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                    U.S. DEPARTMENT OF AGRICULTURE
 Plant, Soil and Nutrition Research: Ithaca, NY
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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 Helen Ware

                                                                (PhD)
                        Plant, Soil and Nutrition Research

                        




                        
                        Computational Biologist
                        Phone: (516) 367-6979
                        
                        
                        Fax: (516) 367-6851(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsComputational and Genomic Resources to Support Plant Genome Function
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 435146Development of Pan-genomic & Computational Resources for Agriculture
                                                    Cooperative Agreement
                                                                    (A)Accession Number: 443248Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits
                                                    In-House Appropriated
                                                                    (D)Accession Number: 445304Coordination and Support for Stewardship of Sorghum Pathway and Phenotype Data in SorghumBase
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 445185**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Long-read sequencing  broadens access to genetic and transcript diversity for high-value traits in sorghum

- (Abstract Only)Sorghum eFP browser to view gene expression anatomograms in gramene

- (Abstract Only)Standardizing biocuration of genetic variation data to promote FAIRification

- (Abstract Only)Unlocking genomic diversity: harnessing the power of FAIR principles in gramene

- (Abstract Only)CLIMtools: A web-based suite of tools for exploring genotype by environment (GxE) associations

- (Abstract Only)Swift pan-genomic methods for comprehensive genome annotation in crop genomes

- (Abstract Only)A large sequenced mutant library- valuable reverse genetic resource that covers 98% of the genes in a Sorghum genome
                                                        

- (Peer Reviewed Journal)Jiao, Y., Singh, D., Barry, K., Daum, C., Yoshinaga, Y., Khan, A., Lu, Z., Wang, X., Wei, X., Tello-Ruiz, M.K., Burow, G.B., Hayes, C.M., Chen, J., Mortimer, J., Ware, D., Xin, Z. 2023. A large sequenced mutant library- valuable reverse genetic resource that covers 98% of the genes in a Sorghum genome. Plant Journal. 117(5):1543-1557. https://doi.org/10.1111/tpj.16582.A large Sequenced Mutant library provides gene leads for breeding and genome editing

- (Abstract Only)Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Pugh, N.A., Ware, D. 2024. A large Sequenced Mutant library provides gene leads for breeding and genome editing. Plant and Animal Genome Conference.GRAS family transcription factor behavior in sorghum and other monocots

- (Abstract Only)DAP-seq hints at potential binding sites of transcription factors for functional studies

- (Abstract Only)Swift pan-genomic methods for comprehensive genome annotation in crop genomes

- (Abstract Only)Decoding nitrogen use efficiency in maize and sorghum: insights from comparative gene regulatory networks for sustainable agriculture

- (Abstract Only)Characterization of key regulators in microRNA-mediated responses to phosphate deficiency in Arabidopsis root involved in root development

- (Abstract Only)HPC-based genome variant calling workflow (HPC-GVCW)
                                                        

- (Pre-print Publication)Zhou, Y., Kathiresan, N., Yu, Z., Rivera, L.F., Thimma, M., Manickam, K., Chebotarov, D., Mauleon, R., Chougule, K., Wei, S., Gao, T., Green, C.D., Zuccolo, A., Zhang, J., Ware, D., Mcnally, K.L., Wing, R.A. 2023. HPC-based genome variant calling workflow (HPC-GVCW). bioRxiv. https://doi.org/10.1101/2023.06.25.546420.Engineering homoeologs provides a fine scale for quantitative traits in polyploid
                                                        

- (Peer Reviewed Journal)Lee, E., Heo, J., Bang, W., Chougule, K., Waminal, N., Hong, N., Kim, M., Beak, H., Kim, Y., Priatama, R.A., Jang, J., Cha, K., Son, S., Rajendran, S., Choo, Y., Bae, J., Kim, C., Lee, Y., Bae, S., Jones, J., Sohn, K., Kim, H., Ware, D., Keunhwa, K. 2023. Engineering homoeologs provides a fine scale for quantitative traits in polyploid. Plant Biotechnology Journal.  https://doi.org/10.1111/pbi.14141.Gramene: comparative plant genome resource

- (Abstract Only)Direct and predicted motif analysis of GRAS family transcription factors in sorghum and other important crop species

