We are focused on how cells adapt to changes in their environment. Several systems are under investigation including innate immunity in plants, pluripotency in stem cells, self-renewal in cancer cells (embryonal carcinoma and chronic lymphocytic leukemia), and environmental stress in microalgae. To facilitate these studies, we are developing and applying technology for peptide mass spectrometry to enable direct observations of protein dynamics and protein networks on a genome-wide scale. Much of our technology development is done in collaboration with Prof. Vineet Bafna and Prof. Pavel Pevzner in the department of Computer Science and Engineering at UCSD with whom we co-mentor students under the auspices of the IGERT Plant Systems Biology Training Grant and the Interdisciplinary Bioinformatics Program. Additional training opportunities are provided by the Center for Algorithmic and Systems Biology, by the San Diego Consortium for Systems Biology, and by the San Diego Center for Molecular Agriculture.
Singer T, Fan Y, Chang HS, Zhu T, Hazen SP, Briggs SP. A high-resolution map of Arabidopsis recombinant inbred lines by whole-genome exon array hybridization. PLoS Genetics 2:1352-1361, 2006.
Tanner S, Shen Z, Ng J, Florea L, Guigó R, Briggs SP, Bafna V. Improving gene annotation using peptide mass spectrometry. Genome Research 17: 231-239, 2007.
Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. Clustering millions of tandem mass spectra. J. Prot. Res. Jan. 7(1):113-122, 2008.
Tanner S, Payne SH, Dasari S, Shen Z, Wilmarth PA, David LL, Loomis WF, Briggs SP, Bafna V. Accurate annotation of peptide modifications through unrestrictive database search. J. Prot. Res. Jan. 7(1):170-181, 2008.
Bischof LJ, Kao CY, Los FC, Gonzalez MR, Shen Z, Briggs SP, van der Goot FG, Aroian RV. Activation of the unfolded protein response is required for defenses against bacterial pore-forming toxin in vivo. PLoS Pathogens Oct. 4(10):e1000176, 2008.
Bellafiore S, Shen Z, Rosso M-N, Abad P, Shih P, Briggs SP. Direct identification of the Meloidogyne incognita secretome reveals proteins with host cell reprogramming potential. PLoS Pathogens Oct. 4(10):e1000192, 2008.
Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. Discovery and revision of Arabidopsis genes by proteogenomics. Proc. Natl. Acad. Sci. USA (in press), 2008.
Steve Briggs received his Ph.D. from Michigan State University and spent the first half of his career in industry, most recently as Sr. Vice President for Corporate Research at Diversa. Previously he was President of Torrey Mesa Research Institute and before that he was Director at Pioneer/DuPont for several research areas including genomics. Briggs has been Co-editor of The Plant Cell; he serves on the Scientific Advisory Board, Keystone Symposia and the Board of Advisors, Plant Sciences Institute, Iowa State University; he is a member of the National Academy of Sciences.