John D. O'Brien
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Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia
O Miotto, J Almagro-Garcia, M Manske, B MacInnis, S Campino, ...
Nature genetics 45 (6), 648-655, 2013
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing
M Manske, O Miotto, S Campino, S Auburn, J Almagro-Garcia, G Maslen, ...
Nature 487 (7407), 375-379, 2012
Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum
A Miles, Z Iqbal, P Vauterin, R Pearson, S Campino, M Theron, K Gould, ...
Genome research 26 (9), 1288-1299, 2016
Learning to count: robust estimates for labeled distances between molecular sequences
JD O'Brien, VN Minin, MA Suchard
Molecular biology and evolution 26 (4), 801-814, 2009
Efficient depletion of host DNA contamination in malaria clinical sequencing
SO Oyola, Y Gu, M Manske, TD Otto, J O'Brien, D Alcock, B MacInnis, ...
Journal of clinical microbiology 51 (3), 745-751, 2013
Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study
CM Ndila, S Uyoga, AW Macharia, G Nyutu, N Peshu, J Ojal, M Shebe, ...
The Lancet Haematology 5 (8), e333-e345, 2018
Tree and rate estimation by local evaluation of heterochronous nucleotide data
Z Yang, JD O'Brien, X Zheng, HQ Zhu, ZS She
Bioinformatics 23 (2), 169-176, 2007
A genome wide association study of Plasmodium falciparum susceptibility to 22 antimalarial drugs in Kenya
JP Wendler, J Okombo, R Amato, O Miotto, SM Kiara, L Mwai, L Pole, ...
PloS one 9 (5), e96486, 2014
Hydrodynamic mean-field solutions of 1D exclusion processes with spatially varying hopping rates
G Lakatos, J O'Brien, T Chou
Journal of Physics A: Mathematical and General 39 (10), 2253, 2006
A Bayesian approach to inferring the phylogenetic structure of communities from metagenomic data
JD O’Brien, X Didelot, Z Iqbal, L Amenga-Etego, B Ahiska, D Falush
Genetics 197 (3), 925-937, 2014
Dating the time of viral subtype divergence
J D O'Brien, ZS She, MA Suchard
BMC evolutionary biology 8 (1), 1-9, 2008
Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data
JD O’Brien, Z Iqbal, J Wendler, L Amenga-Etego
PLoS computational biology 12 (6), e1004824, 2016
Topological Symmetry Groups of K_ {4r+ 3}
D Chambers, E Flapan, JD O'Brien
arXiv preprint arXiv:0911.2794, 2009
The power and pitfalls of Dirichlet-multinomial mixture models for ecological count data
JD O’Brien, NR Record, P Countway
bioRxiv, 045468, 2016
Approaches to estimating inbreeding coefficients in clinical isolates of Plasmodium falciparum from genomic sequence data
JD O’Brien, L Amenga-Etego, R Li
Malaria journal 15 (1), 1-10, 2016
Omic-style statistical clustering reveals old and new patterns in the Gulf of Maine ecosystem
NR Record, JD O’Brien, K Stamieszkin, JA Runge
Canadian Journal of Fisheries and Aquatic Sciences 74 (7), 973-979, 2017
Genome variation and meiotic recombination in Plasmodium falciparum: insights from deep sequencing of genetic crosses
A Miles, Z Iqbal, P Vauterin, R Pearson, S Campino, M Theron, K Gould, ...
bioRxiv, 024182, 2015
An integrative statistical model for inferring strain admixture within clinical Plasmodium falciparum isolates
JD O'Brien, Z Iqbal, L Amenga-Etego
arXiv preprint arXiv:1505.08171, 2015
Imputation estimators partially correct for model misspecification
VN Minin, JD O'Brien, A Seregin
Statistical Applications in Genetics and Molecular Biology 10 (1), 2011
Correlative FRET: new method improves rigor and reproducibility in determining distances within synaptic nanoscale architecture
H Shinogle-Decker, N Martinez-Rivera, J O'Brien, RD Powell, VN Joshi, ...
Three-Dimensional and Multidimensional Microscopy: Image Acquisition and …, 2018
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