I am a Sloan/DOE Postdoctoral Fellow in Computational Molecular Biology with a background in both Computer Science and Molecular Biology. This Genome Scholar Development and Faculty Transition Award will, during the development phase in Michael Levitt's group at Stanford, provide training and research experience in the application of computational methodologies to genome analysis. This will prepare me for the Faculty Transition phase, which directly supports my goal of establishing an innovative and productive independent group focused on computational molecular biology and genomics. The Award will provide resources allowing me to develop a research program in genome analysis as the human genome sequence is completed, structural genomics blossoms, and many other functional genomics data first become available. The principal research aim is to develop computational methods for structural and functional genomics, using the genome both as a base for investigation and as a resource to help answer biological questions. Structural genomics projects attempt to provide an experimental structure or a good theoretical model for every protein in all completed genomes. My work will involve organizing proteins into families according to homology, predicting structure from homology and constructing coordinate models, maintaining an information resource for structural genomics, developing methods for selection of proteins for experimental characterization, and analyzing solved structures to detect homologies and functional information. The computational functional genomics aspect of this project will primarily involve moving beyond pairwise sequence comparison in order to achieve reliable functional annotation of complete genomes. This includes the use of gene genealogies to trace gene histories and functional divergences, and """"""""reverse genomics"""""""" comparison of multiple complete genomes to locate genes associated with characterized cellular or biochemical functions. I also plan to quantitatively combine sequence comparison with expression and other experimental functional data to improve computational molecular and cellular functional characterization.

National Institute of Health (NIH)
National Human Genome Research Institute (NHGRI)
Career Transition Award (K22)
Project #
Application #
Study Section
Ethical, Legal, Social Implications Review Committee (GNOM)
Program Officer
Felsenfeld, Adam
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Berkeley
Other Basic Sciences
Schools of Earth Sciences/Natur
United States
Zip Code
Muratore, Kathryn E; Engelhardt, Barbara E; Srouji, John R et al. (2013) Molecular function prediction for a family exhibiting evolutionary tendencies toward substrate specificity swapping: recurrence of tyrosine aminotransferase activity in the I? subfamily. Proteins 81:1593-609
Bouchard-Cote, Alexandre; Jordan, Michael I (2013) Evolutionary inference via the Poisson Indel Process. Proc Natl Acad Sci U S A 110:1160-6
Engelhardt, Barbara E; Jordan, Michael I; Srouji, John R et al. (2011) Genome-scale phylogenetic function annotation of large and diverse protein families. Genome Res 21:1969-80
Pastuszak, Alexander W; Joachimiak, Marcin P; Blanchette, Marco et al. (2011) An SF1 affinity model to identify branch point sequences in human introns. Nucleic Acids Res 39:2344-56
Lareau, Liana F; Brooks, Angela N; Soergel, David A W et al. (2007) The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv Exp Med Biol 623:190-211
Yooseph, Shibu; Sutton, Granger; Rusch, Douglas B et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5:e16
Smith, Andrew; Chandonia, John-Marc; Brenner, Steven E (2006) ANDY: a general, fault-tolerant tool for database searching on computer clusters. Bioinformatics 22:618-20
Chandonia, John-Marc; Kim, Sung-Hou; Brenner, Steven E (2006) Target selection and deselection at the Berkeley Structural Genomics Center. Proteins 62:356-70
Stefan, Liliana R; Zhang, Rui; Levitan, Aaron G et al. (2006) MeRNA: a database of metal ion binding sites in RNA structures. Nucleic Acids Res 34:D131-4
Chandonia, John-Marc; Brenner, Steven E (2006) The impact of structural genomics: expectations and outcomes. Science 311:347-51

Showing the most recent 10 out of 33 publications