Gerard Manning Razavi-Newman Center for Bioinformatics manning@salk.edu
We, and all of modern life, are the results of over a billion years of evolutionary experimentation and selection carried out on our genomes. The current explosion of genome sequencing means that now, for the very first time, we can read out the results of these experiments and decipher the logic and diversity of sequence evolution.
We are exploring this rich, but still confusing trove of genome information using protein kinases, a set of genes that constitute about 2% of eukaryotic genes, but alter the behavior of up to 30% of all cellular proteins, and control the majority of biological pathways. They are among the most experimentally characterized of proteins and are a major class of drug targets.
By tracking the evolution of many classes of protein kinases in sequenced genomes, we aim to understand the evolutionary history of this group and relate that to organismal biology, and practical interventions in experimental research and medical therapies. They will also be used as a model system to understand the evolution and function of other gene families.
Other research interests include microbial genomics and metagenomics, and the comparative genomics of promoter sequences in vertebrates and model systems.
We also run a collaboration and support service to bring bioinformatics technologies to labs throughout the Salk, including research collaborations with several Salk investigators.
Education
B.Sc., First Class Honors, National University of Ireland, Cork
Ph.D., Stanford University
Selected Publications
Natarajan, K, Taylor, S, Zhai, Y, Venter, C, Manning, G (2007). Structure and function of the microbial kinome. PLoS Biol. 5(3): e17
Yooseph, S., G. Sutton, D.B. Rusch, S. Williamson, A.L. Halpern, K. Remington, J.A. Eisen, K. Heidelberg, G. Manning, W. Li, L. Jaroszewski, P. Cieplak, C. Miller, H. Li, S.T. Mashiyama, M. Joachimiak, C.v. Belle, J.-M. Chandonia, D. Soergel, Y. Zhai, K. Natarajan, S. Lee, B.J. Raphael, V. Bafna, R. Friedman, S.E. Brenner, A. Godzik, D. Eisenberg, J. Dixon, S. Taylor, M. Frazier, R. Strausberg and J.C. Venter (2007). The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families. PLoS Biology. 5(3): e16
Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science 314(5801):941-52.
Bradham, CA, Foltz, KR, Beane, WS, Arnone, MI, Rizzo, F, Coffman, JA, Mushegian, A, Goel, M, Morales, J, Geneviere, A, Lapraz, F, Robertson, AK, Kelkar, H, Loza-Coll, M, Townley, IK, Raisch, M, Rouz, MM, Legpage, T, Gache, C, McClay, DR, Manning, G. (2006). The Sea Urchin Kinome: A First Look. Dev. Biol. 300(1):180-93.
Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, Del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E.(2006). Shotgun sequencing and analysis of the macronuclear genome of the model eukaryote, the ciliate Tetrahymena thermophila.PLoS Biol. 4 (9): e286.
Schröfelbauer, B, Senger, T, Manning, G, Landau, NR. (2006). Alteration of HIV-1 Vif allows functional interaction with primate APOBEC3G. J. Virol. 80 (12), 5984-91.
Goldberg, JM, Manning, G, Liu, A, Fey, P, Pilcher, KE, Xu, Y, Smith, JL. (2006) The Dictyostelium Kinome – Analysis of the Protein Kinases from a Simple Model Organism. PloS Genet 2 (3): e38
Manning, G. (2005). Genomic overview of Protein Kinases (December 13, 2005), WormBook, ed. The C. elegans Research Community, WormBook, doi/10.1895/wormbook.1.60.1, http://www.wormbook.org
Caenepeel, S, Charydczak, G, Sudarsanam, S. Hunter, T., Manning, G. 2004. The Mouse Kinome: Discovery and comparative genomics of all mouse protein kinases. PNAS 101(32), 11707-12.
Manning, G, Whyte, D, Martinez, R. Hunter, T, Sudarsanam, S. 2002. The protein kinase complement of the human genome. Science 298:1912-1934.
Manning, G, Plowman, G, Hunter, T, Sudarsanam, S 2002. Evolution of protein kinase signaling from yeast to man. Trends in Biochemical Sciences 27(10), 514-20.
