Crop ScienceUniversity of Illinois
Matt Hudson Lab - Bioinformatics & Plant Genomics


For an up to date list, try this link to my Google Scholar page


K. Varala, K. Swaminathan, Y. Li and M.E. Hudson (2011) Rapid genotyping of soybean cultivars using high throughput sequencing. PLoS ONE 6(9):e24811. doi:10.1371/journal.pone.0024811

Y. Li, K. Swaminathan, M.E. Hudson (2011) Rapid, Organ-Specific Transcriptional Responses to Light Regulate Photomorphogenic Development in Dicot Seedlings. Plant Physiology August 2011 vol. 156 no. 4 2124-2140

S.H. Woodard, B.J. Fischman, A. Venkat, M.E. Hudson, K. Varala, S.A. Cameron, A.G. Clark, and G.E. Robinson (2011) Genes involved in convergent evolution of eusociality in bees. PNAS May 3, 2011 vol. 108 no. 18 7472-7477


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

A.L. Toth, K. Varala, M.T. Henshaw, S.L. Rodriguez-Zas, M.E. Hudson, and G.E. Robinson (2010) Brain transcriptomic analysis in paper wasps identifies genes associated with behaviour across social insect lineages. Proc. R. Soc. B 22 July 2010 vol. 277 no. 1691 2139-2148

S.D. Findley, S. Cannon, K. Varala, J. Du, J. Ma, M.E. Hudson, J.A. Birchler and G. Stacey (2010) A Fluorescence in Situ Hybridization System for Karyotyping Soybean. Genetics July 2010 vol. 185 no. 3 727-744

M.G. Muellner, M.S. Attene-Ramos, M.E. Hudson, E.D. Wagner, M.J. Plewa (2010) Human cell toxicogenomic analysis of bromoacetic acid: A regulated drinking water disinfection by-product. Environmental and Molecular Mutagenesis Volume 51, Issue 3, pages 205–214, April 2010


D. Schwarz, H.M. Robertson, J.L. Feder, K. Varala, M.E. Hudson, G.J. Ragland, D.A. Hahn and S.H. Berlocher (2009) Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella. BMC Genomics 2009, 10:633

K. Kim, S. Bellendir, K.A. Hudson, C.B. Hill, G.L. Hartman, D.L. Hyten, M.E. Hudson and B.W. Diers (2009) Fine mapping the soybean aphid resistance gene Rag1 in soybean. THEORETICAL AND APPLIED GENETICS Volume 120, Number 5, 1063-1071, DOI: 10.1007/s00122-009-1234-8

JH Tuteja, G Zabala, K Varala, M Hudson, LO Vodkin (2009). Endogenous, Tissue-Specific Short Interfering RNAs Silence the Chalcone Synthase Gene Family in Glycine max Seed Coats. The Plant Cell 21:3063-3077 (2009)

E.A. Kikis, Y. Oka1, M.E. Hudson, A. Nagatani, P.H. Quail (2009) Residues Clustered in the Light-Sensing Knot of Phytochrome B are Necessary for Conformer-Specific Binding to Signaling Partner PIF3. PLoS Genetics 5(1): e1000352. doi:10.1371/journal.pgen.1000352


Podar, M., I. Anderson, K.S. Makarova, J.G. Elkins, N. Ivanova, M. Wall, A. Lykidis, K. Mavrommatis, H. Sun, M.E. Hudson, W. Chen, C. Deciu, D. Hutchison, J.R. Eads, A. Anderson, F. Fernandes, E. Szeto, A. Lapidus., N.C. Kyrpides, M.H. Saier Jr., P.M. Richardson, R. Rachel, H. Huber, J.A. Eisen, E. Koonin, M. Keller, and K.O. Stetter (2008). A genomic analysis of the Archaeal system Ignicoccus hospitalis: Nanoarchaeum equitans. Genome Biology 9:R158.

Kaczorowski, K.A., Kim, K-S., Diers, B.W. and Hudson, M (2008). Microarray-Based Genetic Mapping Using Soybean Near-Isogenic Lines and Generation of SNP Markers in the Rag1 Aphid-Resistance Interval. Plant Genome 1, issue 2.

