People in the Petrov Lab
Show all current and former lab members
Dmitri Petrov is a Kevin and Michelle Douglas Professor of Humanities and Sciences in the Biology Department at Stanford. He received his Ph.D. in 1997 from Harvard University under the guidance of Daniel Hartl and Richard Lewontin. He was a Junior Fellow at the Harvard Society of Fellows and a Research Fellow in the Genetics Department at Harvard Medical School under the guidance of Chao-Ting Wu. Dmitri came to Stanford in 2000 as an Assistant Professor. Petrov Lab does theoretical, computational and experimental work to address questions in molecular evolution and molecular population genetics. The primary focus at the moment is on (i) population genetics and molecular mechanisms of adaptation and (ii) genome evolution. For projects and papers in the Petrov Lab please visit the Research and Publications pages. Petrov CV is here. E-mail: email@example.com.
James Cai is an Assistant Professor in the Department of Veterinary Integrative Biosciences at Texas A&M University. James is interested in the elucidation of genotype-phenotype relationships using computational genomics approaches. His lab seeks evolutionary interpretation of causal and associated variants underlying genetic disorders and complex traits of different organisms. During his time as Postdotoral Fellow in the Petrov Lab (2006-2010) James discovered the first clear signatures of recurrent adaptation in the patterns of human genetic variation, worked on understanding of patterns of evolution of genes of different evolutionary age, and peculiar network and evolutionary properties of genes that can underlie human disease. James develops various statistical tests and computational tools to understand the processes shaping genome variability patterns within and between species and maintains three Matlab toolboxes for population genetics, molecular evolution, and systems biology. The website of his lab at Texas A&M can be accessed here. The lab news story about James can be found here.
Ruth Hershberg is a Senior Lecturer in the Ruth & Bruce Rappaport Faculty of Medicine at the Technion (Israel Institute of Technology), Haifa, Israel. During her time as a postdoc in the Petrov Lab (2006-2011), Ruth studied the ways in which purifying selection changes within and between different organisms. She has 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; that M. tuberculosis evolve under extremely reduced purifying selection, leading to a large proportion of differences among M. tuberculosis strains having functional consequences; that mutation is universally biased towards AT and that the genomic GC content variation in bacteria is most likely driven by selection; and that the choice of optimal codons across organisms is driven by selection at the level of the genomic GC content. She received her Ph.D. from Hebrew University (summa cum laude) under the guidance of Hannah Margalit. The website of her lab in Technion can be accessed here. The lab news story about Ruth can be found here.
Philipp Messer is a Postdoctoral Fellow in the Petrov Lab (2008-now). His primary research interest is evolutionary genomics. In particular, he is interested in the elementary patterns of mutational processes that underlie the generation of genetic changes in DNA. In his Ph.D. work conducted at the Max-Planck Institute for Molecular Genetics in Berlin with Peter Arndt he 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 Philipp's research at Stanford is to investigate the contribution of selection to these processes. For this purpose, he aims at developing sophisticated population genetics simulations of recurrent selective sweeps in a coalescent framework.
Anna-Sophie Fiston-Lavier is a Postdoctoral Fellow in the Petrov Lab (2008-now). She received her Ph.D. from the Pierre and Marie Curie University in Paris under the guidance of Hadi Quesneville in 2008. She investigated the evolutionary dynamics of Transposable Elements (TEs) and their impact on genome structure and evolution combining comparative genomic and phylogenomic approaches. She showed that the gene density is the main force that shapes the TE sequence evolution in Arabidopsis thaliana. Her analysis of segmental duplications in Drosophila melanogaster contributed to propose a mechanistic model of segmental duplication formation based on non-allelic homologous recombination. She provided evidences of TE role in the duplication formation (Fiston-Lavier et al Genome Research 2007). Infering the evolutionary events that have led to the formation of a new operon-like cluster from A. thaliana, she also showed the role of TEs in the formation and the maintenance of duplications (Field, Fiston-Lavier et al PNAS 2011). Anna's research project is to investigate the contribution of TEs on genome adaptive evolution developing accurate and powerful computational tools for TE dynamic analysis. She started designing an interactive tool to estimate the recombination rate along the D. melanogaster genome sequences (Fiston-Lavier et al Gene 2010). Using this tools, she were able to investigate the TE evolutionary dynamics in Drosophila (Petrov, Fiston-Lavier et al MBE 2011 ). She then developped a computational pipeline for TE annotation in population using next-gen sequencing data (Fiston-Lavier et al NAR 2010).
Fabian Staubach is a Postdoctoral Fellow in the Petrov Lab (2010-now). He is primarily interested in the molecular basis of adaptation. During his PhD at the Max Planck Institute for Evolutionary Biology Fabian 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 the Petrov Lab Fabian studies the bacterial flora associated with Drosophila and its contribution to adaptive evolution of the host.
