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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]


Genome-Wide Patterns of Gene Expression in a Wild Primate Indicate Species-Specific Mechanisms Associated with Tolerance to Natural Simian Immunodeficiency Virus Infection.

Simons ND, Eick GN, Ruiz-Lopez MJ, Hyeroba D, Omeja PA, Weny G, Zheng H, Shankar A, Frost SDW, Jones JH, Chapman CA, Switzer WM, Goldberg TL, Sterner KN, Ting N.

Genome Biol Evol. 2019 Jun 1;11(6):1630-1643. doi: 10.1093/gbe/evz099.


Fast hierarchical Bayesian analysis of population structure.

Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J.

Nucleic Acids Res. 2019 Jun 20;47(11):5539-5549. doi: 10.1093/nar/gkz361.


RhierBAPS: An R implementation of the population clustering algorithm hierBAPS.

Tonkin-Hill G, Lees JA, Bentley SD, Frost SDW, Corander J.

Wellcome Open Res. 2018 Jul 30;3:93. doi: 10.12688/wellcomeopenres.14694.1. eCollection 2018.


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.


HIV seroprevalence, self-reported STIs and associated risk factors among men who have sex with men: a cross-sectional study in Rwanda, 2015.

Ntale RS, Rutayisire G, Mujyarugamba P, Shema E, Greatorex J, Frost SDW, Kaleebu P.

Sex Transm Infect. 2019 Feb;95(1):71-74. doi: 10.1136/sextrans-2017-053311. Epub 2018 Apr 21.


The role of venues in structuring HIV, sexually transmitted infections, and risk networks among men who have sex with men.

Drumright LN, Weir SS, Frost SDW.

BMC Public Health. 2018 Feb 7;18(1):225. doi: 10.1186/s12889-018-5140-3.


Biased phylodynamic inferences from analysing clusters of viral sequences.

Dearlove BL, Xiang F, Frost SDW.

Virus Evol. 2017 Aug 3;3(2):vex020. doi: 10.1093/ve/vex020. eCollection 2017 Jul.


The changing molecular epidemiology of HIV in the Philippines.

Salvaña EMT, Schwem BE, Ching PR, Frost SDW, Ganchua SKC, Itable JR.

Int J Infect Dis. 2017 Aug;61:44-50. doi: 10.1016/j.ijid.2017.05.017. Epub 2017 Jun 21.


HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.

Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C.

AIDS Res Hum Retroviruses. 2017 Nov;33(11):1083-1098. doi: 10.1089/AID.2017.0061. Epub 2017 May 25.


Adaptation of avian influenza virus to a swine host.

Bourret V, Lyall J, Frost SDW, Teillaud A, Smith CA, Leclaire S, Fu J, Gandon S, Guérin JL, Tiley LS.

Virus Evol. 2017 Mar 18;3(1):vex007. doi: 10.1093/ve/vex007. eCollection 2017 Jan.


Modeling and analyzing respondent-driven sampling as a counting process.

Berchenko Y, Rosenblatt JD, Frost SDW.

Biometrics. 2017 Dec;73(4):1189-1198. doi: 10.1111/biom.12678. Epub 2017 Mar 3.


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.


Assessing Commitment and Reporting Fidelity to a Text Message-Based Participatory Surveillance in Rural Western Uganda.

Lester J, Paige S, Chapman CA, Gibson M, Holland Jones J, Switzer WM, Ting N, Goldberg TL, Frost SD.

PLoS One. 2016 Jun 9;11(6):e0155971. doi: 10.1371/journal.pone.0155971. eCollection 2016.


Surveys, Serologies, and Sequences Reveal History of Iatrogenic Transmission of HIV-1.

Frost SD, Kwofie SK.

J Infect Dis. 2016 Aug 1;214(3):341-3. doi: 10.1093/infdis/jiw012. Epub 2016 Jan 14. No abstract available.


Assigning and visualizing germline genes in antibody repertoires.

Frost SD, Murrell B, Hossain AS, Silverman GJ, Pond SL.

Philos Trans R Soc Lond B Biol Sci. 2015 Sep 5;370(1676). pii: 20140240. doi: 10.1098/rstb.2014.0240.


Measuring Asymmetry in Time-Stamped Phylogenies.

Dearlove BL, Frost SD.

PLoS Comput Biol. 2015 Jul 6;11(7):e1004312. doi: 10.1371/journal.pcbi.1004312. eCollection 2015 Jul.


Genomic characterization of two novel HIV-1 unique (CRF01_AE/B) recombinant forms among men who have sex with men in Beijing, China.

Li Z, Li J, Feng Y, Kalish ML, Lu H, Yin L, Liao L, Qian HZ, Frost SD, Ruan Y, Vermund SH, Shao Y, Xing H.

AIDS Res Hum Retroviruses. 2015 Sep;31(9):921-5. doi: 10.1089/AID.2015.0076. Epub 2015 Jun 11.


Assessing the use of hospital staff influenza-like absence (ILA) for enhancing hospital preparedness and national surveillance.

