University of Pittsburgh

Welcome to the Clark lab

   Department of Computational and Systems Biology
   University of Pittsburgh

Molecular Co-evolution

Our overarching goal is to understand how the functions of proteins and their networks change over time. We are particularly focused on the process of co-evolution within functional networks and the ways by which proteins influence each other during evolution. We study a variety of organisms ranging from single cells to primates. Currently we perform experiments in yeast and bacteria to retrace the evolution of protein function, while our computational studies are based in yeast species, Drosophila, and mammals.

Specific Research Topics

Convergent Evolution

A powerful way to identify the genetic regions underlying a particular phenotype is to study groups of species that independently adopted that phenotype. We develop and apply comparative genomics methods that use phenotypic convergence to discover genes and regulatory regions related to a phenotype.

Evolution of Female-Male Interactions in the Cabbage White Butterfly

Post-copulatory interactions between males and females have been shaped by a complex set of competitive and conflictive forces, resulting in specialized male and female traits.

Evolutionary Rate Covariation (ERC)

ERC is a phylogenetic signature that reflects co-functionality between genes. We develop genome-wide datasets of ERC to provide co-evolutionary predictions and to interpret major functional shifts during evolution.
ERC Analysis webserver

For further reading visit our research page.

Lab News

Wynn Meyer et al. publish in Science
Posted August 2018
Ancient convergent losses of Paraoxonase 1 yield potential risks for modern marine mammalsFeatered in the New York Times, The Atlantic, National Geographic, Le Monde, and 30 other publications around the world. Congrats!
Melissa Receives Mellon Fellowship
Posted April 2018
Melissa Plakke, PhD Candidate in the lab, has been awarded the Mellon Fellowship for next academic year. She also won a Presentation Award at the Pitt Grad Expo. Way to go, Melissa!
Jerrica selected for Mentor-Mentee Summer Program
Posted March 2018
Long-time lab undergraduate, Jerrica Jamison, was selected for this competitive summer program, during which she will continue her research in seals, sea lions, and other pinnipeds.
Convergent Evolution in Subterranean Mammals
Posted Oct 2017
Moles and mole-rats experienced similar changes to their genomes underground. Here we identify new ocular genes and eye-specific regulatory sequences.
Write-up in the Atlantic
Posted June 2017
This common butterfly has an extraordinary sex life. Males and female butterflies are intertwined in a strange co-evolutionary struggle.
We can be found at:

University of Pittsburgh School of Medicine
3501 Fifth Avenue
Biomedical Science Tower 3
Room 10054
Pittsburgh, PA 15260

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