Alan Bergland is a Postdoctoral Fellow in the Petrov Lab (2010-now). His research aims to integrate the role of environmental variation with long- and short-term evolutionary processes through an understanding of the genetics, physiology, and morphology that regulate life histories. During his graduate work at Brown University under the guidance or Marc Tatar, Alan focused on the relationship between larval nutrition and adult fecundity in Drosophila melanogaster. This research used a combination of evolutionary demography, ecology, molecular and quantitative genetics, and physiology to investigate how life history plasticity evolves in natural populations. As a post-doc, he is investigating the evolution of D. melanogaster and D. simulans in temperate environments. One aspect of this project focuses on exploring the demographic consequences of seasonal population booms and busts. The other aspect focuses on identifying the location, function and evolutionary history of alleles underlying adaptations to temperate environments.
David Enard is a Postdoctoral Fellow in the Petrov Lab (2011-now). He is broadly interested in finding new methods to characterize the prevalence of positive selection. During his PhD in Hugues Roest Crollius's lab at the École normale supérieure in Paris he developed a comparative population genomics approach that allowed him to demonstrate that vertebrates as distant as human and pufferfish often adapt with the same genes. In thePetrov Lab, David focuses on detecting positive selecvtion in the human genome as well as new approaches to detect selection from frequency changes over very few generations.
Nadia Singh is an Assistant Professor in the Department of Genetics at North Carolina State University. She was a graduate student in the Petrov Lab from 2001-2006. Nadia did her undergraduate work at the University of Chicago and Harvard. Prior to joining the lab, she was working as a research technician in the Program for Population Genetics at the Harvard School of Public Health. Nadia's research in the Petrov lab focused on molecular evolutionary genomics in Drosophila. In particular, Nadia investigated variation in single nucleotide substitutional patterns both within and between species, and the implications of this variation for genome evolution. After receiving her Ph.D. from Stanford, Nadia did a postdoc with Andy Clark and Chip Aquadro at Cornell University in the Department of Molecular Biology and Genetics. Nadia joined the faculty of the Department of Genetics at North Carolina State University in 2010 as an Assistant Professor. Her research continues to focus on the joint and individual roles of non-selective evolutionary forces to genome evolution in Drosophila, with a particular interest on recombination rate variation. You can learn more about Nadia's current research here.
David Lawrie is a Graduate Student in Petrov Lab (2007-now). David did his undergraduate work in computational biology at Cornell with Andy Clark and Adam Siepel and came to Stanford Genetics Department as a graduate student in 2007. His main research interests lie in distinguishing selection from non-selective forces such as mutational biases. Past work in this regard has been on explicitly incorporating the action of selection into substitution models and detailing how sequences are expected to change over divergence timescales with both biases from both mutation and fixation. David showed that weak selection and mutational biases can produce unexpected results with, for example, unconstrained sequences evolving slower than constrained ones in the absence of adaptation. The news report about this work can be found here. Current work is focusing on studying the patterns of weak selection and relaxation of constraint in polymorphism and divergence data. Other research interests include modeling the evolution of cis-regulatory elements.
Diamantis Sellis is a Graduate Student in Petrov Lab (2007-now). Diamantis focuses on the effects that diploidy has on the process of adaptive evolution using both modelling and experimental evolution in yeast. He showed that adaptation in diplods might lead to a high prevalence of transient balancing selection and maintenance of much greater amounts of consequential genetic variation than would be expected in haploids. This work was published in PNAS in 2011 and the news report about it can be found here. The experimental evolution work is in progress.
Yuan Zhu is a Graduate Student in Petrov Lab (2008-now). Yuan Zhu did her undergraduate work at Duke with Susan Alberts and came to Stanford Genetics Department as a graduate student in 2008. In the Petrov Lab she focused on the application of next-generation sequencing of whole pooled populations for asking a broad range of questions in genomic evolution, including areas such as genotype phenotype interaction, evolution of complex traits, and population genetics. She showed that pooled resequecing is a remarkably efficient and precise tool for the estimation of allele frequencies and is using this technique now to (i) identify deleterious mutations in mutation-accumulation lines of yeast, (ii) assess genetic variation across S. cerevisiae, and (iii) estimate patterns of mutation using both natural polymorphism and mutation-accumulation data.
Nandita Garud is a Graduate Student in Petrov Lab (2009-now). Nandita did her undergraduate work in computational biology at Cornell with Andy Clark and came to Stanford Genetics Department as a graduate student in 2009. She is interested in understanding how genetic diversity is maintained in a population. Currently, Nandita is studying “soft sweeps” in Drosophila in which whereby multiple copies of a beneficial allele rise in frequency in a population simultaneously. She is also working on a project to characterize the prevalence of balancing selection in the butterfly species, E. gillettii. In her work in the recent past Nandita worked on identifying RNA editing sites in humans and on the demographic inference of rice. She also concurrently works on an M.S. in Statistics at Stanford.
