Peter Freddolino

This page is no longer current. I recently joined the Department of Biological Chemistry at the University of Michigan. Please see my current research page for up-to-date information. The content below was last updated December 2014.

Postdoctoral Research Scientist, Joint Centers for Systems Biology

Contact

Russ Berrie Pavilion, Room 406
1150 St. Nicholas Avenue
New York, NY 10032
Email

Education

Ph.D. in Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 2009
B.S. with Honors in Biology, California Institute of Technology, 2004

Research Interests

I apply a combination of computational and experimental approaches in order to understand how cells sense and respond to their environment, with foci ranging from the molecular details of perception to the evolutionary basis for existing regulatory architectures. In the process, I make heavy use of microbial population genetics and systems biology tools, bioinformatic analysis, and molecular and atomistic-level simulations. Some of my current projects include:

Investigation of the phenotypic and evolutionary consequences of mutations to the bacterial transcription termination factor Rho
Identification of evolved instances of anticipatory regulation in bacterial populations and their link to the corresponding native habitat
Development of more efficient methods for measuring changes in cellular transcriptional regulatory state

Publications

Complete listing and citation information available on my Google Scholar profile

Most recent publications

Revealing the genetic basis of natural bacterial phenotypic divergence. Peter L. Freddolino, Hani Goodarzi, and Saeed Tavazoie. Journal of Bacteriology, in press, 2013. [pdf]
Bacterial Adaptation through Loss of Function. Alison K. Hottes, Peter L. Freddolino, Anupama Khare, Zachary N. Donnell, Julia C. Liu, and Saeed Tavazoie. PLoS Genetics, 9(7): e1003617, 2013. [html]
Signaling mechanisms of LOV domains: new insights from molecular dynamics studies. Peter L. Freddolino, Kevin H. Gardner, and Klaus Schulten. Photochemical and Photobiological Sciences, 12:1158-1170, 2013. [html]
The Dawn of Virtual Cell Biology. Peter L. Freddolino and Saeed Tavazoie. Cell, 150:248-250, 2012. [html]
Fitness landscape transformation through a single amino acid change in the Rho terminator. Peter L. Freddolino, Hani Goodarzi, and Saeed Tavazoie. PLoS Genetics, 8(5): e1002744, 2012. [html]
Beyond Homeostasis: A Predictive-Dynamic Framework for Understanding Cellular Behavior. Peter L. Freddolino and Saeed Tavazoie. Annual Review of Cell and Developmental Biology, 28:363-384, 2012. [html]

Most representative publications

Fitness landscape transformation through a single amino acid change in the Rho terminator. Peter L. Freddolino, Hani Goodarzi, and Saeed Tavazoie. PLoS Genetics, 8(5): e1002744, 2012. [html]
Challenges in protein-folding simulations. Peter L. Freddolino, Christopher B Harrison, Yanxin Liu, Klaus Schulten. Nature Physics, 6:751-758, 2010. [html]
Common structural transitions in explicit-solvent simulations of villin headpiece folding. Peter L. Freddolino and Klaus Schulten. Biophysical Journal, 97:2338-2347, 2009. [html]
Force field bias in protein folding simulations. Peter L. Freddolino, Sanghyun Park, Benoit Roux, and Klaus Schulten. Biophysical Journal, 96:3772-3780, 2009. [html]
Molecular dynamics simulations of the complete satellite tobacco mosaic virus. Peter L. Freddolino, Anton S. Arkhipov, Steven B. Larson, Alexander McPherson, and Klaus Schulten. Structure, 14:437-449, 2006. [html]
Predicted 3D structure for the human β2 adrenergic receptor and its binding site for agonists and antagonists.Peter L. Freddolino, M. Yashar S. Kalani, Nagarajan Vaidehi, Wely B. Floriano, Spencer E. Hall, Rene J. Trabanino, Victor Wai Tak Kam and William A. Goddard III. PNAS 101:2736-2741, 2004. [html]

Professional History

My CV (pdf)

2011-present: Postdoctoral research scientist, Tavazoie Lab, Joint Centers for Systems Biology, Columbia University
2009-2011: Postdoctoral research associate, Tavazoie Lab, Lewis-Sigler Institute for Integrative Genomics, Princeton University
2004-2009: Graduate research fellow, Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
Advisor: Klaus Schulten
Thesis Title: "Application of all-atom and coarse-grained molecular dynamics simulations to long timescale structural transitions of proteins"
2001-2004: Undergraduate research assistant, Department of Chemistry, California Institute of Technology
Advisor: William A. Goddard III

Awards

NIH K99/R00 Pathway to Independence Award (K99 2013-2015; pending R00 2015-2018)
Beckman Institute Graduate Fellowship (2008-2009)
NSF Graduate Research Fellowship (2004-2008)
UIUC Alumni Distinguished Fellowship (2004-2007)
Sigma Xi Award for Undergraduate Research (2004)
Caltech President's Scholarship (2000-2004)