Current Members
Principal Investigator
Dmitri Petrov
Position: Professor of Biology. Academic Interests: I am interested in molecular evolution and evolutionary genetics. For details on some of our projects please visit the Research page of this web site. Publications: A number of publications have come from our lab. For a full listing, go to the Publications page. CV: My CV can be found online.
E-mail: dpetrov@stanford.edu
Post-Docs/Fellows:
Josefa Gonzalez
website 
I am interested in the study of adaptation both at the molecular and phenotypic level. My current research involves the use of transposable elements (TEs) in Drosophila melanogaster as a tool to find adaptive mutations. We searched for TEs that increased in population frequency sharply after the spread out of Africa and identified a set of thirteen elements likely to be adaptive. I am further investigating these elements by sequencing their flanking regions and looking for evidence of selective sweeps. I am analyzing the molecular evolution of the nearby genes and looking for differences in their expression patterns.
I am also interested in the population dynamics of transposable elements, in particular, whether the rate of transposition and the strength of purifying selection against transposable elements is a property of the family to which the elements belong.
Ruth Hershberg
website
I am interested in the ways in which purifying selection changes within and between different organisms. I have demonstrated that the strength of selection changes between different strains of E. coli and Shigella and causes significant differences in the rate of gene loss. I have also shown that strains of tuberculosis are under extremely reduced purifying selection, leading to a large proportion of mutations between these strains having functional consequences. I have recently started examining the ways in which selection affects codon choice in bacteria and am conducting a wide-scale survey of how the strength of purifying selection shifts between different bacteria.
James J. Cai
website
I am interested in applying population-genetic theories to modern molecular genetic data. I develop various statistical tests and computational tools to understand the processes shaping genome variability patterns within and between species. The particular questions I would like to address are something like these--(1) Which mutations in which genes are responsible for adaptive molecular evolution of humans? (2) What proportion of human genetic variation are selectively neutral, advantageous, deleterious? (3) How can we use evolutionary genomics to predict which types of changes in which types of genes may be involved in human disease?
Philipp Messer
My primary research interest is evolutionary genomics. In particular, I am interested in the elementary patterns of mutational processes that underlie the generation of genetic changes in DNA. In my Ph.D. work conducted at the Max-Planck Institute for Molecular Genetics in Berlin I approached this problem by comparative genomics methods using genome-level datasets, as well as by modeling of evolutionary processes with respect to their effect on statistical properties of genomes. The major focus of my proposed research at Stanford is to investigate the contribution of selection to these processes. For this purpose, we aim at developing sophisticated population genetics simulations of recurrent selective sweeps in a coalescent framework.
Anna-sophie Fiston-Lavier website
I am interested by the impact of repeats (transposable elements, segmental duplications and satellites) on the genome structure and evolution. During my PhD, I investigated a repeat dynamics study in eukaryotic genomes. I developed computational tools to detect and analyse repeats. Comparative genomic approach and sequence analysis of segmental duplications contribute to propose a mechanistic model of segmental duplication formation based on a non-allelic homologous recombination model. Using phylogenic and statistic approaches, I investigated the comparative study of sequence turnover of repeats in euchromatin and heterochromatin.
My postdoc research project will focus on genome evolution. The development of a combine approach of population genetics and comparative genomics will allow us to discuss the impact of transposable elements on genome evolution on a short and large scale.
Fabian Staubach
I am interested in the molecular basis of adaptation. During my PhD at the Max Planck Institute for Evolutionary Biology I studied the evolution of gene expression in house mice and discovered a new gene, which emerged from noncoding sequence in the house mouse lineage. In Dmitri's lab I plan to deepen my understanding of adaptive evolution by investigating parallel evolution of latitudinal clines in Drosophila. Three central questions will be: Which genes are subject to selection? How is selection reflected in the genome? What kinds of phenotypes are associated with selective events? I plan to join the lab in February of 2010.
Graduate Student:
Penka
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David Lawrie
Second Year Genetics graduate student
My research interests lie in the evolution of gene regulation and evolutionary genomics. Currently, I am working on substitution models explicitly incorporating the action of selection into how nucleotides change over time. With these models, I aim to study the evolution of cis-regulatory elements as well as the interaction between mutational biases and the strength of selection. I graduated from Cornell in 2007 where I worked with Andy Clark and Adam Siepel.
Diamantis Sellis
Second Year graduate student
I am interested in evolutionary biology, theoretical biology and bioinformatics. I am particularly interested in understanding multilevel selection and for my PhD I would like to study the dynamics of hierarchically structured biological systems undergoing natural selection. I am currently focusing on the genomic and sub-genomic levels by studying interaction networks and population genetics.orem ipsum d
Yuan Zhu
Second Year graduate student in Genetics
I am interested in the theoretical and experimental aspects of genomic evolution, including areas such as genotype phenotype interaction, evolution of complex traits, and population genetics.Lorem ipsu
Research Assistant:
Talia L. Karasov
I am studying adaptation in natural populations of Drosophila. My current research focuses on the process of evolution to pesticide resistance. I am examining how
resistance alleles enter populations--whether through de novo mutation or through migration. Additionally, I am researching how Drosophila adapt to variable climates
along environmental clines. I proudly hail from Madison, Wisconsin and about to leave to start graduate school at the University of Chicago (see the news item from April 15, 2009).
Undergraduate Student:
Philip Bulterys
I am studying the evolution of Human Immunodeficiency Virus-1 (HIV-1) in the context of Mother-to-Child Transmission (MTCT). Together with collaborators at the Stanford School of Medicine and with support of a UAR Major Grant and a Bio-X Undergraduate Research Award, I plan to characterize the relationship among the virus within-host evolutionary characteristics (diversity, strength of selection, phylogenetics) and the risk of vertical perinatal and postnatal HIV transmission.