Faculty Profiles

Daniel Segré

Daniel Segrè

Associate Professor of Biology, Bioinformatics and Biomedical Engineering

PhD, Weizmann Institute of Science, Israel, 2002
Areas of interest: systems biology, evolution of biochemical networks, genomics, metabolic engineering, microbial ecology
(617) 358-2301

Current Research

We develop theoretical approaches and computational models for the study of complex biological networks. We are especially interested in the dynamics and evolution of metabolism, whose complex web of small-molecule transformations underlies fundamental aspects of biological organization, from energy transduction to cell-cell communication. In addition to helping understand how biological systems function and evolve, we seek to apply our methods to the design and optimization of engineered networks for bioenergy and biomedicine applications.

Courses Taught

  • BE 777 Computational Genomics
  • BF 821 Bioinformatics Seminar
  • BF 571 Dynamics and Evolution of Biological Networks

Selected Publications

  • Klitgord N, Segre D (2010). Environments that induce synthetic microbial ecosystems. PLoS Computational Biology, 6(11): e1001002.
  • Riehl WJ, Krapivsky P, Redner S, SegreD (2010). Signatures of Arithmetic Simplicity in Metabolic Network Architecture. PLoS Computational Biology, 6(4): e1000725.
  • Mazumdar V, Snitkin E, Amar S, Segre D (2009). Metabolic network model of a human oral pathogen. Journal of Bacteriology, Jan; 191(1), 74-90.
  • Snitkin ES, Dudley AM, Janse DM, Wong K, Church GM, Segre D (2008). Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biology, 9:R140.
  • Wright MA, Kharchenko P, Church GM, Segrè D. (2007). Chromosomal periodicity of evolutionarily conserved gene pairs, Proc. Natl. Acad. Sci. USA, 104 (25), 10559-10564.
  • Raymond J, Segrè D. (2006). The effect of oxygen on biochemical networks and the evolution of complex life, Science, 311, 1764-1767.
  • Segrè D, De Luna A, Church GM, Kishony R. (2005). Modular epistasis in yeast metabolism, Nature Genetics, 37(1), 77-83.
  • Segrè D, Vitkup D, Church GM. (2002). Analysis of optimality in natural and perturbed metabolic networks, Proc. Natl. Acad. Sci. USA, 99(23), 15112-15117.
  • Segrè D, Ben-Eli D, Deamer DW, Lancet D. (2001). The Lipid World, Origins of Life and Evolution of the Biosphere, 31, 119-145.