Edward Marcotte, Co-Director
The Marcotte Lab is engaged in the quantitative modeling of the behavior of cells and their constituents. Such models let us better define the functions of genes, and identify linkages between genes and diseases. We are also developing mass spectrometry methods for high-throughput proteomics, and high-throughput microscopy methods to measure protein sub-cellular locations and activities, both of which allow us to test and extend our network models. The work is evenly split between computational and experimental approaches for studying thousands of genes/proteins in parallel. We expect that this type of approach will lead to the development of predictive, rather than descriptive, theories of biology. Learn more >
Vishwanath Iyer, Co-Director
Research in The Iyer Lab is aimed at understanding how gene expression is regulated on a genome-wide scale. We employ genomic, molecular, and computational approaches to study important aspects of global regulators and to reconstruct the transcriptional control of stress responses. These studies involve gene expression profiling, chromatin immunoprecipitation, and computational analyses in yeast and human cells. We are also using genomic approaches to study global gene regulation at the post-transcriptional stage. Learn more >
Andrew Ellington, Associate Director
The Ellington Lab is interested in the evolutionary engineering of molecules, pathways, and organisms, and the application of these methods to real-world problems. In particular, we evolve functional RNA molecules to serve as diagnostic and therapeutic reagents, including those that inhibit the replication of HIV-1 and the growth of tumor cells. We combine these functional RNAs and other components into synthetic genetic circuits that can be used to control gene expression during gene therapy. We are also developing novel chimeras between biology and chemistry, including minimal replicators that can evolve outside of cells, light-dependent signal transduction pathways, and organisms that utilize unnatural amino acids in their proteomes. Learn more >
Scott Hunicke-Smith, Coordinator of Bioinformatics Consulting and Training
Dr. Hunicke-Smith serves as Director to the Genome Sequencing and Analysis Facility. The GSAF’s vision is to be a world-class genomic analysis center in terms of data quality, breadth of available methods, and productivity. The mission of the Genome Sequencing and Analysis Facility is to provide the best quality analytical results with the best value to life science researchers. Learn more >
Jeffrey Barrick
Research in The Barrick Lab is aimed at understanding and harnessing molecular evolution as a creative force. To determine how different types of mutations impact the evolutionary potential of microorganisms, we monitor the competitive dynamics of spontaneous beneficial mutations in laboratory populations. Systems biology approaches are used to link the cell physiological effects of adaptive mutations to how they improve competitive fitness. Then, we use bioinformatics and comparative genomics to investigate whether similar mutational pathways are important in natural or pathogenic populations. We use the tools of synthetic biology to manipulate the evolution of bacteria by altering the rates of certain mutational processes and by perturbing and expanding regulatory and metabolic networks. Learn more >
Ilya Finkelstein
The Finkelstein Lab is focused on understanding how our cells are able to stave off genomic instability and avoid cancer. This highly interdisciplinary research program combines aspects of single-molecule biophysics, traditional biochemistry and micro-/nano-scale engineering to directly observe the key biochemical steps of DNA maintenance. The Finkelstein Lab addresses fundamental questions regarding how cells coordinate multi-protein assemblies on DNA, how these biochemical reactions occur on chromatin, a highly condensed DNA-protein substrate, and how defects in these pathways lead to genomic instability. Learn more >
George Georgiou
The Georgiou Lab is currently working primarily on the discovery and development of protein therapeutics and applied immunology by capitalizing on state of the art protein engineering, directed evolution and systems biology technologies: the Engineering of human therapeutic enzymes for the treatment of a variety of malignancies; deconvolution of antibody responses and antibody signatures in disease states; engineering and optimization of therapeutic antibodies; design of proteolytic enzymes that cleave and irreversibly inactivate disease targets. In parallel, our lab has been working for over 20 years on redox homeostasis, disulfide bond formation and protein biogenesis in bacteria, with current projects related to: evolution of novel pathways for rewiring electron transfer in E.coli; dissecting the role of LMW thiols in redox homeostasis and cell physiology. Learn more >
Andreas Matouschek
The Matouschek Lab focuses on the areas of the mechanism of protein unfolding by cellular macromolecular machines and protein unfolding by ATP-dependent proteases.
Sara Sawyer
The Sawyer Lab uses methods in molecular evolution, virology, and comparative genomics to explore how human immunity genes evolve to better sense pathogens in the cell. Learn more >
Chris Sullivan
The Sullivan Lab seeks to understand how viruses interact with the host RNAi machineries to replicate, induce tumors, and cause pathogenesis. In addition, this work will generate meaningful insights into components of host biology. The ultimate mission is a focused team that strives to meet these goals on a daily basis, and that in the process enjoys the work environment they have created. Learn more >
Stephen Trent
The Trent Lab focuses on the remodeling of lipopolysaccharides or LPS. LPS, also referred to as endotoxin, is the major surface component of Gram-negative bacteria and represents one of the microbial molecular signals responsible for activation of the host innate immune system. Their goal is to identify and characterize the molecular mechanisms necessary for the remodeling of LPS, and to determine how alteration of LPS contributes to evasion of the innate immune response during infection. Several pathogenic bacteria are under investigation in our laboratory including Vibrio cholerae, Campylobacter jejuni, Helicobacter pylori, Salmonella typhimurium, and pathogenic strains of Escherichia coli. Understanding how bacteria remodel their cell surface is of fundamental importance and may yield new therapeutic strategies for intervention in bacterial infections. Learn more >
John Wallingford
The Wallingford Lab is taking an integrated approach to understanding this process in chordate embryos. They combine molecular manipulations, time-lapse imaging, bioinformatics and even old-fashioned cut & paste embryology to investigate molecular signaling, individual cell behavior, and tissue rearrangement. By considering all of these components and how they affect the final body plan, The Wallingford Lab hopes to build a comprehensive picture of early embryonic morphogenesis. Learn more >
Marvin Whiteley
The Whiteley Lab uses a multifaceted approach to study two important aspects of infectious disease: chronic infections and polymicrobial infections. By combining gene expression analysis and whole-genome shotgun sequencing, Dr. Whitely is identifying traits that promote chronic infection and common bacterial mutations that promote long-term host colonization. Ongoing studies in Dr. Whiteley’s lab are identifying genes and secreted molecules that enhance polymicrobial synergy, and virulence traits that could be exploited as novel drug targets. Learn more >
Claus Wilke
The Wilke Lab uses computational biology. Bioinformatical and statistical methods are employed to analyze biological data sets, in particular whole-genome and high-throughput data sets; The Wilke Lab also develops mathematical models and computer simulations of biological systems. While the lab is purely computational, they frequently collaborate with experimental groups. Current research covers three broad but interconnected areas: 1. biophysical mechanisms of molecular evolution; 2. microbial adaptation and experimental evolution; 3. disease dynamics. A recurring theme in the research is evolution; modern biomedical research is deeply connected to evolutionary biology. For example, evolutionary methods are used to track and study infectious diseases such as influenza or HIV/AIDS. Many vaccines are developed through experimental evolution. Cancer progression is governed by evolutionary dynamics. Patterns of genome evolution can reveal costs and constraints under which cells operate. Learn more >