Click here for raw data for Kaczorowski et al. (above)

Craig, J.P., S. Bekal, M. Hudson, L. Domier, T. Niblack, and K. N. Lambert (2008). Analysis of a Horizontally Transferred Pathway Involved in Vitamin B6 Biosynthesis from the Soybean Cyst Nematode Heterodera glycines. Mol. Biol. Evol. 25, 2085-2098

Bekal, S., Craig, J., Hudson, M., Niblack, T., Domier, L and Lambert, KN (2008). Genomic DNA sequence comparison between two inbred soybean cyst nematode biotypes facilitated by massively parallel 454 micro-bead sequencing. Mol Genet Genomics 279, 535-543.

Hudson, M (2008). Sequencing breakthroughs for genomic ecology and evolutionary biology. Molecular Ecology Resources 8, 3-17.

Toth, AL, Varala, K, Newman, TC, Miguez, FE, Hutchison, SK, Willoughby, DA, Simons, JF, Egholm, M, Hunt, JH, Hudson, M, and Robinson, GE (2007). Wasp Gene Expression Supports an Evolutionary Link Between Maternal Behavior and Eusociality. Science 318, 441-444.


Walley JW, Coughlan S, Hudson M, Covington MF, Kaspi R, Banu G, Harmer SL and Dehesh K (2007). Mechanical stress induces biotic and abiotic stress responses via a novel cis-element. PLOS Genetics 3:10

Hudson, M., Bruggink, T, Chang, S.H., Yu, W., Han. B., Wang, X., van der Toorn, P. and Zhu, T. (2007). Analysis of Gene Expression during Brassica Seed Germination Using a Cross-Species Microarray Platform. Crop Science 47, 96-112.

Swaminathan, K.*, Varala, K.*, and Hudson, M(2007). Global repeat discovery and estimation of genomic copy number in a large, complex genome using a high-throughput 454 sequence survey. BMC Genomics 8:132.

Older publications

Hudson, M (2006). Photoreceptor Biotechnology. In: Light and Plant Development, G.C. Whitelam, ed., Blackwell, 2006.

Chen, WJ, Chang SH, Hudson M, Kwan WK, Li J, Estes B, Knoll D, Shi L and Zhu T (2005). Contribution of transcriptional regulation to natural variations in Arabidopsis. Genome Biology 6:R32.

Huq, E., Al-Sady, B.,Hudson, M., Kim, C., Apel, K and Quail, P.H. (2004). PHYTOCHROME-INTERACTING FACTOR 1 Is a Critical bHLH Regulator of Chlorophyll Biosynthesis. Science 305, 1937-1941.

Tepperman JM, Hudson M, Khanna R, Zhu T, Chang SH, Wang X, Quail PH. (2004). Expression profiling of phyB mutant demonstrates substantial contribution of other phytochromes to red-light-regulated gene expression during seedling de-etiolation. Plant J. 38, 725-739.

Hudson, M and Quail, P.H. (2003). Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data. Plant Physiol. 133, 1605-1616.

Hudson, M., Lisch, D.R. and Quail, P.H. (2003). The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A signaling pathway. Plant J. 34, 453-471.

Anderson, A, Hudson, M., Chen, W and Zhu, T. (2003). Identification of nutrient partitioning genes participating in rice grain filling by singular value decomposition (SVD) of genome expression data. BMC Genomics 4:26.

Hudson, M. (2000). The genetics of phytochrome signalling in Arabidopsis. Semin. Cell Dev. Biol. 11, 475-583.

Hudson, M*, Ringli, C*, Boylan, M.T. and Quail, P.H. (1999). The FAR1 locus encodes a novel nuclear protein specific to phytochrome A signaling. Genes Dev. 13, 2017-2027.

Halliday, K.J.,Hudson, M., Ni, M., Qin, M.-M. and Quail, P.H. (1999). poc1: An Arabidopsis mutant perturbed in phytochrome signaling because of a T DNA insertion in the promoter of PIF3, a gene encoding a phytochrome-interacting bHLH protein. Proc. Natl. Acad. Sci. USA 96, 5832-5837.

Hudson, M. and Smith, H. (1998). The phytochrome B encoded by the HLG locus of Nicotiana plumbaginifolia is required for detection of photoperiod: hlg mutants show altered regulation of flowering and circadian movement. Plant J. 15, 281-287.

Hudson, M., Robson, P.R.H., Kraepiel, Y, Caboche, M. and Smith, H. (1997). Nicotiana plumbaginifolia hlg mutants have a mutation in a PHYB-type phytochrome gene: they have elongated hypocotyls in red light, but are not elongated as adult plants. Plant J. 12, 1091-1101.

* equal contributors