UW Genome Sciences

Research:

The Borenstein lab is broadly interested in the integration of systems biology approaches, in-silico modeling, and computational metagenomics to address fundamental questions in microbial ecology and in human microbiome research. Our long term goal is to gain a systems-level principled understanding and to develop predictive models of complex microbial ecosystems, specifically those that inhabit the human body. We develop novel computational methods for studying these complex biological systems and for analyzing related high-throughput data. We aim to harness such methods not only for basic research of these complex systems but also for introducing translational applications in microbiome-based therapy with direct impact on human health. Specific research topics include:

Computational modeling and systems biology of the human microbiome. 
Species interaction, community structure, and assembly rules of microbial communities. 
Computational metagenomics and methods development. 
Large scale computational study of biological networks and their evolution

Selected Publications:

Carr R, Shen-Orr SS, and Borenstein E (2013) Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution. PLoS Computational Biology, PLoS Computational Biology, 9(10).

Levy R, and Borenstein E (2013) Metabolic Modeling of Species Interaction in the Human Microbiome Elucidates Community-Level Assembly Rules. PNAS (Proc. Natl. Acad. Sci. USA), PNAS (Proc. Natl. Acad. Sci. USA), 110(31), 12804-12809.

Greenblum S, Chiu HC, Levy R, Carr R, and Borenstein E (2013) Towards a Predictive Systems-Level Model of the Human Microbiome: Progress, Challenges, and Opportunities. Current Opinion in Biotechnology, 24, 810-820.

Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E*, and Stamatoyannopoulos JA* [* co-corresponding authors] (2012) Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150(6), 1274-1286.

Borenstein E (2012) Computational systems biology and in silico modeling of the human microbiome. Briefings in Bioinformatics, 13(6), 769-780.

Greenblum S, Turnbaugh P, and Borenstein E. Metagenomic Systems Biology of the Human Gut Microbiome Reveals Topological Shifts Associated with Obesity and IBD. PNAS (Proc. Natl. Acad. Sci. USA), 109(2), 594-599, 2012.

Borenstein E and Feldman MW (2009) Topological signatures of species interactions in metabolic networks, Journal of Computational Biology, 16(2), 191-200.

Borenstein E, Kupiec M, Feldman MW, and Ruppin E (2008). Large-Scale Reconstruction and Phylogenetic Analysis of Metabolic Environments. PNAS (Proc. Natl. Acad. Sci. USA), 105(38), 14482-14487.

Kreimer A*, Borenstein E*, Gophna U, and Ruppin E [*equal contribution](2008) The Evolution of Modularity in Bacterial Metabolic Networks. PNAS (Proc. Natl. Acad. Sci. USA), 105(19), 6976-6981.

Borenstein E and Ruppin E (2006) Direct Evolution of Genetic Robustness in MicroRNA. PNAS (Proc. Natl. Acad. Sci. USA), 103(17), 6593-6598.

additional publication listings available via PubMed