Skip to main content
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 (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.)

Projects
Development of Pan-genomic & Computational Resources for Agriculture
Cooperative Agreement (A)
  Accession Number: 443248
Championing Improvement of Sorghum and Other Agriculturally Important Species through Data Stewardship and Functional Dissection of Complex Traits
In-House Appropriated (D)
  Accession Number: 445304
Coordination 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.)
Advancing agricultural genomics: Integrating rsIDs for standardized genetic variation and enhanced breeding strategies - (Abstract Only)
Functional diversification within the heme-binding split-barrel family - (Peer Reviewed Journal)
GrameneOryza 2024: A Collaborative Pan-Genome Resource for Rice Diversity, Knowledge Discovery, and Community Engagement - (Abstract Only)
Chougule, K., Wei, S., Lu, Z., Olson, A., Tello-Ruiz, M.K., Gladman, N.P., Zhang, L., Kumar, V., Kumari, S., Ware, D., Kim, S., Dooling, K., Olson, C., Assmann, S., Dyer, S., Jaiswal, P. 2024. GrameneOryza 2024: A Collaborative Pan-Genome Resource for Rice Diversity, Knowledge Discovery, and Community Engagement. International Symposium on Rice Germplasm Evaluation and Enhancement. International Symposium on Rice Functional Genomics Conference, September 9, 2024.
Catalyzing Genomic Discoveries: Leveraging rsIDs for Enhanced Trait-Driven Interoperability and Genomic Function Transfer - (Abstract Only)
Crop Improvement Through Genomics - (Abstract Only)
Characterization of key regulators in microRNA-mediated responses to phosphate deficiency in Arabidopsis root development - (Abstract Only)
Gramene 2024: A comparative resource on plant reference genomes, pan-genomes, and pathways - (Abstract Only)
Binding Behaviors of Diverse GRAS Family Transcription Factors in Monocots - (Abstract Only)
Catalyzing Genomic Discoveries: Leveraging rsIDs for Enhanced Trait-Driven Interoperability and Genomic Function Transfer - (Abstract Only)
Decoding Nitrogen Use Efficiency in Maize and Sorghum: Insights from Comparative Gene Regulatory Networks for Sustainable Agriculture - (Abstract Only)
Gramene Plants And Pan Genome Resources for Plant Communities - (Abstract Only)
SorghumBase 2024: Building Partnerships and Integrating Genetic Knowledge for the Sorghum Community - (Abstract Only)
Transcriptomic Profiles of Developing Meristems Across Sorghum Accessions Reveal Nuanced Regulatory Pathways Towards Panicle Morphology and Grain Content - (Abstract Only)
Sorghum Pan-Transcriptome Reveals Divergent and Constrained Modules for Inflorescence Morphology - (Abstract Only)
Swift Pan-Genomic Methods for Comprehensive Genome Annotation in Crop Genomes. - (Abstract Only)
Gramene: A comparative resource on plant reference genomes, pan-genomes and pathways - (Abstract Only)
Elucidating Nitrogen Use Efficiency in Crops through Comparative Analysis of Gene Regulatory Networks in Maize and Sorghum - (Abstract Only)
Binding Site Preferences of Sorghum GRAS Transcription Factors Across Monocots - (Abstract Only)
Genetic variation standardization (rsIDs) enhances Trait-Driven Interoperability and Genomic Function Transfer - (Abstract Only)
Evaluating Nitrate Tolerance in Male Sterile Sorghum Lines for implications for safe forage Production - (Abstract Only)
Genome-wide Response to Iron Availability and Identification of Leaf-level Metal Acclimation Factors in Four Sorghum Carbon Partitioning NAM Populations. - (Abstract Only)
Characterization of Transcription Factor Family’s Functional Role in Arabidopsis thaliana Primary Root Growth - (Abstract Only)
Sorghum 2.4K SNP panel: a cost-effective, high sample throughput genotyping resource for US sorghum breeding and research community - (Abstract Only)
Unlocking Genomic Diversity: Harnessing the Power of FAIR Principles in SorghumBase - (Abstract Only)
SorghumBase: Fostering Community Engagement for Sustainable Sorghum Research - (Abstract Only)
SorghumBase: Public Genetic and Genomic Database for the Sorghum Research and Breeding Community - (Abstract Only)
Gapless assembly of complete humannand plant chromosomes using only nanopore sequencing - (Pre-print Publication)
Role of moss and Arabidopsis zinc-fnger homeodomain transcription factors in regulating plant architecture Reprint Icon - (Peer Reviewed Journal)
Lee, Y., Kim, K., Ware, D. 2024. Role of moss and Arabidopsis zinc-fnger homeodomain transcription factors in regulating plant architecture. Plant Biotechnology Reports. 18:223-231. https://doi.org/10.1007/s11816-024-00897-2.
