Postdoctoral Fellows

Meredith L. Carpenter
mlcarpen at stanford dot edu
Website

I have always been fascinated by the evolutionary history reflected in the human genome. From pathogens to migrations to environmental changes, the marks of these historical events remain, and many continue to influence our lives today: for example, by making us susceptible to certain diseases and resistant to others. Now, in the age of genomics, we have the tools to reconstruct these events and gain a better understanding of human history and disease. For my dissertation research at UC Berkeley, I worked on the disease side of the equation, studying the role of meiotic recombination machinery in the divergent eukaryotic parasite Giardia intestinalis. This research also allowed me to investigate broader evolutionary questions relating to the evolution of meiosis and sex.

I joined the Bustamante lab in 2011, and I am now applying my expertise in molecular biology to sequence DNA from ancient humans. The resulting data will allow us to address questions about the genetics of European populations after the Neolithic Revolution.

Omar Cornejo
ocornejo at stanford dot edu
Website

I am an evolutionary biologist interested in understanding how recombination, selection and mutation interact to shape genetic variation and determine the genetic structure of populations. I am particularly interested in the evolution of microorganisms. I combine population genetics, genomics analyses, phylogenetics, mathematical modeling and experimentation to address fundamental questions in ecology and evolution. I have started thinking more about the coevolution of host-pathogens and their signature in the genome, and how combining genomic information from both could shed light into the evolutionary race in host-parasite systems. I work under the philosophy that a combination of experimental studies in the laboratory, mathematical modeling driving the experiments and retrospective analyses of DNA sequence data enable us to gain a deeper understanding about the relative contribution of different processes to the generation and maintenance of genetic variation in the populations.

The increasing access to next generation sequencing has opened up an incredible opportunity to ask many question about the evolution of pathogenicity and the genetic bases of adaptive evolution in pathogens and the evolution of host resistance. I am also working on population genomics of cacao plants (Theobroma cacao). Our interest is to employ re-sequencing data from cacao plants to study their demographic history and to identify the genetic basis of traits of interest like the self-incompatibility system, resistance to witch's broom (a disease suffered by cacao and caused by a fungal infection by Moniliophthora perniciosa). Recently, I have started working on the development and application of tools to identify novel variants genome wide, in under-sampled human populations, with a special emphasis in the detection of variants that might be of interest.

Joanna L. Kelley
jokelley at stanford dot edu
Website

I am interested in how populations adapt to their environment. I am passionate about exploring new systems for studying population differentiation. To date, the majority of my research has focused on humans and non-human primates, my interests are by no means limited to primates.

In the Bustamante lab, I am developing several genomics project in the Bustamante lab including the sequencing, de novo assembly and population differentiation analysis of several model fish systems. I am developing genomic resources for two killifish species, one species (Nothobranchius furzeri) that is a model for aging and a second species (Kryptolebias marmoratus) that is a model for behavioral genomics. The third fish species (Poecilia mexicana) I am working with is a model for ecological genetics and genomics, as it has adapted to sulfidic streams in Mexico.

• Developing a method to date the age of selected alleles
• Determining the timing of selective pressures on geographically-restricted selected alleles in the human genome
• Using molecular and proteomic techniques to explore the adaptive evolution of Type III antifreeze proteins in Antarctic eelpouts
• Evolutionary approaches to prioritizing loci identified by association studies.

Andres Moreno Estrada
morenoe at stanford dot edu
Website

I am a Medical Doctor by training and have a strong interest in understanding patterns of human genetic variation and its implications in health and disease, evolution, and population history reconstruction. After graduating from the University of Guadalajara School of Medicine in 2002, I moved from Mexico to Barcelona, Spain to pursue a PhD in Evolutionary Biology and Population Genetics, which I received from the Pompeu Fabra University in 2009.

I joined the Bustamante Lab at Stanford University in January 2010, where I got the opportunity to focus my research on population genomics in the Americas. My current work involves the use of genome-wide data sets to study fine-scale patterns of population structure in both Native Americans and Hispanic/Latino populations from throughout the Americas. One of the major goals is to better understand the evolutionary processes, including natural selection, that have shaped Native American genomes during the last ~10,000 years of independent evolution since the peopling of the Americas and before the European contact.
The other major goal is aimed at understanding the dynamics of the admixture process in present day Hispanic/Latino populations since the European contact. By applying methods of local ancestry estimation we are trying to trace back ancestry-specific segments of the genome to their potential source populations at the sub-continental level. Defining patterns of local variation and sub-continental ancestry in admixed populations and individual genomes is also allowing the field to move towards a more personalized view of medical genomics and to promote the study of diverse populations underrepresented in current catalogs of human variation.

Marina Muzzio
mmuzzio at stanford dot edu
Website

I'm an Argentinean anthropologist graduated from the Universidad Nacional de La Plata, where I also got my PhD. My thesis and early postdoc work was at the IMBICE (Multidisciplinary Institute of Cellular Biology), about Y chromosome lineages in populations from the Argentinean North-West. I'm a Pew Latin American Fellow and my current research interest focuses on a genome-wide analysis of the Argentinean populations.

Karla Sandoval Mendoza
karlasm at stanford dot edu
Website

As an anthropologist, I have always been fascinated by the enormous cultural diversity within both ancient and modern indigenous populations across the Americas and particularly in Mexico, where I'm originally from. My first experience with indigenous communities was to perform ethnographic studies in a small rural village of Southern Mexico. The members of the community then asked me if I could find out more about their origins and population history in their blood. Since then, my main research interest has focused on the intersection between human genetics and anthropology. After being awarded with a CONACYT fellowship from the Mexican government, I moved to Barcelona to do my PhD in population genetics at the Pompeu Fabra University and joined the Bustamante Lab in May 2010. My current research projects include: Native American Exome Diversity of extant indigenous populations within Mexico, Native American ancient DNA recovered from pre-Columbian mummies across Mexico, Exome sequencing project of ancient DNA from Teotihuacan, and correlation between genetic and linguistic differences among different Nahua populations. Another major effort is to coordinate new sampling expeditions and collecting phenotypes across the Americas with a strong commitment to properly conducted fieldwork and community engagement.

Suyash Shringarpure
suyashs at stanford dot edu
Website

I am interested in developing computational and statistical methods that can be used to understand the evolutionary history of human populations and the genetic basis of diseases. My research focuses on developing models that can efficiently analyze large datasets while making realistic assumptions about the evolutionary processes involved. During my PhD at Carnegie Mellon University, I worked on developing hierarchical Bayesian models for the probabilistic clustering of admixed genomes.

Martin Sikora
msikora at stanford dot edu
Website

My research focuses broadly on the inference of selection and demography from genomic data in a variety of species, including domesticated rice, dogs, and humans. I am interested in the development and application of methods for detecting positive selection in the genome, with the aim of gaining a better understanding of the genomic basis of adaptation and the how different evolutionary forces shape genomic variation.