Past Members

imageJames J. Cai website
Position in the Petrov Lab: Postdoctoral Fellow

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?

image Jerel Davis
Position in the Petrov Lab: Graduate student

Current Position: Consultant, McKinsey & Company

Projects in the Petrov Lab: "I am currently studying gene duplication using bioinformatic and population genetic approaches. In particular I am interested in understanding the factors responsible for duplicate gene fixation and duplicate gene preservation. Academic Interests: In general I am interested in questions concerning the evolution of genome complexity. What are the mechanisms by which duplicate genes fix and persist in populations? What are the rules determining how genetic regulatory networks or protein interaction networks change over the course of evolution? Web page: http://www.stanford.edu/~jerel/IndexFiles/BiologyLinks.htm"

imageCurrent 12/2008: "Jerel is a management consultant focusing primarily on the healthcare industry.  He has consulted for major companies across the industry including: medical products, pharmaceuticals, biotech, wholesalers and distribution, and healthcare IT. Most recently, his focus areas included personalized medicine and the development of healthcare in emerging markets.  He recently studied how "market failures" and incentive alignment challenges are impeding the emergence and adoption of personalized medicine tests.  He has worked in both Russia and China studying the development of healthcare systems and the impact on opportunities for pharmaceutical companies."  

image Nadia Singh
Position in the Petrov Lab: Graduate student

Current Position: Postdoctoral Fellow, Andy Clark and Chip Aquadro Labs at Cornell University

 

imageCurrent: "The evolution of a genome is governed by the interplay among mutation, natural selection, biased gene conversion, and random genetic drift. I use laboratory, bioinformatic, and comparative genomic tools to quantify the individual and joint contributions of different evolutionary forces to genome evolution, such that the underlying causes of molecular change can be inferred. My research focuses on three major areas of evolutionary genomics. First, I strive to quantify the contribution of non-selective forces to genome evolution in Drosophila, through comparisons of substitutional patterns in differentially constrained sequences. Second, I exploit the population genetic differences between the sex chromosomes and the autosomes to make inferences about the molecular evolutionary process, such as the distribution of dominance effects of novel mutations and their selective effects. Finally, I am interested in understanding the genomic and temporal scales over which evolutionarily relevant population genetic parameters evolve, such as recombination rate and mutation rate.

image Yael Salzman
Position in the Petrov Lab: Graduate student

Current Position: Postdoctoral Fellow, Hopi Hoekstra Lab at Harvard University

I am interested in understanding the adaptive significance of transposable elements (TEs) in genome evolution. I started by examining the population genetics of non-LTR elements in D.melonagaster in North America and Africa. The main aim of this work was to investigate population dynamics of Tes in Drosophila. In particular, we found new evidence for the importance of ectopic recombination in TE copy number maintenance in Drosophila. I also identified some unusually frequent TE insertions that are likely to confer an adaptive advantage. One TE in particular appears to knockout a gene and yet be selectively advantageous. I am currently investigating the population genetics of this possible adaptive sweep and trying to understand the phenotypic effects of this TE insertion. Academic Interests: Genome evolution and population genetics. I would like to know which processes led to the structures and patterns in the genomes that we see today.

image J. Michael Macpherson
Position in the Petrov Lab: Graduate student

Current Position: Senior Scientist at the consumer genetics startup 23andMe

 Mike is a Senior Scientist at the consumer genetics startup 23andMe,
 where he works mainly on ancestry analysis. His thesis work was
 conducted in the Feldman and Petrov labs, and centered on the
 inference of the signature of natural selection from population
 genomic datasets.

 

imageMisha Lipatov
Position in the Petrov Lab: Graduate student

Current Position: Graduate Fellow, Marc Feldman's lab

Graduate student Projects: Using theoretical modeling and statistics to study the forces that affect (1) genome-wide single nucleotide substitutions in humans and (2) insertion of natural transposable elements in flies. Academic Interests: Contributing to the growth of the mathematical biology.

Current interests: "I work as a non-confrontational community mediator. In this capacity, I build and maintain communication channels between individuals and groups. This work involves gathering information via libraries and the Internet; absorbing it in talks and meetings; processing such information to produce summaries, figures, and mathematical theories; presenting the information in a clear and unbiased fashion to other people; and passing it on to larger audiences via email messages, articles and essays. I have written computer software, published scientific articles, constructed mathematical theories, taught college-level classes and given presentations at international conferences to promote communication among biologists, economists, physicists, statisticians, mathematicians and anthropologists. Currently I live and work in Palo Alto, CA."

