Speaker Biographies

Patsy Babbitt is Professor of Computational Biology in the Department of Bioengineering and Therapeutic Sciences and the California Institute for Quantitative Biosciences.  Her research focuses on protein structure-function relationships in enzyme superfamilies with a primary aim to understand better the “architectural principles” underlying how some protein scaffolds have evolved to enable many different functions. To take advantage of the amount of sequence and structure data now available, her group uses graphical network models to summarize structure-function relationships in very large and functionally diverse superfamilies whose members occur across the biosphere. This large-scale context allows us to estimate the range of functions a given structural scaffold and active site machinery have achieved through divergent evolution. Further, the results show that only a small proportion of these enzymes have been functionally or structurally characterized, suggesting that many chemical capabilities remain undiscovered.

Anne-Ruxandra Carvunis received her Ph.D. at Université Joseph Fourier, France,  and is now a postdoctoral fellow at the University of California working in the laboratory of Trey Ideker. Dr. Carvunis  studies the principles governing the organization and evolution of molecular networks formed by biomolecules that interact with each other within cells. She also developed a model for the emergence of completely novel proteins during evolution, involving the existence and translation of “proto-genes”. Carvunis and colleagues have also observed that, following gene duplications, protein interactions in A. thaliana are dynamically rewired in a way that shows an action of natural selection at the network level

Belinda Chang received her Ph.D. at Harvard University followed by Postdoctoral research at Rockefeller University. Professor Chang’s research program in the Departments of Ecology and Evolutionary Biology and of Cell and Systems Biology is primarily focused on the evolution of vision from a molecular perspective. Within the eye, visual pigments form the first step in the sensory visual pathway of all animals that can see. Aspects of its biochemistry affect the way an organism perceives and functions in its environment. The Chang Research Group uses a variety of molecular methods to study the evolution of visual pigments, with a view toward correlating their function with the vision and behavior of the organisms in which these proteins reside. In addition to comparative studies of visual pigments in a variety of organisms, the Chang Group also studies visual pigment evolution by recreating ancestral proteins in the laboratory. This is done by first inferring the ancestral pigment sequence using phylogenetic methods, then expressing an artificially synthesized ancestral gene in the laboratory. This allows one to study its evolutionary properties directly, instead of extrapolating the evolution of function from present day proteins.

Cassandra Extavour is Professor of Organismic and Evolutionary Biology, and of Molecular and Cellular Biology. She trained in Drosophila genetics with Antonio Garcia-Bellido at the autonomous University of Madrid as a graduate student, and in comparative arthropod development with Michael Akam at the University of Cambridge as a postdoc. Her research focuses on the evolution of developmental mechanisms and cellular behaviours that establish germ cells and reproductive systems in animals. More broadly, she is interested in the origin and evolution of genes, proteins, gene networks and molecular mechanisms that determine early cell fate decisions in multicellular development. Her group uses multiple different model organisms to perform comparative analysis of development, using approaches from developmental genetics, classical embryology, bioinformatics, biochemistry and molecular evolution.

Research in the Goldstein lab focuses on computational modelling of molecular evolution, with an emphasis on proteins and viruses. In order to understand the properties of proteins – how they fold, what determines their stability, how they interact – we need to investigate the evolutionary processes that determined their form and function. Conversely, the evolution of proteins cannot be understood without considering how their form and function constrain the evolutionary process. Finally, the evolutionary record encodes the history of these proteins, providing important clues about their properties, roles, and interactions. Decoding this record requires an understanding of the underlying process of molecular evolution, how genes and proteins respond to varying, multifaceted selective pressures given their various biophysical, biochemical, and functional constraints.

 

Joanna Masel is an evolutionary theorist interested in the robustness and evolvability of biological systems. A theme is the prevalence of errors at the molecular level, and the evolutionary consequences of their inevitable costs. The de novo origin of coding sequences is a major empirical application for this theory, as is the action of the yeast prion [PSI+] as an evolutionary capacitor. She also studies the tension between relative and absolute competitions in evolution, ecology, and economics. Her lab uses a combination of mathematical, computational and bioinformatic approaches.

Mary J. O’Connell graduated with her BSc and PhD from the National University of Ireland Maynooth (NUIM). Her PhD work was on the topic of evolutionary rate heterogeneity in the coding regions of mammal genomes and her postdoctoral work at UCC was on genomic imprinting. These projects spanned protein coding and non-coding aspects of mammal genomics and formed the foundation of her interest in functional comparative genomics and evolutionary medicine. In 2005 she became a fully tenured academic in the School of Biotechnology, Dublin City University where she established the Bioinformatics and Molecular Evolution research group. Her current research spans many areas of evolutionary biology, including phylogenetics and molecular adaptation, and integrates evolutionary predictions with molecular and biochemical analyses. She is focused on understanding the evolution of disease resistance by studying the molecular mechanisms of both protein and regulatory element evolution in the amniota.

Carrie Olson-Manning is interested in the evolution of enzyme activity and metabolic pathways. She is studying how the corticosteroid synthesis pathway evolved in vertebrates as a postdoctoral fellow in Joe Thornton’s laboratory at the University of Chicago. She completed her PhD at Duke University working with Tom Mitchell-Olds, where she studied the biochemical evolution of herbivore resistance in the charismatic relatives of broccoli.  Carrie did her undergraduate research with Tony Dean in Minnesota, so she loves the balmy winters of Chicago..

David Pollock first became interested in molecular evolution while doing a BA in Biochemistry from UC Berkeley with Allan Wilson. He later got a PhD in Biological Sciences from Stanford University (with Ward Watt and Marcus Feldman) and had postdoctoral fellowships that sent him to the National Institute for Medical Research in London, UC Berkeley, and Los Alamos National Laboratory. Dr. Pollock’s laboratory in the Department of Biochemistry and Molecular Genetics studies the relationship between structure/function and sequence evolution. They also have a focus on comparative vertebrate genomics, particularly the genomics of snakes. Molecules of interest include proteins in general, transcription factors and their binding sites, mitochondrial genomes, transposable elements, and microsatellites.

Douglas Theobald’s lab at Brandeis University is interested in diverse unresolved problems in molecular evolution, including: What are the mechanisms by which new functions evolve? What are the physical constraints on protein evolution? Are ancestral enzymes functionally promiscuous? Does specificity increase during evolution? To what extent is evolution adaptive or due to chance events? How many substitutions are required for evolution of a new function? Do novel functions evolve by small or large increments? What is the importance of correlations among mutations (epistasis)? The answers to these questions have broad implications for understanding the protein structure-function relationship, including rational efforts to design (and redesign) proteins for particular functions.

Claus Wilke received his PhD in Theoretical Physics from the University of Bochum in Germany in 1999. He was a postdoc in the Adami lab at Caltech from 2000 to 2005, where he received training in biological physics, evolutionary biology, and artificial life. Dr. Wilke currently works on problems in computational evolutionary biology, bioinformatics, and structural biology. All his research is theoretical or computational, but he frequently collaborates with experimental groups. Much of his research addresses questions of molecular evolution, in particular about the evolution of viruses and the biophysical mechanisms of protein evolution. Other areas of interest are systems biology, metabolic modeling, and biostatistics.