My group is interested in using genetic, genomic, and proteomic data to understand and model the biology of cancer and to develop methods to effectively deploy therapeutic agents in the age of personalized medicine. The group collaborates extensively with researchers from Berkeley Lab, UC Berkeley, and UCSF in this work.
Cancer Genomics. My group participates in numerous collaborations to understand the effects of genomic dysregulation in cancer. These efforts include development of new methodologies for identifying aberrations in the cancer genome, systematic integration of multiple genomic data types (copy number, expression, and mutation) to better understand the process by which cancer develops, and the application of cell line systems as models for the genetic heterogeneity within cancers. We are funded in these efforts by the NCI Integrative Cancer Biology Program (icbp.nci.nih.gov/), The Cancer Genome Atlas (cancergenome.nih.gov), the Bay Area Breast SPORE, and collaborations with private industry.
Modeling of Signaling Systems. In collaboration with Terry Speed, and Sach Mukherjee the group is developing methods for computationally modeling the signaling that occurs in cancer cells. The idea behind the current work is to create Bayesian estimates of signaling systems from both dynamic and static signaling processes.
Cancer Bioinformatics.My group also supports data redistribution for numerous LBL and UCSF efforts such as the UCSF Bay Area Breast SPORE and collaborations between Dr Gray’s group and private industry. We focus on practical methods for sharing data using open source technologies such as extensions to Java TreeView that allow heat-map based visualization of genomic data.
The Cancer Genome Atlas Research Network; Lawrence Berkeley National Laboratory, Spellman PT, Purdom E, Jakkula LR, Lapuk AV, Marr H, Dorton S, Gi Choi Y, Han J, Ray A, Wang V, Durinck S, Robinson M, Wang NJ, Vranizan K, Peng V, Van Name E, Fontenay GV, Ngai J, Conboy JG, Parvin B, Feiler HS, Speed TP, Gray JW; Nature. 2008 Sep 4., PMID: 18772890.
Y. Wang, M. Moorhead, G. Karlin-Neumann, N. Wang, J. Ireland, S. Lin, C. Chen, L.M. Heiser, K. Chin, L. Esserman, J.W. Gray, P.T. Spellman., M. Faham. Performance of Molecular Inversion Probes (MIP) in Allele Copy Number Determination. Genome Biology. 8:R246, 2007.
A.R. Jones, M. Miller, R. Aebersold, R. Apweiler, C.A. Ball, A. Brazma, J. Degreef, N. Hardy, H. Hermjakob, S.J. Hubbard, P. Hussey, M. Igra, H. Jenkins, R.K. Julian, K. Laursen, S.G. Oliver, N.W. Paton, S.A. Sansone, U. Sarkans, C.J. Stoeckert, C.F. Taylor, P.L. Whetzel, J.A. White, P. Spellman, A. Pizarro. The Functional Genomics Experiment model (FuGE): an extensible framework for standards in functional genomics. Nat. Biotechnology. 25:1127-33, 2007.
R.M. Neve, K. Chin, J. Fridlyand, J. Yeh, F.L. Baehner, T. Fevr, L. Clark, N. Bayani, J.P. Coppe JP, F. Tong, T. Speed, P.T. Spellman, S. DeVries, A. Lapuk, N.J. Wang, W.L. Kuo, J.L. Stilwell, D. Pinkel, D.G. Albertson, F.M. Waldman, F. McCormick, R.B. Dickson, M.D. Johnson, M. Lippman, S. Ethier, A. Gazdar, J.W. Gray. A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes. Cancer Cell. 6:515-27, 2006.
K. Chin K, S. DeVries, J. Fridlyand, P.T. Spellman, R. Roydasgupta, W.L. Kuo, A. Lapuk, R.M. Neve, Z. Qian, T. Ryder, F. Chen, H. Feiler, T. Tokuyasu, C. Kingsley, S. Daikree, Z. Meng, K. Chew, D. Pinkel, A. Jain, B.M. Ljung, L. Esserman, D.G. Albertson, F.M. Waldman, J.W. Gray. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 6:529-41, 2006.
E. De Gregorio, P. T. Spellman, P. Tzou, G. M. Rubin and B. Lemaitre. The Toll and Imd pathways are the major regulators of the immune response in Drosophila. Embo Journal 21: 2568-79, 2002.
P. T. Spellman, M. Miller, J. Stewart, C. Troup, U. Sarkans, S. Chervitz, D. Bernhart, G. Sherlock, C. Ball, M. Lepage, M. Swiatek, W. L. Marks, J. Goncalves, S. Markel, D. Iordan, M. Shojatalab, A. Pizarro, J. White, R. Hubley, E. Deutsch, M. Senger, B. J. Aronow, A. Robinson, D. Bassett, C. J. Stoeckert, Jr. and A. Brazma. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biology 3: RESEARCH0046, 2002.
E. De Gregorio, P. T. Spellman, G. M. Rubin and B. Lemaitre. Genome-wide analysis of the Drosophila immune response by using oligonucleotide microarrays. Proceedings of the National Academy of Sciences, U.S.A. 98: 12590-5, 2001.
G. Zhu, P.T. Spellman, T. Volpe, P. O. Brown, D. Botstein, T. N. Davis and B. Futcher. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 406: 90-4, 2000.
P.T. Spellman, G. Sherlock, M. Q. Zhang, V. R. Iyer, K. Anders, M. B. Eisen, P. O. Brown, D. Botstein and B. Futcher. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9: 3273-97, 1998.
M. B. Eisen, P.T. Spellman, P. O. Brown and D. Botstein. Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences, U.S.A. 95: 14863-8, 1998.