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

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.
Co-evolution's Witness -Feature Article
Posted Sept 2015
Our work on co-evolution signatures between disease genes was recently featured at PittMed. Along with our work with the Morehouse lab on butterfly reproductive proteins.
Featured on the Saccharomyces Genome Blog
Posted April 2015
Our recent paper on the evolution and function of the Shu complex was written up on the Saccharomyces Genome Database.
How do novel organs get their genes?
Posted March 2015
A derived butterfly reproductive organ, the bursa copulatrix, is a powerful model to study how new organ systems are equiped with their gene repertoire. Our new publication in MBE lays out the case for extensive gene borrowing.
ERC in Medical Genetics
Posted February 2015
Our recent publication in PLOS Genetics outlines ERC as a tool in disease gene discovery and validation.
Recommended Reading
Access the recommendation on F1000Prime
Posted January 2015
Our ERC publication with the Findlay and Wolfner labs was recently highlighed by Norman Johnson (UMass) on the Faculty of 1000 website.
Kaufman Foundation
Posted August 2014
We were recently awarded a Charles E. Kaufman Foundation New Investigator Grant to develop evolutionary signatures as a method to predict gene function. Abstracts and media coverage.
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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