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

Location: Plant, Soil and Nutrition Research

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

A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset - (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.

Expression atlas update: insights from sequencing data at both bulk and single cell level - (Peer Reviewed Journal)

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)

Decoding nitrogen use efficiency in maize and sorghum: insights from comparative gene regulatory networks for sustainable agriculture - (Abstract Only)

Swift pan-genomic methods for comprehensive genome annotation in crop genomes - (Abstract Only)

Characterization of key regulators in microRNA-mediated responses to phosphate deficiency in Arabidopsis root involved in root development - (Abstract Only)

HPC-based genome variant calling workflow (HPC-GVCW) - (Pre-print Publication)
Zhou, Y., Kathiresan, N., Yu, Z., Rivera, L.F., Thimma, M., Manickam, K., Chebotarov, D., Mauleon, R., Chougule, K., Wei, S., Gao, T., Green, C.D., Zuccolo, A., Zhang, J., Ware, D., Mcnally, K.L., Wing, R.A. 2023. HPC-based genome variant calling workflow (HPC-GVCW). bioRxiv. https://doi.org/10.1101/2023.06.25.546420.

Engineering homoeologs provides a fine scale for quantitative traits in polyploid - (Peer Reviewed Journal)
Lee, E., Heo, J., Bang, W., Chougule, K., Waminal, N., Hong, N., Kim, M., Beak, H., Kim, Y., Priatama, R.A., Jang, J., Cha, K., Son, S., Rajendran, S., Choo, Y., Bae, J., Kim, C., Lee, Y., Bae, S., Jones, J., Sohn, K., Kim, H., Ware, D., Keunhwa, K. 2023. Engineering homoeologs provides a fine scale for quantitative traits in polyploid. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.14141.

Gramene: comparative plant genome resource - (Abstract Only)

Direct and predicted motif analysis of GRAS family transcription factors in sorghum and other important crop species - (Abstract Only)

Gramene PanMaize: One-stop pan-genome browser for exploring the rich genetic diversity in maize - (Abstract Only)

Regulatory networks governing nitrogen use efficiency in maize and sorghum - (Abstract Only)

An improved reference of the grapevine genome reasserts the origin of the PN40024 highly-homozygous genotype - (Peer Reviewed Journal)
Velt, A., Frommer, B., Blanc, S., Holtgrawe, D., Dumas, V., Grimplet, J., Hugueney, P., Lahaye, M., Kim, C., Matus, J., Navarro-Paya, D., Orduna, L., Tello-Ruiz, M.K., Vitulo, N., Ware, D., Rustenholz, C. 2023. An improved reference of the grapevine genome reasserts the origin of the PN40024 highly-homozygous genotype. G3, Genes/Genomes/Genetics. https://10.1093/g3journal/jkad067.

Towards standards for biocuration and interoperability of genetic variation data - (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)

Pan-genomic approaches to consistent annotation of rice genomes - (Abstract Only)

Guidelines for standardizing gene model nomenclature and genome assembly quality metrics - (Abstract Only)

Ten new high quality genome assemblies for diverse bioenergy sorghum genotypes - (Peer Reviewed Journal)
Voelker, W.G., Krishnan, K., Chougule, K., Alexander, L.C., Lu, Z., Olson, A., Ware, D., Songsomboon, K., Ponce, C., Brenton, Z.W., Boatwright, L., Cooper, E.A. 2023. Ten new high quality genome assemblies for diverse bioenergy sorghum genotypes. Frontiers in Plant Science. 13:1040909. https://doi.org/10.3389/fpls.2022.1040909.

Sorghumbase: an integrated pan-genome resource on sorghum genomics and genetics data set for the sorghum community - (Abstract Only)

Gramene Oryza: a dedicated pan-genome resource to map rice diversity - (Abstract Only)

Creating a FAIR data ecosystem for incorporating single cell genomics data into agricultural G2P research - (Abstract Only)

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

Role of a ZF-HD transcription factor in miR157-mediated feed-forward regulatory module that determines plant architecture in arabidopsis - (Peer Reviewed Journal)
Lee, Y., Kumari, S., Olson, A., Hauser, F., Ware, D. 2022. Role of a ZF-HD transcription factor in miR157-mediated feed-forward regulatory module that determines plant architecture in arabidopsis. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms23158665.

