Joel Wertheim
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Detecting individual sites subject to episodic diversifying selection
B Murrell, JO Wertheim, S Moola, T Weighill, K Scheffler, SLK Pond
PLoS genet 8 (7), e1002764, 2012
Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection
MD Smith, JO Wertheim, S Weaver, B Murrell, K Scheffler, ...
Molecular biology and evolution 32 (5), 1342-1353, 2015
RELAX: detecting relaxed selection in a phylogenetic framework
JO Wertheim, B Murrell, MD Smith, SL Kosakovsky Pond, K Scheffler
Molecular biology and evolution 32 (3), 820-832, 2015
Dating the age of the SIV lineages that gave rise to HIV-1 and HIV-2
JO Wertheim, M Worobey
PLoS Comput Biol 5 (5), e1000377, 2009
Gene-wide identification of episodic selection
B Murrell, S Weaver, MD Smith, JO Wertheim, S Murrell, A Aylward, ...
Molecular biology and evolution 32 (5), 1365-1371, 2015
The global transmission network of HIV-1
JO Wertheim, AJ Leigh Brown, NL Hepler, SR Mehta, DD Richman, ...
The Journal of infectious diseases 209 (2), 304-313, 2014
Purifying selection can obscure the ancient age of viral lineages
JO Wertheim, SL Kosakovsky Pond
Molecular biology and evolution 28 (12), 3355-3365, 2011
A case for the ancient origin of coronaviruses
JO Wertheim, DKW Chu, JSM Peiris, SLK Pond, LLM Poon
Journal of Virology 87 (12), 7039-7045, 2013
HIV-TRACE (TRAnsmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens
SL Kosakovsky Pond, S Weaver, AJ Leigh Brown, JO Wertheim
Molecular biology and evolution 35 (7), 1812-1819, 2018
Using molecular HIV surveillance data to understand transmission between subpopulations in the United States
AM Oster, JO Wertheim, AL Hernandez, MCB Ocfemia, N Saduvala, ...
Journal of acquired immune deficiency syndromes (1999) 70 (4), 444, 2015
Social and genetic networks of HIV-1 transmission in New York City
JO Wertheim, SL Kosakovsky Pond, LA Forgione, SR Mehta, B Murrell, ...
PLoS pathogens 13 (1), e1006000, 2017
Using HIV networks to inform real time prevention interventions
SJ Little, SLK Pond, CM Anderson, JA Young, JO Wertheim, SR Mehta, ...
PloS one 9 (6), e98443, 2014
Evolutionary origins of human herpes simplex viruses 1 and 2
JO Wertheim, MD Smith, DM Smith, K Scheffler, SLK Pond
Molecular biology and evolution, msu185, 2014
The emergence of SARS-CoV-2 in Europe and North America
M Worobey, J Pekar, BB Larsen, MI Nelson, V Hill, JB Joy, A Rambaut, ...
Science 370 (6516), 564-570, 2020
Relaxed molecular clocks, the bias–variance trade-off, and the quality of phylogenetic inference
JO Wertheim, MJ Sanderson, M Worobey, A Bjork
Systematic biology 59 (1), 1-8, 2010
The sordid affair between human herpesvirus and HIV
S Gianella, M Massanella, JO Wertheim, DM Smith
The Journal of infectious diseases 212 (6), 845-852, 2015
Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy
JO Wertheim, M Fourment, SL Kosakovsky Pond
Molecular biology and evolution 29 (2), 451-456, 2012
Evolutionary history of chimpanzees inferred from complete mitochondrial genomes
A Bjork, W Liu, JO Wertheim, BH Hahn, M Worobey
Molecular biology and evolution 28 (1), 615-623, 2011
A challenge to the ancient origin of SIVagm based on African green monkey mitochondrial genomes
JO Wertheim, M Worobey
PLoS pathogens 3 (7), e95, 2007
Targeting HIV prevention based on molecular epidemiology among deeply sampled subnetworks of men who have sex with men
X Wang, Y Wu, L Mao, W Xia, W Zhang, L Dai, SR Mehta, JO Wertheim, ...
Clinical Infectious Diseases 61 (9), 1462-1468, 2015
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