Large-scale efforts in genome sequencing have elucidated much of the "parts list" for thousands of species, but a general description of how genes collectively interact to produce functioning systems eludes us. We use statistical analysis of genome sequences drawn from thousands of organisms to distill out general patterns describing the organization of cellular systems. These statistical models are then tested for their ability to explain, predict, and design cellular behaviors in the lab.
Kim is a Moore Investigator in Data-Driven Discovery. She completed a PhD in biophysics at UC Berkeley with Dr. Tracy Handel, where she studied the computational design of protein-protein interfaces. As a postdoctoral researcher, she developed a model for the evolution of new allosteric regulation and experimentally tested the idea of allosteric "hot spots" with Dr. Rama Ranganathan (at UT Southwestern).
- evolution and engineering of cellular systems
- protein regulation and inter-protein communication
- statistical analysis of genomes and prediction of functional interactions
- An evolutionary module in central metabolism
- Schober AF, Ingle C, Park JO, Chen L, Rabinowitz JD, Junier I, Rivoire O, Reynolds KA BioRXiv 2017
- Evolution-Based Functional Decomposition of Proteins.
- Rivoire O, Reynolds KA, Ranganathan R PLoS Comput. Biol. 2016 Jun 12 6 e1004817
- Hot spots for allosteric regulation on protein surfaces.
- Reynolds KA, McLaughlin RN, Ranganathan R Cell 2011 Dec 147 7 1564-75
- Conserved amino acid networks modulate discrete functional properties in an enzyme superfamily.
- Narayanan C, Gagné D, Reynolds KA, Doucet N Sci Rep 2017 Jun 7 1 3207
- An evolution-based strategy for engineering allosteric regulation.
- Pincus D, Resnekov O, Reynolds KA Phys Biol 2017 Apr 14 2 025002
- Evolution-based design of proteins.
- Reynolds KA, Russ WP, Socolich M, Ranganathan R Meth. Enzymol. 2013 523 213-35
- Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface.
- Reynolds KA, Hanes MS, Thomson JM, Antczak AJ, Berger JM, Bonomo RA, Kirsch JF, Handel TM J. Mol. Biol. 2008 Oct 382 5 1265-75
- An object-oriented library for computational protein design.
- Chowdry AB, Reynolds KA, Hanes MS, Voorhies M, Pokala N, Handel TM J Comput Chem 2007 Nov 28 14 2378-88
- Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface.
- Reynolds KA, Thomson JM, Corbett KD, Bethel CR, Berger JM, Kirsch JF, Bonomo RA, Handel TM J. Biol. Chem. 2006 Sep 281 36 26745-53