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

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.

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.

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.

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.

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.

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.

Genome-wide characterization of maize miRNA genes - (Peer Reviewed Journal)

Zhang, L., Chia, J., Kumari, S., Stein, J.C., Liu, Z., Narechania, A., Maher, C.A., Guill, K., Mcmullen, M.D., Ware, D. 2009. Genome-wide characterization of maize miRNA genes. PLoS Genetics. 5(11): e1000716. DOI: 10.1371/journal.pgen.1000716.

A single molecule scaffold for the maize genome - (Peer Reviewed Journal)

Zhou, S., Fusheng, W., Pasternak, S., Ware, D., Wing, R., Livny, M., Schwartz, D.C. 2009. A single molecule scaffold for the maize genome. PLoS Genetics. 5(11):1-14.

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.

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.

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.