Selected Publications

pf.inbreeding Lucas Amegna-Etego, Ruiqi Li, and John D. O’Brien. 2015. Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data. In draft.

pf.mixture  Zamin Iqbal, Lucas Amenga-Etego, and John D. O’Brien. 2015. An integrative statistical model for inferring strain admixture within clinical Plasmodium falciparum isolates. Under review.

lineage  John D. O’Brien, Xavier Didelot, Zamin Iqbal, Lucas Amenga-Etego, Bartu Ahiska, and Daniel Falush. 2014. A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data. Genetics. 197(3), 925-937.

pf.wgs  Magnus Manske et al. (statistician), 2012, Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing, Nature. 487(7407), 375-379.

tsg Dwayne Chambers, Erica Flapan, and John O’Brien. 2011. Topological symmetry groups of $K_{4r+ 3}$. Discrete and Continuous Dynamical Systems – Series S. 4(6), 1401-1411.

count John D O’Brien and Vladimir N. Minin and Marc A. Suchard, 2009. Learning to count: robust estimates for labeled distances between molecular sequences, Molecular Biology and Evolution. 26(4), 801-814.

treble John D. O’Brien and Zhen-Su She and Marc A. Suchard. 2008. Dating the time of viral subtype divergence. BMC evolutionary biology. 8(1). 172-177.

(Need link)  Zhu Yang* and John O’Brien*  and Xiaobin Zheng and Huai-Qiu Zhu and Zhen-Su She. 2007. Tree and rate estimation by local evaluation of heterochronous nucleotide data. Bioinformatics. 23(3), 169-176.

For a full list of my citations, see my Google Scholar citations:


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