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Relative evolutionary rate inference in HyPhy with LEISR.

Spielman SJ, Kosakovsky Pond SL.

PeerJ. 2018 Feb 5;6:e4339. doi: 10.7717/peerj.4339. eCollection 2018.


HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.

Kosakovsky Pond SL, Weaver S, Leigh Brown AJ, Wertheim JO.

Mol Biol Evol. 2018 Jan 31. doi: 10.1093/molbev/msy016. [Epub ahead of print]


Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes.

Weaver S, Shank SD, Spielman SJ, Li M, Muse SV, Kosakovsky Pond SL.

Mol Biol Evol. 2018 Jan 2. doi: 10.1093/molbev/msx335. [Epub ahead of print]


Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites.

Pacheco MA, Matta NE, Valkiunas G, Parker PG, Mello B, Stanley CE Jr, Lentino M, Garcia-Amado MA, Cranfield M, Kosakovsky Pond SL, Escalante AA.

Mol Biol Evol. 2018 Feb 1;35(2):383-403. doi: 10.1093/molbev/msx285.


Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas.

Forrester NL, Wertheim JO, Dugan VG, Auguste AJ, Lin D, Adams AP, Chen R, Gorchakov R, Leal G, Estrada-Franco JG, Pandya J, Halpin RA, Hari K, Jain R, Stockwell TB, Das SR, Wentworth DE, Smith MD, Kosakovsky Pond SL, Weaver SC.

PLoS Negl Trop Dis. 2017 Aug 3;11(8):e0005693. doi: 10.1371/journal.pntd.0005693. eCollection 2017 Aug.


Intrasubtype B HIV-1 Superinfection Correlates with Delayed Neutralizing Antibody Response.

Wagner GA, Landais E, Caballero G, Phung P, Kosakovsky Pond SL, Poignard P, Richman DD, Little SJ, Smith DM.

J Virol. 2017 Aug 10;91(17). pii: e00475-17. doi: 10.1128/JVI.00475-17. Print 2017 Sep 1.


Genotype-Specific Evolution of Hepatitis E Virus.

Brayne AB, Dearlove BL, Lester JS, Kosakovsky Pond SL, Frost SD.

J Virol. 2017 Apr 13;91(9). pii: e02241-16. doi: 10.1128/JVI.02241-16. Print 2017 May 1.


Social and Genetic Networks of HIV-1 Transmission in New York City.

Wertheim JO, Kosakovsky Pond SL, Forgione LA, Mehta SR, Murrell B, Shah S, Smith DM, Scheffler K, Torian LV.

PLoS Pathog. 2017 Jan 9;13(1):e1006000. doi: 10.1371/journal.ppat.1006000. eCollection 2017 Jan.


Partner services in adults with acute and early HIV infection.

Green N, Hoenigl M, Chaillon A, Anderson CM, Kosakovsky Pond SL, Smith DM, Little SJ.

AIDS. 2017 Jan 14;31(2):287-293. doi: 10.1097/QAD.0000000000001308.


HIV-associated neurocognitive disorder is associated with HIV-1 dual infection.

Wagner GA, Chaillon A, Liu S, Franklin DR Jr, Caballero G, Kosakovsky Pond SL, Vaida F, Heaton RK, Letendre SL, Grant I, Richman DD, Smith DM.

AIDS. 2016 Nov 13;30(17):2591-2597.


Compartmentalized HIV rebound in the central nervous system after interruption of antiretroviral therapy.

Gianella S, Kosakovsky Pond SL, Oliveira MF, Scheffler K, Strain MC, De la Torre A, Letendre S, Smith DM, Ellis RJ.

Virus Evol. 2016 Aug 3;2(2):vew020. eCollection 2016 Jul.


Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples.

Laird Smith M, Murrell B, Eren K, Ignacio C, Landais E, Weaver S, Phung P, Ludka C, Hepler L, Caballero G, Pollner T, Guo Y, Richman D; IAVI Protocol C Investigators & The IAVI African HIV Research Network, Poignard P, Paxinos EE, Kosakovsky Pond SL, Smith DM.

Virus Evol. 2016 Jul 8;2(2):vew018. doi: 10.1093/ve/vew018. eCollection 2016 Jul.


Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch.

MacLeod DT, Choi NM, Briney B, Garces F, Ver LS, Landais E, Murrell B, Wrin T, Kilembe W, Liang CH, Ramos A, Bian CB, Wickramasinghe L, Kong L, Eren K, Wu CY, Wong CH; IAVI Protocol C Investigators & The IAVI African HIV Research Network, Kosakovsky Pond SL, Wilson IA, Burton DR, Poignard P.