- (Abstract Only)Gramene PanMaize: One-stop pan-genome browser for exploring the rich genetic diversity in maize

- (Abstract Only)Regulatory networks governing nitrogen use efficiency in maize and sorghum

- (Abstract Only)Registration of 252 sequenced sorghum mutants as a community reverse genetic resource
                                                        

- (Peer Reviewed Journal)Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Burke, J.J., Pugh, N.A., Ware, D. 2023. Registration of 252 sequenced sorghum mutants as a community reverse genetic resource. Journal of Plant Registrations. 17(3):599-604. https://doi.org/10.1002/plr2.20296.An improved reference of the grapevine genome reasserts the origin of the PN40024 highly-homozygous genotype
                                                        

- (Peer Reviewed Journal)Velt, A., Frommer, B., Blanc, S., Holtgrawe, D., Dumas, V., Grimplet, J., Hugueney, P., Lahaye, M., Kim, C., Matus, J., Navarro-Paya, D., Orduna, L., Tello-Ruiz, M.K., Vitulo, N., Ware, D., Rustenholz, C. 2023. An improved reference of the grapevine genome reasserts the origin of the PN40024 highly-homozygous genotype. G3, Genes/Genomes/Genetics. https://10.1093/g3journal/jkad067.Pan-genomic approaches to consistent annotation of rice genomes

- (Abstract Only)Gramene 2023: An online resource for plant reference genomes, pan-genomes and plant reactome pathways

- (Abstract Only)SorghumBase 2023: Building partnerships and integrating genetic knowledge for the sorghum community

- (Abstract Only)Towards standards for biocuration and interoperability of genetic variation data

- (Abstract Only)Ten new high quality genome assemblies for diverse bioenergy sorghum genotypes
                                                        

- (Peer Reviewed Journal)Voelker, W.G., Krishnan, K., Chougule, K., Alexander, L.C., Lu, Z., Olson, A., Ware, D., Songsomboon, K., Ponce, C., Brenton, Z.W., Boatwright, L., Cooper, E.A. 2023. Ten new high quality genome assemblies for diverse bioenergy sorghum genotypes. Frontiers in Plant Science. 13:1040909. https://doi.org/10.3389/fpls.2022.1040909.Sorghumbase: an integrated pan-genome resource on sorghum genomics and genetics data set for the sorghum community

- (Abstract Only)Gramene Oryza: a dedicated pan-genome resource to map rice diversity

- (Abstract Only)Creating a FAIR data ecosystem for incorporating single cell genomics data into agricultural G2P research

- (Abstract Only)A data infrastructure for the plant cell atlas

- (Review Article)Sequenced Mutants as a Resource for Reverse Genetics in Sorghum

- (Abstract Only)Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Pugh, N.A., Ware, D. 2022. Sequenced Mutants as a Resource for Reverse Genetics in Sorghum. ASA-CSSA-SSSA Annual Meeting Abstracts.Role of a ZF-HD transcription factor in miR157-mediated feed-forward regulatory module that determines plant architecture in arabidopsis
                                                        

- (Peer Reviewed Journal)Lee, Y., Kumari, S., Olson, A., Hauser, F., Ware, D. 2022. Role of a ZF-HD transcription factor in miR157-mediated feed-forward regulatory module that determines plant architecture in arabidopsis. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms23158665.Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (Oryza sativa)
                                                        

- (Peer Reviewed Journal)Zhou, Y., Yu, Z., Chebotarov, D., Chougule, K., Ly, Z., Rivera, L.F., Kathiresan, N., Al-Bader, N., Mohammed, N., Alsantely, A., Mussurova, S., Santos, J., Thimma, M., Troukhan, M., Fornasiero, A., Green, C., Copetti, D., Kudrna, D., Llaca, V., Lorieux, M., Zuccolo, A., Ware, D., McNally, K., Zhang, J., Wing, R., Kudrna, D. 2023. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (Oryza sativa). Nature Genetics. 14:1567. https://doi.org/10.1038/s41467-023-37004-y.Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (oryza sativa)
                                                        

