Sameer Soi

Sameer Soi

Graduate Student

Department of Genetics
School of Medicine
University of Pennsylvania
Philadelphia, PA 19104

ssoi@mail.med.upenn.edu
(215) 746-2683

Research Interests

I am broadly interested in the statistical properties of evolutionary forces shaping genome-wide variation. I am currently studying how complex demographic scenarios, typical of African populations, confound signatures of natural selection; to accomplish this I am using coalescent theory, approximate bayesian computation, and principal components.

Education

Fall 2007 - Present

Graduate Studies, University of Pennsylvania, Computational Biology

Fall 2006 - Summer 2007

M.S., Georgetown University, Biochemistry

Summer 2003 - Spring 2006

B.S., Pennsylvania State University, Premed-Med/Life Sciences

Research Experience

2008

Rotation Student, University of Pennsylvania (Summer)
Studied genetic variation in NRAMP1, a tuberculosis candidate gene, within worldwide populations using sequence analysis and estimators of selection in the lab of Dr Sarah Tishkoff.

Rotation Student, University of Pennsylvania (Spring)
Constructed a phylogeny of cancer patient gene expression profiles to correlate risk and progression for Drs. John Maris and Li-san Wang. Employed the beta-splitting model of species evolution to identify non-random nodes. Developed a bootstrap test of significance for this model.

2007

Rotation Student, University of Pennsylvania (Fall)
Tested and optimized an efficient method developed by Drs. Li-san Wang and Shane Jensen for the differential allocation of resamples in multiple hypothesis testing scenarios. Modified method for use in GWAS studies.

2006

Graduate Research Assistant, Georgetown/NCI (Fall)
Utilized microarray expression data and gene ontology to find statistically reliable housekeeping genes for reference in NCI60 cell line and other data sets with the guidance of Drs Hongfang Liu and Barry Zeeberg.

Research Student, Pennsylvania State University (Spring)
Developed a high-throughput tool for aligning genes with MLAGAN for Dr Hiroshi Akashi.

2005

Research Student, Pennsylvania State University (Fall)
Developed a high-throughput tool for aligning genes with MLAGAN for Dr Hiroshi Akashi.

Research Intern, Windber Research Institute (Summer)
Analyzed co-occurence of clinical diagnoses within an at-risk breast cancer population using a Bayesian network for Dr Hai Hu.

Publications and Posters

  • Laura B Scheinfeldt, Sameer Soi, Simon Thompson, Alessia Ranciaro, Dawit Wolde Meskel, William Beggs, Charla Lambert, Joseph P Jarvis, Dawit Abate, Gurja Belay, Sarah A Tishkoff. (2012) Genetic adaptation to high altitude in the Ethiopian highlands. Genome Biology 13:R1.
  • Scheinfeldt L., Soi S., Tishkoff S. (2010)  Colloquium paper: working toward a synthesis of archaeological, linguistic, and genetic data for inferring African population history. PNAS May 11; 107(2):8931-8938.
  • Jensen S., Soi S., Wang L. (2009) A Bayesian approach to efficient differential allocation for resampling-based significance testing. BMC Bioinformatics 10:198.
  • Liu H., Soi S. and Zeeberg B. (2007) Identifying housekeeping genes from microarray gene expression.  [Poster presented at the NIH Summer Research Poster Day Program. August 2007].
  • Liu H., Soi S. and Zeeberg B. (2007) Identifying housekeeping genes from microarray gene expression.  [Poster presented at the Georgetown Masters Biochemistry Research Presentation. August 2007].