Immunity. 2016 May 17;44(5):1215-26. doi: 10.1016/j.immuni.2016.04.016.


Using HIV Sequence and Epidemiologic Data to Assess the Effect of Self-referral Testing for Acute HIV Infection on Incident Diagnoses in San Diego, California.

Mehta SR, Murrell B, Anderson CM, Kosakovsky Pond SL, Wertheim JO, Young JA, Freitas L, Richman DD, Mathews WC, Scheffler K, Little SJ, Smith DM.

Clin Infect Dis. 2016 Jul 1;63(1):101-107. doi: 10.1093/cid/ciw161. Epub 2016 May 11.


Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus.

Tully DC, Ogilvie CB, Batorsky RE, Bean DJ, Power KA, Ghebremichael M, Bedard HE, Gladden AD, Seese AM, Amero MA, Lane K, McGrath G, Bazner SB, Tinsley J, Lennon NJ, Henn MR, Brumme ZL, Norris PJ, Rosenberg ES, Mayer KH, Jessen H, Kosakovsky Pond SL, Walker BD, Altfeld M, Carlson JM, Allen TM.

PLoS Pathog. 2016 May 10;12(5):e1005619. doi: 10.1371/journal.ppat.1005619. eCollection 2016 May.


Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort.

Landais E, Huang X, Havenar-Daughton C, Murrell B, Price MA, Wickramasinghe L, Ramos A, Bian CB, Simek M, Allen S, Karita E, Kilembe W, Lakhi S, Inambao M, Kamali A, Sanders EJ, Anzala O, Edward V, Bekker LG, Tang J, Gilmour J, Kosakovsky-Pond SL, Phung P, Wrin T, Crotty S, Godzik A, Poignard P.

PLoS Pathog. 2016 Jan 14;12(1):e1005369. doi: 10.1371/journal.ppat.1005369. eCollection 2016 Jan.


Comparative Analysis of Cell-Associated HIV DNA Levels in Cerebrospinal Fluid and Peripheral Blood by Droplet Digital PCR.

de Oliveira MF, Gianella S, Letendre S, Scheffler K, Kosakovsky Pond SL, Smith DM, Strain M, Ellis RJ.

PLoS One. 2015 Oct 2;10(10):e0139510. doi: 10.1371/journal.pone.0139510. eCollection 2015.


Gene-wide identification of episodic selection.

Murrell B, Weaver S, Smith MD, Wertheim JO, Murrell S, Aylward A, Eren K, Pollner T, Martin DP, Smith DM, Scheffler K, Kosakovsky Pond SL.

Mol Biol Evol. 2015 May;32(5):1365-71. doi: 10.1093/molbev/msv035. Epub 2015 Feb 19.


Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection.

Smith MD, Wertheim JO, Weaver S, Murrell B, Scheffler K, Kosakovsky Pond SL.

Mol Biol Evol. 2015 May;32(5):1342-53. doi: 10.1093/molbev/msv022. Epub 2015 Feb 19.


Next generation sequencing improves detection of drug resistance mutations in infants after PMTCT failure.

Fisher RG, Smith DM, Murrell B, Slabbert R, Kirby BM, Edson C, Cotton MF, Haubrich RH, Kosakovsky Pond SL, Van Zyl GU.

J Clin Virol. 2015 Jan;62:48-53. doi: 10.1016/j.jcv.2014.11.014. Epub 2014 Nov 20.


RELAX: detecting relaxed selection in a phylogenetic framework.

Wertheim JO, Murrell B, Smith MD, Kosakovsky Pond SL, Scheffler K.

Mol Biol Evol. 2015 Mar;32(3):820-32. doi: 10.1093/molbev/msu400. Epub 2014 Dec 23.


IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform.

Hepler NL, Scheffler K, Weaver S, Murrell B, Richman DD, Burton DR, Poignard P, Smith DM, Kosakovsky Pond SL.

PLoS Comput Biol. 2014 Sep 25;10(9):e1003842. doi: 10.1371/journal.pcbi.1003842. eCollection 2014 Sep.


Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2.

Nayak A, Pattabiraman N, Fadra N, Goldman R, Kosakovsky Pond SL, Mazumder R.

J Biomol Struct Dyn. 2015;33(8):1682-94. doi: 10.1080/07391102.2014.967300. Epub 2014 Oct 15.


