Ben Murrell

Ben Murrell

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Ben Murrell

Ben Murrell

Publications by authors named "Ben Murrell"

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Long-read amplicon denoising.

Nucleic Acids Res 2019 Oct;47(18):e104

Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17177, Sweden.

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http://dx.doi.org/10.1093/nar/gkz657DOI Listing
October 2019

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

Immunity 2019 Jul;51(1):141-154.e6

International AIDS Vaccine Initiative Neutralizing Antibody Center, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2019.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642152PMC
July 2019

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

Immunity 2019 01 11;50(1):241-252.e6. Epub 2018 Dec 11.

Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), The Scripps Research Institute, La Jolla, CA 92037, USA; IAVI Neutralizing Antibody Center and the Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613183049
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http://dx.doi.org/10.1016/j.immuni.2018.11.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6335502PMC
January 2019

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

PLoS Comput Biol 2018 12 13;14(12):e1006498. Epub 2018 Dec 13.

Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1006498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314628PMC
December 2018

RIFRAF: a frame-resolving consensus algorithm.

Bioinformatics 2018 11;34(22):3817-3824

Department of Medicine, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1093/bioinformatics/bty426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223371PMC
November 2018

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

Cell Host Microbe 2018 10 27;24(4):593-599.e3. Epub 2018 Sep 27.

Division of Medical Virology, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu- Natal, Durban 4013, South Africa; National Health Laboratory Services of South Africa, Cape Town 7925, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.chom.2018.09.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6185870PMC
October 2018

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

Virus Evol 2018 Jul 4;4(2):vey030. Epub 2018 Dec 4.

Division of HIV/AIDS Prevention, Centers for Disease Control and Prevention, Atlanta, USA.

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https://academic.oup.com/ve/article/doi/10.1093/ve/vey030/52
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http://dx.doi.org/10.1093/ve/vey030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6279948PMC
July 2018

Detecting and Analyzing Genetic Recombination Using RDP4.

Methods Mol Biol 2017 ;1525:433-460

Institute of Infectious Diseases and Molecular Medicine, Computational Biology Group, University of Cape Town, Cape Town, 7549, South Africa.

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http://dx.doi.org/10.1007/978-1-4939-6622-6_17DOI Listing
January 2018

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

Immunity 2017 11;47(5):990-1003.e9

International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10004, USA; Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat a l'Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, 38044 Grenoble, France. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2017.11.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736302PMC
November 2017

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

PLoS Pathog 2017 01 9;13(1):e1006000. Epub 2017 Jan 9.

New York City Department of Health and Mental Hygiene, New York, New York, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1006000DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5221827PMC
January 2017

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

J Virol 2016 09 26;90(18):8085-9. Epub 2016 Aug 26.

Department of Medicine, University of California, San Diego, San Diego, California, USA

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http://dx.doi.org/10.1128/JVI.00972-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008085PMC
September 2016

Discovering General Multidimensional Associations.

PLoS One 2016 18;11(3):e0151551. Epub 2016 Mar 18.

Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151551PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4798755PMC
August 2016

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

Immunity 2016 05;44(5):1215-26

International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA; International AIDS Vaccine Initiative, New York, NY 10038, USA; Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2016.04.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003182PMC
May 2016

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

EBioMedicine 2015 Oct 18;2(10):1456-63. Epub 2015 Jul 18.

Division of Infectious Diseases, University of California San Diego, #8208 200 W. Arbor St. San Diego, CA 92103, United States ; Division of Infectious Diseases, San Diego Veterans Affairs Medical Center, 3350 La Jolla Village Drive, San Diego, CA 92161, United States.

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http://dx.doi.org/10.1016/j.ebiom.2015.07.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634195PMC
October 2015

Assigning and visualizing germline genes in antibody repertoires.

Philos Trans R Soc Lond B Biol Sci 2015 Sep;370(1676)

Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA

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http://dx.doi.org/10.1098/rstb.2014.0240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528417PMC
September 2015

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

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

Department of Integrative Biomedical Sciences, Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road Observatory 7549, Cape Town, South Africa.

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http://dx.doi.org/10.1093/ve/vev003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5014473PMC
May 2015

RELAX: detecting relaxed selection in a phylogenetic framework.

Mol Biol Evol 2015 Mar 23;32(3):820-32. Epub 2014 Dec 23.

Department of Medicine, University of California, San Diego Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa

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http://dx.doi.org/10.1093/molbev/msu400DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4327161PMC
March 2015

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

J Clin Virol 2015 Jan 20;62:48-53. Epub 2014 Nov 20.

Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie van Zilj Drive, Parow 7500, South Africa; National Health Laboratory Service, Tygerberg, Francie van Zijl Drive, Parow 7500, South Africa. Electronic address:

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http://dx.doi.org/10.1016/j.jcv.2014.11.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4279108PMC
January 2015

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

PLoS One 2014 10;9(4):e94534. Epub 2014 Apr 10.

Department of Medicine, University of California San Diego, San Diego, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0094534PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3983186PMC
December 2014

R2-equitability is satisfiable.

Proc Natl Acad Sci U S A 2014 May 29;111(21):E2160. Epub 2014 Apr 29.

Computer Science, University of KwaZulu-Natal, Pietermaritzburg 3201, South Africa.

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http://dx.doi.org/10.1073/pnas.1403623111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4040619PMC
May 2014

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

Mol Biol Evol 2013 May 18;30(5):1196-205. Epub 2013 Feb 18.

Department of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa.

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http://dx.doi.org/10.1093/molbev/mst030DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3670733PMC
May 2013

Detecting individual sites subject to episodic diversifying selection.

PLoS Genet 2012 12;8(7):e1002764. Epub 2012 Jul 12.

Biomedical Informatics Research Division, eHealth Research and Innovation Platform, Medical Research Council, Tygerberg, South Africa.

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http://dx.doi.org/10.1371/journal.pgen.1002764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3395634PMC
January 2013

Modeling HIV-1 drug resistance as episodic directional selection.

PLoS Comput Biol 2012 10;8(5):e1002507. Epub 2012 May 10.

Biomedical Informatics Research Division, eHealth Research and Innovation Platform, Medical Research Council, Tygerberg, South Africa.

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http://dx.doi.org/10.1371/journal.pcbi.1002507DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3349733PMC
September 2012

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

Methods Mol Biol 2012 ;856:239-72

Department of Medicine, University of California, San Diego, CA, USA.

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http://dx.doi.org/10.1007/978-1-61779-585-5_10DOI Listing
July 2012

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

PLoS One 2011 22;6(12):e28898. Epub 2011 Dec 22.

Biomedical Informatics Research Division, eHealth Research and Innovation Platform, Medical Research Council, Cape Town, Western Cape, South Africa.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028898PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245233PMC
May 2012

Degenerate Primer IDs and the birthday problem.

Proc Natl Acad Sci U S A 2012 May 19;109(21):E1330; author reply E1331. Epub 2012 Apr 19.

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http://dx.doi.org/10.1073/pnas.1203613109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361375PMC
May 2012