Department of Crop Sciences
Matthew Hudson
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Matthew Hudson

334 National Soybean Res Ctr
1101 West Peabody Drive
Urbana, IL 61801
(217) 244-8096


Ph.D.: Biology, University of Leicester — 1998
M.A.: Natural Sciences, University of Cambridge — 1997
B.A.: Natural Sciences, University of Cambridge — 1994


Professor, University of Illinois (2014 - present)
Associate Professor, University of Illinois (2010 - 2014)
Assistant Professor, University of Illinois (2004 - 2010)
Bioinformatics Scientist, Diversa Corporation, San Diego, CA. (2003 - 2004)
Bioinformatics Specialist, Torrey Mesa Research Institute (2002 - 2003)
Postdoctoral Fellow, University of California, Berkeley (1998 - 2002)

Journal Articles

Kim, K-S, Bellendir, S., Hudson, K., Hill, C., Hartman, G., Hyten, D., Hudson, M., Diers, B. 2010. Fine Mapping the Soybean Aphid Resistance Gene Rag1 in Soybean. Theoretical App. Genet.;120, 1063-71.
K. Swaminathan, M.S. Alabady, K. Varala, E. De Paoli, I. Ho, D.S. Rokhsar, A.K. Arumuganathan, R. Ming, P.J. Green, B.C. Meyers, S.P. Moose and M.E. Hudson (2010). Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biology 2010, 11:R12
Kim KS, Hill CB, Hartman GL, Hyten DL, Hudson ME, Diers BW. 2010. Fine mapping of the soybean aphid-resistance gene Rag2 in soybean PI 200538. Theor Appl Genet. 2010 121:599-610.
Wang J, Roe B, Macmil S, Yu Q, Murray J, Tang H, Chen C, Najar F, Wiley G, Bowers J, Van Sluys MA, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, Ming R. 2010. Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics. 11:261
Findley S.D, Cannon S., Varala K., Hudson M.E., Birchler J, Stacey G. 2010. A Fluorescence In Situ Hybridization System for Karyotyping Soybean. Genetics. 185:727-44.
Toth A., Varala, K., Henshaw M., Rodriguez-Zas S., Hudson M., Robinson, G. 2010. Brain transcriptomic analysis in paper wasps identifies genes associated with behavior across social insect lineages. Proc. Roy. Soc. B., 277:2139-2148.
Woodard S.H., Fischman B.J., Venkat A., Hudson M.E., Varala K., Cameron S.A., Clark A.G., Robinson G.E. 2011. Genes involved in convergent evolution of eusociality in bees. Proc. Natl. Acad. Sci. USA. 108:7472-7477.
Li Y., Swaminathan K., Hudson M.E. 2011. Rapid, organ-specific transcriptional responses to light regulate photomorphogenic development in dicot seedlings. Plant Physiol. 156:2124-40.
Varala K., Swaminathan K., Li Y., Hudson M.E. 2011. Rapid genotyping of soybean cultivars using high throughput sequencing. PLoS ONE 6, e24811
Swaminathan, K., Chae, W.B., Mitros, T., Varala, K., Xie, L., Barling, A., Glowacka, K., Hall, M., Jezowski, S., Ming, R., Hudson, M., Juvik, J., Moose, S., Rokhsar, D.S. 2012. Deep sequencing identifies markers for a framework genetic map and reveals recent allotetraploidy in Miscanthus. BMC Genomics, 13:142.
Barber, W.T., Zhang, W., Win, H., Varala, K., Dorweiler, J.E., Hudson, M. and Moose, S.P. 2012. Repeat associated small RNAs vary among parents and following hybridization in maize. Proc. Natl. Acad. Sci. USA, in press.
James, Brandon T., Cuixia Chen, Arthur Rudolph, Kankshita Swaminathan, Jan E Murray, Jong-Kuk Na, Ashley K Spence, Brandon Smith, Matthew E Hudson, Stephen P Moose, Ray Ming 2012. Development of microsatellite markers in autopolyploid sugarcane and comparative analysis of conserved microsatellites in sorghum and sugarcane. Molecular Breeding 30, 661-669.
Cook, David E., Tong Geon Lee, Xiaoli Guo, Sara Melito, Kai Wang, Adam M Bayless, Jianping Wang, Teresa J Hughes, David K Willis, Thomas E Clemente, Brian W Diers, Jiming Jiang, Matthew E Hudson*, Andrew F Bent* 2012. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 338, 1206-1209.
Li, Y., K Varala, SP Moose, ME Hudson 2012. The Inheritance Pattern of 24 nt siRNA Clusters in Arabidopsis Hybrids Is Influenced by Proximity to Transposable Elements. PloS ONE 7 (10), e47043.
Zabala, Gracia, Edhilvia Campos, Kranthi K Varala, Sean Bloomfield, Sarah I Jones, Hlaing Win, Jigyasa H Tuteja, Bernarda Calla, Steven J Clough, Matthew Hudson and Lila O Vodkin 2012. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. BMC Plant Biology 12, 177
Ming, R., R VanBuren, Y Liu, M Yang, Y Han, L Li, Q Zhang, MJ Kim, MC Schatz et al 2013. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology 14, R41.
Cingolani P, Cao X., Khetani, RS, Chen, C-C, Coon, M, Sammak, A, Bollig-Fischer, A, Land, S, Huang Y., Hudson M E, Garfinkel MD, Zhong S, Robinson GE and Ruden DM 2013. Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees. BMC Genomics 14:666.
Davis C, Kota K, Baldhandapani V, Gong W, Abubucker S, Becker E, Martin J, Wyle KM, Khetani R, Hudson ME, Weinstock GM and Mitreva M. 2013. mBLAST: Keeping up with the Sequencing Explosion for (Meta) Genome Analysis. J Data Mining Genomics Proteomics 4:135.
Barling A, Swaminathan K, Mitros T, James BT, Morris J, Ngamboma O, Hall MC, Kirkpatrick J, Alabady M, Spence AK, Hudson ME, Rokhsar DS, Moose SP. 2013. A detailed expression study of the Miscanthus genus reveals changes in the transcriptome associated with the rejuvenation of spring rhizomes. BMC Genomics 14: 864
Honey Bee Genome Sequencing Consortium (see publication for full author list). 2014. Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics 15: 86
Hudson, KA and Hudson, ME. 2014. The basic helix-loop-helix transcription factor family in Sacred lotus (Nelumbo nucifera). Tropical Plant Biol. 7: 65.
Li, Y., Varala, K and Hudson, ME. 2014. A survey of the small RNA population during far-red light-induced apical hook opening. Front. Plant. Sci. 5: 156.