Postdoctoral Fellows

María Ávila-Arcos
maria.avila at stanford dot edu
Website

I received my B.S. in genomic sciences from the National Autonomous University of Mexico and subsequently moved to Denmark to do my PhD under the supervision of Tom Gilbert at the Centre for GeoGenetics. My PhD research was focused on the optimization and analysis of next-gen sequencing data generated from a variety of ancient DNA (aDNA) sources, including maize, humans, koalas, whales and viruses, among others. For the last part of my PhD and one additional year of postdoc at the Center for GeoGenetics, I focused on the study of aDNA from ancient individuals from the Americas. My goal at the Bustamante lab is to combine ancient and modern genomic data to investigate demographic parameters, such as population size and split times within Mexico during the peopling of Mesoamerica as well as to identify candidate regions in the genome underlying events of adaptive evolution in Native Mexicans.


Meredith L. Carpenter
mlcarpen at stanford dot edu
Website

I am a molecular biologist and geneticist working in the field of human genomics. I am fascinated by the evolutionary history reflected in the human genome and the ways in which it has impacted disease susceptibilities in different populations.

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.

Now, for my postdoctoral work, I am applying my expertise in molecular biology to develop new tools for working with and analyzing ancient DNA. This project has enabled me to build a solid background in human genomics and population genetics, which will serve as a foundation for my future work. I am now involved in several projects related to clinical genomics and genome interpretation.


Rosa Fregel
rfregel at stanford dot edu
Website

I am a population genetics researcher interested in the ancient DNA field. My main aim is to understand human migration processes by the analysis of human remains and its comparison with modern populations. My PhD thesis consisted of the analysis of uniparental markers both in Canarian prehispanic aborigines and XVIII century samples, and their comparison with the current population with the aim of determining aborigines' origin and understanding the effect of European colonization in the islands. In theBustamante Lab, I am involved in the study of the human migrations related with the transoceanic slave trade and indentured laborers in Mauritius, in collaboration with the Mauritian Archaeology and Cultural Heritage project. I'm analyzing historical human remains from two archaeological sites, Le Morne (S.XVIII) and Bois Marchand (S.XIX), and modern human samples using NGS and genome-wide SNPs in order to determine the genetic temporal evolution of Mauritius.


Chris Gignoux
cgignoux at stanford dot edu
Website

I am a population geneticist interested in understanding human history and the impact that has had on diseases found in diverse populations. I use a combination of methods from evolutionary genetics and epidemiology to uncover novel ancestry signals in genetic data and better empower association studies.

In graduate school at UCSF I studied admixture, or mixed ancestry, in diverse populations of the Americas using genomic data. I also worked on methods to leverage admixture to identify novel genes associated with asthma and other complex traits. Before that, I developed ancestry features for 23andMe, worked in an Anthropology lab and pursued a Master's in Anthropological Sciences.

In the Bustamante Lab I am continuing my research in broad and fine-scale patterns of ancestry, and developing better association study methods that incorporate these important aspects of genetic information. I work with large genetic consortia to develop novel genotyping arrays and interpret findings across different ethnic groups. I am also continuing fieldwork and my interest in mapping traits both in American and Southern African populations.


Nilah Monnier Ioannidis
nilah at stanford dot edu
Website

As part of the Clinical Genomics project, I am developing new methods to interpret the pathogenicity of rare genetic variants from whole exome and whole genome sequencing studies. I received my PhD in Biophysics from Harvard University while working in the Biological Engineering department at MIT, where I developed methods for analyzing intracellular particle trajectories using Bayesian inference and hidden Markov models. Prior to my PhD, I worked as research director at the Jain Foundation, a private foundation focused on the rare genetic disease of dysferlinopathy, and held internships at the National Academy of Sciences and the journal Science. I also have an MPhil in Chemistry from the University of Cambridge and BA in Biochemical Sciences from Harvard College.



Fernando Mendez
flmendez at stanford dot edu
Website

I am a population geneticist interested in the evolution of human populations. I received my PhD in ecology and evolutionary biology at the University of Arizona in 2012, working mainly on the detection of archaic introgression in modern populations.

I am currently studying the use of long read sequencing and other technologies to improve phasing, SNP calling, as well as imputation of genetic data in pedigrees.

 



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.


Morten Rasmussen
mortenr2 at stanford dot edu
Website

I am a molecular biologist, and spent my PhD working on ancient DNA, applying the (then new) second generation sequencing technologies to various applications within ancient DNA. In particular I worked on ancient human genomes. During my postdoc I will work on de novo human genomes, using different long read technologies.

 

 

 


Anna Rychkova
rychkova at stanford dot edu
Website

I have always been passionate about biology and curious about the physical mechanisms that underlie biological functions. I received an MS in Biophysics from the Physics Department of Moscow State University, and then a PhD in Computational Chemistry from the Chemistry Department of the University of Southern California. With my background in physics and experience in protein simulations I have decided to switch into the field of human genetics, as I am very excited about its application to human health and personalized medicine. I joined the group of Carlos Bustamante in September 2013 and am currently working on the Clinical Genome project, where I am trying to improve methods for variant assessment using information about protein structure.

 


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.

 

 

 


Genevieve Wojcik
gwojcik at stanford dot edu
Website

I am a genetic epidemiologist interested in human-pathogen co-evolution. Specifically, I am interested in how host-pathogen interactions have shaped human genetics and how it can inform better treatment for infectious diseases, as well as vaccine development. I received an MHS in Human Genetics/Genetic Epidemiology, followed by a PhD in Epidemiology from Johns Hopkins University Bloomberg School of Public Health. My dissertation work focused on the evaluation of secondary methods for genome-wide association studies, as well as the genetics underlying the infant response to oral poliovirus vaccine. I joined the Bustamante lab in January 2014, where I am focusing on genetic epidemiology across diverse populations as part of a large genetics consortium while continuing to examine the consequences of selective pressures that pathogens exert upon human populations.


 

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