Evolutionary origins of human herpes simplex viruses 1 and 2.

Wertheim JO, Smith MD, Smith DM, Scheffler K, Kosakovsky Pond SL.

Mol Biol Evol. 2014 Sep;31(9):2356-64. doi: 10.1093/molbev/msu185. Epub 2014 Jun 10.


Using HIV networks to inform real time prevention interventions.

Little SJ, Kosakovsky Pond SL, Anderson CM, Young JA, Wertheim JO, Mehta SR, May S, Smith DM.

PLoS One. 2014 Jun 5;9(6):e98443. doi: 10.1371/journal.pone.0098443. eCollection 2014.


On the validity of evolutionary models with site-specific parameters.

Scheffler K, Murrell B, Kosakovsky Pond SL.

PLoS One. 2014 Apr 10;9(4):e94534. doi: 10.1371/journal.pone.0094534. eCollection 2014.


Neuropathy- and myopathy-associated mutations in human small heat shock proteins: Characteristics and evolutionary history of the mutation sites.

Benndorf R, Martin JL, Kosakovsky Pond SL, Wertheim JO.

Mutat Res Rev Mutat Res. 2014 Mar 6. pii: S1383-5742(14)00018-0. doi: 10.1016/j.mrrev.2014.02.004. [Epub ahead of print] Review.


Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States.

Wagner GA, Pacold ME, Kosakovsky Pond SL, Caballero G, Chaillon A, Rudolph AE, Morris SR, Little SJ, Richman DD, Smith DM.

J Infect Dis. 2014 Apr 1;209(7):1032-8. doi: 10.1093/infdis/jit633. Epub 2013 Nov 22. Erratum in: J Infect Dis. 2014 Oct 1;210(7):1166.


The global transmission network of HIV-1.

Wertheim JO, Leigh Brown AJ, Hepler NL, Mehta SR, Richman DD, Smith DM, Kosakovsky Pond SL.

J Infect Dis. 2014 Jan 15;209(2):304-13. doi: 10.1093/infdis/jit524. Epub 2013 Oct 22.


Dynamics of viral evolution and neutralizing antibody response after HIV-1 superinfection.

Chaillon A, Wagner GA, Hepler NL, Little SJ, Kosakovsky Pond SL, Caballero G, Pacold ME, Phung P, Wrin T, Richman DD, Wertheim JO, Smith DM.

J Virol. 2013 Dec;87(23):12737-44. doi: 10.1128/JVI.02260-13. Epub 2013 Sep 18.


Suppressors of RNAi from plant viruses are subject to episodic positive selection.

Murray GG, Kosakovsky Pond SL, Obbard DJ.

Proc Biol Sci. 2013 Jun 26;280(1765):20130965. doi: 10.1098/rspb.2013.0965. Print 2013 Aug 22.


Using ultradeep pyrosequencing to study HIV-1 coreceptor usage in primary and dual infection.

Wagner GA, Pacold ME, Vigil E, Caballero G, Morris SR, Kosakovsky Pond SL, Little SJ, Richman DD, Gianella S, Smith DM.

J Infect Dis. 2013 Jul 15;208(2):271-4. doi: 10.1093/infdis/jit168. Epub 2013 Apr 18.


A case for the ancient origin of coronaviruses.

Wertheim JO, Chu DK, Peiris JS, Kosakovsky Pond SL, Poon LL.

J Virol. 2013 Jun;87(12):7039-45. doi: 10.1128/JVI.03273-12. Epub 2013 Apr 17.


FUBAR: a fast, unconstrained bayesian approximation for inferring selection.

Murrell B, Moola S, Mabona A, Weighill T, Sheward D, Kosakovsky Pond SL, Scheffler K.

Mol Biol Evol. 2013 May;30(5):1196-205. doi: 10.1093/molbev/mst030. Epub 2013 Feb 18.


Phylogenetic relatedness of HIV-1 donor and recipient populations.

Wertheim JO, Scheffler K, Choi JY, Smith DM, Kosakovsky Pond SL.

J Infect Dis. 2013 Apr;207(7):1181-2. doi: 10.1093/infdis/jit021. Epub 2013 Jan 11. No abstract available.


A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection.

Lemey P, Minin VN, Bielejec F, Kosakovsky Pond SL, Suchard MA.

Bioinformatics. 2012 Dec 15;28(24):3248-56. doi: 10.1093/bioinformatics/bts580. Epub 2012 Oct 12.


