Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 56

1.

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
2.

Long-read amplicon denoising.

Kumar V, Vollbrecht T, Chernyshev M, Mohan S, Hanst B, Bavafa N, Lorenzo A, Kumar N, Ketteringham R, Eren K, Golden M, Oliveira MF, Murrell B.

Nucleic Acids Res. 2019 Aug 16. pii: gkz657. doi: 10.1093/nar/gkz657. [Epub ahead of print]

PMID:
31418021
3.

Rapid and Focused Maturation of a VRC01-Class HIV Broadly Neutralizing Antibody Lineage Involves Both Binding and Accommodation of the N276-Glycan.

Umotoy J, Bagaya BS, Joyce C, Schiffner T, Menis S, Saye-Francisco KL, Biddle T, Mohan S, Vollbrecht T, Kalyuzhniy O, Madzorera S, Kitchin D, Lambson B, Nonyane M, Kilembe W; IAVI Protocol C Investigators; IAVI African HIV Research Network, Poignard P, Schief WR, Burton DR, Murrell B, Moore PL, Briney B, Sok D, Landais E.

Immunity. 2019 Jul 16;51(1):141-154.e6. doi: 10.1016/j.immuni.2019.06.004.

4.

Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance.

Cirelli KM, Carnathan DG, Nogal B, Martin JT, Rodriguez OL, Upadhyay AA, Enemuo CA, Gebru EH, Choe Y, Viviano F, Nakao C, Pauthner MG, Reiss S, Cottrell CA, Smith ML, Bastidas R, Gibson W, Wolabaugh AN, Melo MB, Cossette B, Kumar V, Patel NB, Tokatlian T, Menis S, Kulp DW, Burton DR, Murrell B, Schief WR, Bosinger SE, Ward AB, Watson CT, Silvestri G, Irvine DJ, Crotty S.

Cell. 2019 May 16;177(5):1153-1171.e28. doi: 10.1016/j.cell.2019.04.012. Epub 2019 May 9.

PMID:
31080066
5.

Reprogramming the antigen specificity of B cells using genome-editing technologies.

Voss JE, Gonzalez-Martin A, Andrabi R, Fuller RP, Murrell B, McCoy LE, Porter K, Huang D, Li W, Sok D, Le K, Briney B, Chateau M, Rogers G, Hangartner L, Feeney AJ, Nemazee D, Cannon P, Burton DR.

Elife. 2019 Jan 17;8. pii: e42995. doi: 10.7554/eLife.42995.

6.

Vaccine-Induced Protection from Homologous Tier 2 SHIV Challenge in Nonhuman Primates Depends on Serum-Neutralizing Antibody Titers.

Pauthner MG, Nkolola JP, Havenar-Daughton C, Murrell B, Reiss SM, Bastidas R, Prévost J, Nedellec R, von Bredow B, Abbink P, Cottrell CA, Kulp DW, Tokatlian T, Nogal B, Bianchi M, Li H, Lee JH, Butera ST, Evans DT, Hangartner L, Finzi A, Wilson IA, Wyatt RT, Irvine DJ, Schief WR, Ward AB, Sanders RW, Crotty S, Shaw GM, Barouch DH, Burton DR.

Immunity. 2019 Jan 15;50(1):241-252.e6. doi: 10.1016/j.immuni.2018.11.011. Epub 2018 Dec 11.

7.

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.

8.

Maintenance and reappearance of extremely divergent intra-host HIV-1 variants.

Wertheim JO, Oster AM, Murrell B, Saduvala N, Heneine W, Switzer WM, Johnson JA.

Virus Evol. 2018 Dec 4;4(2):vey030. doi: 10.1093/ve/vey030. eCollection 2018 Jul.

9.

HIV Superinfection Drives De Novo Antibody Responses and Not Neutralization Breadth.

Sheward DJ, Marais J, Bekker V, Murrell B, Eren K, Bhiman JN, Nonyane M, Garrett N, Woodman ZL, Abdool Karim Q, Abdool Karim SS, Morris L, Moore PL, Williamson C.

Cell Host Microbe. 2018 Oct 10;24(4):593-599.e3. doi: 10.1016/j.chom.2018.09.001. Epub 2018 Sep 27.

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.

PMID:
30010850
11.

RIFRAF: a frame-resolving consensus algorithm.

Eren K, Murrell B.

Bioinformatics. 2018 Nov 15;34(22):3817-3824. doi: 10.1093/bioinformatics/bty426.

PMID:
29850783
12.

Glycoengineering HIV-1 Env creates 'supercharged' and 'hybrid' glycans to increase neutralizing antibody potency, breadth and saturation.

