Jon David McAuliffe Faculty Profile

Jon David McAuliffe
Assistant Professor of Statistics

PhD, University of California, Berkeley, 2005; MS, Harvard University, 1995; BA, Harvard University, 1995

Research Areas
Comparative genomics; methods for bioinformatics; nonparametric inference; statistical computing

Current Projects
Analysis of the relationship between phylogenetic tree structure and the power to detect evolutionary conservation. Implications for choosing species to sequence. Efforts to synthesize phylogenetic substitution models and hidden Markov models of biological function: multi-species gene finding, multi-species cis-regulatory module detection. Smooth nonparametric empirical Bayes for Dirichlet process mixture models.

Other Positions
Statistician, Affymetrix, summer 2003; Statistician, Amazon.com, 1999-2000; Quantitative analyst, D. E. Shaw & Co., 1995-1999

Career and Recent Professional Awards; Teaching Awards
Lehmann Citation for outstanding thesis in theoretical statistics, UC Berkeley Statistics Department, 2005; Regents Fellow, University of California, 2000-2004; Outstanding Graduate Student Instructor, UC Berkeley, 2003; Outstanding Teaching Fellow, Harvard CUE Guide, 1994

Representative Publications
(with M. I. Jordan and L. Pachter)
“Subtree Power Analysis and Species Selection for Comparative Genomics.” Proc. of the National Academy of Sciences 102(22): 7900-5 (May 31, 2005).

(with L. Pachter and M. I. Jordan
“Multiple-Sequence Functional Annotation and the Generalized Hidden Markov Phylogeny.” Bioinformatics 20(12): 1850-60 (August 12, 2004).

(with D. Boffelli, D. Ovcharenko, K.D. Lewis, I. Ovcharenko, L. Pachter, and E.M. Rubin)
“Phylogenetic shadowing of primate sequences to find functional regions of the human genome.” Science 299(5611): 1391-4 (Feburary 28, 2003).

(with P.L. Bartlett and M.I. Jordan)
“Convexity, Classification, and Risk Bounds.” Journal of the American Statistical Association (forthcoming).