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 Education Research Experience Publications and Posters

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

University of Pennsylvania, Computational Biology (Fall 2007 - present)

MS, Georgetown University, Biochemistry (Fall 2006 - Summer 2007)

BS, Pennsylvania State University, Premed-Med/Life Sciences (Summer 2003 - Spring 2006)

Research Experience

• Rotation Student, University of Pennsylvania (Summer 2008)
  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 2008)
  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.
• Rotation Student, University of Pennsylvania (Fall 2007)
  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.
• Graduate Research Assistant, Georgetown/NCI (Fall 2006 - Summer 2007)
  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 (Fall 2005 - Spring 2006)
  Developed a high-throughput tool for aligning genes with MLAGAN for Dr Hiroshi Akashi.
• Research Intern, Windber Research Institute (Summer 2005)
  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].