- (Pre-print Publication)Zhou, Y., Yu, Z., Chebotarov, D., Chougule, K., Lu, Z., Rivera, L.F., Kathiresan, N., Al-Bader, N., Mohammed, N., Alsantely, A., Musssurova, S., Santos, J., Thimma, M., Troukhan, M., Green, C.D., Copetti, D., Kudrna, D., Llaca, V., Lorieux, M., Zuccolo, A., Ware, D., Mcnally, K., Zhang, J., Wing, R.A., Kudrna, D. 2022. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (oryza sativa). bioRxiv. https://doi.org/10.1101/2022.06.11.495682.Gramene 2022: an online resource for plant reference genomes, pan-genomes and plant reactome pathways

- (Abstract Only)SorghumBase: supporting the sorghum community with pangenomes resources and community news

- (Abstract Only)Characterization of a novel zinc chaperone in arabidopsis

- (Abstract Only)Regulatory networks governing nitrogen use efficiency in maize and sorghum

- (Abstract Only)Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in arabidopsis
                                                        

- (Peer Reviewed Journal)Ferroro-Serrano, A., Sylvia, M.M., Forstmeier, P.C., Olson, A.J., Ware, D., Bevilacqua, P.C., Assmann, S.M. 2022. Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in arabidopsis. Genome Biology. 23:101. https://doi.org/10.1186/s13059-022-02656-4.Sorghum root epigenetic landscape during limiting phosphorus conditions
                                                        

- (Peer Reviewed Journal)Gladman, N.P., Hufnagel, B., Regulski, M., Liu, Z., Wang, X., Chougule, K., Kochian, L., Magalhaes, J., Ware, D. 2022. Sorghum root epigenetic landscape during limiting phosphorus conditions. Plant Direct. 6(5):e393. https://doi.org/10.1002/pld3.393.Mutation breeding in the age of next-generation sequencing and genome editing

- (Abstract Only)Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Ware, D. 2022. Mutation breeding in the age of next-generation sequencing and genome editing. Plant and Animal Genome Conference.SorghumBase: a web-based portal for sorghum genetic information and community advancement
                                                        

- (Peer Reviewed Journal)Gladman, N., Olson, A., Wei, S., Chogule, K., Lu, Z., Tello0ruiz, M., Meijs, I., Van Buren, P., Jiao, Y., Wang, B., Kumar, V., Kumari, S., Zhang, L., Burke, J.J., Chen, J., Burow, G.B., Hayes, C.M., Emendack, Y., Xin, Z., Ware, D. 2022. SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta. 255:35. https://doi.org/10.1007/s00425-022-03821-6.Ensembl Genomes 2022: an expanding genome resource for non-vertebrates
                                                        

- (Peer Reviewed Journal)Yates, A.D., Allen, J., Amode, R.M., Azov, A.G., Barba, M., Becerra, A., Bhai, J., Campbell, L.I., Carbajo Manuel, M., Chakiachvili, M., Chougule, K., Christensen, M., Contreras-Moreira, B., Cuzick, A., Fioretto, L., Davis, P., De Silva, N.H., Diamantakis, S., Dyer, S., Elster, J., Filippi, C.V., Gall, A., Grigoriadis, D., Guijarro-Clarke, C., Gupta, P., Hammond-Kosack, K.E., Howe, K.L., Jaiswal, P., Kaikala, V., Kumar, V., Kumari, S., Langridge, N., Le, T., Luypaert, M., Maslen, G.L., Maurel, T., Moore, B., Muffato, M., Mushtaq, A., Naamati, G., Naithani, S., Olson, A., Parker, A., Paulini, M., Pedro, H., Perry, E., Preece, J., Quinton-Tulloch, M., Rodgers, F., Rosello, M., Ruffier, M., Seager, J., Sitnik, V., Szpak, M., Tate, J., Tello-Ruiz, M.K., Trevanion, S.J., Urban, M., Ware, D., Wei, S., Williams, G., Winterbottom, A., Zarowiecki, M., Finn, R.D., Flicek, P. 2021. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. 50(D1):D996-D1003. https://doi.org/10.1093/nar/gkab1007.A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in sorghum
                                                        

