Matthew Hudson


Dr. Hudson uses supercomputing and DNA sequencing to solve problems in plant, animal, and human genetics. His current research focuses on how crops are bred and on ways to treat and prevent plant, animal, and human diseases. He is particularly interested in the genetics of crop traits and the genetic and molecular interactions of soybeans with pathogens, pests, and other organisms.

Primary Disciplines


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

Academic Positions

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

Selected Articles in Journals

  • HX Chang, L Domier, O Radwan, C Yendrek, M Hudson, GL Hartman. 2015. Identification of multiple phytotoxins produced by Fusarium virguliforme including a phytotoxic effector (FvNIS1) associated with sudden death syndrome foliar symptoms. Molecular Plant-Microbe Interactions, online before print.
  • Kapheim KM, Pan H, Li C, Salzberg SL, Puiu D, Magoc T, Robertson HM, Hudson ME and 46 other authors. 2015. Genomic Signatures of Evolutionary Transitions from Solitary to Group Living. Science 348, 1139-1143.
  • Li Q, Li Y, Moose SP, Hudson ME. 2015. Transposable elements, mRNA expression level and strand-specificity of small RNAs are associated with non-additive inheritance of gene expression in hybrid plants. BMC Plant Bio 15: 168.
  • AE Lipka, CB Kandianis, ME Hudson, J Yu, J Drnevich, PJ Bradbury, MA Gore. 2015. From association to prediction: statistical methods for the dissection and selection of complex traits in plants
  • Curr. Op. Plant Biol. 24, 110-118
  • Sadd, BM, Barriebeau, SM, Bloch, G and 156 other authors, 2015. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biology 16, 76.
  • Lee, T.G., Kumar, I, Diers, B. and Hudson, M. 2015. Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus. Molecular Ecology 24, 1774-1791.
  • Hudson, KA and Hudson, M. 2015. A classification of basic helix-loop-helix transcription factors of soybean. International Journal of Genomics, Article ID 603182
  • Hudson, KA and Hudson, M. 2014. The basic helix-loop-helix transcription factor family in the sacred lotus, Nelumbo nucifera. Tropical Plant Biology 7:65-70.
  • Akperty, A., Belaffif, M., Graef, G.L., Mian, M.A. R., Shannon, J.G., Cregan, P.B., Hudson, M.E., Diers, B.W. and Nelson, R.L. 2014. Effects of selective genetic introgression from wild soybean to soybean. Crop Science 54: 2683-2695.
  • 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.
  • 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 14: 864.
  • 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, in press.
  • 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.
  • 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.
  • 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.
  • 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
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Varala K., Swaminathan K., Li Y., Hudson M.E. 2011. Rapid genotyping of soybean cultivars using high throughput sequencing. PLoS ONE 6, e24811
  • 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.
  • 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.