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (Oryza sativa) - (Peer Reviewed Journal)
Zhou, Y., Yu, Z., Chebotarov, D., Chougule, K., Ly, Z., Rivera, L.F., Kathiresan, N., Al-Bader, N., Mohammed, N., Alsantely, A., Mussurova, S., Santos, J., Thimma, M., Troukhan, M., Fornasiero, A., Green, C., Copetti, D., Kudrna, D., Llaca, V., Lorieux, M., Zuccolo, A., Ware, D., McNally, K., Zhang, J., Wing, R., Kudrna, D. 2023. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (Oryza sativa). Nature Genetics. 14:1567. https://doi.org/10.1038/s41467-023-37004-y.

Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (oryza sativa) - (Pre-print Publication)
Zhou, Y., Yu, Z., Chebotarov, D., Chougule, K., Lu, Z., Rivera, L.F., Kathiresan, N., Al-Bader, N., Mohammed, N., Alsantely, A., Musssurova, S., Santos, J., Thimma, M., Troukhan, M., Green, C.D., Copetti, D., Kudrna, D., Llaca, V., Lorieux, M., Zuccolo, A., Ware, D., Mcnally, K., Zhang, J., Wing, R.A., Kudrna, D. 2022. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian Rice (oryza sativa). bioRxiv. https://doi.org/10.1101/2022.06.11.495682.

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 - (Peer Reviewed Journal)
Ferroro-Serrano, A., Sylvia, M.M., Forstmeier, P.C., Olson, A.J., Ware, D., Bevilacqua, P.C., Assmann, S.M. 2022. Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in arabidopsis. Genome Biology. 23:101. https://doi.org/10.1186/s13059-022-02656-4.

Sorghum root epigenetic landscape during limiting phosphorus conditions - (Peer Reviewed Journal)
Gladman, N.P., Hufnagel, B., Regulski, M., Liu, Z., Wang, X., Chougule, K., Kochian, L., Magalhaes, J., Ware, D. 2022. Sorghum root epigenetic landscape during limiting phosphorus conditions. Plant Direct. 6(5):e393. https://doi.org/10.1002/pld3.393.

SorghumBase: a web-based portal for sorghum genetic information and community advancement - (Peer Reviewed Journal)
Gladman, N., Olson, A., Wei, S., Chogule, K., Lu, Z., Tello0ruiz, M., Meijs, I., Van Buren, P., Jiao, Y., Wang, B., Kumar, V., Kumari, S., Zhang, L., Burke, J.J., Chen, J., Burow, G.B., Hayes, C.M., Emendack, Y., Xin, Z., Ware, D. 2022. SorghumBase: a web-based portal for sorghum genetic information and community advancement. Planta. 255:35. https://doi.org/10.1007/s00425-022-03821-6.

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates - (Peer Reviewed Journal)
Yates, A.D., Allen, J., Amode, R.M., Azov, A.G., Barba, M., Becerra, A., Bhai, J., Campbell, L.I., Carbajo Manuel, M., Chakiachvili, M., Chougule, K., Christensen, M., Contreras-Moreira, B., Cuzick, A., Fioretto, L., Davis, P., De Silva, N.H., Diamantakis, S., Dyer, S., Elster, J., Filippi, C.V., Gall, A., Grigoriadis, D., Guijarro-Clarke, C., Gupta, P., Hammond-Kosack, K.E., Howe, K.L., Jaiswal, P., Kaikala, V., Kumar, V., Kumari, S., Langridge, N., Le, T., Luypaert, M., Maslen, G.L., Maurel, T., Moore, B., Muffato, M., Mushtaq, A., Naamati, G., Naithani, S., Olson, A., Parker, A., Paulini, M., Pedro, H., Perry, E., Preece, J., Quinton-Tulloch, M., Rodgers, F., Rosello, M., Ruffier, M., Seager, J., Sitnik, V., Szpak, M., Tate, J., Tello-Ruiz, M.K., Trevanion, S.J., Urban, M., Ware, D., Wei, S., Williams, G., Winterbottom, A., Zarowiecki, M., Finn, R.D., Flicek, P. 2021. Ensembl Genomes 2022: an expanding genome resource for non-vertebrates. Nucleic Acids Research. 50(D1):D996-D1003. https://doi.org/10.1093/nar/gkab1007.

A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in sorghum - (Peer Reviewed Journal)
Kumari, S., Kumar, V., Beilsmith, K., Seaver, S., Canon, S., Dehal, P., Gu, T., Joachimiak, M., Lerma-Ortiz, C., Liu, F., Zhenyuan, L., Pearson, E., Ranjan, P., Riel, W., Henry, C.S., Arkin, A.P., Ware, D. 2021. A KBase case study on genome-wide transcriptomics and plant primary metabolism in response to drought stress in sorghum. Current Plant Biology. https://doi.org/10.1016/j.cpb.2021.100229.

