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Items: 30

1.

HIV Diversity and Genetic Compartmentalization in Blood and Testes during Suppressive Antiretroviral Therapy.

Miller RL, Ponte R, Jones BR, Kinloch NN, Omondi FH, Jenabian MA, Dupuy FP, Fromentin R, Brassard P, Mehraj V, Chomont N, Poon AFY, Joy JB, Brumme ZL, Routy JP; ORCHID Study Group.

J Virol. 2019 Aug 13;93(17). pii: e00755-19. doi: 10.1128/JVI.00755-19. Print 2019 Sep 1.

PMID:
31189714
2.

Prevalence of Human Immunodeficiency Virus-1 Integrase Strand Transfer Inhibitor Resistance in British Columbia, Canada Between 2009 and 2016: A Longitudinal Analysis.

Kamelian K, Lepik KJ, Chau W, Yip B, Zhang WW, Lima VD, Robbins MA, Woods C, Olmstead A, Joy JB, Barrios R, Harrigan PR.

Open Forum Infect Dis. 2019 Feb 12;6(3):ofz060. doi: 10.1093/ofid/ofz060. eCollection 2019 Mar.

3.

A systematic, deep sequencing-based methodology for identification of mixed-genotype hepatitis C virus infections.

Olmstead AD, Montoya V, Chui CK, Dong W, Joy JB, Tai V, Poon AFY, Nguyen T, Brumme CJ, Martinello M, Matthews GV, Richard Harrigan P, Dore GJ, Applegate TL, Grebely J, Howe AYM.

Infect Genet Evol. 2019 Apr;69:76-84. doi: 10.1016/j.meegid.2019.01.016. Epub 2019 Jan 14.

PMID:
30654177
4.

Genetic complexity in the replication-competent latent HIV reservoir increases with untreated infection duration in infected youth.

Brumme ZL, Sudderuddin H, Ziemniak C, Luzuriaga K, Jones BR, Joy JB, Cunningham CK, Greenough T, Persaud D.

AIDS. 2019 Feb 1;33(2):211-218. doi: 10.1097/QAD.0000000000002045.

PMID:
30325763
5.

Phylogenetic approach to recover integration dates of latent HIV sequences within-host.

Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Harrigan PR, Jones RB, Brockman MA, Joy JB, Poon AFY, Brumme ZL.

Proc Natl Acad Sci U S A. 2018 Sep 18;115(38):E8958-E8967. doi: 10.1073/pnas.1802028115. Epub 2018 Sep 5.

6.

Extensive host immune adaptation in a concentrated North American HIV epidemic.

Brumme ZL, Kinloch NN, Sanche S, Wong A, Martin E, Cobarrubias KD, Sandstrom P, Levett PN, Harrigan PR, Joy JB.

AIDS. 2018 Sep 10;32(14):1927-1938. doi: 10.1097/QAD.0000000000001912.

7.

The global origins of resistance-associated variants in the non-structural proteins 5A and 5B of the hepatitis C virus.

Jones BR, Howe AYM, Harrigan PR, Joy JB.

Virus Evol. 2018 Jan 16;4(1):vex041. doi: 10.1093/ve/vex041. eCollection 2018 Jan.

8.

Global priorities for conserving the evolutionary history of sharks, rays and chimaeras.

Stein RW, Mull CG, Kuhn TS, Aschliman NC, Davidson LNK, Joy JB, Smith GJ, Dulvy NK, Mooers AO.

Nat Ecol Evol. 2018 Feb;2(2):288-298. doi: 10.1038/s41559-017-0448-4. Epub 2018 Jan 18.

PMID:
29348644
9.

Genomic Environment Impacts Color Vision Evolution in a Family with Visually Based Sexual Selection.

Sandkam BA, Joy JB, Watson CT, Breden F.

Genome Biol Evol. 2017 Nov 1;9(11):3100-3107. doi: 10.1093/gbe/evx228.

