JCVI: About / Bios / Shibu Yooseph
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Shibu Yooseph, Ph.D.

Research Interests and Accomplishments

Shibu Yooseph's main research interest is in designing algorithms for solving problems in computational biology. He currently works on the analysis and interpretation of metagenomic sequence data, with a goal to assess microbial diversity. His research interests also include phylogenetics, sequence analysis, clustering, synthetic genomics, proteomics, and SNP analysis.

He received his Bachelor of Technology in Computer Science and Engineering in 1992 from the Institute of Technology, Banaras Hindu University, India, and his Ph.D. in Computer and Information Science in 1997 from the University of Pennsylvania. He was a postdoctoral fellow at the Center for Discrete Mathematics and Theoretical Computer Science (DIMACS), Rutgers University from 1997-98. He was also a consultant at Lucent Technologies (Bell Labs), Murray Hill during this period. From 1998-2000 he was a research associate in the Department of Mathematics at the University of Southern California. Following that, he was a computer scientist in the Informatics Research Group at Celera Genomics and Applied Biosystems, during which time he contributed to the mouse genome project and also to the functional genomics and proteomics efforts. He joined the Institute for Biological Energy Alternatives (now JCVI) in 2003.

In addition to his research, he has contributed to science research support and education. He has been a reviewer for several journals and conferences, including Journal of Computational Biology, Bioinformatics, and Annual International Conference on Computational Molecular Biology (RECOMB). He has also organized several symposiums and workshops in the past, including DIMACS Workshop on Analysis of Gene Expression Data and DIMACS Minisymposium on Advances in Phylogenetics Inference Methods.

Select Publications

Brim H, Yooseph S, et al.
Microbiome Analysis of Stool Samples from African Americans With Colon Polyps.

PloS One. 2013 Jan 01; 8: e81352.[more]

Yooseph S, Li W, et al.
Gene Identification and Protein Classification in Microbial Metagenomic Sequence Data via Incremental Clustering.

BMC Bioinformatics. 2008 Apr 01; 9(1): 182.[more]

Williamson, S. J., Rusch, D. B., et al.
The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses Within Aquatic Microbial Samples

PLoS ONE. 2008 Jan 23; 3(1): e1456.[more]

Kannan, N., Wu, J., et al.
Evolution of Allostery In the Cyclic Nucleotide Binding Module

Genome Biol. 2007 Dec 12; 8(12): R264.[more]

Rusch, D. B., Halpern, A. L., et al.
The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic Through Eastern Tropical Pacific

PLoS Biol. 2007 Mar 13; 5(3): e77.[more]

Yooseph S, Sutton G, et al.
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families.

PLoS Biology. 2007 Mar 01; 5(3): e16.[more]

Glass JI, Assad-Garcia N, et al.
Essential Genes of a Minimal Bacterium.

Proceedings of the National Academy of Sciences of the United States of America. 2006 Jan 10; 103(2): 425-30.[more]

Halldorsson, B.V., Bafna, V., et al.
A Survey of Computational Methods for Determining Haplotypes

Computational Methods for Snps and Haplotype Inference. 2004 Feb 14; 2983: 26-47.[more]