Matthew E. Hudson

   Research Responsibilities and Goals

My research effort aims to combine bioinformatics with genetic and genomic techniques for the next generation of crop improvement. We are interested in the use of next-generation sequencing technology for crop plants and other non-model organisms. We also have research programs in bioinformatics, mechanism and evolution of transcriptional networks, light-regulated plant development, DNA binding proteins and regulatory DNA sequence.

   Professional experience

Assistant Professor	University of Illinois	2004 -
Bioinformatics Scientist	Diversa corporation, San Diego	2003 to 2004
Bioinformatics Specialist	Torrey Mesa Research Institute	2002 to 2003
Postdoctoral Fellow	University of California, Berkeley	1998 to 2002

   Education

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

   Publications

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.

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.

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

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