Pan-genome resources for grapevine - (Proceedings)

Ranked choice voting for representative transcripts with TRaCE - (Peer Reviewed Journal)
Olson, A., Ware, D. 2021. Ranked choice voting for representative transcripts with TRaCE. Bioinformatics. 2021, btab542. https://doi.org/10.1093/bioinformatics/btab542.

Comparative analysis of sorghum EMS mutants and natural populations - (Pre-print Publication)
Wang, L., Lipzen, A., Lu, Z., Chen, J., Wang, X., Tello-Ruiz, M.K., Barry, K., Mortimer, J., Ware, D., Xin, Z. 2021. Comparative analysis of sorghum EMS mutants and natural populations. bioRxiv. https://doi.org/10.1101/2021.06.06.447271.

Sorghum root epigenetic landscape during limiting phosphorus conditions - (Pre-print Publication)
Gladman, N., Hufnagel, B., Regulski, M., Liu, Z., Wang, X., Chougule, K., Kochian, L., Magalhaes, J., Ware, D. 2021. Sorghum root epigenetic landscape during limiting phosphorus conditions. bioRxiv. https://doi.org/10.1101/2021.05.25.445633.

Single-cell RNA sequencing of developing ears facilitates functional analysis and trait gene discovery in maize - (Peer Reviewed Journal)
Xu, X., Crow, M., Rice, B.R., Li, F., Harris, B., Liu, L., Arevalo, E.D., Lu, Z., Jackson, D., Ware, D., Wang, L., Fox, N., Wang, X., Drenkow, J., Luo, A., Char, S., Yang, B., Sylvester, A., Gingeras, T., Schmitz, R., Lipka, A., Gillis, J. 2021. Single-cell RNA sequencing of developing ears facilitates functional analysis and trait gene discovery in maize. Developmental Cell. 56:557-568. https://doi.org/10.1016/j.devcel.2020.12.015.

Pan-genome analysis in sorghum highlights the extent of genomic variation and sugarcane aphid resistance genes - (Pre-print Publication)
Wang, B., Jiao, Y., Chougule, K., Olson, A., Huang, J., Llaca, V., Fengler, K., Wei, X., Wang, L., Wang, X., Regulski, M., Drenkow, J., Gingeras, T., Hayes, C.M., Armstrong, J.S., Huang, Y., Xin, Z., Ware, D. 2021. Pan-genome Analysis in Sorghum Highlights the Extent of Genomic Variation and Sugarcane Aphid Resistance Genes. bioRxiv. https://doi.org/10.1101/2021.01.03.424980.

Amino acid and carbohydrate metabolism are coordinated to maintain energetic balance during drought in sugarcane - (Peer Reviewed Journal)
Diniz, A., Da Silva, D. ., Lembke, C.A., Costa, M.B., Ten-Caten, F., Li, F., Vilela, R., Menossi, M., Ware, D., Engres, L., Souza, G. 2020. Amino acid and carbohydrate metabolism are coordinated to maintain energetic balance during drought in sugarcane. International Journal of Molecular Sciences. 21(23):9124. https://doi.org/10.3390/ijms21239124.

Gramene: a resource for comparative analysis of plants genomes and pathways - (Book / Chapter)
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 - (Peer Reviewed Journal)
Hon, T., Mars, K., Young, G., Tsai, Y., Kauralis, J., Landolin, J.M., Maurer, N., Kudrna, D., Hardigan, M.A., Steiner, C.C., Knapp, S., Ware, D., Shapiro, B., Peluso, P., Rank, D.R. 2020. Highly accurate HiFi long read sequencing data for five complex genome samples. Scientific Data - Nature. 7. Article e399. https://doi.org/10.1038/s41597-020-00743-4.

SciApps: an automated platform for processing and distribution of plant genomics data - (Book / Chapter)

Amino acid metabolism and carbohydrate metabolism in sugarcane are coordinated to maintain energetic balance during drought - (Peer Reviewed Journal)
Diniz, A.L., Silva, D.I., Lembke, C.G., Costa, M.D., Ten-Caten, F., Li, F., Vilela, R.D., Menossi, M., Endres, L., Ware, D., Souza, G.M. 2020. Amino acid metabolism and carbohydrate metabolism in sugarcane are coordinated to maintain energetic balance during drought. International Journal of Molecular Sciences. 21:9124. https://doi.org/10.3390/ijms21239124.

