswari, U., Maurel, T., Mcdowall, M.D., Moore, B., Muffato, M., Naamati, G., Naithani, S., Olson, A., Papatheodorou, I., Patricio, M., Paulini, M., Pedro, H., Perry, E., Preece, J., Rosello, M., Russell, M., Sitnik, V., Staines, D.M., Stein, J., Tello-Ruiz, M.K., Trevanion, S.J., Urban, M., Wei, S., Ware, D., Williams, G., Yates, A.D., Flicek, P. 2020. Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Research. 48(D1,8):D689-D695. https://doi.org/10.1093/nar/gkz890.
EMS-induced mutant library as a tool for fast trait discovery - (Abstract Only)
Xin, Z., Burow, G.B., Hayes, C.M., Emendack, Y., Chen, J., Ware, D. 2019. EMS-induced mutant library as a tool for fast trait discovery. ASA-CSSA-SSSA Annual Meeting Abstracts. https://scisoc.confex.com/scisoc/2019am/meetingapp.cgi/Person/368671. online.
Identification of the first nuclear male sterility gene (Male-sterile 9) in sorghum Reprint Icon - (Peer Reviewed Journal)
Chen, J., Jiao, Y., Echevarria Laza, H.J., Payton, P.R., Ware, D., Xin, Z. 2019. Identification of the first nuclear male sterility gene (Male-sterile 9) in sorghum. The Plant Genome. 12. https://doi.org/10.3835/plantgenome2019.03.0020.
Reviving the Transcriptome Studies: An insight into the emergence of Single-Molecule Transcriptome Sequencing Reprint Icon - (Peer Reviewed Journal)
Wang, B., Kumar, V., Olson, A., Ware, D. 2019. Reviving the Transcriptome Studies: An insight into the emergence of Single-Molecule Transcriptome Sequencing. Frontiers in Genetics. 10:384. https://doi.org/10.3389/fgene.2019.00384.
The dominant and poorly penetrant phenotypes of maize unstable factor for orange1 are caused by DNA methylation changes at a linked transposon Reprint Icon - (Peer Reviewed Journal)
Wittmeyer, K., Cui, J., Chaterjee, D., Lee, T., Tan, Q., Jiao, Y., Wang, P., Gaffoora, I., Ware, D., Meyers, B., Chopra, S. 2018. The dominant and poorly penetrant phenotypes of maize unstable factor for orange1 are caused by DNA methylation changes at a linked transposon. The Plant Cell. https://doi.org/10.1105/tpc.18.00546.
Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species Reprint Icon ()
Kersey, P., Allen, J., Allot, A., Barba, M., Boddu, S., Bolt, B., Carvalho-Silva, D., Christensen, M., Davis, P., Grabmueller, C., Kumar, N., Liu, Z., Maurel, T., Moore, B., Mcdowall, M., Maheswari, U., Naamati, G., Newman, V., Ong, C., Paulini, M., Pedro, H., Perry, E., Russell, M., Sparrow, H., Tapanari, E., Taylor, K., Vullo, A., Williams, G., Zadissia, A., Olson, A., Stein, J., Wei, S., Tello-Ruiz, M., Ware, D., Luciani, A., Potter, S., Finn, R., Urban, M., Hammond-Kosack, K., Bolser, D., Nishadi, D., Howe, K., Langridge, N., Maslen, G., Staines, D., Yates, A. 2018. Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species. Nucleic Acids Research. 46(D1):D802-D808. doi: 10.1093/nar/gkx1011.
Transcriptional regulation of nitrogen and nitrogen-related metabolism in Arabidopsis Reprint Icon - (Peer Reviewed Journal)
Gaudinier, A., Rodrigues-Medina, J., Zhang, L., Olson, A., Liseron-Monfils, C., Ware, D. 2018. Transcriptional regulation of nitrogen and nitrogen-related metabolism in Arabidopsis. Nature. 563:259-264. https://doi.org/10.1038/s41586-018-0656-3.
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture Reprint Icon - (Peer Reviewed Journal)
Harper, E.C., Campbell, J., Cannon, E.K., Jung, S., Main, D., Poelchau, M.F., Walls, R.L., Andorf, C.M., Arnaud, E., Berardini, T.Z., Birkett, C.L., Cannon, S.B., Carson, J., Condon, B., Cooper, L., Dunn, N., Elsik, C., Farmer, A., Ficklin, S., Grant, D.M., Grau, E., Hendon, N., Hu, Z., Humann, J., Jaiswal, P., Jonquet, C., Laporte, M., Larmande, P., Lazo, G.R., McCarthy, F., Menda, N., Mungall, C., Munoz-Torres, M., Naithani, S., Nelson, R., Nesdill, D., Park, C., Reecy, J., Reiser, L., Sanderson, L., Sen, T.Z., Staton, M., Subramaniam, S., Karey, T., Unda, V., Unni, D., Wang, L., Ware, D., Wegrzyn, J., Williams, J., Woodhouse, M. 2018. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database: The Journal of Biological Databases and Curation. 2018(1):1-32. https://doi.org/10.1093/database/bay088.
SciApps: a bioinformatics workflow platform powered by XSEDE and CyVerse Reprint Icon - (Proceedings)
Wang, L., Lu, Z., Van Buren, P., Ware, D. 2018. SciApps: a bioinformatics workflow platform powered by XSEDE and CyVerse. In: Proceedings of PEARC18. p. 1-7. doi: 10.1145/3219104.3219109.
Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes Reprint Icon - (Peer Reviewed Journal)
Sun, S., Zhou, Y., Chen, J., Shi, J., Zhao, H., Zhao, H., Song, W., Zhang, M., Cui, Y., Dong, X., Liu, H., Ma, X., Yinping, J., Bo, W., Wei, X., Stein, J., Glaubitz, J., Lu, F., Yu, G., Liang, C., Fengler, K., Li, B., Rafalski, A., Schnable, P., Ware, D., Buckler Iv, E.S., Lai, J. 2018. Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nature Genetics. https://doi.org/10.1038/s41588-018-0182-0.
SciApps: A cloud-based platform for reproducible bioinformatics workflows Reprint Icon - (Peer Reviewed Journal)
Wang, L., Zu, Z., Van Buren, P., Ware, D. 2018. SciApps: A cloud-based platform for reproducible bioinformatics workflows. Bioinformatics. https://doi.org/10.1093/bioinformatics/bty439.
Improved RNA-seq workflows using cyVerse cyberinfrastructure Reprint Icon - (Peer Reviewed Journal)
Chougule, K., Wang, L., Stein, J., Wang, X., Devisetty, U., Klein, R.R., Ware, D. 2018. Improved RNA-seq workflows using cyVerse cyberinfrastructure. Current Protocols in Bioinformatics. 63(1):e53. https://doi.org/10.1002/cpbi.53.
NECorr, a Tool to Rank Gene Importance in Biological Processes using Molecular Networks and Transcriptome Data Reprint Icon ()
Liseron-Monfils, C., Olson, A.J., Ware, D. 2018. NECorr, a Tool to Rank Gene Importance in Biological Processes using Molecular Networks and Transcriptome Data. bioRxiv. 1-11. https://doi.org/10.1101/326868.
Predicting gene structure changes resulting from genetic variants via exon definition features - (Peer Reviewed Journal)
Majoros, W., Holt, C., Campbell, M., Ware, D., Yandell, M., Reddy, T. 2018. Predicting gene structure changes resulting from genetic variants via exon definition features. Bioinformatics. 34(21):3616-3623.
