Computational Systems Biology
at the University of Virginia


HS68 Fibroblast Crosstalk with Melanoma Public data from the study of crosstalk between HS68 fibroblast and melanoma.

Cowpea Genomics Initiative Cowpea genespace sequencing and analysis project

Cowpea Genespace Knowledgebase Data mining and tools to use the cowpea genespace reads. Includes BLAST annotations, SSRs, and downloads.

UVa OMSSA Web Introduction UVa's free, improved web interface to OMSSA

UVa OMSSA Web (password required)

TOBFAC: Tobacco Transcription Factors

Open source XLST scripts for use with OMSSA
OMSSA and pepXML XSLT scripts tar format
OMSSA and pepXML XSLT scripts zip format

Sites currently being developed. Not open to the public yet.
TOBGEN: Tobacco Genomics
COPFAC: Cowpea Transcription Factors


The North Carolina State University Tobacco Genomics Initiative data can be found at:
NCSU TGI data

We have used this data for several projects and wish to extend our thanks to Dr. Charlie Opperman and his team. The data is hosted at the NCSU Center for the Biology of Nematode Parasitism. At the PNGG web site you will find the tobacco (Nicotiana tabacum) gene space sequences (aka gene space reads), as well as .qual files, BACs and an assembly prepare by Dr. Betsy Scholl. The sequences are from libraries enriched by methyl filtration.

Cowpea and tobacco contacts

Dr. Mike Timko (Primary investigator, cowpea, tobacco) mpt9g@virginia.edu
Dr. Xianfeng Jeff Chen (Computational biologist) xc3m@virginia.edu
Dr. Paul Rushton (Senior scientist, tobacco, transcription factors) pr8y@virginia.edu
Marta Bokowiec (Scientist) mtb8u@virginia.edu
Jen Brannock (Scientist) jrf5s@virginia.edu
Tom Laudeman (Software engineer, bioinformatics, DBA, Linux sysadmin) twl8n@virginia.edu
Jim Roberts (Software engineer, bioinformatics, DBA, Linux and Windows sysadmin) jhr2b@virginia.edu