Drumright LN, Frost SD, Elliot AJ, Catchpole M, Pebody RG, Atkins M, Harrison J, Parker P, Holmes AH.

BMC Infect Dis. 2015 Mar 1;15:110. doi: 10.1186/s12879-015-0789-z.


Eight challenges in phylodynamic inference.

Frost SD, Pybus OG, Gog JR, Viboud C, Bonhoeffer S, Bedford T.

Epidemics. 2015 Mar;10:88-92. doi: 10.1016/j.epidem.2014.09.001. Epub 2014 Sep 16.


Modeling infectious disease dynamics in the complex landscape of global health.

Heesterbeek H, Anderson RM, Andreasen V, Bansal S, De Angelis D, Dye C, Eames KT, Edmunds WJ, Frost SD, Funk S, Hollingsworth TD, House T, Isham V, Klepac P, Lessler J, Lloyd-Smith JO, Metcalf CJ, Mollison D, Pellis L, Pulliam JR, Roberts MG, Viboud C; Isaac Newton Institute IDD Collaboration.

Science. 2015 Mar 13;347(6227):aaa4339. doi: 10.1126/science.aaa4339. Review.


Genomic characterization of two novel HIV-1 second-generation recombinant forms among men who have sex with men in Beijing, China.

Li Z, Wei H, Feng Y, Li J, Kalish ML, Lu H, Yin L, Liao L, Qian HZ, Frost SD, Ruan Y, Vermund SH, Shao Y, Xing H.

AIDS Res Hum Retroviruses. 2015 Mar;31(3):342-6. doi: 10.1089/AID.2014.0307. Epub 2015 Jan 8.


Sampling through time and phylodynamic inference with coalescent and birth-death models.

Volz EM, Frost SD.

J R Soc Interface. 2014 Dec 6;11(101):20140945.


Understanding drivers of phylogenetic clustering in molecular epidemiological studies of HIV.

Frost SD, Pillay D.

J Infect Dis. 2015 Mar 15;211(6):856-8. doi: 10.1093/infdis/jiu563. Epub 2014 Oct 13. No abstract available.


Beyond bushmeat: animal contact, injury, and zoonotic disease risk in Western Uganda.

Paige SB, Frost SD, Gibson MA, Jones JH, Shankar A, Switzer WM, Ting N, Goldberg TL.

Ecohealth. 2014 Dec;11(4):534-43. doi: 10.1007/s10393-014-0942-y. Epub 2014 May 21.


Inferring the source of transmission with phylogenetic data.

Volz EM, Frost SD.

PLoS Comput Biol. 2013;9(12):e1003397. doi: 10.1371/journal.pcbi.1003397. Epub 2013 Dec 19.


Can non-lytic CD8+ T cells drive HIV-1 escape?

Seich Al Basatena NK, Chatzimichalis K, Graw F, Frost SD, Regoes RR, Asquith B.

PLoS Pathog. 2013;9(11):e1003656. doi: 10.1371/journal.ppat.1003656. Epub 2013 Nov 14.


Respondent driven sampling: determinants of recruitment and a method to improve point estimation.

McCreesh N, Copas A, Seeley J, Johnston LG, Sonnenberg P, Hayes RJ, Frost SD, White RG.

PLoS One. 2013 Oct 31;8(10):e78402. doi: 10.1371/journal.pone.0078402. eCollection 2013.


Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in rhesus macaques.

Varela M, Verschoor E, Lai RP, Hughes J, Mooj P, McKinley TJ, Fitzmaurice TJ, Landskron L, Willett BJ, Frost SD, Bogers WM, Heeney JL.

PLoS One. 2013 Aug 14;8(8):e70814. doi: 10.1371/journal.pone.0070814. eCollection 2013.


Modelling tree shape and structure in viral phylodynamics.

Frost SD, Volz EM.

Philos Trans R Soc Lond B Biol Sci. 2013 Feb 4;368(1614):20120208. doi: 10.1098/rstb.2012.0208. Print 2013 Mar 19.


Individual and network factors associated with prevalent hepatitis C infection among rural Appalachian injection drug users.

Havens JR, Lofwall MR, Frost SD, Oser CB, Leukefeld CG, Crosby RA.

Am J Public Health. 2013 Jan;103(1):e44-52. doi: 10.2105/AJPH.2012.300874. Epub 2012 Nov 15.


Respondent driven sampling--where we are and where should we be going?

White RG, Lansky A, Goel S, Wilson D, Hladik W, Hakim A, Frost SD.

Sex Transm Infect. 2012 Oct;88(6):397-9. No abstract available.


Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection.

Volz EM, Koopman JS, Ward MJ, Brown AL, Frost SD.

PLoS Comput Biol. 2012;8(6):e1002552. doi: 10.1371/journal.pcbi.1002552. Epub 2012 Jun 28.


Mixed adjuvant formulations reveal a new combination that elicit antibody response comparable to Freund's adjuvants.