Sexual transmission of predicted CXCR4-tropic HIV-1 likely originating from the source partner's seminal cells.

Gianella S, Mehta SR, Young JA, Vargas MV, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM.

Virology. 2012 Dec 5;434(1):2-4. doi: 10.1016/j.virol.2012.09.010. Epub 2012 Oct 3.


Higher HIV-1 genetic diversity is associated with AIDS and neuropsychological impairment.

Hightower GK, Wong JK, Letendre SL, Umlauf AA, Ellis RJ, Ignacio CC, Heaton RK, Collier AC, Marra CM, Clifford DB, Gelman BB, McArthur JC, Morgello S, Simpson DM, McCutchan JA, Grant I, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM; CHARTER Study Group.

Virology. 2012 Nov 25;433(2):498-505. doi: 10.1016/j.virol.2012.08.028. Epub 2012 Sep 20.


Impact of seminal cytomegalovirus replication on HIV-1 dynamics between blood and semen.

Gianella S, Mehta SR, Strain MC, Young JA, Vargas MV, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM.

J Med Virol. 2012 Nov;84(11):1703-9. doi: 10.1002/jmv.23398.


Detecting individual sites subject to episodic diversifying selection.

Murrell B, Wertheim JO, Moola S, Weighill T, Scheffler K, Kosakovsky Pond SL.

PLoS Genet. 2012;8(7):e1002764. doi: 10.1371/journal.pgen.1002764. Epub 2012 Jul 12.


In vivo VL-targeted microbial superantigen induced global shifts in the B cell repertoire.

Grönwall C, Kosakovsky Pond SL, Young JA, Silverman GJ.

J Immunol. 2012 Jul 15;189(2):850-9. doi: 10.4049/jimmunol.1200245. Epub 2012 Jun 13.


Modeling HIV-1 drug resistance as episodic directional selection.

Murrell B, de Oliveira T, Seebregts C, Kosakovsky Pond SL, Scheffler K; Southern African Treatment and Resistance Network-SATuRN Consortium.

PLoS Comput Biol. 2012;8(5):e1002507. doi: 10.1371/journal.pcbi.1002507. Epub 2012 May 10.


Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen.

Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, Engelbrech S, Murrell B, Scheffler K, Smith D.

J Virol. 2012 Jun;86(11):6231-7. doi: 10.1128/JVI.06541-11. Epub 2012 Mar 28.


Associations between phylogenetic clustering and HLA profile among HIV-infected individuals in San Diego, California.

Mehta SR, Kosakovsky Pond SL, Young JA, Richman D, Little S, Smith DM.

J Infect Dis. 2012 May 15;205(10):1529-33. doi: 10.1093/infdis/jis231. Epub 2012 Mar 23.


Using HIV transmission networks to investigate community effects in HIV prevention trials.

Wertheim JO, Kosakovsky Pond SL, Little SJ, De Gruttola V.

PLoS One. 2011;6(11):e27775. doi: 10.1371/journal.pone.0027775. Epub 2011 Nov 16.


Inconsistencies in estimating the age of HIV-1 subtypes due to heterotachy.

Wertheim JO, Fourment M, Kosakovsky Pond SL.

Mol Biol Evol. 2012 Feb;29(2):451-6. doi: 10.1093/molbev/msr266. Epub 2011 Oct 31.


Statistics and truth in phylogenomics.

Kumar S, Filipski AJ, Battistuzzi FU, Kosakovsky Pond SL, Tamura K.

Mol Biol Evol. 2012 Feb;29(2):457-72. doi: 10.1093/molbev/msr202. Epub 2011 Aug 26. Review.


A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses.

Goto H, Ryder OA, Fisher AR, Schultz B, Kosakovsky Pond SL, Nekrutenko A, Makova KD.

Genome Biol Evol. 2011;3:1096-106. doi: 10.1093/gbe/evr067. Epub 2011 Jul 29.


Purifying selection can obscure the ancient age of viral lineages.

Wertheim JO, Kosakovsky Pond SL.

Mol Biol Evol. 2011 Dec;28(12):3355-65. doi: 10.1093/molbev/msr170. Epub 2011 Jun 24.


A random effects branch-site model for detecting episodic diversifying selection.

Kosakovsky Pond SL, Murrell B, Fourment M, Frost SD, Delport W, Scheffler K.

Mol Biol Evol. 2011 Nov;28(11):3033-43. doi: 10.1093/molbev/msr125. Epub 2011 Jun 13.

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