A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing Reprint Icon - (Peer Reviewed Journal)
Wang, B., Regulski, M., Tseng, E., Olson, A., Goodwin, S., Mccombie, R., Ware, D. 2018. A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. Genome Research. doi:10.1101/gr.227462.117.
The maize W22 genome provides a foundation for functional genomics and transposon biology Reprint Icon - (Peer Reviewed Journal)
Springer, N., Anderson, S., Andorf, C.M., Ahern, K., Bai, F., Barad, O., Barbazuk, W., Bass, H.W., Baruch, K., Gen-Zvi, G., Buckler IV, E.S., Bukowski, R., Campbell, M.S., Cannon, E.K., Chomet, P., Dawe, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K., Gault, C., Guan, J., Jander, G., Hunter III, C.T., Jiao, Y., Koch, K.E., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D.R., Noshay, J., Portwood II, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Shi, J., Soifer, I., Stein, J.C., Suzuki, M., Vera, D.L., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wei, X., Wimalanathan, K., Woodhouse, M.R., Xiong, W., Brutnell, T.P. 2018. The maize W22 genome provides a foundation for functional genomics and transposon biology. Nature Genetics. 50:1282-1288. https://doi.org/10.1038/s41588-018-0158-0.
Construction of the third generation Zea mays haplotype map - (Peer Reviewed Journal)
Bukowski, R., Guo, X., Lu, Y., Zou, C., He, B., Rong, Z., Yang, B., Wang, B., Xu, D., Xie, C., Fan, L., Gao, S., Xy, X., Zhang, G., Li, Y., Jiao, Y., Doebley, J., Ross-Ibarra, J., Buffalo, V., Romay, C., Buckler IV, E.S., Wu, Y., Lai, J., Ware, D., Sun, Q. 2018. Construction of the third generation Zea mays haplotype map. Gigascience. 7(4):1-12.
A Reference Genome for US Rice - (Abstract Only)
Scheffler, B.E., Edwards, J., Stein, J., Ware, D., Vaughn, J.N., Schmutz, J., Peterson, D., Youngblood, C., Duke, M.V., Grimwood, J., Simpson, S.A., Mcclung, A.M. 2018. A Reference Genome for US Rice. Meeting Abstract. 37th Rice Technical Working Group.p.50.
KBase: the United States Department of Energy systems biology knowledgebase - (Peer Reviewed Journal)
Arkin, A., Stevens, R., Cottingham, R., Maslov, S., Henry, C., Dehal, P., Ware, D., Perez, F., Harris, N., Canon, S., Sneddon, M., Henderson, M., Riehl, W., Gunter, D., Murphy-Olson, D., Chen, S., Kamimura, R., Brettin, T., Meyer, F., Chivian, D., Weston, D., Glass, E., Davison, B., Kumari, S., Allen, B., Baumohl, J., Best, A., Bowen, B., Brenner, S., Bun, C., Chandonia, J., Chia, J., Colasanti, R., Conrad, N., David, J., Dejongh, M., Devoid, S., Dietrich, E., Drake, M., Dubchak, I., Edirisinghe, J., Fang, G., Faria, J., Frybarger, P., Gerlach, W., Gerstein, M., Gurtowski, J., Haun, H., He, F., Jain, R., Joachimiak, M., Keegan, K., Kondo, S., Kumar, V., Land, M., Mills, M., Novichkov, P., Oh, T., Olson, G., Olson, B., Parrello, B., Pasternak, S., Pearson, E., Poon, S., Price, G., Ramakrishnan, S., Ranjan, P., Ronald, P., Schatz, M., Seaver, S., Shukla, M., Sutormin, R., Syed, M., Thomason, J., Tintle, N., Wang, D., Xia, F., Yoo, H., Yoo, S. 2018. KBase: the United States Department of Energy systems biology knowledgebase. Nature Biotechnology. 36:566-569.
Efficient identification of causal mutations through sequencing of bulked F2 from two allelic bloomless mutants - (Peer Reviewed Journal)
Jiao, Y., Burow, G.B., Gladman, N., Acosta Martinez, V., Chen, J., Burke, J.J., Ware, D., Xin, Z. 2018. Efficient identification of causal mutations through sequencing of bulked F2 from two allelic bloomless mutants. Frontiers in Plant Science. doi.org/10.3389/fpls.2017.02267.
Genomes of 11 rice relatives unveil genetic conservation, turnover and innovation across the genus Oryza - (Peer Reviewed Journal)
Sequenced sorghum mutant library- an efficient platform for discovery of causal gene mutations - (Abstract Only)
Jiao, Y., Burke, J.J., Chuang, K.J., Burow, P.D., Chen, J., Hayes, C.M., Emendack, Y., Ware, D., Xin, Z. 2017. Sequenced sorghum mutant library- an efficient platform for discovery of causal gene mutations [abstract]. Meeting Abstract. Paper No. 001.
Rapid identification of causal gene mutations through sequencing bulked F2 derived from independent alleles - (Abstract Only)
Jiao, Y., Burow, G.B., Gladman, N., Acosta Martinez, V., Chen, J., Burke, J.J., Ware, D., Xin, Z. 2017. Rapid identification of causal gene mutations through sequencing bulked F2 derived from independent alleles [abstract]. ASA-CSSA-SSSA Annual Meeting. Paper No. 001.
SMRT sequencing of the Vitis vinifera cv. ‘Flame seedless’ genome using a SMRTbell-free library preparation from Swift Biosciences - (Abstract Only)
Goodwin, S., Cadle Davidson, L.E., Campbell, M., Xu, X., Wappel, R., Regulski, M., Ledbetter, C.A., Naegele, R.P., Mccombie, R., Ware, D. 2018. SMRT sequencing of the Vitis vinifera cv. ‘Flame seedless’ genome using a SMRTbell-free library preparation from Swift Biosciences. Annual International Plant & Animal Genome Conference. 1.
The next generation of training for Arabidopsis researchers: bioinformatics and quantitative biology - (Peer Reviewed Journal)
Friesner, J., Assmann, S., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., Buell, R., Bucksch, A., Demura, T., Dinneny, J., Doherty, C., Eveland, A., Falter-Braun, P., Gehan, M., Gonzales, M., Grotewold, E., Gutierrez, R., Kramer, U., Krouk, G., Ma, S., Markelz, R., Megraw, M., Meyers, B., Murray, J., Provart, N., Rhee, S., Smith, R., Spalding, E., Teal, T., Torii, K., Town, C., Vaughn, M., Vierstra, R., Ware, D., Wilkins, O., Williams, C., Brady, S. 2017. The next generation of training for Arabidopsis researchers: bioinformatics and quantitative biology. Plant Physiology. 175:1499-1509.
The plastid and mitochondrial peptidase network in Arabidopsis thaliana: a foundation for testing genetic interactions and functions in organellar proteostasis Reprint Icon - (Peer Reviewed Journal)
Majsec, K., Bhuiyan, N., Sun, Q., Kumari, S., Kumar, V., Ware, D., Van Wijk, K. 2017. The plastid and mitochondrial peptidase network in Arabidopsis thaliana: a foundation for testing genetic interactions and functions in organellar proteostasis. The Plant Cell. https://doi.org/10.1105/tpc.1700481.
