B. Murrell

Sergei L. Kosakovsky Pond, R. Haubrich, Davey M. Smith, 2015, Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology.

An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction

D. Sheward, B. Murrell, M. Corcoran, 2020, Nature Communications.

Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study

J. Dillner, S. Reddy, R. Dyrdak, 2022, The Lancet Infectious Diseases.

Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors

Michele D. Sobolewski, Wei-Shau Hu, S. Hughes, 2019, Proceedings of the National Academy of Sciences.

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

I. Grant, R. Ellis, S. Gianella, 2016, Scientific Reports.

Protection against SARS-CoV-2 transmission by a parenteral prime—Intranasal boost vaccine strategy

J. Bukh, D. Sheward, B. Murrell, 2022, eBioMedicine.

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

R. Shafer, P. Lemey, A. Nekrutenko, 2022, Molecular biology and evolution.

HIV Transmission Networks in the San Diego–Tijuana Border Region

Kimberly C. Brouwer, T. Patterson, S. Little, 2015, EBioMedicine.

Evasion of neutralising antibodies by omicron sublineage BA.2.75

S. Reddy, J. Albert, D. Sheward, 2022, bioRxiv.

Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies

G. B. Karlsson Hedestam, D. Sheward, B. Murrell, 2022, Immunity.

SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden

H. Tegel, P. Nilsson, M. Hedhammar, 2020, Nature Communications.

Antibody responses to SARS-CoV-2 train machine learning to assign likelihood of past infection during virus emergence in Sweden

C. Wallace, J. Dillner, J. Albert, 2020 .

Disease-associated antibody phenotypes and probabilistic seroprevalence estimates during the emergence of SARS-CoV-2

C. Wallace, G. B. Karlsson Hedestam, D. Sheward, 2020, medRxiv.

Seropositivity in blood donors and pregnant women during the first year of SARS‐CoV‐2 transmission in Stockholm, Sweden

G. B. Karlsson Hedestam, D. Sheward, B. Murrell, 2021, Journal of internal medicine.

Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage

B. Murrell, C. Sarrazin, C. Hedskog, 2019, Virus evolution.

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

Daniel W. Kulp, D. Irvine, D. Burton, 2018, Cell.

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

Ben Murrell, Terri Wrin, Sergei L. Kosakovsky Pond, 2017, Immunity.

Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort

Ben Murrell, Jianming Tang, Adam Godzik, 2016, PLoS pathogens.

Adjuvanted SARS-CoV-2 spike protein elicits neutralizing antibodies and CD4 T cell responses after a single immunization in mice

G. B. Karlsson Hedestam, D. Sheward, B. Murrell, 2020, EBioMedicine.

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

Ben Murrell, Nico Pfeifer, Florian Klein, 2017, Nature Medicine.

SARS-CoV-2 protein subunit vaccination of mice and rhesus macaques elicits potent and durable neutralizing antibody responses

D. Sheward, B. Murrell, G. Mcinerney, 2021, Cell Reports Medicine.

RELAX: detecting relaxed selection in a phylogenetic framework.

Ben Murrell, Konrad Scheffler, Sergei L. Kosakovsky Pond, 2014, Molecular biology and evolution.

GPR43 regulates marginal zone B‐cell responses to foreign and endogenous antigens

B. Murrell, M. Bohlooly-y, M. Ádori, 2020, Immunology and cell biology.

Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps

C. Bachert, B. Murrell, L. Cardell, 2021, Science Immunology.

An MPER antibody neutralizes HIV-1 using germline features shared among donors

D. Burton, I. Wilson, A. Ward, 2019, Nature Communications.

Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2

J. Schwenk, J. Dillner, N. Roxhed, 2021, Nature Communications.

Seropositivity in blood donors and pregnant women during 9-months of SARS-CoV-2 transmission in Stockholm, Sweden

C. Wallace, D. Sheward, B. Murrell, 2020, medRxiv.

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

Ben Murrell, Thomas Vollbrecht, Joel O Wertheim, 2016, Journal of Virology.

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Sergei L. Kosakovsky Pond, P. Lemey, D. Robertson, 2021, Cell.

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

R. Ellis, S. Gianella, S. Letendre, 2016, Journal of NeuroVirology.

Evolutionary analysis of base-pairing interactions in DNA and RNA secondary structures

Ben Murrell, Jotun Hein, Michael Golden, 2018, bioRxiv.

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

W. Heneine, B. Murrell, W. Switzer, 2018, Virus evolution.

Modeling HIV-1 Drug Resistance as Episodic Directional Selection

Ben Murrell, Tulio de Oliveira, Christopher J. Seebregts, 2012, PLoS Comput. Biol..

Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution

Ben Murrell, Konrad Scheffler, Daniel Kaliski, 2011, PloS one.

A translational multiplex serology approach to profile the prevalence of anti-SARS-CoV-2 antibodies in home-sampled blood

J. Schwenk, J. Dillner, N. Roxhed, 2020, medRxiv.

Conserved recombination patterns across coronavirus subgenera

D. Robertson, M. Stanhope, B. Murrell, 2021, bioRxiv.

RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets

Ben Murrell, Venkatesh Kumar, Gerrit Botha, 2020, Virus evolution.

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

Ben Murrell, Sergei L. Kosakovsky Pond, Sergei L Kosakovsky Pond, 2018, The Journal of infectious diseases.

Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function

R. Shafer, P. Lemey, A. Nekrutenko, 2022, bioRxiv.

The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape

Sergei L. Kosakovsky Pond, P. Lemey, D. Robertson, 2021, medRxiv.

HIV Superinfection Drives De Novo Antibody Responses and Not Neutralization Breadth

L. Morris, P. Moore, J. Bhiman, 2018, Cell host & microbe.

Estimating the timing of HIV infection from unmutated sequences

Ben Murrell, Alec Pankow, Murray Christian, 2020, bioRxiv.

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.

Sergei L. Kosakovsky Pond, D. Richman, S. Little, 2016, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

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

Ben Murrell, Konrad Scheffler, Joel O. Wertheim, 2017, PLoS pathogens.

Detecting and Analyzing Genetic Recombination Using RDP4.

Ben Murrell, Darren P Martin, Arjun Khoosal, 2017, Methods in molecular biology.

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

Ben Murrell, William R. Schief, Thomas Vollbrecht, 2019, Immunity.

Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples.

Yan Guo, Ben Murrell, Pham Phung, 2016, Virus evolution.

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

Ben Murrell, Lynn Morris, Hongmei Gao, 2013, Virology Journal.

Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies

D. Sheward, B. Murrell, S. Ekström, 2022, Science advances.

HIV Coinfection Provides Insights for the Design of Vaccine Cocktails to Elicit Broadly Neutralizing Antibodies

L. Morris, P. Moore, N. Garrett, 2022, Journal of virology.

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

Ben Murrell, Sergei L. Kosakovsky Pond, Steven Weaver, 2017, bioRxiv.

Antigen receptor stimulation drives selection against pathogenic mtDNA variants that dysregulate lymphocyte responses

M. Pekalski, R. Holmdahl, D. Sheward, 2021, medRxiv.

Probabilistic classification of anti‐SARS‐CoV‐2 antibody responses improves seroprevalence estimates

J. Dillner, D. Sheward, B. Murrell, 2022, Clinical & translational immunology.

Rapid Germinal Center and Antibody Responses in Non-human Primates after a Single Nanoparticle Vaccine Immunization

D. Irvine, D. Burton, W. Schief, 2019, Cell reports.

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

Ben Murrell, Terri Wrin, Sergei L. Kosakovsky Pond, 2016, Immunity.

DNA-launched RNA replicon vaccines induce potent anti-SARS-CoV-2 immune responses in mice

D. Sheward, B. Murrell, G. Mcinerney, 2021, Scientific Reports.

Structural basis of Omicron neutralization by affinity-matured public antibodies

R. Dyrdak, J. Albert, D. Sheward, 2022, bioRxiv.

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

B. Haynes, J. Mascola, J. Binley, 2018, PLoS pathogens.

Sublingual allergen immunotherapy with recombinant dog allergens prevents airway hyperresponsiveness in a model of asthma marked by vigorous TH2 and TH17 cell responses

H. Grönlund, B. Murrell, J. Coquet, 2021, bioRxiv.

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

P. Ryan, B. Murrell, J. Coetzee, 2015, PloS one.

A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo

D. Sheward, B. Murrell, O. Fernandez-Capetillo, 2021, bioRxiv.

Variable loss of antibody potency against SARS-CoV-2 B.1.1.529 (Omicron)

J. Dillner, J. Albert, G. B. Karlsson Hedestam, 2021, bioRxiv.

Systematic evaluation of SARS‐CoV‐2 antigens enables a highly specific and sensitive multiplex serological COVID‐19 assay

H. Tegel, P. Nilsson, J. Dillner, 2021, Clinical & translational immunology.

SARS-CoV-2 protein subunit vaccination elicits potent neutralizing antibody responses

D. Sheward, B. Murrell, G. Mcinerney, 2020, bioRxiv.

Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses

J. Mascola, R. Wyatt, L. Shapiro, 2019, The Journal of experimental medicine.

Longitudinally Tracked, Rapid and Robust Antigen-Specific Germinal Center Responses in Non-Human Primates after a Single Nanoparticle Vaccine Immunization

