MY COORDINATES: I can be found at the Center for Comparative Genomics and Bioinformatics of the
I was born in
PASSING ON SOME WISDOM: I taught many graduate and undergraduate courses, often concerning regression methods, bioinformatics, and the statistical analysis of data produced by high-throughput genomic technologies. Here are links to a few representative course websites: Applied Regression Analysis, Bioinformatics II, Current Research in Statistical Genomics. My colleagues (including statisticians, computer scientists and biologists) and I maintain a close-knit co-advising network to train and mentor students working at the interfaces between our disciplines. Examples of recent graduates mentored through this network are Erika Kvikstad (PhD in Genetics, 2009, now a post-doc at the University Claude Bernard Lyon 1 in France), Svitlana Tyekucheva (PhD in Statistics, 2008, then a post-doc at Johns Hopkins and now at Harvard), James Taylor (PhD in Computer Science, 2006, now a Biology and Math&CS faculty at Emory University), and Shan Yang (PhD in Biochemistry and Molecular Biology, 2004, now a senior bioinformatics scientist at Applied Biosystems).
MY WORK IN STATISTICS: My interests as a statistician cover multivariate analysis and regression (including dimension reduction, supervised and unsupervised classification, non-parametric tools and parametric regression modeling), computational techniques (including re-sampling, perturbation and permutation schemes for the empirical assessment of significance), approaches to the analysis of high-dimensional and under-sampled data (which are very common in genomics applications), and Markov models (as applied to genomic sequences and alignments). With funding from the NSF, R. Dennis Cook (Statistics, U of MN), Bing Li (Statistics, Penn State) and I have pursued research on Sufficient Dimension Reduction, a body of theory and methods for handling high-dimensional regression and classification problems, which is also closely related to graphics and data visualization. Representative publications.
MY WORK IN BIOINFORMATICS AND GENOMICS: Most of my research occurs at the interfaces between statistics, bioinformatics and genomics. Over the years, this work has comprised NIH and NSF funded collaborations with Ross Hardison, Kateryna Makova, Webb Miller, Anton Nekrutenko, Mary Poss and other researchers at the Center for Comparative Genomics and Bioinformatics, the Center for Medical Genomics, and the Center for Infectious Disease Dynamics of Penn State, as well as other institutions (e.g. the Center for Biomolecular Science and Engineering of UC Santa Cruz). Starting with our participation in several genome Consortia (e.g. Mouse, Rat, Chicken), we used sequence and alignment data to investigate various aspects of evolution and function. Among others, I have been involved in projects concerning alignment scoring methodology, estimation of the share of the human genome under purifying selection, genome-wide computational prediction of regulatory elements (see ESPERR and RP scores), local variation and co-variation of divergence processes and the determinants of mutagenesis, X chromosome inactivation, etc. Recently, we have begun utilizing data from next generation sequencing technologies both in our studies of mutagenesis and genome dynamics, and in studies associating epigenomic signatures to sequence, alignment and transcriptional information. We are also initiating projects in which genomic information is linked to aspects of the spatio-temporal dynamics of infectious diseases, investigated in in vitro and in vivo systems. Representative publications.
MY WORK IN METEOROLOGY: Through an NSF funded collaboration with Jenni Evans (Meteorology, PSU), I also work on the application of dimension reduction, clustering, regression and re-sampling methods to large-scale meteorological data. In particular, we investigate the structure and lifecycle evolution of cyclones with a focus on the process of extra-tropical transition. Representative publications.
(last updated Sept 2010)