Improved maize reference genome with single-molecule technologies - (Peer Reviewed Journal)
Jiao, Y., Peluso, P., Liang, T., Shi, J., Stitzer, M., Wang, B., Campbell, M., Stein, J., Wei, X., Chin, J., Guill, K.E., Regulski, M., Sunita, K., Olson, A., Gent, J., Schneider, K., Wolfgruber, T., May, M., Springer, N., Antoniou, E., McCombie, R., Presting, G., McMullen, M.D., Ross-Ibarra, J., Kelly, D., Hastie, A., Rank, D., Ware, D. 2017. Improved maize reference genome with single-molecule technologies. Nature. doi: 10.1038/nature22971.
Genome-wide annotation of mutations in a phenotyped mutant library provides an efficient platform for discovery of casual gene mutations - (Abstract Only)
Jiao, Y., Burke, J.J., Chopra, R., Burow, G.B., Chen, J., Wang, J., Hayes, C.M., Emendack, Y., Ware, D., Xin, Z. 2016. Genome-wide annotation of mutations in a phenotyped mutant library provides an efficient platform for discovery of casual gene mutations [abstract]. January 8-14, 2016, San Diego, CA. Paper No. W852-112.
High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE - (Peer Reviewed Journal)
Majoros, W.H., Campbell, M.S., Holt, C., Denardo, E., Ware, D., Allen, A.S., Yandell, M., Reddy, T. 2016. High-throughput interpretation of gene structure changes in human and nonhuman resequencing data, using ACE. Bioinformatics. doi: 10.1093/bioinformatics/btw799.
Gramene database: navigating plant comparative genomics resources - (Peer Reviewed Journal)
Gupta, P., Naithani, S., Tello-Ruiz, M., Chougule, K., D'Eustachio, P., Fabregat, A., Jiao, J., Keays, M., Lee, Y., Kumari, S., Mulvaney, J., Olson, A., Preece, J., Stein, J., Wei, S., Weiser, J., Huerta, L., Petryszak, R., Kersey, P., Stein, L., Ware, D., Jaiswal, P. 2016. Gramene database: navigating plant comparative genomics resources. Current Biology. DOI: 10.1016/j.cpb.2016.12.005.
Towards an open grapevine information system - (Peer Reviewed Journal)
Adam-Blondon, A., Alaux, M., Pommier, C., Cantu, D., Cheng, Z., Cramer, G.R., Davies, C., Delrot, S., Deluc, L., Di Gaspero, G., Grimplet, J., Fennell, A., Londo, J.P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B., Topfer, R., Vivier, M., Ware, D., Quesneville, H. 2016. Towards an open grapevine information system. Horticulture Research. doi: 10.1038/hortres.2016.56.
Towards an open grapevine information system ()
Adam-Blondon, A., Alaux, M., Pommier, C., Cantu, D., Cheng, Z., Cramer, G., Davies, C., Delrot, S., Deluc, L., Di Gaspero, G., Grimplet, J., Fennell, A., Londo, J.P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B., Topfer, R., Vivier, M., Ware, D., Quesneville, H. 2016. Towards an open grapevine information system. Horticulture Research. 3:16056. doi:10.1038/hortres.2016.56.
A sorghum mutant resource as an efficient platform for gene discovery in grasses - (Peer Reviewed Journal)
Jiao, Y., Burke, J.J., Chopra, R., Burow, G.B., Chen, J., Wang, B., Hayes, C.M., Emendack, Y., Ware, D., Xin, Z. 2016. A sorghum mutant resource as an efficient platform for gene discovery in grasses. The Plant Cell. 28:1551-1562.
Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing - (Peer Reviewed Journal)
Wang, B., Tseng, E., Regulski, M., Clark, T., Hon, T., Jiao, Y., Lu, Z., Olson, A., Stein, J., Ware, D. 2016. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nature Communications. 7:11708 doi: 10.1038/ncomms11708.
Large-scale atlas of microarray data reveals biological landscape of gene expression in Arabidopsis - (Peer Reviewed Journal)
He, F., Yoo, S., Wang, D., Kumari, S., Gerstein, M., Ware, D., Maslov, S. 2016. Large-scale atlas of microarray data reveals biological landscape of gene expression in Arabidopsis. Plant Journal. 86(6):472-480.
Stewardship of the Maize B73 feference genome assembly - (Abstract Only)
Cannon, E., Rezaie, T., Dunfee, B., Jiao, Y., Schneider, V., Ware, D., Andorf, C.M. 2016. Stewardship of the Maize B73 feference genome assembly. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 64.
Sequence, assembly and annotation of the maize W22 genome - (Abstract Only)
Andorf, C.M., Ahem, K., Bai, F., Barad, O., Barbazuk, B.W., Bass, H.W., Baruch, K., Ben-Zvi, G., Buckler Iv, E.S., Bukowski, R., Davenport, R., Dooner, H.K., He Du, L., Du, C., Easterling, K.A., Gault, C.M., Guan, J., Jander, G., Jiao, Y., Koch, K., Kol, G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D., Portwood II, J.L., Ronen, G., Settles, M.A., Shem-Tov, D., Soifer, I., Springer, N.M., Suzuki, M., Vera, D., Vollbrecht, E., Vrebalov, J.T., Ware, D., Wimalanathan, K., Xiong, W., Brutnell, T. 2016. Sequence, assembly and annotation of the maize W22 genome. In: 58th Annual Maize Genetics Conference, March 17-20, 2016, Jacksonville, Florida. p. 91.
The iPlant collaborative: cyberinfrastructure for enabling data to discovery for the life sciences - (Peer Reviewed Journal)
Merchant, N., Lyons, E., Goff, S., Vaughn, M., Ware, D., Micklos, D., Antin, P. 2016. The iPlant collaborative: cyberinfrastructure for enabling data to discovery for the life sciences. PLoS Biology. 14(1):e1002342.
An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize - (Peer Reviewed Journal)
Liu, H., Niu, Y., Gonzales-Portillo, P.J., Zhou, H., Wang, L., Ware, D. 2015. An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize. Biomed Central (BMC) Genomics. 16:1078.
Revealing gene regulation and association through biological networks Reprint Icon - (Peer Reviewed Journal)
Liseron-Monfils, C., Ware, D. 2015. Revealing gene regulation and association through biological networks. Current Biology. 3-4:30-39.
Ensembl genomes 2016: more genomes, more complexity Reprint Icon - (Peer Reviewed Journal)
Kersey, P.J., Allen, J., Armean, I., Boddu, S., Bolt, B.J., Carvalho-Silva, D., Christensen, M., Davis, P., Falin, L.J., Grabmueller, C., Humphrey, J., Kerhornou, A., Khobova, J., Aranganathan, N.K., Langridge, N., Lowy, E., Mcdowall, M.D., Maheswari, U., Nuhn, M., Ong, C., Overduin, B., Paulini, M., Pedro, H., Perry, E., Spudich, G., Tapanari, E., Walts, B., Williams, G., Marcela-Tello, M., Stein, J., Wei, S., Ware, D., Boiser, D.M., Howe, K.L., Kulesha, E., Lawson, D., Maslen, G., Staines, D.M. 2016. Ensembl genomes 2016: more genomes, more complexity. Nucleic Acids Research. 44:D574-D580.