10.

Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison.

Ratmann O, Hodcroft EB, Pickles M, Cori A, Hall M, Lycett S, Colijn C, Dearlove B, Didelot X, Frost S, Hossain AS, Joy JB, Kendall M, K├╝hnert D, Leventhal GE, Liang R, Plazzotta G, Poon AF, Rasmussen DA, Stadler T, Volz E, Weis C, Leigh Brown AJ, Fraser C; PANGEA-HIV Consortium.

Mol Biol Evol. 2017 Jan;34(1):185-203. doi: 10.1093/molbev/msw217. Epub 2016 Oct 7.

11.

Ancestral Reconstruction.

Joy JB, Liang RH, McCloskey RM, Nguyen T, Poon AF.

PLoS Comput Biol. 2016 Jul 12;12(7):e1004763. doi: 10.1371/journal.pcbi.1004763. eCollection 2016 Jul. No abstract available.

12.

The spread of hepatitis C virus genotype 1a in North America: a retrospective phylogenetic study.

Joy JB, McCloskey RM, Nguyen T, Liang RH, Khudyakov Y, Olmstead A, Krajden M, Ward JW, Harrigan PR, Montaner JSG, Poon AFY.

Lancet Infect Dis. 2016 Jun;16(6):698-702. doi: 10.1016/S1473-3099(16)00124-9. Epub 2016 Mar 30.

13.

Transmission of hepatitis C virus infection among younger and older people who inject drugs in Vancouver, Canada.

Jacka B, Applegate T, Poon AF, Raghwani J, Harrigan PR, DeBeck K, Milloy MJ, Krajden M, Olmstead A, Joy JB, Marshall BD, Hayashi K, Pybus OG, Lima VD, Magiorkinis G, Montaner J, Lamoury F, Dore GJ, Wood E, Grebely J.

J Hepatol. 2016 Jun;64(6):1247-55. doi: 10.1016/j.jhep.2016.02.031. Epub 2016 Feb 26.

14.

Development and Validation of Two Screening Assays for the Hepatitis C Virus NS3 Q80K Polymorphism Associated with Reduced Response to Combination Treatment Regimens Containing Simeprevir.

Chui CK, Dong WW, Joy JB, Poon AF, Dong WY, Mo T, Woods CK, Beatty C, Hew H, Harrigan PR, Brumme CJ.

J Clin Microbiol. 2015 Sep;53(9):2942-50. doi: 10.1128/JCM.00650-15. Epub 2015 Jul 1.

15.

A molecular phylogenetics-based approach for identifying recent hepatitis C virus transmission events.

Olmstead AD, Joy JB, Montoya V, Luo I, Poon AF, Jacka B, Lamoury F, Applegate T, Montaner J, Khudyakov Y, Grebely J, Cook D, Harrigan PR, Krajden M.

Infect Genet Evol. 2015 Jul;33:101-9. doi: 10.1016/j.meegid.2015.04.017. Epub 2015 Apr 24.

16.

Global origin and transmission of hepatitis C virus nonstructural protein 3 Q80K polymorphism.

McCloskey RM, Liang RH, Joy JB, Krajden M, Montaner JS, Harrigan PR, Poon AF.

J Infect Dis. 2015 Apr 15;211(8):1288-95. doi: 10.1093/infdis/jiu613. Epub 2014 Nov 10.

PMID:
25389307
17.

The impact of clinical, demographic and risk factors on rates of HIV transmission: a population-based phylogenetic analysis in British Columbia, Canada.

Poon AF, Joy JB, Woods CK, Shurgold S, Colley G, Brumme CJ, Hogg RS, Montaner JS, Harrigan PR.

J Infect Dis. 2015 Mar 15;211(6):926-35. doi: 10.1093/infdis/jiu560. Epub 2014 Oct 13.

18.

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing.

Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, Woods CK, Brumme CJ, Ho CK, Schinkel J, Joy JB, Harrigan PR, Poon AF.

Nucleic Acids Res. 2014 Jul;42(12):e98. doi: 10.1093/nar/gku355. Epub 2014 May 7.

19.

Global distribution and conservation of evolutionary distinctness in birds.

Jetz W, Thomas GH, Joy JB, Redding DW, Hartmann K, Mooers AO.

Curr Biol. 2014 May 5;24(9):919-30. doi: 10.1016/j.cub.2014.03.011. Epub 2014 Apr 10.

20.

Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation.

Watson CT, Steinberg KM, Huddleston J, Warren RL, Malig M, Schein J, Willsey AJ, Joy JB, Scott JK, Graves TA, Wilson RK, Holt RA, Eichler EE, Breden F.

Am J Hum Genet. 2013 Apr 4;92(4):530-46. doi: 10.1016/j.ajhg.2013.03.004. Epub 2013 Mar 28.

21.

Symbiosis catalyses niche expansion and diversification.

Joy JB.

Proc Biol Sci. 2013 Feb 6;280(1756):20122820. doi: 10.1098/rspb.2012.2820. Print 2013 Apr 7.

22.

Hybridization leads to sensory repertoire expansion in a gynogenetic fish, the Amazon molly (poecilia formosa): a test of the hybrid-sensory expansion hypothesis.

Sandkam BA, Joy JB, Watson CT, Gonzalez-Bendiksen P, Gabor CR, Breden F.

Evolution. 2013 Jan;67(1):120-30. doi: 10.1111/j.1558-5646.2012.01779.x. Epub 2012 Sep 7.

PMID:
23289566
23.

The global diversity of birds in space and time.

Jetz W, Thomas GH, Joy JB, Hartmann K, Mooers AO.

Nature. 2012 Nov 15;491(7424):444-8. doi: 10.1038/nature11631. Epub 2012 Oct 31.

PMID:
23123857
24.

Island phytophagy: explaining the remarkable diversity of plant-feeding insects.

Joy JB, Crespi BJ.

Proc Biol Sci. 2012 Aug 22;279(1741):3250-5. doi: 10.1098/rspb.2012.0397. Epub 2012 May 2.

25.

Prolixicin: a novel antimicrobial peptide isolated from Rhodnius prolixus with differential activity against bacteria and Trypanosoma cruzi.

Ursic-Bedoya R, Buchhop J, Joy JB, Durvasula R, Lowenberger C.

Insect Mol Biol. 2011 Dec;20(6):775-86. doi: 10.1111/j.1365-2583.2011.01107.x. Epub 2011 Sep 12.

PMID:
21906194
26.

Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata.

Watson CT, Gray SM, Hoffmann M, Lubieniecki KP, Joy JB, Sandkam BA, Weigel D, Loew E, Dreyer C, Davidson WS, Breden F.

J Mol Evol. 2011 Feb;72(2):240-52. doi: 10.1007/s00239-010-9426-z. Epub 2010 Dec 18.

PMID:
21170644
27.

Evolution of embryonic developmental period in the marine bird families Alcidae and Spheniscidae: roles for nutrition and predation?

Hipfner JM, Gorman KB, Vos RA, Joy JB.

BMC Evol Biol. 2010 Jun 14;10:179. doi: 10.1186/1471-2148-10-179.

28.
29.

Adaptive radiation of gall-inducing insects within a single host-plant species.

Joy JB, Crespi BJ.

Evolution. 2007 Apr;61(4):784-95.

PMID:
17439611
30.

Origin of AIDS: contaminated polio vaccine theory refuted.

Worobey M, Santiago ML, Keele BF, Ndjango JB, Joy JB, Labama BL, Dhed'A BD, Rambaut A, Sharp PM, Shaw GM, Hahn BH.

Nature. 2004 Apr 22;428(6985):820.

PMID:
15103367

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