D. Irvine, D. Burton, W. Schief, 2019, SSRN Electronic Journal.

Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells

R. Fuller, D. Burton, W. Schief, 2020, Nature Communications.

Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles

B. Murrell, M. Corcoran, X. Castro Dopico, 2021, Immunity.

Driving potent neutralization of a SARS-CoV-2 Variant of Concern with a heterotypic boost

D. Sheward, B. Murrell, G. Mcinerney, 2021, bioRxiv.

A bispecific monomeric nanobody induces SARS-COV-2 spike 2 trimer dimers 3 4

D. Sheward, B. Murrell, G. Mcinerney, 2021 .

Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models

D. Sheward, B. Murrell, G. Mcinerney, 2021, Cell Reports Medicine.

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

David Nemazee, Ben Murrell, Bryan Briney, 2018, bioRxiv.

SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display

Cédric R. Weber, Andreas P. Cuny, A. Yermanos, 2021, Cell Reports.

Single-cell sequencing of plasma cells from COVID-19 patients reveals highly expanded clonal lineages produce specific and neutralizing antibodies to SARS-CoV-2

Cédric R. Weber, Andreas P. Cuny, A. Yermanos, 2021, bioRxiv.

Recombinant multimeric dog allergen prevents airway hyperresponsiveness in a model of asthma marked by vigorous TH2 and TH17 cell responses

H. Grönlund, B. Murrell, J. Coquet, 2022, Allergy.

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

Ben Murrell, Sergei L. Kosakovsky Pond, Konrad Scheffler, 2014, PLoS Comput. Biol..

The genomes of several plant species contain endogenous geminiviral sequences

P. Roumagnac, B. Murrell, S. Winter, 2016 .

Measuring Dispositions to Bundle Choices

B. Murrell, D. Spurrett, 2010 .

Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study

D. Sheward, B. Murrell, J. Klingström, 2023, The Lancet Regional Health - Europe.

Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies

D. Burton, B. Briney, Collin Joyce, 2023, PLoS pathogens.

Vaccination of SARS-CoV-2-infected individuals expands a broad range of clonally diverse affinity-matured B cell lineages

L. Walker, D. Sheward, B. Murrell, 2023, Nature communications.

Phenotypic characterization of single CD4+ T cells harboring genetically intact and inducible HIV genomes

J. Routy, B. Murrell, M. Massanella, 2023, Nature Communications.

A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo

D. Sheward, B. Murrell, O. Fernandez-Capetillo, 2022, Nature Communications.

Degenerate Primer IDs and the Birthday Problem

D. Sheward, C. Williamson, B. Murrell, 2012, Proceedings of the National Academy of Sciences.

Evaluation of Archival HIV DNA in Brain and Lymphoid Tissues

R. Ellis, S. Gianella, C. Ignacio, 2023, Journal of virology.

Emergence and antibody evasion of BQ, BA.2.75 and SARS-CoV-2 recombinant sub-lineages in the face of maturing antibody breadth at the population level

S. Tangye, D. Stark, A. Kelleher, 2023, eBioMedicine.

Sensitivity of BA.2.86 to prevailing neutralising antibody responses

D. Sheward, B. Murrell, S. Muschiol, 2023, bioRxiv.

Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations

Yong Liu, L. Bäckdahl, M. Pekalski, 2023, JCI insight.

SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden

H. Tegel, P. Nilsson, M. Hedhammar, 2020, Nature Communications.

UC Office of the President Recent Work Title Assigning and visualizing germline genes in antibody repertoires Permalink

S. Frost, B. Murrell, G. Silverman, 2015 .

A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo

D. Sheward, B. Murrell, O. Fernandez-Capetillo, 2022, Nature Communications.

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

R. Ellis, S. Gianella, S. Letendre, 2015, Journal of NeuroVirology.

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

Stephanie J. Spielman, Sergei L. Kosakovsky Pond, A. Poon, 2019, Methods in molecular biology.

SARS-CoV-2 evolution in the Omicron era

O. Pybus, A. Rambaut, D. Sheward, 2023, Nature Microbiology.

RIFRAF: a frame-resolving consensus algorithm

Ben Murrell, Kemal Eren, B. Murrell, 2017, bioRxiv.

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

D. Richman, D. Burton, P. Poignard, 2014 .

Antigen receptor stimulation drives selection against pathogenic mtDNA 1 variants that dysregulate lymphocyte responses 2 the 4 development of adaptive immune responses

Yong Liu, L. Bäckdahl, M. Pekalski, 2021 .