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. In recent work, we have used statistical sequence analysis to re-wire kinase signalling pathways, and to understand genetic interactions in folate metabolism. We are particularly interested in the idea that cellular systems might be decomposed into simpler, modular building blocks.
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).

Research Interest

  • evolution and engineering of cellular systems
  • protein regulation and inter-protein communication
  • statistical analysis of genomes and prediction of functional interactions


Featured Publications LegendFeatured Publications

High-Order Epistasis in Catalytic Power of Dihydrofolate Reductase Gives Rise to a Rugged Fitness Landscape in the Presence of Trimethoprim Selection.
Tamer YT, Gaszek IK, Abdizadeh H, Batur TA, Reynolds KA, Atilgan AR, Atilgan C, Toprak E, Mol. Biol. Evol. 2019 Jul 36 7 1533-1550
An evolution-based strategy for engineering allosteric regulation.
Pincus D, Resnekov O, Reynolds KA Phys Biol 2017 Apr 14 2 025002
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