Gramene 2016: comparative plant genomics and pathway resources - (Peer Reviewed Journal)
Tello-Ruiz, M., Stein, J., Wei, S., Preece, J., Olson, A., Naithani, S., Amarashinghe, V., Dharmawardhana, P., Jiao, Y., Mulvaney, J., Kumari, S., Chougule, K., Elser, J., Wang, B., Thomason, J., Bolser, D., Kerhornou, A., Walts, B., Fonseca, N., Huerta, L., Keays, M., Tang, Y., Parkinson, H., Fabregat, A., Mckay, S., Weiser, J., D'Eustachio, P., Stein, L., Petryszak, R., Kersey, P., Jaiswal, P., Ware, D. 2015. Gramene 2016: comparative plant genomics and pathway resources. Nucleic Acids Research. doi: 10.1093/nar/gkv1179.
Sequence-indexed mutant library for fast discovery of casual gene mutations for drought tolerance in sorghum - (Abstract Only)
Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Burke, J.J., Ware, D. 2015. Sequence-indexed mutant library for fast discovery of casual gene mutations for drought tolerance in sorghum [abstract]. Sorghum Improvement Conference of North America, September 1-3, 2014, Manhattan, Kansas. p. 1.
The BioMart community portal: an innovative alternative to large, centralized data repositories Reprint Icon - (Peer Reviewed Journal)
Smedley, D., Haider, S., Spooner, W., Ware, D., Youens-Clark, K., Kasprzyk, A. 2015. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research. 43(W1):W589-598.
Metabolomic profiling of the nectars of Aquilegia pubescens and A. canadensis Reprint Icon - (Peer Reviewed Journal)
Noutsos, C., Perera, M., Nikolau, B.J., Seaver, S., Ware, D. 2015. Metabolomic profiling of the nectars of Aquilegia pubescens and A. canadensis. PLoS One. 10(5):e0124501.
An arabidopsis gene regulatory network for secondary cell wall synthesis - (Peer Reviewed Journal)
Taylor-Teeples, M., Lin, L., De Lucas, M., Zhang, L., Ware, D., Brady, S. 2014. An arabidopsis gene regulatory network for secondary cell wall synthesis. Nature. 517:571-575.
Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes Reprint Icon - (Peer Reviewed Journal)
Law, M., Childs, K.L., Campbell, M.S., Stein, J.C., Olson, A.J., Holt, C., Panchy, N., Lei, J., Jiao, D., Andorf, C.M., Lawrence, C.J., Ware, D., Shiu, S., Sun, Y., Jiang, N., Yandell, M. 2015. Automated update, revision, and quality control of the maize genome annotations using MAKER-P improves the B73 RefGen_v3 gene models and identifies new genes. Plant Physiology. 167(1):25-39.
New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica Reprint Icon - (Peer Reviewed Journal)
Schatz, M.C., Maron, L.G., Stein, J.C., Hernandez, W.A., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., Wright, M.H., Chia, J., Ware, D., Mccouch, S.R., Mccombia, W.R. 2014. New whole genome de novo assemblies of three divergent strains of rice (O. sativa) documents novel gene space of aus and indica. Genome Biology. 15:506-521.
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource Reprint Icon - (Peer Reviewed Journal)
Seaver, S.M., Gerdesa, S., Frelind, O., Lerma-Ortize, C., Bradburyd, L.M., Zallote, R., Hasnaind, G., Niehausd, T.D., El Yacoubie, B., Pasternak, S., Olson, R., Pusch, G., Overbeek, R., Stevens, R., De Crecy-Lagarde, V., Ware, D., Hanson, A.D., Henry, C.S. 2014. High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. Proceedings of the National Academy of Sciences. 111(26):9645-9650.
Disentangling methodological and biological sources of gene tree discordance on oryza (poaceae) chromosome 3 - (Peer Reviewed Journal)
Zwickl, D.J., Stein, J.C., Wing, R.A., Ware, D., Sanderson, M.J. 2014. Disentangling methodological and biological sources of gene tree discordance on oryza (poaceae) chromosome 3. Systematic Biology. DOI: 10.1093/sysbio/syu027.
Sources of gene tree discordance on oryza (poaceae) chromosome 3 - (Peer Reviewed Journal)
Zwickl, D.J., Stein, J.C., Wing, R.A., Ware, D., Sanderson, M.J. 2014. Sources of gene tree discordance on oryza (poaceae) chromosome 3. Systematic Biology. DOI: 10.101093/sysbio/syu027.
A genome-wide association study platform built on iPlant cyber-infrastructure - (Peer Reviewed Journal)
Wang, L., Ware, D., Lushbough, C., Merchang, N., Stein, L. 2014. A genome-wide association study platform built on iPlant cyber-infrastructure. Concurrency and Computation: Practice and Experience. DOI: 10.1002/cpe.3236.
MAKER-P: a tool-kit for the creation, management, and quality control of plant genome annotations - (Peer Reviewed Journal)
Campbell, M.S., Law, M., Holt, C., Stein, J., Moghe, G., Hunagel, D., Lei, J., Achawanantakun, R., Lawrence, C.J., Ware, D., Shiu, S., Childs, K.L., Sun, Y., Jiang, N., Yandell, M. 2014. MAKER-P: a tool-kit for the creation, management, and quality control of plant genome annotations. Plant Physiology. 164(2):513-24.
Regulatory modules controlling maize inflorescence architecture - (Peer Reviewed Journal)
Eveland, A.L., Goldschmidt, A., Pautler, M., Morohashi, K., Liseron-Monfils, C., Lewis, M.W., Kumari, S., Yang, F., Hiraga, S., Unger-Wallace, E., Olson, A., Stanfield, S., Hake, S.C., Schmidt, R.J., Vollbrecht, E., Grotewold, E., Ware, D., Jackson, D. 2013. Regulatory modules controlling maize inflorescence architecture. Genome Research. 24:431-443.
Gramene 2013: Comparative plant genomics resources Reprint Icon - (Peer Reviewed Journal)
Monaco, M.K., Stein, J., Naithani, S., Wei, S., Dharmawardhana, P., Kumari, S., Amarasinghe, V., Youens-Clark, K., Thomason, J., Preece, J., Pasternak, S., Olson, A., Jiao, Y., Lu, Z., Bolser, D., Kerhornou, A., Staines, D., Watts, B., Wu, G., D'Eustachio, P., Haw, R., Croft, D., Kersey, P., Stein, L., Jaiswal, P., Ware, D. 2014. Gramene 2013: Comparative plant genomics resources. Nucleic Acids Research. 42:D1193-D1199.
Ensembl Genomes 2013: scaling up access to genome-wide data Reprint Icon - (Peer Reviewed Journal)
Kersey, P.J., Allen, J.E., Christensen, M., Davis, P., Falin, L.J., Grabmueller, C., Hughes, D.S., Humphrey, J., Kerhornou, A., Khobova, J., Langridge, N., Mcdowall, M.D., Maheswari, U., Maslen, G., Nuhn, M., Ong, C.K., Paulini, M., Pedro, H., Toneva, I., Tuli, M., Walts, B., Williams, G., Wilson, D., Youens-Clark, K., Monaco, M.K., Stein, J., Wei, X., Ware, D., Bolser, D.M., Howe, K.L., Kulesha, E. 2014. Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Research. 45:D546-D552.
Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots Reprint Icon - (Peer Reviewed Journal)
Kumari, S., Ware, D. 2013. Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots. PLoS One. 8(10):e79011.
Expanding and vetting Sorghum bicolor gene annotations through transcriptome and methylome sequencing - (Peer Reviewed Journal)
Olson, A.J., Klein, R.R., Dugas, D.V., Lu, Z., Regulski, M., Klein, P., Ware, D. 2014. Expanding and vetting Sorghum bicolor gene annotations through transcriptome and methylome sequencing. The Plant Genome. 7(2). Available: https://www.crops.org/publications/tpg/articles/7/2/plantgenome2013.08.0025.
The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA - (Peer Reviewed Journal)
Regulski, M., Lu, Z., Kendall, J., Donoghue, M.T., Reinders, J., Llaca, V., Deschamps, S., Smith, A., Levy, D., Mccombie, R., Tingey, S., Rafalski, A., Hicks, J., Ware, D., Martienssen, R.A. 2013. The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA. Genome Research. DOI: 10.1101/gr.153510.112.
A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress - (Peer Reviewed Journal)
Dharmawardhana, P., Ren, L., Amarasinghe, V., Monaco, M.K., Thomason, J., Ravenscroft, D., Mccouch, S., Ware, D., Jaiswal, P. 2013. A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. Rice. 6(1):1-15.
A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor Reprint Icon - (Peer Reviewed Journal)
Lou, M., Gu, Y.Q., You, F., Deal, K., Ma, Y., Hu, Y., Huo, N., Wang, Y., Wang, J., Chen, S., Jorgensen, C., Zhang, Y., Mcguire, P., Pasternak, S., Stein, J., Ware, D., Kramer, M., Mccombie, W., Kianian, S., Martis, M., Mayer, K., Sehgal, K., Li, W., Gill, B., Bevan, M., Simkova, H., Dolezel, J., Weining, S., Lazo, G.R., Anderson, O.D., Dvorak, J. 2013. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. Proceedings of the National Academy of Sciences. 110(19):7940-7945.
Metabolic pathway resources at MaizeGDB - (Abstract Only)
Sen, T.Z., Monaco, M., Chae, L., Dharmawardhana, P., Schaeffer, M.L., Dreher, K., Zhang, P., Naithani, S., Thomason, J., Harper, E.C., Gardiner, J., Cannon, E., Andorf, C.M., Campbell, D.A., Rhee, S.Y., Ware, D., Jaiswal, P., Lawrence, C.J. 2013. Metabolic pathway resources at MaizeGDB [abstract]. In: Proceedings of Maize Genetics Conference, March 14-17, St. Charles, Illinois. p. 3.
Maize metabolic network construction and transcriptome analysis - (Peer Reviewed Journal)
Monaco, M.K., Sen, T.Z., Dharmawardhana, P., Ren, L., Schaeffer, M.L., Amarasinghe, V., Thomason, J., Harper, E.C., Gardiner, J.M., Lawrence, C.J., Ware, D., Jaiswal, P., Naithani, S., Cannon, E. 2013. Maize metabolic network construction and transcriptome analysis. The Plant Genome. 6(1):DOI:10.3835/plantgenome2012.09.0025.
Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays - (Peer Reviewed Journal)
Liu, Z., Kumari, S., Zhang, L., Zheng, Y., Ware, D. 2012. Characterization of miRNAs in response to short-term waterlogging in three inbred lines of Zea mays. PLoS One. 7(6):e39786.
ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize - (Peer Reviewed Journal)
Hung, H., Shannon, L.M., Tian, F., Bradbury, P., Chen, C., Flint Garcia, S.A., McMullen, M.D., Ware, D., Buckler IV, E.S., Doebley, J.F., Holland, J.B. 2012. ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proceedings of the National Academy of Sciences. 109:E1913–E1921.
The tomato genome sequence provides insight into fleshy fruit evolution - (Peer Reviewed Journal)
Ware, D., Thannhauser, T.W., White, R.A., Giovannoni, J.J. 2012. The tomato genome sequence provides insight into fleshy fruit evolution. Nature. 485:635-641. DOI: 10.1038/nature11119.
Maize HapMap2 identifies extant variation from a genome in flux - (Peer Reviewed Journal)
Chia, J., Song, C., Bradbury, P., Costich, D., De Leon, N., Doebley, J., Elshire, R., Gaut, B., Geller, L., Glaubitz, J., Gore, M.A., Guill, K., Holland, J., Hufford, M., Lai, J., Li, M., Liu, X., Lu, Y., McCombie, R., Nelson, R., Poland, J.A., Prasanna, B., Phyajarvi, T., Rong, T., Sekhon, R., Sun, Q., Tenaillon, M., Tian, F., Wang, J., Xu, X., Zhang, Z., Kaeppler, S.M., Ross-Ibarra, J., McMullen, M.D., Buckler IV, E.S., Zhang, G., Xu, Y., Ware, D. 2012. Maize HapMap2 identifies extant variation from a genome in flux. Nature Genetics. 40:803-807. DOI: 10.1038/ng.2313.
Comparative population genomics of maize domestication and improvement - (Peer Reviewed Journal)
Hufford, M., Xu, X., Van Heerwaarden, J., Pyhajarvi, T., Chia, J., Cartwright, R., Elshire, R., Glaubitz, J., Guill, K.E., Kaeppler, S., Lai, J., Morrell, P., Shannon, L., Song, C., Springer, N., Swanson-Wagner, R., Tiffin, P., Wang, J., Zhang, G., Doebley, J., McMullen, M.D., Ware, D., Buckler IV, E.S., Yang, S., Ross-Ibarra, J. 2012. Comparative population genomics of maize domestication and improvement. Nature Genetics. 44:808-811. DOI: 10.1038/ng.2309.
GrameneMart: the biomart data portal for the gramene project - (Peer Reviewed Journal)
Spooner, W., Youens-Clark, K., Staines, D., Ware, D. 2012. GrameneMart: the biomart data portal for the gramene project. Database: The Journal of Biological Databases and Curation. DOI: 10.1093/database/bar056.
MaizeCyc: Metabolic networks in maize - (Abstract Only)
Monaco, M., Sen, T.Z., Ren, L., Dharmawardhana, P., Schaeffer, M.L., Amarasinghe, V., Thomason, J., Harper, E.C., Naithani, S., Gardiner, J.M., Lawrence, C.J., Ware, D., Pankaj, J. 2012. MaizeCyc: Metabolic networks in maize. Plant and Animal Genome Conference. 4:100-110.
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid - (Peer Reviewed Journal)
Dugas, D.V., Monaco, M.K., Olsen, A., Klein, R.R., Kumari, S., Ware, D., Klein, P.E. 2011. Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid. Biomed Central (BMC) Genomics. 12:Article 514.
Metabolic and regulatory networks in gramene - (Abstract Only)
Dharmawardhana, P., Monaco, M., Amarasinghe, V., Preece, J., Wu, G., D'Eustachio, P., Thomason, J., Sen, T.Z., Gardiner, J.M., Harper, E.C., Schaeffer, M.L., Lawrence, C.J., Ware, D., Jaiswal, P. 2011. Metabolic and regulatory networks in gramene. Meeting Abstract. Paper No. 2.