- (Peer Reviewed Journal)Kumari, S., Kumar, V., Beilsmith, K., Seaver, S., Canon, S., Dehal, P., Gu, T., Joachimiak, M., Lerma-Ortiz, C., Liu, F., Zhenyuan, L., Pearson, E., Ranjan, P., Riel, W., Henry, C.S., Arkin, A.P., Ware, D. 2021. A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in sorghum. Current Plant Biology. https://doi.org/10.1016/j.cpb.2021.100229.Pedigreed mutant library as an efficient resource to discover targets for genome editing

- (Abstract Only)Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Ware, D. 2021. Pedigreed mutant library as an efficient resource to discover targets for genome editing. Meeting Abstract.Ranked choice voting for representative transcripts with TRaCE
                                                        

- (Peer Reviewed Journal)Olson, A., Ware, D. 2021. Ranked choice voting for representative transcripts with TRaCE. Bioinformatics. 2021, btab542. https://doi.org/10.1093/bioinformatics/btab542.De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
                                                        

- (Peer Reviewed Journal)Hufford, M.B., Seetharam, A.S., Woodhouse, M.H., Chougle, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Portwood II, J.L., Cannon, E.K., Andorf, C.M., Ware, D., Dawe, K.R. et al. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science. 373(6555):655-662. https://doi.org/10.1126/science.abg5289.Comparative analysis of sorghum EMS mutants and natural populations
                                                        

- (Pre-print Publication)Wang, L., Lipzen, A., Lu, Z., Chen, J., Wang, X., Tello-Ruiz, M.K., Barry, K., Mortimer, J., Ware, D., Xin, Z. 2021. Comparative analysis of sorghum EMS mutants and natural populations. bioRxiv. https://doi.org/10.1101/2021.06.06.447271.Sorghum root epigenetic landscape during limiting phosphorus conditions
                                                        

- (Pre-print Publication)Gladman, N., Hufnagel, B., Regulski, M., Liu, Z., Wang, X., Chougule, K., Kochian, L., Magalhaes, J., Ware, D. 2021. Sorghum root epigenetic landscape during limiting phosphorus conditions. bioRxiv. https://doi.org/10.1101/2021.05.25.445633.Sequence, assembly and annotation of maize inbred B104

- (Abstract Only)Manchanda, N., Chougule, K., Olson, A., Fengler, K., Seetharam, A., Liaca, V., Zastrow-Hayes, G., Wei, S., Braun, I., Lopez, M.D., Ployaram, W., Zarecor, S., Lu, Z., Walley, J., Yandeau-Nelson, M., Wang, K., Adams, D., Ware, D., Schmitz, B., Woodhouse, M.H., Lauter, N.C., Andorf, C.M., Lawrence-Dill, C., Hufford, M. 2021. Sequence, assembly and annotation of maize inbred B104. Maize Annual Meetings. 76.Single-cell RNA sequencing of developing ears facilitates functional analysis and trait gene discovery in maize
                                                        

- (Peer Reviewed Journal)Xu, X., Crow, M., Rice, B.R., Li, F., Harris, B., Liu, L., Arevalo, E.D., Lu, Z., Jackson, D., Ware, D., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S., Yang, B., Sylvester, A., Gingeras, T., Schmitz, R., Lipka, A., Gillis, J. 2021. Single-cell RNA sequencing of developing ears facilitates functional analysis and trait gene discovery in maize. Developmental Cell. 56:557-568. https://doi.org/10.1016/j.devcel.2020.12.015.Gene disruption by structural mutations drives selection in US rice breeding over the last century
                                                        

- (Peer Reviewed Journal)Vaughn, J.N., Korani, W., Stein, J.C., Edwards, J., Peterson, D.G., Simpson, S.A., Youngblood, R.C., Grimwood, J., Ware, D., Mcclung, A.M., Scheffler, B.E. 2021. Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genetics. 17(3): e1009389. https://doi.org/10.1371/journal.pgen.1009389.De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
                                                        

- (Pre-print Publication)Hufford, M.B., Seetharam, A.S., Woodhouse, M.H., Chougie, K.M., Ou, S., Liu, J., Ricci, W.A., Guo, T., Olson, A., Qiu, Y., Portwood Ii, J.L., Cannon, E.K., Andorf, C.M., Ware, D., Dawe, K.R., et all. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. bioRxiv. https://doi.org/10.1101/2021.01.14.426684.Pan-genome analysis in sorghum highlights the extent of genomic variation and sugarcane aphid resistance genes
                                                        

