Graduate Students

Tom Cooke
cooketho at stanford dot edu
Website

I am interested in animal pigmentation, which has long served as a model for cellular and developmental processes, and the molecular mechanisms that lead to natural variation in phenotype. In the budgerigar (Melopsittacus undulatus, or common parakeet), captive breeding since the 19th century has led to a dazzling array of plumage color morphs. I am using high-throughput DNA sequencing to identify the genes responsible for this variation. Knowledge of these genes can tell us more about the unique class of psittacofulvin pigments, found only in parrots, and how the enzymes that produce them evolved.

 


Helio Costa
hcosta at stanford dot edu
Website

I received my B.S. in Genetics from UC Davis in 2010. As an undergraduate I spent three years studying Drosophila development and evolution in Dr. Artyom Kopp's lab at UC Davis. Additionally, in the summer of 2009, I worked in Dr. Nevan Krogan's lab at UCSF studying protein-protein interaction networks in fission yeast.

I am now a Genetics Ph.D. student and am broadly interested in applying genomic approaches, such as DNA and RNA sequencing, to understand human genetic diversity and its relevance to human health and disease susceptibility.

 


Roxana Daneshjou
roxanad at stanford dot edu
Website

I received my B.S. in Bioengineering from Rice University in 2009. As an undergraduate, I worked in the tissue engineering lab of Dr. Antonios Mikos. I was also involved in engineering design projects through Beyond Traditional Borders, which created lower cost solutions for medical needs in developing countries.

I started medical school at Stanford in Fall of 2009 and became interested in Genetics. I joined the lab of Russ Altman in 2010, and completed a Howard Hughes Medical Institute Fellowship before joining the Medical Scientist Training Program. As a Genetics Ph.D. student with the Altman lab and Bustamante lab, I am leading the Iranian Genome project. I am also interested in pharmacogenetics in diverse populations.


Joe Davis
joed3 at stanford dot edu
Website

I completed a B.A. in Biological Sciences with a minor in Statistics from the University of Chicago in 2012. During my time in Chicago, I worked in Dr. Neil Shubin's lab on a project to determine the role of a Hox gene enhancer in the development of the tetrapod limb bud. I also worked in the labs of Dr. Justin Borevitz and Dr. Abraham Palmer to develop a Genotyping-By-Sequenicng (GBS) protocol and analysis pipeline for mouse inbred lines.

As a Genetics PhD student with the Bustamante lab and the Montgomery lab, I am interested in the forces of selection and demography that shape regulatory variation in humans. I am currently developing statistical methods to leverage population level gene expression and variation data to characterize functional variation.


Julian Homburger
jhomburg at stanford dot edu
Website

I graduated from Cornell in May 2013 where I studied both Statistics and Biological Sciences. During this time I worked with Dr. Nathan Sutter studying the population genetic history of dogs and horses. I also spent a summer working with Dr. Mickey Atwal at Cold Spring Harbor Laboratory assessing the effectiveness of rare variant tests for diseases. I started graduate school in the Department of Genetics at Stanford University in September 2013.

I am a student in both the Bustamante laboratory the Ashley laboratory. My work focuses on intersecting the fields of population genetics and clinical genetics to gain a better understanding of the genetic basis of disease.


Brian Keith Maples
bmaples at stanford dot edu
Website

I received a B.A. in Science and Management from Claremont McKenna College in 2004. I then worked for a small biotech startup where I invented and developed a rapid and isothermal method for DNA amplification before joining the Stanford Biomedical Informatics PhD program in 2010. My interests include developing statistical and machine learning-based methods for solving genetics problems.

I am currently developing a method for inferring local ancestry.

 

 


Alicia Martin
armartin at stanford dot edu
Website

I received my B.S. in Bioengineering from the University of Washington. During my time at UW, I studied organ formation with Celeste Berg using Drosophila melanogaster as a model organism and dorsal appendages or "breathing tubes" on fruit fly eggs as a model system. Additionally, I worked to develop the fruit fly as a model for aminoglycoside antibiotic toxicity.

Since coming to Stanford, my research interests have shifted toward genetic and expression variation in diverse human populations. I am currently studying transcriptome variation across global populations that have undergone serial bottlenecks. I am also working to understand the genetic basis of the large phenotypic variation in skin pigmentation in the #Khomani San, one of the most genetically diverse human population yet studied.


Kimberly McManus
kfm at stanford dot edu

I graduated from MIT with a B.S. in Biology in 2011. As an undergrad my research focused on a jointed MIT (Dr. Maria Zuber) and Harvard (Dr. Gary Ruvkun) research endeavor called SETG (Search for Extraterrestrial Genomes), whose goal is to develop an instrument to go to Mars and test for ancient remnants of DNA. I worked on multiple levels of this project including: design of universal DNA primers, efficient methods of DNA extraction from soil, and application of new Next Generation Sequencing techniques.

As a Biology PhD student at Stanford I am broadly interested in evolutionary genomics and continuing to push technology further to understand selection and variation between and within species here on Earth. Specifically, I am working on projects related to the origin of the Duffy allele (which provides resistance to Plasmodium vivax), as well as exploring selection and diversity among Western Gorillas.


Shaila Musharoff
shailam at stanford dot edu

I received my B.S. in Computer Science and Genetics from Rutgers University and my M.S. in Computer Science from NYU's Courant Institute. I did my first year of Ph.D. studies at Cornell University and moved to Stanford with the Bustamante lab in the summer of 2010.

I am currently interested in how human migrations shape patterns of variation on the X chromosome, and in inferring signatures of sex-biased demographic events from whole-genome sequence data. I am also interested in how the recent extreme population growth of the human population has affected the site frequency spectrum, and more generally in the implications of non-equilibrium conditions on processes such as the retention of deleterious alleles.


Patricia Ortiz-Tello
paortiz at stanford dot edu
Website

My research has two components. The first component is to elucidate population structure among the Native Americans in South America. Based on their genomic data, my goal is to understand migration patterns, infer bottlenecks, admixture events, and relationships between the different indigenous populations of South America. The second part of my research deals with the genetic basis of preeclampsia, specifically in admixed populations which have undergone positive adaption. This work is done in collaboration with the Hospital Manuel Nunez Butron in Puno, Peru, where the prevalence of preeclampsia is much higher than the world-wide estimate of 3-8%. In conjunction with our genotypic studies, I will be looking at gene expression studies of placental sections of women with and without preeclampsia. My goal as an MSTP student is to elucidate the genetic mechanism for this condition and continue its study from a clinical perspective as I go on to do my residency in obstetrics and gynecology.


David Poznik
dpoznik at stanford dot edu

Following a year teaching high school physics and 16 months studying the human and geographic diversity of Asia first-hand, I served as senior research analyst for the Department of Genetics & Epidemiology at Harvard Medical School's Joslin Diabetes Center, where I led the analysis for a number of linkage and GWAS studies aimed at identifying genes underlying diabetic nephropathy. In the fall of 2010, I joined Stanford's Department of Biomedical Informatics and the Bustamante lab, where my interests in computer science, statistics, genomics, and history/anthropology coalesce. The motivating goal of my research is to utilize genomic data to gain insight into the process by which the planet was peopled. I am currently working to leverage high-throughput Y Chromosome sequence data for demographic inference.


 

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