Professor, Bioengineering 308C Stanley Hall  mailcode: MC 1762  (510) 642-9932  fax: (510) 642-5835  Lab home page: Berkeley Phylogenomics Group

Research Interests

My research focus is the development of novel 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

Brown DP, Krishnamurthy N, Sjölander K, "Automated Protein Subfamily Identification and Classification," PLoS Computational Biology 2007, 3(8): e160 doi:10.1371/journal.pcbi.0030160.

Jake Gunn Glanville, Dan Kirshner, Nandini Krishnamurthy and Kimmen Sjölander, "Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis," Nucleic Acids Research 2007; doi:10.1093/nar/gkm325. 

Nandini Krishnamurthy, Duncan Brown and Kimmen Sjölander, "FlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function", BMC Evolutionary Biology 2007, 7 Suppl 1:S12 doi:10.1186/1471-2148-7-S1-S12.

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

Sjölander, K., "Phylogenomic inference of protein molecular function: advances and challenges," Bioinformatics 2004 (20)2:170-179. Oxford University Press access.

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

Venter, C. et al., "The sequence of the human genome," Science, 2001 Feb 16;291(5507):1304-51. (My contributions: the algorithms used for the Panther HMM library construction and functional classification of the human genome. (1) FlowerPower clustering and alignment of homologs; (2) Bayesian Evolutionary Tree Estimation and subfamily identification; (3) Subfamily HMM construction.) Science Online access.

Personal Home Page

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