Kimmen Sjölander

Associate Professor, Bioengineering Core Member, UCB/UCSF Graduate Group in Bioengineering 308C Stanley Hall mailcode: MC 1762 (510) 642-9932 fax: 510-642-5835 This e-mail address is being protected from spambots. You need JavaScript enabled to view it http://phylogenomics.berkeley.edu/ Membership effective July 2001

Research Interests

My research focus is the application of computational methods for biological discovery.

Research Summary

I am primarily interested in phylogenetic tree reconstruction, remote homolog recognition, protein structure prediction, subfamily classification, prediction of critical positions in molecules, multiple sequence alignment, protein-protein interaction, pathway inference, computational prediction of protein domain structure, and other aspects of protein function and structure. The medical applications of genomics and bioinformatics, for the detection of genes involved in disease, or conferring virulence to microbes, and similar problems, is a particular area of interest. My experience in industry, prior to re-joining academia, made me aware of many of the issues confronting scientists working on target and drug discovery, and I have various research interests in these areas as well.

Selected Publications

Venter, C. et al, "The sequence of the human genome," Science, 2001 Feb 16;291(5507):1304-5

Edgar, R., and Sjölander, K., "SATCHMO: Sequence Alignment and Tree Construction using Hidden Markov models," Bioinformatics. 2003 Jul 22;19(11):1404-11. Selected by the Faculty of 1000 as a "Must Read" for Technological Advance (rating 6.0).

Nandini Krishnamurthy, Duncan Brown, Dan Kirshner and Kimmen Sjölander, "PhyloFacts: An online structural phylogenomic encyclopedia for protein functional and structural classification", Genome Biology 2006, 7:R83

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy and Kimmen Sjölander, "Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis," Nucleic Acids Research 2007

Brown DP, Krishnamurthy N, Sjölander K, "Automated Protein Subfamily Identification and Classification," PLoS Computational Biology 2007, 3(8)