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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #434556

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

A data infrastructure for the plant cell atlas - (Review Article)

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (Oryza sativa) - (Peer Reviewed Journal)

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.

Characterization of a novel zinc chaperone in arabidopsis - (Abstract Only)

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)

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.

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.

Pan-genome resources for grapevine - (Proceedings)

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.

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.

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.

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 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

Gramene: a resource for comparative analysis of plants genomes and pathways - (Book / Chapter)

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.

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.

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.

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.

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.

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.

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.

Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy Reprint Icon - (Review Article)
Gault, C., Kremling, K., Buckler IV, E.S. 2018. Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy. The Plant Genome. https://doi.org/10.1101/267682.

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.

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.