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research - (Peer Reviewed Journal)
Tello-Ruiz, M.K., Naithani, S., Gupta, P., Olson, A., Wei, S., Preece, J., Jiao, Y., Wang, B., Chougule, K., Garg, P., Elser, J., Kumari, S., Kumar, V., Contreras-Moreira, B., Naamati, G., George, N., Cook, J., Bolser, D.M., D'Eustachio, P., Stein, L.D., Gupta, A., Xu, W., Regala, J., Papatheodorou, I., Kersey, P.J., Flicek, P., Taylor, C., Jaiswal, P., Ware, D. 2020. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Research. 49:D1452-D1463. https://doi.org/10.1093/nar/gkaa979.

Current status of the multinational Arabidopsis community - (Peer Reviewed Journal)
Parry, G., Provart, N.J., Brady, S.M., Uzilday, B., Adams, K., Araujo, W., Aubourg, S., Baginsky, S., Bakker, E., Barenfaller, K., Batley, J., Beale, M., Beilstein, M., Belkhadir, Y., Berardini, T., Bergelson, J., Blanco-Herrera, F., Brady, S., Braun, H., Briggs, S., Brownfield, L., Cardarelli, M., Castellanos-Uribe, M., Coruzzi, G., Dassanayake, M., De Jaeger, G., Dilkes, B., Doherty, C., Ecker, J., Edger, P., Edwards, D., El Kasmi, F., Eriksson, M., Exposito-Alonso, M., Falter-Braun, P., Fernie, A., Ferro, M., Fiehn, O., Friesner, J., Greenham, K., Guo, Y., Hamann, T., Hancock, A., Hauser, M., Heazlewood, J., Ho, C., Horak, H., Huala, E., Hwang, I., Iuchi, S., Jaiswal, P., Jakobson, L., Jiang, Y., Jiao, Y., Jones, A., Kadota, Y., Khurana, J., Kliebenstein, D., Knee, E., Kobayashi, M., Koch, M., Krouk, G., Larson, T., Last, R., Lepiniec, L., Li, S., Lurin, C., Lysak, M., Maere, S., Malinowski, R., Maumus, F., May, S., Mayer, K., Mendoza-Cozatl, D., Mendoza-Poudereux, I., Meyers, B., Micol, J., Millar, H., Mock, H., Mukhtar, K., Mukhtar, S., Murcha, M., Nakagami, H., Nakamura, Y., Nicolov, L., Nikolau, B., Nowack, M., Nunes-Nesi, A., Palmgren, M., Parry, G., Patron, N., Peck, S., Pedmale, U., Perrot-Rechenmann, C., Pieruschka, R., Pio-Beltran, J., Pires, J., Provart, Rajjou, L., Reiser, L., Reumann, S., N., Rhee, S., Rigas, S., Ware, D. 2020. Current status of the multinational Arabidopsis community. Plant Direct. 00:1-9. https://doi.org/10.1002/pld3.248.

Management, analyses, and distribution of the MaizeCODE Data on the Cloud - (Peer Reviewed Journal)
Wang, L., Lu, Z., Delabastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Ware, D., Gingeras, T., Xu, X., Ramirez, C., Fernandez Marco, C., Williams, J., Dobin, A., Birnbaum, K., Jackson, D., Martienssen, R., Mccombie, R.W., Micklos, D., Schatz, M. 2020. Management, analyses, and distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science. 31. https://doi.org/10.3389/fpls.2020.00289.

Variant phasing and haplotypic expression from long-read sequencing in maize - (Peer Reviewed Journal)
Wang, B., Tseng, E., Baybayan, P., Eng, K., Regulski, M., Jiao, Y., Wang, L., Olson, A., Chougule, K., Van Buren, P., Ware, D. 2020. Variant phasing and haplotypic expression from long-read sequencing in maize. Communications Biology. 3(78). https://doi.org/10.1038/s42003-020-0805-8.

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline - (Peer Reviewed Journal)
Ou, S., Su, W., Liao, Y., Chougule, K.M., Agda, J.R., Hellinga, A.J., Lugo, C., Elliott, T.A., Ware, D., Peterson, T., Jiang, N., Hirsch, C.N., Hufford, M.B. 2019. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 20(1):275. https://doi.org/10.1186/s13059-019-1905-y.

