Jack O'Brien

Associate Professor of Mathematics

Jack O'Brien

Contact Information


Searles Science Building - 202

Teaching this semester

MATH 1300. Biostatistics

An introduction to the statistical methods used in the life sciences. Emphasizes conceptual understanding and includes topics from exploratory data analysis, the planning and design of experiments, probability, and statistical inference. One and two sample t-procedures and their non-parametric analogs, one-way ANOVA, simple linear regression, goodness of fit tests, and the chi-square test for independence are discussed. An average of four to five hours of class meetings and computer laboratory sessions per week. Not open to students who have credit for Mathematics 1200 or have credit or are concurrently enrolled in Mathematics 1400.

MATH 2206. Probability

A study of the mathematical models used to formalize nondeterministic or “chance” phenomena. General topics include combinatorial models, probability spaces, conditional probability, discrete and continuous random variables, independence and expected values. Specific probability densities, such as the binomial, Poisson, exponential, and normal, are discussed in depth.


  • Ph.D., Biomathematics, University of California, Los Angeles, 2008
  • B.A., Mathematics (Honors), Pomona College, 2002

Selected Publications

MalariaGEN Consortium (statistician). “Next-generation sequencing reveals the world-wide population structure of Plasmodium falciparum .” Nature. forthcoming

Vladimir Minin, John D. O’Brien, Arseni Seregin. 2011. “Imputation estimators partially correct for model misspecification.” Statistical Applications in Genetics and Molecular Biology. (10):1201-1218.

John D. O’Brien, Vladimir N. Minin, and Marc A. Suchard. 2009. “Learning to count: robust estimates for labeled distances between molecular sequences”, Molecular Biology and Evolution, (26):801-814.

John D. O’Brien, Zhen-Su She, and Marc A Suchard. 2008. “Dating the time of viral subtype divergence.” BMC Evolutionary Biology, (8).

Zhu Yang, John D. OBrien (joint first author), Xiao-Bin Zheng, Huai-Qu Zhu, Zhen-Su She. 2007. “Tree and rate estimation by local evaluation of heterochronous nucleotide data.” Bioinformatics, (23):169-176;


Genetic Epidemiology of Malaria Conference June 2012
• “Testing pipelines with crosses.” (Invited)

International Biogeographic Society Conference September 2011 
• “Towards a reconstruction of the historical migration patterns of P. falciparum through its organelles.” (Contributed)

Bristol Complexity Seminar March 2010
• “Simulataneously estimating mircrobial ecology and evolution.” (Invited)

Oxford Mathematical Biology Seminar November 2009
• “The lineage model for microbial community composition.” (Invited)

Joint Statistical Meeting August 2009
• “The lineage model for microbial community composition.” (Contributed)

Stochastic Processes and their Applications General Meeting August 2009
• “A more general model of the evolution of influenza subtypes.” (Contributed)

Gordon Research Conference in Applied Microbiology July 2009
• “A Bayesian model for metagenomic population structure.” (Contributed)

University of Bath June 2009
• “Phylogenetics and GMRFs to model conformational changes.” (Invited)

European Bioinformatics Institute October 2008
• “Robust counting for unusual distances.” (Invited)

Centers for Disease Control - Influenza Division April 2008
• “Modeling distance, rates and nonneutrality in viral systems.” (Invited)

Joint Statistical Meeting July 2007
• “Counting codon changes carefully: Markov-chain-induced counting processes for robust distance estimation.” (Contributed)

Peking University - Center for Theoretical Biology July 2006 
• “Watching change in influenza A viruses.” (Invited)

DIMACS Workshop on Rapidly Evolving Pathogens July 2006 
• “Characterizing the rate of nucleotide substitution along branches in inuenza phylogenies.” (Contributed)

Society for Molecular Biology and Evolution General Meeting May 2006
• “Breaking the molecular clock (assumption).” (Contributed)

University of Bergen - Department of Lingusitics March 2003
• “Cognitive aspects of the grammar of Norwegian Sign Language.” (Invited)


  • Royal Society:  International Travel Grant, 2009
  • University of California: Chancellor’s Fellowship, 2003-2004 and 2007-2008
  • National Institutes of Health:  NIH Systems and Integrative Biology Fellowship, 2004-2007
  • Fulbright Scholar, Norway, 2002-2003
  • Pomona College, Department of Mathematics: Honors Thesis, 2002