Crooks ET, Grimley SL, Cully M, Osawa K, Dekkers G, Saunders K, Rämisch S, Menis S, Schief WR, Doria-Rose N, Haynes B, Murrell B, Cale EM, Pegu A, Mascola JR, Vidarsson G, Binley JM.

PLoS Pathog. 2018 May 2;14(5):e1007024. doi: 10.1371/journal.ppat.1007024. eCollection 2018 May.

13.

HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage.

Landais E, Murrell B, Briney B, Murrell S, Rantalainen K, Berndsen ZT, Ramos A, Wickramasinghe L, Smith ML, Eren K, de Val N, Wu M, Cappelletti A, Umotoy J, Lie Y, Wrin T, Algate P, Chan-Hui PY, Karita E; IAVI Protocol C Investigators; IAVI African HIV Research Network, Ward AB, Wilson IA, Burton DR, Smith D, Pond SLK, Poignard P.

Immunity. 2017 Nov 21;47(5):990-1003.e9. doi: 10.1016/j.immuni.2017.11.002.

14.

Intrapatient viral diversity and treatment outcome in patients with genotype 3a hepatitis C virus infection on sofosbuvir-containing regimens.

Bhardwaj N, Ragonnet-Cronin M, Murrell B, Chodavarapu K, Martin R, Chang S, Miller MD, Feld JJ, Sulkowski M, Mangia A, Wertheim JO, Osinusi A, McNally J, Brainard D, Mo H, Svarovskaia ES.

J Viral Hepat. 2018 Apr;25(4):344-353. doi: 10.1111/jvh.12825. Epub 2017 Dec 28.

PMID:
29112331
15.

Extra-epitopic hepatitis C virus polymorphisms confer resistance to broadly neutralizing antibodies by modulating binding to scavenger receptor B1.

El-Diwany R, Cohen VJ, Mankowski MC, Wasilewski LN, Brady JK, Snider AE, Osburn WO, Murrell B, Ray SC, Bailey JR.

PLoS Pathog. 2017 Feb 24;13(2):e1006235. doi: 10.1371/journal.ppat.1006235. eCollection 2017 Feb.

16.

Influence of intraoperative radiation therapy on locally advanced and recurrent colorectal tumors: A 16-year experience.

Brady JT, Crawshaw BP, Murrell B, Dosokey EM, Jabir MA, Steele SR, Stein SL, Reynolds HL Jr.

Am J Surg. 2017 Mar;213(3):586-589. doi: 10.1016/j.amjsurg.2016.10.036. Epub 2017 Jan 3.

PMID:
28160966
17.

Antibody 10-1074 suppresses viremia in HIV-1-infected individuals.

Caskey M, Schoofs T, Gruell H, Settler A, Karagounis T, Kreider EF, Murrell B, Pfeifer N, Nogueira L, Oliveira TY, Learn GH, Cohen YZ, Lehmann C, Gillor D, Shimeliovich I, Unson-O'Brien C, Weiland D, Robles A, Kümmerle T, Wyen C, Levin R, Witmer-Pack M, Eren K, Ignacio C, Kiss S, West AP Jr, Mouquet H, Zingman BS, Gulick RM, Keler T, Bjorkman PJ, Seaman MS, Hahn BH, Fätkenheuer G, Schlesinger SJ, Nussenzweig MC, Klein F.

Nat Med. 2017 Feb;23(2):185-191. doi: 10.1038/nm.4268. Epub 2017 Jan 16.

18.

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.

19.

Detecting and Analyzing Genetic Recombination Using RDP4.

Martin DP, Murrell B, Khoosal A, Muhire B.

Methods Mol Biol. 2017;1525:433-460.

PMID:
27896731
20.

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.

21.

The Evolutionary Histories of Antiretroviral Proteins SERINC3 and SERINC5 Do Not Support an Evolutionary Arms Race in Primates.

Murrell B, Vollbrecht T, Guatelli J, Wertheim JO.

J Virol. 2016 Aug 26;90(18):8085-9. doi: 10.1128/JVI.00972-16. Print 2016 Sep 15.

22.

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.

23.

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.

24.

Discovering General Multidimensional Associations.

Murrell B, Murrell D, Murrell H.

PLoS One. 2016 Mar 18;11(3):e0151551. doi: 10.1371/journal.pone.0151551. eCollection 2016.

25.

Corrigendum: Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART.

de Oliveira MF, Murrell B, Pérez-Santiago J, Vargas M, Ellis RJ, Letendre S, Grant I, Smith DM, Woods SP, Gianella S.

Sci Rep. 2016 Jan 19;6:19387. doi: 10.1038/srep19387. No abstract available.

26.

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.

27.

HIV Transmission Networks in the San Diego-Tijuana Border Region.

Mehta SR, Wertheim JO, Brouwer KC, Wagner KD, Chaillon A, Strathdee S, Patterson TL, Rangel MG, Vargas M, Murrell B, Garfein R, Little SJ, Smith DM.

