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Items: 1 to 50 of 98

1.

A new method for inferring timetrees from temporally sampled molecular sequences.

Miura S, Tamura K, Tao Q, Huuki LA, Kosakovsky Pond SL, Priest J, Deng J, Kumar S.

PLoS Comput Biol. 2020 Jan 17;16(1):e1007046. doi: 10.1371/journal.pcbi.1007046. [Epub ahead of print]

2.

Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates.

Yan Y, Maurer-Alcalá XX, Knight R, Kosakovsky Pond SL, Katz LA.

mBio. 2019 Dec 24;10(6). pii: e02524-19. doi: 10.1128/mBio.02524-19.

3.

A structural basis for antibody-mediated neutralization of Nipah virus reveals a site of vulnerability at the fusion glycoprotein apex.

Avanzato VA, Oguntuyo KY, Escalera-Zamudio M, Gutierrez B, Golden M, Kosakovsky Pond SL, Pryce R, Walter TS, Seow J, Doores KJ, Pybus OG, Munster VJ, Lee B, Bowden TA.

Proc Natl Acad Sci U S A. 2019 Dec 10;116(50):25057-25067. doi: 10.1073/pnas.1912503116. Epub 2019 Nov 25.

4.

HyPhy 2.5 - a customizable platform for evolutionary hypothesis testing using phylogenies.

Kosakovsky Pond SL, Poon AFY, Velazquez R, Weaver S, Hepler NL, Murrell B, Shank SD, Magalis BR, Bouvier D, Nekrutenko A, Wisotsky S, Spielman SJ, Frost SDW, Muse SV.

Mol Biol Evol. 2019 Aug 27. pii: msz197. doi: 10.1093/molbev/msz197. [Epub ahead of print]

PMID:
31504749
5.

Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces.

Spielman SJ, Weaver S, Shank SD, Magalis BR, Li M, Kosakovsky Pond SL.

Methods Mol Biol. 2019;1910:427-468. doi: 10.1007/978-1-4939-9074-0_14.

PMID:
31278673
6.

National and International Dimensions of Human Immunodeficiency Virus-1 Sequence Clusters in a Northern California Clinical Cohort.

Rhee SY, Magalis BR, Hurley L, Silverberg MJ, Marcus JL, Slome S, Kosakovsky Pond SL, Shafer RW.

Open Forum Infect Dis. 2019 Mar 14;6(4):ofz135. doi: 10.1093/ofid/ofz135. eCollection 2019 Apr.

7.

Combining Phylogenetic and Network Approaches to Identify HIV-1 Transmission Links in San Mateo County, California.

Dalai SC, Junqueira DM, Wilkinson E, Mehra R, Kosakovsky Pond SL, Levy V, Israelski D, de Oliveira T, Katzenstein D.

Front Microbiol. 2018 Dec 6;9:2799. doi: 10.3389/fmicb.2018.02799. eCollection 2018.

8.

Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons.

Eren K, Weaver S, Ketteringham R, Valentyn M, Laird Smith M, Kumar V, Mohan S, Kosakovsky Pond SL, Murrell B.

PLoS Comput Biol. 2018 Dec 13;14(12):e1006498. doi: 10.1371/journal.pcbi.1006498. eCollection 2018 Dec.

9.

phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics.

Shank SD, Weaver S, Kosakovsky Pond SL.

BMC Bioinformatics. 2018 Jul 25;19(1):276. doi: 10.1186/s12859-018-2283-2.

10.

Growth of HIV-1 Molecular Transmission Clusters in New York City.

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

J Infect Dis. 2018 Nov 5;218(12):1943-1953. doi: 10.1093/infdis/jiy431.

11.

Evaluation of global HIV/SIV envelope gp120 RNA structure and evolution within and among infected hosts.

Rife Magalis B, Kosakovsky Pond SL, Summers MF, Salemi M.

Virus Evol. 2018 Jun 21;4(1):vey018. doi: 10.1093/ve/vey018. eCollection 2018 Jan.

12.

Relative evolutionary rates in proteins are largely insensitive to the substitution model.

Spielman SJ, Kosakovsky Pond SL.

Mol Biol Evol. 2018 Jun 19. doi: 10.1093/molbev/msy127. [Epub ahead of print]

13.

Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population.

Rhee SY, Clutter D, Fessel WJ, Klein D, Slome S, Pinsky BA, Marcus JL, Hurley L, Silverberg MJ, Kosakovsky Pond SL, Shafer RW.

Clin Infect Dis. 2019 Jan 7;68(2):213-221. doi: 10.1093/cid/ciy453.

14.

Neutral Theory and Rapidly Evolving Viral Pathogens.

Frost SDW, Magalis BR, Kosakovsky Pond SL.

Mol Biol Evol. 2018 Jun 1;35(6):1348-1354. doi: 10.1093/molbev/msy088.

15.

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.

16.

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 Jul 1;35(7):1812-1819. doi: 10.1093/molbev/msy016.

17.

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 Mar 1;35(3):773-777. doi: 10.1093/molbev/msx335.

18.

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.

19.

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.

20.

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.

21.

Genotype-Specific Evolution of Hepatitis E Virus.

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

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

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

31.

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.

32.

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.

33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

42.

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.

43.

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.

44.

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.

45.

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.

46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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