- (Pre-print Publication)Wang, B., Jiao, Y., Chougule, K., Olson, A., Huang, J., Llaca, V., Fengler, K., Wei, X., Wang, L., Wang, X., Regulski, M., Drenkow, J., Gingeras, T., Hayes, C.M., Armstrong, J.S., Huang, Y., Xin, Z., Ware, D. 2021. Pan-genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes. bioRxiv. https://doi.org/10.1101/2021.01.03.424980.Amino acid and carbohydrate metabolism are coordinated to maintain energetic balance during drought in sugarcane
                                                        

- (Peer Reviewed Journal)Diniz, A., Da Silva, D. ., Lembke, C.A., Costa, M.B., Ten-Caten, F., Li, F., Vilela, R., Menossi, M., Ware, D., Engres, L., Souza, G. 2020. Amino acid and carbohydrate metabolism are coordinated to maintain energetic balance during drought in sugarcane. International Journal of Molecular Sciences. 21(23):9124. https://doi.org/10.3390/ijms21239124.Gramene: a resource for comparative analysis of plants genomes and pathways

- (Book / Chapter)Gramene: a resource for comparative analysis of plants genomes and pathways
                                                        

- (Book / Chapter)Tello-Ruiz, M.K., Jaiswal, P., Ware, D. 2022. Gramene: a resource for comparative analysis of plants genomes and pathways. In: Edwards, D. Plant Bioinformatics Methods and Protocols. 3rd edition. Hertfordshire, UK:Humana Press. p.101-131. https://doi.org/10.1007/978-1-0716-2067-0_5#DOIHighly accurate HiFi long read sequencing data for five complex genome samples
                                                        

- (Peer Reviewed Journal)Hon, T., Mars, K., Young, G., Tsai, Y., Kauralis, J., Landolin, J.M., Maurer, N., Kudrna, D., Hardigan, M.A., Steiner, C.C., Knapp, S., Ware, D., Shapiro, B., Peluso, P., Rank, D.R. 2020. Highly accurate HiFi long read sequencing data for five complex genome samples. Scientific Data - Nature. 7. Article e399. https://doi.org/10.1038/s41597-020-00743-4.SciApps: an automated platform for processing and distribution of plant genomics data

- (Book / Chapter)Amino acid metabolism and carbohydrate metabolism in sugarcane are coordinated to maintain energetic balance during drought
                                                        

- (Peer Reviewed Journal)Diniz, A.L., Silva, D.I., Lembke, C.G., Costa, M.D., Ten-Caten, F., Li, F., Vilela, R.D., Menossi, M., Endres, L., Ware, D., Souza, G.M. 2020. Amino acid metabolism and carbohydrate metabolism in sugarcane are coordinated to maintain energetic balance during drought. International Journal of Molecular Sciences. 21:9124. https://doi.org/10.3390/ijms21239124.Gramene 2021: harnessing the power of comparative genomics and pathways for plant research
                                                        

- (Peer Reviewed Journal)Tello-Ruiz, M.K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D.M., D'Eustachio, P., Stein, L.D., Gupta, A., Xu, W., Regala, J., Papatheodorou, I., Kersey, P.J., Flicek, P., Taylor, C., Jaiswal, P., Ware, D. 2020. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research. 49:D1452-D1463. https://doi.org/10.1093/nar/gkaa979.BSAseq: An interactive and integrated web-based workflow for identification of causal mutations in bulked f2 populations
                                                        

- (Peer Reviewed Journal)Wang, L., Lu, Z., Regulski, M., Jiao, Y., Chen, J., Ware, D., Xin, Z. 2021. BSAseq: An interactive and integrated web-based workflow for identification of causal mutations in bulked f2 populations. Bioinformatics. 37(3):382-387. https://doi.org/10.1093/bioinformatics/btaa709.Current status of the multinational Arabidopsis community
                                                        