Transcriptomic Profiles of Developing Meristems Across Sorghum Accessions Reveal Nuanced Regulatory Pathways Towards Panicle Morphology - (Abstract Only)
Gramene PanMaize: One-Stop Pan-Genome Browser for Exploring the Rich Genetic Diversity in Maize - (Abstract Only)
Decoding Nitrogen Use Efficiency in Maize and Sorghum: Insights from Comparative Gene Regulatory Networks for Sustainable Agriculture - (Abstract Only)
Gramene 2024: A comparative resource on plant reference genomes, pan-genomes and pathways - (Abstract Only)
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. Reprint Icon - (Pre-print Publication)
Cahn, J., Regulski, M., Lynn, J., Ernst, E., De Santis Alves, C., Ramakrishnan, S., Chougule, K., Wei, S., Lu, Z., Martienssen, R.A., Xiaosa, X., Drenkow, J., Kramer, M., Mccombie, R., Ware, D., Jackson, D., Schatz, M., Gingeras, T. 2024. MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.. bioRxiv. https://doi.org/10.1101/2024.02.22.581585.
Functional genomics enabled by the large scale sequence indexed sorghum mutant population - (Abstract Only)
Jiao, Y., Tian, R., Chen, J., Ware, D., Xin, Z. 2024. Functional genomics enabled by the large scale sequence indexed sorghum mutant population. Plant Biology Annual Meeting.
Leveraging Biomedicine Resources to Understand Single-Cell Data in Agriculture: The Faang Experience - (Abstract Only)
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)
A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset Reprint Icon - (Peer Reviewed Journal)
Zhou, Y., Kathiresan, N., Yu, Z., Rivera, L.F., Thimma, M., Manickam, K., Chebotarov, D., Mauleon, R., Chougule, K., Wing, R.A., Wei, S., Gao, T., Green, C., Zuccolo, A., Ware, D., Zhang, J., Mcnally, K.L., Yang, Y., Xie, W. 2024. A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset. BMC Biology. 22:13. https://doi.org/10.1186/s12915-024-01820-5.
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 Reprint Icon - (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.
A large sequenced mutant library as a community resource for sorghum breeding and genomics - (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 as a community resource for sorghum breeding and genomics. Meeting Abstract.
Expression atlas update: insights from sequencing data at both bulk and single cell level Reprint Icon - (Peer Reviewed Journal)
Ensembl 2024 Reprint Icon - (Peer Reviewed Journal)
Harrison, P.W., Amode, R., Austine-Orimoloye, O., Aziv, A.G., Barba, M., Barnes, I., Becker, A., Bennett, R., Berry, A., Yates, A.D., Bhai, J., Bhurji, S., Boddu, S., Branco Lins, P.R., Brooks, L., Budhanuru Ramaraju, S., Campbell, L.I., Carbajo Martinez, M., Charkhchi, M., Chougule, K., Cockburn, A., Davidson, C.E., De Silva, N.H., Dodiya, K., Donaldson, S., El Houdaigui, B., El Naboulsi, T., Fatima, R., Garcia Giron, C., Genez, T., Grigoriadis, D., Ghattaoraya, G., Gonzalez Martinez, J., Gurbich, T.A., Hardy, M.E., Hollis, Z., Hourlier, T.E., Hunt, T., Kay, M., Kaykala, V., Le, T., Lelmos, D., Lodha, D., Marques-Coelho, D., Maslen, G., Merino, G.A., Mirabueno, L., Mushtaq, A.E., Nakib Hossain, S., Ogeh, D.N., Pandian Sakthivel, M., Parker, A., Perry, M., Pilizota, I., Poppleton, D., Prosovetskaia, I., Raj, S., Perez-Silva, J.G., Salam, A.A., Saraf, S., Saraiva-Agostinho, N., Sheppard, D., Sinha, S., Sipos, B., Sitnik, V., Stark, W., Steed, E., Suner, M., Surapaneni, L., Sutinen, K., Tricomi, F.F., Urbina-Gomez, D., Veidenberg, A.E., Walsh, T.A., Ware, D., Wass, E., Willhoft, N.L., Allen, J., Alvarez-Jarreta, J., Chakiachvili, M., Flint, B., Giorgetti, S., Haggerty, L., Ilsley, G.R., Keatley, J., Loveland, J.E., Moore, B., Mudge, J.M., Naamati, G., Tate, J., Trevanion, S.J., Winterbottom, A., Frankish, A., Hunt, S.E., Cunningham, F.E., Dyser, S., Finn, R.D., Martin, F. 2023. Ensembl 2024. Nucleic Acids Research. Vol.52, p. D891-899. https://doi.org/10.1093/nar/gkad1049.
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) Reprint Icon - (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 Reprint Icon - (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.
A large Sequenced Mutant library covers 98% of the genes in the genome of the inbred line BTx623 - (Abstract Only)
Xin, Z., Jiao, Y., Burow, G.B., Hayes, C.M., Chen, J., Pugh, N.A., Ware, D. 2023. A large Sequenced Mutant library covers 98% of the genes in the genome of the inbred line BTx623. ASA-CSSA-SSSA Annual Meeting Abstracts.
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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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) Reprint Icon - (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) Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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#DOI
Highly accurate HiFi long read sequencing data for five complex genome samples Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 Reprint Icon - (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 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.
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 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 - (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 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 - (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 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.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 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 - (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 - (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.
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.
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.
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., 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.
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.
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 - (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 143:587-599
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.
ARS News Articles