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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » People & Locations » Nathan Weeks
Nathan T Weeks
Corn Insects and Crop Genetics Research
Information Technology Specialist

Phone: (509) 415-3745
Fax:

(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)

Projects
Legume Information System and Network - a Legume Bioinformatics Resource
Non-Assistance Cooperative Agreement (S)
  Accession Number: 442240

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole genome duplications Reprint Icon - (Peer Reviewed Journal)
Cannon, S.B., Lee, H., Weeks, N.T., Berendzen, J. 2024. Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole genome duplications. Bioinformatics. https://doi.org/10.1093/bioinformatics/btae526.
Doing genetic and genomic biology using the Legume Information System and associated resources Reprint Icon - (Book / Chapter)
Redsun, S., Hokin, S., Cameron, C.T., Cleary, A.M., Berendzen, J., Dash, S., Brown, A.V., Wilkey, A., Campbell, J.D., Huang, W., Kalberer, S.R., Weeks, N.T., Cannon, S.B., Farmer, A.D. 2022. Doing genetic and genomic biology using the Legume Information System and associated resources. Methods in Molecular Biology. 2443. https://doi.org/10.1007/978-1-0716-2067-0_4.
The legume information system and associated online genomic resources Reprint Icon - (Peer Reviewed Journal)
Berendzen, J., Brown, A.V., Cameron, C.T., Campbell, J.D., Cleary, A.M., Dash, S., Hokin, S., Huang, W., Kalberer, S.R., Nelson, R., Redsun, S., Weeks, N.T., Wilkey, A., Farmer, A.D., Cannon, S.B. 2021. The legume information system and associated online genomic resources. Legume Science. Article e74. https://doi.org/10.1002/leg3.74.
A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database Reprint Icon - (Peer Reviewed Journal)
Brown, A.V., Connors, S., Huang, W., Wilkey, A., Grant, D.M., Weeks, N.T., Cannon, S.B., Graham, M.A., Nelson, R. 2020. A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database. Nucleic Acids Research. 49(D1):D1496-D1501. https://doi.org/10.1093/nar/gkaa1107.
The genome sequence of segmental allotetraploid peanut Arachis hypogaea Reprint Icon - (Peer Reviewed Journal)
Bertioli, D.J., Jenkins, J., Clevenger, J., Dudchenko, O., Gao, D., Seijo, G., Leal-Bertioli, S., Ren, L., Farmer, A., Pandey, M., Samoluk, S.S., Abernathy, B., Agarwal, G., Ballen-Taborda, C., Cameron, C., Campbell, J., Chavarro, C., Chitikineni, A., Chu, Y., Dash, S., El Baidouri, M., Guo, B., Huang, W., Kim, K.D., Korani, W., Lanciano, S., Lui, C.G., Mirouze, M., Moretzsohn, M.C., Pham, M., Shin, J.H., Shirasawa, K., Sinharoy, S., Sreedasyam, A., Weeks, N.T., Zhang, X., Zheng, Z., Sun, Z., Froenicke, L., Aiden, E.L., Michelmore, R., Varshney, R.K., Holbrook Jr, C.C., Cannon, E.K., Scheffler, B.E., Grimwwood, J., Ozias-Akins, P., Cannon, S.B., Jackson, S.A., Schmutz, J. 2019. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nature Genetics. 51:877-884. https://doi.org/10.1038/s41588-019-0405-z.
Ten quick tips for sharing open genomic data Reprint Icon - (Peer Reviewed Journal)
Brown, A.V., Campbell, J.D., Assefa, T., Grant, D.M., Nelson, R., Weeks, N.T., Cannon, S.B. 2018. Ten quick tips for sharing open genomic data. PLoS Computational Biology. https://doi.org/10.1371/journal.pcbi.1006472.
Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume - (Peer Reviewed Journal)
Belamkar, V., Farmer, A.D., Weeks, N.T., Kalberer, S.R., Blackmon, W.J., Cannon, S.B. 2016. Genomics-assisted characterization of a breeding collection of Apios americana, an edible tuberous legume. Nature Scientific Reports. 6:34908. doi: 10.1038/srep34908.