Plant Reactome: a knowledgebase and resource for comparative pathway analysis - (Peer Reviewed Journal)
Naithani, S., Gupta, P., Preece, J., D'Eustachio, P., Elser, J.L., Garg, P., Dikeman, D.A., Kiff, J., Cook, J., Olson, A., Wei, S., Tello-Ruiz, M.K., Mundo, A.F., Munoz-Pomer, A., Mohammed, S., Cheng, T., Bolton, E., Papatheodorou, I., Stein, L., Ware, D., Jaiswal, P. 2020. Plant Reactome: a knowledgebase and resource for comparative pathway analysis. Nucleic Acids Research. 48(D1):D1093-D1103. https://doi.org/10.1093/nar/gkz996.

Double triage to identify poorly annotated genes in maize: The missing link in community curation - (Peer Reviewed Journal)
Tello-Ruiz, M.K., Marco, C.F., Hsu, F., Khangura, R.S., Qiao, P., Sapkota, S., Stiszer, M.C., Wasikowski, R., Wu, H., Junpeng, Z., Chougule, K., Barone, L.C., Ghiban, C., Muna, D., Olson, A.C., Wang, L.C., Ware, D., Micklos, D.A. 2019. Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLoS Computational Biology. 14(10). https://doi.org/10.1371/journal.pone.0224086.

A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits - (Peer Reviewed Journal)
Knauer, S., Javell, M., Li, L., Li, X., Ma, X., Wimalanathan, K., Kumari, S., Johnston, R., Leiboff, S., Meeley, R., Schnable, P.S., Ware, D., Lawrence-Dill, C., Yu, J., Muehlbauer, G.J., Scanlon, M.J., Timmermans, M.C. 2019. A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits. Genome Research. 29(12):1962-1973. https://doi.org/10.1101/gr.250878.119.

Fertility of pedicellate spikelets in sorghum is controlled by a jasmonic acid regulatory module - (Peer Reviewed Journal)
Gladman, N.P., Jiao, Y., Lee, Y., Zhang, L., Chopra, R., Regulski, M., Burow, G.B., Hayes, C.M., Christensen, S.A., Dampanaboina, L., Chen, J., Burke, J.J., Ware, D., Xin, Z. 2019. Fertility of pedicellate spikelets in sorghum is controlled by a jasmonic acid regulatory module. Nature Plants. 20(19). https://doi.org/10.3390/ijms20194951.

Ensembl Genomes 2020-enabling non-vertebrate genomic research - (Peer Reviewed Journal)
Howe, K.L., Contreras-Moreira, B., De Silva, N., Maslen, G., Akanni, W., Allen, J., Alvarez-Jarreta, J., Barba, M., Bolser, D.M., Cambell, L., Carbajo, M., Chakiachvili, M., Christensen, M., Cummins, C., Cuzick, A., Davis, P., Fexova, S., Gall, A., George, N., Gil, L., Gupta, P., Hammond-Kosack, K.E., Haskell, E., Hunt, S.E., Jaiswal, P., Janacek, S.H., Kersey, P.J., Langridge, N., Maheswari, U., Maurel, T., Mcdowall, M.D., Moore, B., Muffato, M., Naamati, G., Naithani, S., Olson, A., Papatheodorou, I., Patricio, M., Paulini, M., Pedro, H., Perry, E., Preece, J., Rosello, M., Russell, M., Sitnik, V., Staines, D.M., Stein, J., Tello-Ruiz, M.K., Trevanion, S.J., Urban, M., Wei, S., Ware, D., Williams, G., Yates, A.D., Flicek, P. 2020. Ensembl Genomes 2020-enabling non-vertebrate genomic research. Nucleic Acids Research. 48(D1,8):D689-D695. https://doi.org/10.1093/nar/gkz890.

Reviving the Transcriptome Studies: An insight into the emergence of Single-Molecule Transcriptome Sequencing - (Peer Reviewed Journal)
Wang, B., Kumar, V., Olson, A., Ware, D. 2019. Reviving the Transcriptome Studies: An insight into the emergence of Single-Molecule Transcriptome Sequencing. Frontiers in Genetics. 10:384. https://doi.org/10.3389/fgene.2019.00384.

The dominant and poorly penetrant phenotypes of maize unstable factor for orange1 are caused by DNA methylation changes at a linked transposon - (Peer Reviewed Journal)
Wittmeyer, K., Cui, J., Chaterjee, D., Lee, T., Tan, Q., Jiao, Y., Wang, P., Gaffoora, I., Ware, D., Meyers, B., Chopra, S. 2018. The dominant and poorly penetrant phenotypes of maize unstable factor for orange1 are caused by DNA methylation changes at a linked transposon. The Plant Cell. https://doi.org/10.1105/tpc.18.00546.

Tripsacum de novo transcriptome assemblies reveal parallel gene evolution with maize after ancient polyploidy - (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 - (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 - (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.