Heather Machado is a Graduate Student in Petrov Lab (2010-now). She received both her B.S. and M.S. from Portland State University where she worked with Mitch Cruzan and then worked as a Research associate in Suzy Renn's lab at Reed. Heather joined the Stanford Biology Department as a graduate student in 2010. In the Petrov Lab she is planning to work on understanding adaptation particularly in the context of recent radiations or environmental shifts.
Sandeep Venkataram is a Graduate Student in Petrov Lab (2010-now). He received his B.S. from the Washington University in St.Louis where he worked with Justin Fay. In the Petrov Lab Sandeep is using artificial evolution in yeast to shed light on the patterns of compensatory evolution.
Ben Wilson is a Graduate Student in Petrov Lab (2010-now). He received his B.S. from the University of Arizona where he worked with Joanna Mazel. Ben is interested in the theoretical population genetics of adaptation, particularly in populations that fluctuate in size over various time-scales. He is also interested in how complex adaptive landscapes contribute to the evolutionary trajectories we see in adaptation. Ben uses a combination of theoretical approaches with experimental evolution and genomic inference to test theoretical predictions.
Zoe Assaf is a Graduate Student in Petrov Lab (2010-now). Zoe did her undergraduate work in molecular and developmental biology at Berkeley and then stayed a year working as a Research Technician in Zach Cande's lab. Zoe came to Stanford Genetics Department as graduate student in 2010. Zoe is interested in studying the theoretical, computational, and experimental aspects of evolutionary biology. Shew is combiningmodelling and experimental evolution in Drosophila to study adaptation from standing variation.
Jacqueline Ou is a Graduate Student in Petrov and Sherlock Labs (2010-now). Jackie did her undergraduate work in mathematics at Duke and then spent several years working for a number of companies (Foundation Medicine / Third Rock Ventures, Bain & Company, HIV/AIDS Initiative in Southern & Eastern Africa at Clinton Foundation). Jackie came to Stanford to pursue her graduate work at Stanford Genetics Department in 2010. Jackie is interested in the potential repeatability and predictability of evolution, using both theoretical and directed evolution approaches. Recent literature has theoretically suggested that evolutionary paths to drug resistance are constrained by their fitness landscapes in various settings. Working in both the Petrov and Sherlock laboratories, she is interested in experimentally exploring whether these theoretical models are accurate and in further developing theoretical approaches to predict evolution in constrained fitness landscapes. Jacie is currently on leave.
Rajiv McCoy is a Graduate Student in the Boggs and Petrov Labs (2010-now). He received his B.S. in Biology and Ecosystem Science & Policy from the University of Miami where he worked in Barbara Whitlock's lab. Rajiv is interested in evolution of small populations, working at the intersection of evolutionary and ecological genomics. His current project in the Petrov lab investigates the prevalence of balancing selection in an introduced population of the checkerspot butterfly Euphydryas gillettii.
Talia Karasov is a Graduate Student at the University of Chicago in the laboratory of Joy Bergelson. Talia did her undergraduate work at Stanford, and joined the Petrov lab during her Sophomore year in 2006. She also worked as a reserarch assistant in the lab on a joint project with Gretchen Daily. Her research in the lab focused primarily on the evolution of insecticide resistance in Drosophila. The work culminated in a paper published in PLoS Genetics that challenged the conventional wisdom and suggested that adaptation in Drosophila is not mutation limited and that Drosophila populations are more than 100-fold larger in their effective size than was previously thought. The news story about this work can be found here. In 2009 she moved to Chicago to start her PhD. She is currently investigating the evolution of host-pathogen interactions in Arabidopsis.
Philip Bulterys is currently a second-year MD/PhD student in the UCLA/Caltech Medical Scientist Training Program (MSTP). He received his B.S. in Biology from Stanford University in 2010, and worked on an HIV evolution project in the Petrov lab from 2008 to 2010. He is interested in the ecology and evolution of infectious diseases and firmly committed to public health. Philip is a recepient of the Paul & Daisy Soros Fellowship for New Americans.The lab news story about Philip can be found here.
Felicia King Felicia King is an Undergraduate Student in Petrov Lab (2010-now). Felicia is currently studying adaptation of Drosophila to local climate change in Northern California populations under the guidance of Postodoctoral Fellow Alan Bergland. To test for local adaptation, Felicia is collecting flies along an elevational gradient from the Central Valley to the Sierra Nevadas and assays them for genetic markers and traits known to be winter-adaptive.