Legume Information System (LegumeInfo.org): a key component of a set of federated data resources for the legume family - (Peer Reviewed Journal)
Dash, S., Campbell, J.D., Cannon, E., Cleary, A.M., Huang, W., Kalberer, S.R., Karingula, V., Rice, A.G., Singh, J., Umale, P.E., Weeks, N.T., Wilkey, A.P., Farmer, A.D., Cannon, S.B. 2015. Legume Information System (LegumeInfo.org): a key component of a set of federated data resources for the legume family. 2016. Nucleic Acids Research. 44 (D1):D1181-D1188. doi: 10.1093/nar/gkv1159.
Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress - (Peer Reviewed Journal)
Belamkar, V., Weeks, N.T., Bharti, A.K., Farmer, A.D., Graham, M.A., Cannon, S.B. 2014. Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. Biomed Central (BMC) Genomics. 15:950. DOI:10.1186/1471-2164-15-950.
De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity - (Peer Reviewed Journal)
Haas, B.J., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, P.D., Bowden, J., Couger, M.B., Eccles, D., Li, B., Lieber, M., Weeks, N.T. 2013. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity. Nature Protocols. 8(8):1494-1512.
A comprehensive transcriptome assembly of pigeonpea (Cajanauscajan L.) using sanger and second-generation sequencing platforms - (Peer Reviewed Journal)
Kudapa, H., Bharti, A.K., Cannon, S.B., Farmer, A.D., Deonovic, B., Kramer, R., Bohra, A., Weeks, N.T., Crow, J.A., Tuteja, R., Shah, T., Dutta, S., Gupta, D.K., Singh, A., Gaikwad, K., Sharma, T.R., May, G.D., Singh, N.K., Varshney, R.K. 2012. A comprehensive transcriptome assembly of pigeonpea (Cajanauscajan L.) using sanger and second-generation sequencing platforms. Molecular Plant. 5(5):1020-1028.
Gene expression patterns are correlated with genomic and genic structure in soybean - (Peer Reviewed Journal)
Woody, J.L., Severin, A., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.T., Weeks, N.T., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2011. Gene expression patterns are correlated with genomic and genic structure in soybean. Genome. 54(1):10-18.
RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome - (Peer Reviewed Journal)
Severin, A.J., Woody, J.L., Bolon, Y.E., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R., Grant, D.M., Specht, J.E., Graham, M.A., Cannon, S.B., May, G.D., Vance, C.P., Shoemaker, R.C. 2010. RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome. Biomed Central (BMC) Plant Biology. 10:610.
Complementary Genetic and Genomic Approaches Help Characterize the Linkage Group I Seed Protein QTL in Soybean - (Peer Reviewed Journal)
Bolon, Y.E., Joseph, B., Cannon, S.B., Graham, M.A., Diers, B.W., Farmer, A.D., May, G.D., Muehlbauer, G.J., Specht, J.E., Tu, Z., Weeks, N.T., Xu, W.W., Shoemaker, R.C., Vance, C.P. 2010. Complementary Genetic and Genomic Approaches Help Characterize the Linkage Group I Seed Protein QTL in Soybean. Biomed Central (BMC) Plant Biology. 10:41. Available: http://www.biomedcentral.com/1471-2229/10/41.
High-Throughput SNP Discovery through Deep Resequencing of a Reduced Representation Library to Anchor and Orient Scaffolds in the Soybean Whole Genome Sequence - (Peer Reviewed Journal)
Hyten, D.L., Cannon, S.B., Song, Q., Weeks, N.T., Fickus, E.W., Shoemaker, R.C., Specht, J.E., May, G.D., Cregan, P.B. 2010. High-Throughput SNP Discovery through Deep Resequencing of a Reduced Representation Library to Anchor and Orient Scaffolds in the Soybean Whole Genome Sequence. Biomed Central (BMC) Genomics. 11:38.