Who are we?
We are a laboratory in the Crop Sciences department at the University of Illinois, Urbana-Champaign.
We work together with other departments and centers on campus in a number of collaborative projects.
GC See also Matthew Hudson’s faculty page
What do we do?
We work in computational biology, bioinformatics, high-performance computing, genome sequencing, and molecular biology.
We develop and implement computational tools to allow us and others to analyze large datasets common in modern biology.
Our focus is to combine these techniques to try to understand more about crop plants, crop breeding, and genetics.
Mass Sequencing
Download Polistes wasp 454 EST data
(unigenes)
Download Polistes wasp 454 EST data
(all raw sequence reads)
Crop Plant Biology: Research Projects
We have projects on several aspects of crop plant biology, including disease resistance, heterosis, biomass production, phytochrome mediated seedling development and canopy development. We also work with organisms associated with crops, such as pollinators, root-associated fungi and pathogens.
Heterosis is essentially the same as “hybrid vigor”, a key aspect of breeding and yield in many crops
Phytochrome is a plant photoreceptor, that allows plants to perceive light in the red and far-red region of the spectrum.
We will have more introduction to this subject soon, in the meantime for heterosis click here and for phytochrome click here to learn more.
Web Tools
Arabidopsis Promoter Element Discovery Tools
New Degenerate
New degenerate promoter element search method
elefinder
Looks for already known motifs, gives statistical significance scores
Promoter Retrieval Tool
The first two tools need sets of 2kb promoters, get these from the promoter retrieval tool
Original Sift Method
Now available as a website (Hudson et al., 2003), for gene lists
Promoter Retrieval
For gene lists
Old Sift Script
Download old Sift script
FASTA and BLAST searches are currently available to collaborators only.
Downloads
Looking for the web-based promoter element search tool?
Download sift package from Hudson and Quail, 2003 (contains Perl scripts and a promoter database):
Opportunities
Coming Soon!
Publications
2011
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
2010
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
2009
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
2008
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.
2007
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
People
PI
Matt Hudson
mhudson (@uiuc.edu)
Tel. 217 244 8096, fax 217 333 8046
334 NSRC,
1101 W. Peabody Dr.
Urbana IL 61801 USA
Job Title
Kankshita Swaminathan
kank (@uiuc.edu)
Tel. 217 265 6988, fax 217 333 8046
Job Title
Indrajit Kumar
ikumar2 (@uiuc.edu)
Tel. 217 265 6988, fax 217 333 8046
325 NSRC,
1101 W. Peabody Dr.
Urbana IL 61801 USA
Job Title
Christina Fliege
cfliege2 (@uiuc.edu)
190 NSRC,
1101 W Peabody Dr.
Urbana
IL 61801
USA
Job Title
Gopal Battu
gbattu (@illinois.edu)
Tel. 217 265 6988, fax 217 333 8046
190 NSRC,
1101 W. Peabody Dr.
Urbana
IL 61801
USA
Job Title
Mohammad B Belaffif
belafif2 (@illinois.edu)
Tel. 217 265 6988, fax 217 333 8046
190 NSRC,
1101 W. Peabody Dr.
Urbana
IL 61801
USA
Job Title
Tong Geon Lee
agrospel (@illinois.edu)
Tel. 217 265 6998, fax 217 333 8046
190 NSRC,
1101 W. Peabody Dr.
Urbana
IL 61801
USA
Alumni
Job Title
Kathleen M Keating
kmkeati2 (@illinois.edu)
Tel. 217 265 6988, fax 217 333 8046
Job Title
Luda Yafremava
lsy (@illinois.edu)
Tel. 217 265 6998, fax 217 333 8046
190 NSRC,
1101 W. Peabody Dr.
Urbana
IL 61801
USA
Job Title
Magdy S. Alabady
msalabad (@illinois.edu)
Tel. 217 265 6998, fax 217 333 8046
190 NSRC,
1101 W. Peabody Dr.
Urbana
IL 61801
USA
Job Title
Radhika Khetani
rkhetani (@igb.uiuc.edu)
Tel. 217 333 2448, fax 217 333 8046
2112 IGB,
1206 W. Gregory Dr.
Urbana
IL 61801
USA
Job Title
Wendy
hwin2 (@uiuc.edu)
Tel. 217 265 6988, fax 217 333 8046
325 NSRC,
1101 W. Peabody Dr.
Urbana
IL 61801
USA
Courses
CPSC 565: Perl and Unix for Bioinformatics
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean ullamcorper lobortis purus, in tincidunt sem finibus id. Mauris pulvinar justo sed aliquam feugiat. Maecenas a orci vitae leo laoreet mollis in ac erat. Quisque eget efficitur ex, lobortis congue nibh. Maecenas tempor tellus eget massa facilisis dictum. Ut pulvinar felis at turpis pulvinar maximus. Aliquam erat volutpat.