Enhanced Y1H Assays for Arabidopis Reprint Icon - (Peer Reviewed Journal)
Gaudinier, A., Zhang, L., Reece-Hoyes, J.S., Taylor-Teeples, M., Pu, L., Liu, Z., Breton, G., Pruneda-Paz, J.L., Kim, D., Kay, S.A., Walhout, A.J., Ware, D., Brady, S.M. 2011. Enhanced Y1H Assays for Arabidopis. Nature Methods. 8:1053-1055.
MaizeCyc: Metabolic networks in maize - (Abstract Only)
Monaco, M., Sen, T.Z., Ren, L., Dharmawardhana, P., Schaeffer, M.L., Amarasinghe, V., Thomason, J., Harper, E.C., Naithani, S., Gardiner, J.M., Lawrence, C.J., Ware, D., Jaiswal, P. 2011. MaizeCyc: Metabolic networks in maize [abstract]. In: Conference on Genome Informatics, November 2-5, 2011, Cold Spring Harbor, New York. p. 1.
Evidence for network evolution in an arabidopsis interactome map - (Peer Reviewed Journal)
Matija, D., Ruxandra Carvunis, A., Charloteaux, B., Galli, M., Pevzner, S.J., Tasan, M., Stein, J., Spooner, W., Ware, D., Braun, P., Ecker, J.R., Hill, D.E., Roth, F.P., Vidal, M. 2011. Evidence for network evolution in an arabidopsis interactome map. Science. 333(6042):601-607.
The iPlant collaborative: cyberinfrastructure for plant biology Reprint Icon - (Peer Reviewed Journal)
Goff, S.A., Vaughn, M., Mckay, S., Lyons, E., Stapleton, A.E., Gessler, D., Matasci, N., Wang, L., Hanlon, M., Lenards, A., Muir, A., Merchant, N., Lowry, S., Mock, S., Helmke, M., Kubach, A., Narro, M., Hopkins, N., Micklos, D., Hilgert, U., Gonzales, M., Jordan, C., Skidmore, E.L., Dooley, R., Cazes, J., Mclay, R., Lu, Z., Pasternak, S., Piel, W.H., Grene, R., Noutsos, C., Gendler, K., Feng, X., Tang, C., Lent, M., Kim, S., Kvilekval, K., Manjunath, B., Tannen, V., Stamatakis, A., Sanderson, M., Welch, S.M., Cranston, K.A., Soltis, P., Soltis, D., O'Meara, B., Ann, C., Brutnell, T., Kleibenstein, D.J., White, J.W., Leebens-Mack, J., Donoghue, M.J., Spalding, E.P., Vision, T.J., Myers, C.R., Lowenthal, D., Enquist, B.J., Boyle, B., Akoglu, A., Andrews, G., Ram, S., Ware, D., Stein, L., Stanzione, D. 2011. The iPlant collaborative: cyberinfrastructure for plant biology. Frontiers in Plant Genetics and Genomics. DOI: 10.3389/fpls.2011.00034. 2:34.
Metabolic and regulatory networks for cereals - (Abstract Only)
Dharmawardhana, P., Monaco, M., Amarasinghe, V., Preece, J., D'Eustachio, P., Ren, L., Thomason, J., Sen, T.Z., Gardiner, J.M., Harper, E.C., Schaeffer, M.L., Lawrence, C.J., Ware, D., Jaiswal, P. 2011. Metabolic and regulatory networks for cereals. American Society of Plant Biologists Annual Meeting, August 6-10, 2011, Minneapolis, MN. Available: http://abstracts.aspb.org/pb2011/public/P21/P21021.html.
Sequencing for the cream of the crop ()
Chia, J., Ware, D. 2011. Sequencing for the cream of the crop. Nature Biotechnology. 29:138-139. DOI: 10.1038/nbt.1756.
Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population - (Peer Reviewed Journal)
Kump, K., Bradbury, P., Buckler IV, E.S., Belcher, A., Oropeza-Rosas, M., Wisser, R., Zwonitzer, J., Kresovich, S., McMullen, M.D., Ware, D., Balint Kurti, P.J., Holland, J.B. 2011. Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nature Genetics. 43:163-168.
Genetic structure and domestication history of the grape - (Peer Reviewed Journal)
Myles, S., Boyko, A., Owens, C.L., Brown, P., Fabrizio, G., Aradhya, M.K., Prins, B.H., Reynolds, A., Chia, J., Ware, D., Bustamante, C., Buckler IV, E.S. 2011. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences. 10.1073/pnas.1009363108.
Genetic structure and domestication history of the grape - (Peer Reviewed Journal)
Myles, S., Boyko, A.R., Owens, C.L., Brown, P.J., Grassi, F., Aradhya, M.K., Prins, B.H., Reynolds, A., Chia, J., Ware, D., Bustamante, C.D., Buckler, E.S. 2011. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences. 108:3530-3535.
A stele-enriched gene regulatory network in the arabidopsis root - (Peer Reviewed Journal)
Brady, S.M., Zhang, L., Megraw, M., Martinez, N.J., Jiang, E., Yi, C.S., Ware, D., Walhout, A.J., Benfey, P.N. 2011. A stele-enriched gene regulatory network in the arabidopsis root. EMBO Journal. 7:459.
Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor - (Peer Reviewed Journal)
Swanson-Wagner, R.A., Eichten, S.R., Kumari, S., Tiffin, P., Stein, J.C., Ware, D., Springer, N.M. 2010. Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor. Genome Research. 20(12):1689-1699.
Digital gene expression signatures for maize development - (Peer Reviewed Journal)
Eveland, A.L., Nagasawa, N., Goldshmidt, A., Meyer, S., Beatty, M., Sakai, H., Ware, D., Jackson, D. 2010. Digital gene expression signatures for maize development. Plant Physiology. 154(3):1024-1039.
An International Bioinformatics Infrastructure to Underpin the Arabidopsis Community - (Peer Reviewed Journal)
Bastow, R., Beynon, J., Estelle, M., Friesner, J., Grotewold, E., Lavagi, I., Lindsey, K., Meyers, B., Provart, N., Benfey, P., Birney, E., Braun, P., Brendel, V., Buell, R., Caccamo, M., Carrington, J., Cherry, M., Ecker, J., Eppig, J., Forster, M., Gutierrez, R., Hilson, P., Huala, E., Katari, M., Kersey, P., Kudla, J., Ma, H., Matsui, M., Matthews, K., May, S., Mayer, K., Millar, A., Millar, H., Mjolsness, E., Mockler, T., Nikolau, B., Nordborg, M., Rawlings, C., Schofield, P., Schoof, H., Schroeder, J., Sen, T.Z., Stanzione, D., Town, C., Toyoda, T., Vision, T., Walsh, S., Wang, X., Ware, D., Weckwerth, W., Yang, W. 2010. An international bioinformatics infrastructure to underpin the Arabidopsis community. The Plant Cell. 22(8):2530-2536.
Rapid genomic characterization of the genus Vitis - (Peer Reviewed Journal)
Myles, S., Chia, J., Hurwitz, B., Simon, C.J., Zhong, G., Buckler IV, E.S., Ware, D. 2010. Rapid genomic characterization of the genus Vitis. PLoS One. 5(1):e8219.
The B73maize genome: complexity, diversity, dynamics - (Peer Reviewed Journal)
Schnable, P., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang, C., Wing, R., Wilson, R., Zhang, L., Chia, J., Narechania, A. 2009. The B73maize genome: complexity, diversity, dynamics. Science. 326(5956):1112-1115.