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Research Assistant:

image 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).

image Abraham Bassan
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image Stanford Tran
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. In egestas nisl sit amet odio. Duis iaculis metus eu nulla. Donec venenatis sapien sed urna. Donec et felis ut elit elementum pellentesque. Praesent bibendum turpis semper lacus. Sed quis risus vitae eros nonummy aliquet. Curabitur congue, purus eget auctor egestas, nunc pede suscipit erat, a egestas nisi eros non orci. Fusce dolor. Etiam dictum ipsum in turpis. Nunc elit nibh, facilisis vitae, iaculis sed, sodales vel, sapien. Cras est massa, sodales at, commodo a, ultrices ac, urna. Nam eu turpis sed ante sagittis vestibulum.

image Konrad Scheffler
I completed my PhD in 2002 at the Cambridge University Engineering Department, where I was a member of the Speech, Vision and Robotics group (now called the Machine Intelligence group). My thesis dealt with automatic design of spoken dialogue systems, including quantitative modelling of speech recognition systems along with their users, quantitative simulation of human-computer dialogue, and the application of reinforcement learning to strategy design in spoken dialogue systems. Prior to this I obtained the B.Eng and M.Eng degrees in Electronic Engineering (specialising in speech recognition) at the University of Stellenbosch. After a year and a half as lecturer in Computer Science at the University of the Western Cape, I started working as a postdoctoral research fellow first at the South African National Bioinformatics Institute (SANBI) and then at the computational biology group at the University of Cape Town, where I have been since January 2005. My current interests focus on applying probabilistic models to biological problems, particularly evolution.


image Guy Sella
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. In egestas nisl sit amet odio. Duis iaculis metus eu nulla. Donec venenatis sapien sed urna. Donec et felis ut elit elementum pellentesque. Praesent bibendum turpis semper lacus. Sed quis risus vitae eros nonummy aliquet. Curabitur congue, purus eget auctor egestas, nunc pede suscipit erat, a egestas nisi eros non orci. Fusce dolor. Etiam dictum ipsum in turpis. Nunc elit nibh, facilisis vitae, iaculis sed, sodales vel, sapien. Cras est massa, sodales at, commodo a, ultrices ac, urna. Nam eu turpis sed ante sagittis vestibulum.

image Alfredo Ruíz Panadero
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. In egestas nisl sit amet odio. Duis iaculis metus eu nulla. Donec venenatis sapien sed urna. Donec et felis ut elit elementum pellentesque. Praesent bibendum turpis semper lacus. Sed quis risus vitae eros nonummy aliquet. Curabitur congue, purus eget auctor egestas, nunc pede suscipit erat, a egestas nisi eros non orci. Fusce dolor. Etiam dictum ipsum in turpis. Nunc elit nibh, facilisis vitae, iaculis sed, sodales vel, sapien. Cras est massa, sodales at, commodo a, ultrices ac, urna. Nam eu turpis sed ante sagittis vestibulum.

image Gayle Davidson
Lorem ipsum dolor sit amet, consectetuer adipiscing elit. In egestas nisl sit amet odio. Duis iaculis metus eu nulla. Donec venenatis sapien sed urna. Donec et felis ut elit elementum pellentesque. Praesent bibendum turpis semper lacus. Sed quis risus vitae eros nonummy aliquet. Curabitur congue, purus eget auctor egestas, nunc pede suscipit erat, a egestas nisi eros non orci. Fusce dolor. Etiam dictum ipsum in turpis. Nunc elit nibh, facilisis vitae, iaculis sed, sodales vel, sapien. Cras est massa, sodales at, commodo a, ultrices ac, urna. Nam eu turpis sed ante sagittis vestibulum.

image Kapa Lenkov
kapa@stanford.edu, Position: Research Assistant




image Michael Wiser
mwiser@stanford.edu Position: Graduate student Projects: Currently I am working on assaying the relative fitness effects of knockouts of unrelated pairs of singleton genes vs pairs of  duplicate genes in yeast. I would like to determine whether the effects of knocking out both members of a duplicate pair are additive, multiplicative, or epistatic, and whether individuals can adapt more quickly and/or more successfully to the loss of a duplicated gene than to the loss of a singleton. Academic Interests: In general, I am interested in molecular and evolutionary genetics. As I am an experimental evolutionist, this virtually necessitates working in microorganisms, due to their dense population sizes and extremely rapid generation times.  I’ve done previous work in E. coli, and am now branching into S. cerivisiae. The resolution of genetic conflict (be it host/parasite, parent/offspring, male/female, or predator/prey) and the mechanisms of speciation look quite intriguing, but I’m sticking to somewhat more tractable problems within a single species for the moment.


image Peter Carlson
pcarlson@stanford.edu Position: Second Year Undegraduate Projects: Academic Interests:

 

imagePhilip 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.

image 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.