CPSC 265: Genetic Engineering Laboratory
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Aenean ullamcorper lobortis purus, in tincidunt sem finibus id. Mauris pulvinar justo sed aliquam feugiat. Maecenas a orci vitae leo laoreet mollis in ac erat. Quisque eget efficitur ex, lobortis congue nibh. Maecenas tempor tellus eget massa facilisis dictum. Ut pulvinar felis at turpis pulvinar maximus. Aliquam erat volutpat.
Links
A
- AlignACE (Cambridge, MA)
- Arabidopsis Gene Regulatory Information Server (Columbus, OH)
B
- BII (BioInformatics Institute, Singapore)
- BIMAS (NIH BioInformatics & Molecular Analysis Section)
- The Barton Group (University of Dundee, Scotland)
- Bioinformatics & Evolutionary Genomics (Ghent, Belgium)
- Bioinformatics Centre (University of Pune, India)
- Bioinformatics Research Centre, University of Glasgow (Scotland)
- Blueprint (Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto)
- Brutlag Bioinformatics Group (Stanford University, CA)6d
C
- CBCB (Center for Bioinformatics and Computational Biology)
- CMS Molecular Biology Resource (San Diego Supercomputing Center)
- Community Sequencing Program (Department of Energy / Joint Genome Institute)
- Computational Biology Research Center (National Institute of Advanced Industrial Science and Technology, Japan)
- Computational Molecular Biology at NIH (Bethesda, Maryland)
E
G
- Gene Ontology Consortium
- Genome Institute of Singapore
- Genome Sciences Centre (BC Cancer Agency, Vancouver)
- Gerstein Group (Yale University)
H
- Harvard – Lipper Center for Computational Genomics (Harvard Medical School)
- Helmholtz Network for Bioinformatics (Germany)
- Human Genome Center (Institute of Medical Science, University of Tokyo)
I
- IGB (University of California Institute for Genomics and Bioinformatics)
- ISREC (Swiss Institute for Experimental Cancer Research)
- Insititute of Medical Technology Bioinformatics Group (University of Tampere, Finland)
J
- JCSG (Joint Center for Structural Genomics – Stanford, UCSD and Scripps Institute)
- Japanese Society for Bioinformatics (Kyoto University, Japan)
- Jim Kent’s Website (Santa Cruz, CA)
L
- Leeds Bioinformatics Group (University of Leeds, UK)
- Linnaeus Centre for Bioinformatics (Uppsala, Sweden)
M
- MaizeGDB (Ames, IA)
- MRC Laboratory of Molecular Biology (Cambridge, UK)
N
O
- OGMP Informatics Division (Organelle Megasequencing Program, Canada)
- Oak Ridge National Laboratory – Computational Biosciences Section (Oak Ridge, Tennessee)
P
- PGA Directory (Programs for Genomic Applications, NHLBI)
- PlantCARE (Ghent, Belgium)
- Protein Structure Prediction Center (Lawrence Livermore Laboratory, CA)
Q
- QB3 (Institute for Bioengineering, Biotechnology and Quantitative Biomedical Research, CA)
S
- SANBI – South African National Bioinformatics Institute (University of the Western Cape)
- SIB – Swiss Institute for Bioinformatics (Geneva, Switzerland)
- SocBiN (Society for Bioinformatics in the Nordic Countries)
- Sonnhammer Bioinformatics Group (Karolinska Institute, Sweden)
T
- The Arabidopsis Information Resource (Stanford, CA)
- TBR (Human Genome Mapping Project Resource Centre, UK)
- The Jackson Laboratory (Maine)
- The Virtual Institute of Bioinformatics (Eire) (Ireland)
U
- UCL Bioinformatics Unit (University College London)
- UCLA Bioinformatics Institute
- UCSC Bioinformatics (Santa Cruz, CA)
- UC Center for Genomics and Bioinformatics (University of Cincinnati, OH)
- UMBER (University of Manchester, UK)
W
- WEHI Genetics and Bioinformatics Group (The Walter and Eliza Hill Institute, Australia)
- WIS Bioinformatics and Biological Computing (Weizmann Institute)
Contact Us
- Turner Hall, 1102 S Goodwin Ave, Urbana, IL 61801
- mhudson@illinois.edu
- (217) 244-8096