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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Research Project #425427

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

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

Application of molecular simulations toward understanding cellulase mechanisms Reprint Icon - (Peer Reviewed Journal)
Arora, M., Yennamalli, R.M., Sen, T.Z. 2018. Application of molecular simulations toward understanding cellulase mechanisms. BioEnergy Research. 11:850-867. https://doi.org/10.1007/s12155-018-9944-x.

The art of curation at a biological database: principles and application Reprint Icon - (Peer Reviewed Journal)
Odell, S.G., Lazo, G.R., Woodhouse, M.R., Hane, D.L., Sen, T.Z. 2017. The art of curation at a biological database: principles and application. Current Plant Biology. 11-12:2-11. https://doi.org/10.1016/j.cpb.2017.11.001.

Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation - (Peer Reviewed Journal)
Sen, T.Z., Braun, B., Schott, D., Portwood II, J.L., Schaeffer, M.L., Harper, E.C., Cannon, E.K., Andorf, C.M. 2017. Surveying the maize community for their diversity and pedigree visualization needs to prioritize tool development and curation. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bax031.

Lipase catalyzed methanolysis of tri-(12-hydroxy stearoyl)-glycerol in organic solvents - (Peer Reviewed Journal)
Kang, S., McKeon, T.A. 2016. Lipase catalyzed methanolysis of tri-(12-hydroxy stearoyl)-glycerol in organic solvents. Advances in Enzyme Research. 4(4):152-157. doi: 10.4236/aer.2016.44014.

The quality of metabolic pathway resources depends on initial enzymatic function assignments and level of manual curation: A case for maize - (Peer Reviewed Journal)
Walsh, J., Schaeffer, M.L., Zhang, P., Rhee, S., Dickerson, J., Sen, T.Z. 2016. The quality of metabolic pathway resources depends on initial enzymatic function assignments and level of manual curation: A case for maize. BMC Systems Biology. 10:129.

Genome resources for climate-resilient cowpea, an essential crop for food security - (Peer Reviewed Journal)
Munoz-Amatriain, M., Mirebrahim, H., Xu, P., Wannamaker, S., Luo, M., Alhakami, H., Alpert, M., Atokple, I.K., Batieno, J., Boukar, O., Bozdag, S., Cisse, N., Drabo, I., Ehlers, J., Farmer, A., Fatokun, C., Gu, Y.Q., Guo, Y., Huynh, B., Jackson, S., Kusi, F., Lawley, C.T., Lucas, M.R., Ma, Y., Timko, M.P., Wu, J., You, F., Barkley, N.L., Roberts, P.A., Lonardi, S., Close, T.J. 2017. Genome resources for climate-resilient cowpea, an essential crop for food security. Plant Journal. 89:1042-1054 doi: 10.1111/tpj.13404.

Fatty acid composition of seed oil from Fremontodendron californicum - (Peer Reviewed Journal)
McKeon, T.A. 2016. Fatty acid composition of seed oil from Fremontodendron californicum. American Journal of Plant Sciences. 7(15):2107-2111. doi: 10.4326/ajps.2013.715188.

PIECE 2.0: an update for the plant gene structure comparison and evolution database Reprint Icon - (Peer Reviewed Journal)
Wang, Y., Xu, L., Thilmony, R.L., You, F., Gu, Y.Q., Coleman-Derr, D.A. 2016. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Research. 45(D1):1015-1020. https://doi.org/10.1093/nar/gkw935.

GSP: A web-based platform for designing genome-specific primers in polyploids - (Peer Reviewed Journal)
Wang, Y., Tiwari, T., Coleman-Derr, D.A., Rawda, N., Gill, B., Huo, N., You, F., Gu, Y.Q. 2016. GSP: A web-based platform for designing genome-specific primers in polyploids. Bioinformatics. doi: 10.1093/bioinformatics/btw/34.

WheatExp: an RNA-seq expression database for polypoid wheat - (Peer Reviewed Journal)
Pearce, S., Vazquez-Cross, H., Herin, S.Y., Hane, D., Wang, Y., Gu, Y.Q., Dubcovsky, J. 2015. WheatExp: an RNA-seq expression database for polypoid wheat. Biomed Central (BMC) Plant Biology. 15:299.

GrainGenes: Changing Times, Changing Databases, Digital Evolution. Reprint Icon - (Abstract Only)
Tobias, C.M., Lazo, G.R., Gu, Y.Q., Matthews, D.E. 2015. GrainGenes: Changing Times, Changing Databases, Digital Evolution. Meeting Abstract. scisoc.confex.com/scisoc/2015am/webprogram/Paper94726.html.

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species - (Peer Reviewed Journal)
Wang, Y., Coleman-Derr, D.A., Chen, G., Gu, Y.Q. 2015. OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 43(W1):W78-W84. doi: 10.1093/nar/gkv487.

Bacterial pathogen genomics: liberibacters from around the world. - (Abstract Only)

AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants - (Peer Reviewed Journal)
Wang, Y., Thilmony, R.L., Zhao, Y., Chen, G., Gu, Y.Q. 2014. AIM: A comprehensive Arabidopsis Interactome Module database and related interologs in plants. Database: The Journal of Biological Databases and Curation. doi: 10.1093/database/bau117.

The Oat Newsletter: where we've been and where we're going - (Abstract Only)

De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum - (Peer Reviewed Journal)
Fox, S.E., Geniza, M., Hanumappa, M., Naihani, S., Sullivan, C., Preece, J., Tiwari, V.K., Elser, J., Leonard, J.M., Sage, A., Gresham, C., Kerhornou, A., Bolser, D., Mccarthy, F., Kersey, P., Lazo, G.R., Jaiswal, P. 2014. De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. PLoS One. 9:E96855.

Net Venn - An integrated network analysis web platform for gene lists - (Peer Reviewed Journal)
Wang, Y., Thilmony, R.L., Gu, Y.Q. 2014. Net Venn - An integrated network analysis web platform for gene lists. Nucleic Acids Research. DOI: 10.1093/narlgku331.