A first generation haplotype map of maize - (Peer Reviewed Journal)
Gore, M.A., Chia, J., Elshire, R.J., Sun, Q., Ersoz, E.S., Hurwitz, B.L., Peiffer, J.A., Mcmullen, M.D., Grills, G.S., Ross-Ibarra, J., Ware, D., Buckler Iv, E.S. 2009. A first generation haplotype map of maize. Science. 326(5956):1115-1117.
Genome-wide characterization of maize miRNA genes - (Peer Reviewed Journal)
Zhang, L., Chia, J., Kumari, S., Stein, J.C., Liu, Z., Narechania, A., Maher, C.A., Guill, K., Mcmullen, M.D., Ware, D. 2009. Genome-wide characterization of maize miRNA genes. PLoS Genetics. 5(11): e1000716. DOI: 10.1371/journal.pgen.1000716.
The Physical and Genetic Framework of the B73 Maize Genome - (Peer Reviewed Journal)
Wei, F., Zhang, J., Zhou, S., He, R., Schaeffer, M.L., Collura, K., Kudrna, D., Faga, B., Wissotski, M., Golser, W., Fulton, L., Courtney, W., Fronick, C., Fulton, B., Coe, E., Schwartz, D.C., Ware, D., Clifton, S., Wilson, R.K., Wing, R.A. 2009. The Physical and Genetic Framework of the B73 Maize Genome. PLoS Genetics. 5(11):e1000715.
A single molecule scaffold for the maize genome - (Peer Reviewed Journal)
Zhou, S., Fusheng, W., Pasternak, S., Ware, D., Wing, R., Livny, M., Schwartz, D.C. 2009. A single molecule scaffold for the maize genome. PLoS Genetics. 5(11):1-14.
A Single Molecule Scaffold for the Maize Genome - (Peer Reviewed Journal)
Zhou, S., Wei, F., Nguyen, J., Bechner, M., Potamousis, K., Goldstein, S., Pape, L., Mehan, M.R., Churas, C., Pasternak, S., Forrest, D.K., Wise, R.P., Ware, D., Wing, R., Waterman, M., Livny, M., Schwartz, D.C. 2009. A Single Molecule Scaffold for the Maize Genome. PLoS Genetics. 5(11):1-14.
Applications and Methods Utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for Bioinformatics Resource Discovery and Disparate Data and Service Integration - (Peer Reviewed Journal)
Nelson, R., Avraham, S., Shoemaker, R.C., May, G., Ware, D., Gessler, D.D. 2009. Applications and Methods Utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for Bioinformatics Resource Discovery and Disparate Data and Service Integration. BioMed Central (BMC) BioData Mining. 10:309.
Evidence-based gene predictions in plant genomes - (Peer Reviewed Journal)
Liang, C., Mao, L., Ware, D., Stein, L. 2009. Evidence-based gene predictions in plant genomes. Genome Research. 10(2):1912-1923.
CMap 1.01: a comparative mapping application for the internet - (Peer Reviewed Journal)
Youens-Clark, K., Faga, B., Stein, L., Ware, D. 2009. CMap 1.01: a comparative mapping application for the internet. Bioinformatics. 25(22):3040-3042.
Genetic Properties of the Maize Nested Association Mapping Population - (Peer Reviewed Journal)
Mcmullen, M.D., Kresovich, S., Sanchez-Villeda, H., Bradbury, P., Li, H., Sun, Q., Flint Garcia, S.A., Thornsberry, J., Acharya, C., Bottoms, C., Brown, P., Browne, C.J., Eller, M.S., Guill, K.E., Harjes, C., Kroon, D., Lepak, N.K., Mitchell, S., Peterson, B.E., Pressoir, G., Romero, S.M., Oropeza Rosas, M., Salvo, S.A., Yates, H., Hanson, M., Jones, E., Smith, S., Glaubitz, J., Goodman, M., Ware, D., Holland, J.B., Buckler Iv, E.S. 2009. Genetic Properties of the Maize Nested Association Mapping Population. Science. 325:737-740.
The Genetic Architecture of Maize Flowering Time - (Peer Reviewed Journal)
Buckler Iv, E.S., Holland, J.B., Mcmullen, M.D., Kresovich, S., Acharya, C., Bradbury, P., Brown, P., Browne, C.J., Eller, M.S., Ersoz, E., Flint Garcia, S.A., Garcia, A., Glaubitz, J.C., Goodman, M., Haries, C., Guill, K.E., Kroon, D., Larsson, S., Lepak, N.K., Li, H., Mitchell, S.E., Pressoir, G., Peiffer, J., Oropeza Rosas, M., Rocheford, T., Romay, C., Romero, S., Salvo, S.A., Sanchez Villeda, H., Sun, Q., Tian, F., Upadyayula, N., Ware, D., Yates, H., Yu, J., Zhang, Z. 2009. The Genetic Architecture of Maize Flowering Time. Science. 325(5941):714-718.
Microdissection of Shoot Meristem Functional Domains - (Peer Reviewed Journal)
Brook, Iii, L., Strable, J., Ware, D., Nettleton, D., Scanlon, M.J. 2009. Microdissection of Shoot Meristem Functional Domains. PLoS Genetics. 5(5): e1000476. DOI: 10.1371/journal.pgen.1000476.
Large-scale enrichment and discovery of gene-associated SNPs - (Peer Reviewed Journal)
Buckler Iv, E.S., Gore, M., Wright, M., Ersoz, E., Bouffard, P., Jarvie, T., Hurwitz, B., Narechania, A., Harkins, T., Grills, G., Ware, D. 2009. Large-scale enrichment and discovery of gene-associated SNPs. The Plant Genome. 2:121-133.
Panzea: An Update on New Content and Features - (Peer Reviewed Journal)
Canaran, P., Buckler Iv, E.S., Glaubitz, J., Stein, L., Sun, Q., Zhao, W., Ware, D. 2009. Panzea: An Update on New Content and Features. Nucleic Acids Research. 36:D1041-D1043.
The Sorghum bicolor genome and the diversification of grasses - (Peer Reviewed Journal)
Paterson, A.H., Bowers, J.E., Maher, C.A., Narechania, A., Zhang, L., Ware, D., Messing, J., Rokhsar, D.S. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature. 457:551-556.
Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats - (Peer Reviewed Journal)
Wicker, T., Narechania, A., Sabot, F., Stein, J., Giang, V., Graner, A., Ware, D., Stein, N. 2008. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. Biomed Central (BMC) Genomics. 9:518.
Genome-wide analysis for discovery of new rice miRNA reveals natural antisense miRNA (nat-miRNAs) - (Peer Reviewed Journal)
Lu, C., Jeong, D., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, D., Maher, C., Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B., Green, P. 2008. Genome-wide analysis for discovery of new rice miRNA reveals natural antisense miRNA (nat-miRNAs). Proceedings of the National Academy of Sciences. 105(12):4951-4956.
The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza - (Peer Reviewed Journal)
Kim, H., Hurwitz, B., Yu, Y., Collura, K., Gill, N., Miguel, P.S., Mullikin, J., Nelson, W., Wissotski, M., Braidotti, M., Kudrna, D., Goicoechea, J.L., Stein, L., Ware, D., Jackson, S., Soderlund, C., Wing, R. 2008. The Oryza map alignment project: Construction, alignment and analysis of 12 BAC fingerprint/end sequence framework physical maps that represent the 10 genome types of genus Oryza. Genome Research. 9:R45.1-R45.15.
