Ben Logsdon ~ Graduate Student Ph.D. (December 2010) Ben is a postdoctoral associate in Dr. Charles Kooperberg's group at the Fred Hutchinson Cancer Research Center



Office:
Current: Fred Hutchinson Cancer Research Center Division of Public Health Sciences
Seattle, WA 98109-1024

Contact:
Email: blogsdon at fhcrc dot org

Research Interests:
My research interests fall into two broad categories: 1) multiple locus genome-wide association studies, 2) regulatory network reconstruction from genome-wide genotype and gene expression data. To study these problems I have developed both stochastic and deterministic inference algorithms applied to Bayesian and likelihood based statistical models. Some of the inference methods I use are Markov chain Monte Carlo (MCMC) samplers, convex optimization with regularized regression (interior point methods), and variational Bayes algorithms (Mean field approximations), among others. I am interested in developing algorithms to solve these model selection problems that 1) scale to genome-wide data-sets, 2) have sound statistical properties, and 3) are robust in terms of power and controlling for false positives when applied to real data.


Graduate Field and Fellowships:
  • Computational Biology
  • Presidential Life Sciences Fellowship
  • Cornell Provost Award Fellowship
  • Center for Vertebrate Genomics, Scholars' Fellowship

 
Papers:
  • Logsdon B., Mezey J. 2011. Mouse obesity network reconstruction with a variational Bayes algorithm to employ agressive false positive control. submitted, April 2011.
  • Logsdon, B., Mezey, J. 2010. Gene expression network reconstruction by convex feature selection while incorporating genetic perturbations. PLoS Computational Biology. Link
  • Logsdon, B., Hoffman, G., Mezey, J. 2010. A variational Bayes algorithm for fast and accurate multiple locus genome-wide association analysis. BMC Bioinformatics. Link
  • C.K. Griswold, B. Logsdon, R. Gomulkiewicz. 2007. Neutral evolution of multiple quantitative characters: a genealogical approach. Genetics 176(1):455-66. Link
  • T.S. kim, B.A. Logsdon, S. Park, J.G. mezey, K. Lee. 2007. Quantitative trait loci for the circadian clock in Neurospora crassa. Genetics 177(4):2335-47. Link