EBioMedicine. 2015 Jul 18;2(10):1456-63. doi: 10.1016/j.ebiom.2015.07.024. eCollection 2015 Oct.

28.

Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART.

de Oliveira MF, Murrell B, Pérez-Santiago J, Vargas M, Ellis RJ, Letendre S, Grant I, Smith DM, Woods SP, Gianella S.

Sci Rep. 2015 Nov 25;5:17094. doi: 10.1038/srep17094. Erratum in: Sci Rep. 2016;6:19387. Murrel, Ben [corrected to Murrell, Ben].

29.

Recreational Fish-Finders--An Inexpensive Alternative to Scientific Echo-Sounders for Unravelling the Links between Marine Top Predators and Their Prey.

McInnes AM, Khoosal A, Murrell B, Merkle D, Lacerda M, Nyengera R, Coetzee JC, Edwards LC, Ryan PG, Rademan J, van der Westhuizen JJ, Pichegru L.

PLoS One. 2015 Nov 23;10(11):e0140936. doi: 10.1371/journal.pone.0140936. eCollection 2015.

30.

Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infection.

Pérez-Santiago J, Schrier RD, de Oliveira MF, Gianella S, Var SR, Day TR, Ramirez-Gaona M, Suben JD, Murrell B, Massanella M, Cherner M, Smith DM, Ellis RJ, Letendre SL, Mehta SR.

J Neurovirol. 2016 Apr;22(2):191-200. doi: 10.1007/s13365-015-0384-5. Epub 2015 Oct 1.

31.

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.

32.

RDP4: Detection and analysis of recombination patterns in virus genomes.

Martin DP, Murrell B, Golden M, Khoosal A, Muhire B.

Virus Evol. 2015 May 26;1(1):vev003. eCollection 2015.

33.

The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed.

Filloux D, Murrell S, Koohapitagtam M, Golden M, Julian C, Galzi S, Uzest M, Rodier-Goud M, D'Hont A, Vernerey MS, Wilkin P, Peterschmitt M, Winter S, Murrell B, Martin DP, Roumagnac P.

Virus Evol. 2015 May 26;1(1):vev002. eCollection 2015.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

R2-equitability is satisfiable.

Murrell B, Murrell D, Murrell H.

Proc Natl Acad Sci U S A. 2014 May 27;111(21):E2160. doi: 10.1073/pnas.1403623111. Epub 2014 Apr 29. No abstract available.

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.

Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models.

Lacerda M, Moore PL, Ngandu NK, Seaman M, Gray ES, Murrell B, Krishnamoorthy M, Nonyane M, Madiga M, Wibmer CK, Sheward D, Bailer RT, Gao H, Greene KM, Karim SS, Mascola JR, Korber BT, Montefiori DC, Morris L, Williamson C, Seoighe C; CAVD-NSDP Consortium.

Virol J. 2013 Dec 2;10:347. doi: 10.1186/1743-422X-10-347.

42.

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

Muhire BM, Golden M, Murrell B, Lefeuvre P, Lett JM, Gray A, Poon AY, Ngandu NK, Semegni Y, Tanov EP, Monjane AL, Harkins GW, Varsani A, Shepherd DN, Martin DP.

J Virol. 2014 Feb;88(4):1972-89. doi: 10.1128/JVI.03031-13. Epub 2013 Nov 27.

43.

Effects of misalignment on static torsional strength of anterior cervical plate systems.

Chin KR, Cumming VB, Henson M, Murrell B, Chan FW.

Spine J. 2013 Nov;13(11):1544-8. doi: 10.1016/j.spinee.2013.05.027. Epub 2013 Jun 22.

PMID:
23800821
44.

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.

45.

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.

46.

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.

47.

Degenerate Primer IDs and the birthday problem.

Sheward DJ, Murrell B, Williamson C.

Proc Natl Acad Sci U S A. 2012 May 22;109(21):E1330; author reply E1331. doi: 10.1073/pnas.1203613109. Epub 2012 Apr 19. No abstract available.

48.

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.

49.

Evolution of viral genomes: interplay between selection, recombination, and other forces.

Pond SL, Murrell B, Poon AF.

Methods Mol Biol. 2012;856:239-72. doi: 10.1007/978-1-61779-585-5_10. Review.

PMID:
22399462
50.

Non-negative matrix factorization for learning alignment-specific models of protein evolution.

Murrell B, Weighill T, Buys J, Ketteringham R, Moola S, Benade G, du Buisson L, Kaliski D, Hands T, Scheffler K.

PLoS One. 2011;6(12):e28898. doi: 10.1371/journal.pone.0028898. Epub 2011 Dec 22.

Supplemental Content

Loading ...
Support Center