HTML::GMap-A High Level Perl Wrapper Around the Google Maps(TM) API - (Peer Reviewed Journal)
Canaran, P., Glaubitz, J., Ware, D. 2008. HTML::GMap-A High Level Perl Wrapper Around the Google Maps(TM) API. Bioinformatics. 36(1):1041-1043.
Gramene: a growing plant comparative genomics resource - (Peer Reviewed Journal)
Jaiswal, P., Avraham, S., Buckler Iv, E.S., Casstevens, T., Hebbard, C., Liang, C., Ni, J., Ravenscroft, D., Ren, L., Stein, L., Spooner, W., Tecle, I., Thomason, J., Wei Xuehong, Ware, D., Youens-Clark, K., Yap, I., Mccouch, S., Tung, C. 2008. Gramene: a growing plant comparative genomics resource. Nucleic Acids Research. 36:D947-D953.
The Plant Ontology Database: A community resource for plant structure and developmental stages controlled vocabulary and annotations - (Peer Reviewed Journal)
Avraham, S., Tung, C., Jaiswal, P., Ilic, K., Kellogg, E., Mccouch, S., Pujar, A., Reiser, L., Rhee, S., Sachs, M.M., Schaeffer, M.L., Stein, L., Stevens, P., Vincent, L., Zapata, F., Ware, D. 2008. The Plant Ontology Database: A community resource for plant structure and developmental stages controlled vocabulary and annotations. Nucleic Acids Research. 36:D449-D454.
The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages Controlled Vocabulary and Annotations - (Peer Reviewed Journal)
Avraham, S., Tung, C., Jaiswal, P., Ilic, K., Kellogg, E.A., Mccouch, S.R., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M.L., Stein, L.D., Stevens, P.F., Vincent, L.P., Zapata, F., Ware, D. 2007. The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages Controlled Vocabulary and Annotations. Nucleic Acids Research 36: Database issue D449-D454
Databases and data mining ()
Lawrence, C.J., Ware, D. 2009. Databases and data mining. In: Bennetzen, J.L., Hake, S., editors. Handbook of Maize. Vol. 2, Genetics and Genomics. 1st edition. New York, NY: Springer Science and Business Media, LLC. p. 659-672.
Plant Structure Ontology, Unified Vocabulary of Anatomy and Morphology of a Flowering Plant - (Peer Reviewed Journal)
Ilic, K., Kellogg, E., Jaiswal, P., Zapata, F., Stevens, P., Vincent, L., Avraham, S., Reiser, L., Pujar, A., Sachs, M.M., Whitman, N., Mccouch, S., Schaeffer, M.L., Ware, D., Stein, L., Rhee, S. 2007. Plant Structure Ontology, Unified Vocabulary of Anatomy and Morphology of a Flowering Plant. Plant Physiology. 143:587-599.
Gramene: a bird's eye view of cereal genomes - (Peer Reviewed Journal)
Jaiswal, P., Ni, J., Yap, I., Ware, D., Spooner, W., Youens-Clark, K., Ren, L., Liang, C., Zhao, W., Ratnapu, K., Faga, B., Canaran, P., Fogleman, M., Hebbard, C., Avraham, S., Schmidt, S., Casstevens, T., Buckler Iv, E.S., Stein, L., Mccouch, S. 2007. Gramene: a bird's eye view of cereal genomes. Nucleic Acids Research. 34:D717-D723. Available: http://nar.oxfordjournals.org/
Tissue-specific expression of maize domestication and crop improvement loci - (Peer Reviewed Journal)
Hufford, K., Canaran, P., Ware, D., Mcmullen, M.D., Gaut, B. 2007. Tissue-specific expression of maize domestication and crop improvement loci. Plant Physiology. 144:1642-1653.
Evolution of Arabidopsis microRNA families through duplication events - (Peer Reviewed Journal)
Maher, C., Stein, L., Ware, D. 2007. Evolution of Arabidopsis microRNA families through duplication events. Genome Research. 16:510-519.
Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum - (Peer Reviewed Journal)
Hass-Jacobus, B., Futrell-Griggs, M., Abernathy, B., Westerman, R., Goicoechea, J., Stein, J., Ware, D. 2007. Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum. Biomed Central (BMC) Genomics. 7:199.
Panzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome - (Peer Reviewed Journal)
Zhao, W., Canaran, P., Jurkuta, R., Fulton, T., Glaubitz, J., Buckler Iv, E.S., Doebley, J., Gaut, B., Goodman, M., Holland, J.B., Kresovich, S., Mcmullen, M.D., Stein, L., Ware, D. 2007. Panzea: A Database and Resource for Molecular and Functional Diversity in the Maize Genome. Nucleic Acids Research. 34:D752-D757.
Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support - (Peer Reviewed Journal)
Canaran, P., Stein, L., Ware, D. 2007. Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support. Bioinformatics. 22(7):885-886.
Plant Structure Ontology. Unified Vocabulary of Anatomy and Morphology of a Flowering Plant - (Peer Reviewed Journal)
Ilic, K., Kellogg, E.A., Jaiswal, P., Zapata, F., Stevens, P.F., Vincent, L.P., Avraham, S., Reiser, L., Pujar, A., Sachs, M.M., Whitman, N.T., Mccouch, S.R., Schaeffer, M.L., Ware, D., Stein, L.D., Rhee, S.Y. 2006. Plant Structure Ontology. Unified Vocabulary of Anatomy and Morphology of a Flowering Plant. Plant Physiology 143:587-599
WHOLE-PLANT GROWTH STAGE ONTOLOGY FOR ANGIOSPERMS AND ITS APPLICATION IN PLANT BIOLOGY - (Peer Reviewed Journal)
Pujar, A., Jaiswal, P., Kellogg, E., Ilic, K., Vincent, L., Avraham, S., Stevens, P., Zapata, F., Reiser, L., Rhee, S., Sachs, M.M., Schaeffer, M.L., Stein, L., Ware, D., McCouch, S. 2006. Whole-plant growth stage ontology for angiosperms and its application in plant biology. Plant Physiology. 142:414-428.
PLANT ONTOLOGY (PO): A CONTROLLED VOCABULARY OF PLANT STRUCTURES AND GROWTH STAGES - (Peer Reviewed Journal)
Jaiswal, P., Avraham, S., Ilic, K., Kellogg, E.A., Mccouch, S., Pujar, A., Reiser, L., Rhee, S.Y., Sachs, M.M., Schaeffer, M.L., Stein, L., Stevens, P., Vincent, L., Ware, D., Zapata, F. 2005. Plant ontology (po): a controlled vocabulary of plant structures and growth stages. Comparative and Functional Genomics. 6:388-397.
MOLECULAR AND FUNCTIONAL DIVERSITY IN THE MAIZE GENOME - (Abstract Only)
Briggs, W., Buckler Iv, E.S., Canaran, P., Doebley, J., Fulton, T., Gaut, B., Goodman, M., Holland, J.B., Kresovich, S., Mcmullen, M.D., Stein, L., Ware, D., Wright, S., Zhao, W. 2005. Molecular and functional diversity in the maize genome [abstract]. Maize Genetics Conference. Paper No. 177. p. 126.
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