- (Peer Reviewed Journal)Parry, G., Provart, N.J., Brady, S.M., Uzilday, B., Adams, K., Araujo, W., Aubourg, S., Baginsky, S., Bakker, E., Barenfaller, K., Batley, J., Beale, M., Beilstein, M., Belkhadir, Y., Berardini, T., Bergelson, J., Blanco-Herrera, F., Brady, S., Braun, H., Briggs, S., Brownfield, L., Cardarelli, M., Castellanos-Uribe, M., Coruzzi, G., Dassanayake, M., De Jaeger, G., Dilkes, B., Doherty, C., Ecker, J., Edger, P., Edwards, D., El Kasmi, F., Eriksson, M., Exposito-Alonso, M., Falter-Braun, P., Fernie, A., Ferro, M., Fiehn, O., Friesner, J., Greenham, K., Guo, Y., Hamann, T., Hancock, A., Hauser, M., Heazlewood, J., Ho, C., Horak, H., Huala, E., Hwang, I., Iuchi, S., Jaiswal, P., Jakobson, L., Jiang, Y., Jiao, Y., Jones, A., Kadota, Y., Khurana, J., Kliebenstein, D., Knee, E., Kobayashi, M., Koch, M., Krouk, G., Larson, T., Last, R., Lepiniec, L., Li, S., Lurin, C., Lysak, M., Maere, S., Malinowski, R., Maumus, F., May, S., Mayer, K., Mendoza-Cozatl, D., Mendoza-Poudereux, I., Meyers, B., Micol, J., Millar, H., Mock, H., Mukhtar, K., Mukhtar, S., Murcha, M., Nakagami, H., Nakamura, Y., Nicolov, L., Nikolau, B., Nowack, M., Nunes-Nesi, A., Palmgren, M., Parry, G., Patron, N., Peck, S., Pedmale, U., Perrot-Rechenmann, C., Pieruschka, R., Pio-Beltran, J., Pires, J., Provart, Rajjou, L., Reiser, L., Reumann, S., N., Rhee, S., Rigas, S., Ware, D. 2020. Current status of the multinational Arabidopsis community. Plant Direct. 00:1-9. https://doi.org/10.1002/pld3.248.Gapless assembly of maize chromosomes using long-read technologies
                                                        

- (Peer Reviewed Journal)Liu, J., Seetharam, A.S., Chougule, K.M., Ou, S., Swentowsky, K.W., Gent, J.I., Llaca, V., Woodhouse, M.H., Manchanda, N., Presting, G.G., Kurdna, D.A., Alabady, M., Hirsch, C.N., Fengler, K.A., Ware, D., Michael, T.P., Hufford, M.B., Dawe, R.K. 2020. Gapless assembly of maize chromosomes using long-read technologies. Genome Biology. 21. https://doi.org/10.1186/s13059-020-02029-9.Effect of sequence depth and length in long-read assembly of the maize inbred NC358
                                                        

- (Peer Reviewed Journal)Ou, S., Liu, J., Chougule, K., Fungtammasan, A., Seetharam, A., Stein, J., Llaca, V., Manchanda, N., Gilbert, A., Wei, S., Ware, D., Woodhouse, M.H., et all. 2020. Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature Communications. 11. https://doi.org/10.1038/s41467-020-16037-7.Management, analyses, and distribution of the MaizeCODE Data on the Cloud
                                                        

- (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
                                                        

- (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.Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in 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. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nature Communications. https://doi.org/10.1038/s41467-019-14280-1.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.Gene disruption by structural mutations drives selection in U.S. rice breeding over the last century

- (Proceedings)Vaughn, J.N., Stein, J.C., Korani, W., Edwards, J., Peterson, D.G., Simpson, S.A., Grimwood, J., Ware, D., McClung, A.M., Scheffler, B.E. 2021. Gene disruption by structural mutations drives selection in U.S. rice breeding over the last century. Proceedings of 38th Rice Technical Working Group Meeting, February 24-27, 2020, Orange Beach, Alabama. p 77. Electronic Publication.Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (Review Article)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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (Other)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
                                                        

- (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
                                                        

- (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
                                                        

- (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.17.00481.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

- (Review Article)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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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
                                                        

- (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

- (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

- (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

- (Other)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.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.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.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.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.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.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-D454Databases and data mining

- (Book / Chapter)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 143:587-599WHOLE-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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