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Publications

I publish as John D. O’Brien

Full list also on Google Scholar.

In draft

  • John O’Brien. “The topological analysis of mixture models.”
  • John O’Brien and Aaron Kaufman. “The shape of local political space.”

Peer-reviewed publications

  • John D. O’Brien. 2026. “A Bayesian mixture model captures temporal and spatial structure of voting blocs within longitudinal referendum data.” Political Science Research and Methods, 1–22. doi:10.1017/psrm.2025.10050. [journal] [arXiv]
  • Felicia McBride, Nur Schettino, John D. O’Brien, Wilder Harwood, Liz Perot, Grant Temple, Hugo Ayalo Solares, et al. 2025. “A radio-quiet AGN as a candidate counterpart to neutrino event IceCube–200615A.” Monthly Notices of the Royal Astronomical Society 541(2). [journal]
  • Dhiraj Murthy, John D. O’Brien, Alex Gross, Nathan Meyers. 2021. “Variations in the temporal structure of sociability across American cities.” Sociology 55(1): 30–55. Nominated for paper of the year by the British Sociological Association.
  • Nicholas Record, John D. O’Brien, Karen Stamieszkin, Jeffrey A. Runge. 2019. “Omic-style statistical clustering reveals old and new patterns in Gulf of Maine ecosystem.” Canadian Journal of Fisheries and Aquatic Sciences.
  • C. M. Ndila, S. Uyoga, A. W. Macharia, G. Nyutu, N. Peshu, J. Ojal, M. Shebe, et al. 2018. “Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study.” The Lancet Haematology 5(8): e333–e345.
  • John D. O’Brien, Lucas Amenga-Etego, Ruiqi Li. 2017. “Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data.” Malaria Journal 15(1): 473–484.
  • Alistair Miles, Zamin Iqbal, Paul Vauterin, Richard Pearson, Susanna Campino, Marie Theron, Keith Gould, Daniel Mead, Elizabeth Drury, John D. O’Brien, Valentin Rubio, et al. 2016. “Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum.” Genome Research 26(9): 1288–99.
  • John D. O’Brien, Kathryn Lin, Scott MacEachern. 2016. “Mixture model of pottery decorations from Lake Chad Basin archaeological sites reveals ancient segregation patterns.” Proceedings of the Royal Society B 283(1827): 2824.
  • John D. O’Brien, Zamin Iqbal, Jason Wendler, Lucas Amenga-Etego. 2016. “Inferring strain mixture within clinical Plasmodium falciparum isolates using genomic sequence data.” PLoS Computational Biology 12(6): e1004824.
  • Vladimir Douhovnikoff, Samuel Taylor, Eric Hazelton, Cindi Smith, John D. O’Brien. 2015. “Maximal stomatal conductance to water and plasticity in stomatal traits differ between native and invasive introduced lineages of Phragmites australis in North America.” AoB Plants 8: plw006.
  • John D. O’Brien, Xavier Didelot, Lucas Amenga-Etego, Zamin Iqbal, Daniel Falush. 2014. “A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data.” Genetics 10(3): 114–119.
  • Jason Wendler, John Okombo, Roberto Amato, Olivo Miotto, Steven Kiara, Leah Mwai, Lewa Pole, John D. O’Brien, Magnus Manske, Daniel Alcock, et al. 2014. “A genome-wide association study of Plasmodium falciparum susceptibility to 22 antimalarial drugs in Kenya.” PLoS ONE 9(5): e96486.
  • Olivo Miotto, Jacob Almagro-Garcia, Magnus Manske, Bronwyn MacInnis, Susana Campino, Kirk A. Rockett, Chanaki Amaratunga, et al. 2013. “Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia.” Nature Genetics 45(6): 648–655.
  • Samuel Oyola, Yong Gu, Magnus Manske, Thomas Otto, John D. O’Brien, Daniel Alcock, Bronwyn MacInnis, Matthew Berriman, Chris Newbold, Dominic Kwiatkowski, et al. 2013. “Efficient depletion of host DNA contamination in malaria clinical sequencing.” Journal of Clinical Microbiology 51(3): 745–751.
  • Magnus Manske, Olivo Miotto, Susanna Campino, Sarah Auburn, Jacob Almagro-Garcia, Gareth Maslen, John D. O’Brien, Abdoulaye Djimde, et al. 2012. “Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing.” Nature 487(7407): 375–9.
  • Vladimir Minin, John D. O’Brien, Arseni Seregin. 2011. “Imputation estimators partially correct for model misspecification.” Statistical Applications in Genetics and Molecular Biology 10(1): 1201–1218.
  • Dwayne Chambers, Erica Flapan, John D. O’Brien. 2010. “The topological symmetry groups of complete graphs with 4n+3 vertices.” Discrete and Continuous Dynamical Systems, Series S 4: 1401–1412.
  • John D. O’Brien, Vladimir N. Minin, 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, Marc A. Suchard. 2008. “Dating the time of viral subtype divergence.” BMC Evolutionary Biology 8(1): 172–179.
  • Zhu Yang, John D. O’Brien (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(1): 169–176.
  • Greg Lakatos, John D. O’Brien, Tom Chou. 2006. “Hydrodynamic mean field solutions of 1D exclusion processes with spatially varying hopping rates.” Journal of Physics A: Mathematical and General 39(10): 2253–2264.

Awards and fellowships

  • Royal Society International Travel Grant, 2009
  • University of California Chancellor’s Fellowship, 2003–2004 and 2007–2008
  • NIH Systems and Integrative Biology Fellowship, 2004–2007
  • Fulbright Scholar, U.S. Department of State, 2002–2003
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