Lai RP, Seaman MS, Tonks P, Wegmann F, Seilly DJ, Frost SD, LaBranche CC, Montefiori DC, Dey AK, Srivastava IK, Sattentau Q, Barnett SW, Heeney JL.

PLoS One. 2012;7(4):e35083. doi: 10.1371/journal.pone.0035083. Epub 2012 Apr 11.


Evaluation of respondent-driven sampling.

McCreesh N, Frost SD, Seeley J, Katongole J, Tarsh MN, Ndunguse R, Jichi F, Lunel NL, Maher D, Johnston LG, Sonnenberg P, Copas AJ, Hayes RJ, White RG.

Epidemiology. 2012 Jan;23(1):138-47. doi: 10.1097/EDE.0b013e31823ac17c.


Deep molecular characterization of HIV-1 dynamics under suppressive HAART.

Buzón MJ, Codoñer FM, Frost SD, Pou C, Puertas MC, Massanella M, Dalmau J, Llibre JM, Stevenson M, Blanco J, Clotet B, Paredes R, Martinez-Picado J.

PLoS Pathog. 2011 Oct;7(10):e1002314. doi: 10.1371/journal.ppat.1002314. Epub 2011 Oct 27.


Evaluation of the role of location and distance in recruitment in respondent-driven sampling.

McCreesh N, Johnston LG, Copas A, Sonnenberg P, Seeley J, Hayes RJ, Frost SD, White RG.

Int J Health Geogr. 2011 Oct 18;10:56. doi: 10.1186/1476-072X-10-56.


Molecular evolution analysis of the human immunodeficiency virus type 1 envelope in simian/human immunodeficiency virus-infected macaques: implications for challenge dose selection.

Varela M, Landskron L, Lai RP, McKinley TJ, Bogers WM, Verschoor EJ, Dubbes R, Barnett SW, Frost SD, Heeney JL.

J Virol. 2011 Oct;85(19):10332-45. doi: 10.1128/JVI.05290-11. Epub 2011 Jul 27.


Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load.

Poon AF, Aldous JL, Mathews WC, Kitahata M, Kahn JS, Saag MS, Rodríguez B, Boswell SL, Frost SD, Haubrich RH.

PLoS One. 2011;6(6):e21189. doi: 10.1371/journal.pone.0021189. Epub 2011 Jun 20.


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.


Capture-recapture methods and respondent-driven sampling: their potential and limitations.

Berchenko Y, Frost SD.

Sex Transm Infect. 2011 Jun;87(4):267-8. doi: 10.1136/sti.2011.049171. No abstract available.


Epidemiological bridging by injection drug use drives an early HIV epidemic.

Volz E, Frost SDW, Rothenberg R, Meyers LA.

Epidemics. 2010 Sep;2(3):155-164. doi: 10.1016/j.epidem.2010.06.003. Epub 2010 Jun 19.


Risk of intraoperative hypotension with loop diuretics: a randomized controlled trial.

Khan NA, Campbell NR, Frost SD, Gilbert K, Michota FA, Usmani A, Seal D, Ghali WA.

Am J Med. 2010 Nov;123(11):1059.e1-8. doi: 10.1016/j.amjmed.2010.07.019.


Rapid social network assessment for predicting HIV and STI risk among men attending bars and clubs in San Diego, California.

Drumright LN, Frost SD.

Sex Transm Infect. 2010 Dec;86 Suppl 3:iii17-23. doi: 10.1136/sti.2010.045914. Epub 2010 Oct 21.


Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology.

Delport W, Poon AF, Frost SD, Kosakovsky Pond SL.

Bioinformatics. 2010 Oct 1;26(19):2455-7. doi: 10.1093/bioinformatics/btq429. Epub 2010 Jul 29.


Viral phylodynamics and the search for an 'effective number of infections'.

Frost SD, Volz EM.

Philos Trans R Soc Lond B Biol Sci. 2010 Jun 27;365(1548):1879-90. doi: 10.1098/rstb.2010.0060.


An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.

Kosakovsky Pond SL, Posada D, Stawiski E, Chappey C, Poon AF, Hughes G, Fearnhill E, Gravenor MB, Leigh Brown AJ, Frost SD.

PLoS Comput Biol. 2009 Nov;5(11):e1000581. doi: 10.1371/journal.pcbi.1000581. Epub 2009 Nov 26.


Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD.

Mol Biol Evol. 2010 Apr;27(4):819-32. doi: 10.1093/molbev/msp289. Epub 2009 Dec 2.


Evolutionary fingerprinting of genes.

Pond SL, Scheffler K, Gravenor MB, Poon AF, Frost SD.

Mol Biol Evol. 2010 Mar;27(3):520-36. doi: 10.1093/molbev/msp260. Epub 2009 Oct 28.


Phylodynamics of infectious disease epidemics.

Volz EM, Kosakovsky Pond SL, Ward MJ, Leigh Brown AJ, Frost SD.

Genetics. 2009 Dec;183(4):1421-30. doi: 10.1534/genetics.109.106021. Epub 2009 Sep 21.

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