Benjamin Murrell

About me
Publications
Public outreach and news

About me

The Murrell lab works on various topics related to Computational Biology,
Virology, and Immunology. The lab's current focus is on questions related to
SARS-CoV-2/COVID-19 vaccines and therapeutics.

Articles

Article: NATURE COMMUNICATIONS. 2024;15(1):6338
Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques
Mandolesi M; Das H; de Vries L; Yang Y; Kim C; Dhinakaran M; Castro Dopico X; Fischbach J; Kim S; Guryleva MV; Adori M; Chernyshev M; Stalmarck A; Hanke L; Mcinerney GM; Sheward DJ; Corcoran M; Haellberg BM; Murrell B; Karlsson Hedestam GB
Article: NATURE. 2024;631(8021):617-626
Spike deep mutational scanning helps predict success of SARS-CoV-2 clades
Dadonaite B; Brown J; McMahon TE; Farrell AG; Figgins MD; Asarnow D; Stewart C; Lee J; Logue J; Bedford T; Murrell B; Chu HY; Veesler D; Bloom JD
Article: CELL REPORTS MEDICINE. 2024;5(6):101577
Structural basis of broad SARS-CoV-2 cross-neutralization by affinity-matured public antibodies
Sheward DJ; Pushparaj P; Das H; Greaney AJ; Kim C; Kim S; Hanke L; Hyllner E; Dyrdak R; Lee J; Dopico XC; Dosenovic P; Peacock TP; McInerney GM; Albert J; Corcoran M; Bloom JD; Murrell B; Hedestam GBK; Hallberg BM
Article: VIRUS EVOLUTION. 2024;10(1):veae019
Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations-Application to HIV-1 quasispecies
Westfall DH; Deng W; Pankow A; Chen L; Zhao H; Williamson C; Rolland M; Murrell B; Mullins JI
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2024;121(4):e2308942121
Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features
Juraska M; Bai H; deCamp AC; Magaret CA; Li L; Gillespie K; Carpp LN; Giorgi EE; Ludwig J; Molitor C; Hudson A; Williamson BD; Espy N; Simpkins B; Rudnicki E; Shao D; Rossenkhan R; Edlefsen PT; Westfall DH; Deng W; Chen L; Zhao H; Bhattacharya T; Pankow A; Murrell B; Yssel A; Matten D; York T; Beaume N; Gwashu-Nyangiwe A; Ndabambi N; Thebus R; Karuna ST; Morris L; Montefiori DC; Hural JA; Cohen MS; Corey L; Rolland M; Gilbert PB; Williamson C; Mullins JI
Article: NPJ VACCINES. 2024;9(1):17
Three immunizations with Novavax's protein vaccines increase antibody breadth and provide durable protection from SARS-CoV-2
Lenart K; Cerveira RA; Hellgren F; Ols S; Sheward DJ; Kim C; Cagigi A; Gagne M; Davis B; Germosen D; Roy V; Alter G; Letscher H; Van Wassenhove J; Gros W; Gallouet A-S; Le Grand R; Kleanthous H; Guebre-Xabier M; Murrell B; Patel N; Glenn G; Smith G; Lore K
Article: CLINICAL & TRANSLATIONAL IMMUNOLOGY. 2024;13(5):e1508
Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque
Dopico XC; Guryleva M; Mandolesi M; Corcoran M; Coquet JM; Murrell B; Hedestam GBK
Article: JCI INSIGHT. 2023;8(17):e167656
Antigen receptor stimulation induces purifying selection against pathogenic mitochondrial tRNA mutations
Zhang J; Koolmeister C; Han J; Filograna R; Hanke L; Adori M; Sheward DJ; Teifel S; Gopalakrishna S; Shao Q; Liu Y; Zhu K; Harris RA; Mcinerney G; Murrell B; Aoun M; Baeckdahl L; Holmdahl R; Pekalski M; Wedell A; Engvall M; Wredenberg A; Hedestam GBK; Dopico XC; Rorbach J
Article: JOURNAL OF VIROLOGY. 2023;97(6):e0054323-e00523
Evaluation of Archival HIV DNA in Brain and Lymphoid Tissues
Oliveira MF; Pankow A; Vollbrecht T; Kumar NM; Cabalero G; Ignacio C; Zhao M; Vitomirov A; Gouaux B; Nakawawa M; Murrell B; Ellis RJ; Gianella S
Article: PLOS PATHOGENS. 2023;19(6):e1011416
Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies
Joyce C; Murrell S; Murrell B; Omorodion O; Ver LS; Carrico N; Bastidas R; Nedellec R; Bick M; Woehl J; Zhao F; Burns A; Barman S; Appel M; Ramos A; Wickramasinghe L; Eren K; Vollbrecht T; Smith DM; Pond SLK; McBride R; Worth C; Batista F; Sok D; Poignard P; Briney B; Wilson IA; Landais E; Burton DR
Article: NANO LETTERS. 2023;23(9):3701-3707
A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens
Schlegel J; Porebski B; Andronico L; Hanke L; Edwards S; Brismar H; Murrell B; McInerney GM; Fernandez-Capetillo O; Sezgin E
Article: THE LANCET REGIONAL HEALTH. EUROPE. 2023;30:100646
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.
Vikström L; Fjällström P; Gwon Y-D; Sheward DJ; Wigren-Byström J; Evander M; Bladh O; Widerström M; Molnar C; Rasmussen G; Bennet L; Åberg M; Björk J; Tevell S; Thålin C; Blom K; Klingström J; Murrell B; Ahlm C; Normark J; Johansson AF; Forsell MNE
Article: NATURE COMMUNICATIONS. 2023;14(1):2249
Vaccination of SARS-CoV-2-infected individuals expands a broad range of clonally diverse affinity-matured B cell lineages
Chernyshev M; Sakharkar M; Connor RI; Dugan HL; Sheward DJ; Rappazzo CG; Stalmarck A; Forsell MNE; Wright PF; Corcoran M; Murrell B; Walker LM; Hedestam GKB
Article: EBIOMEDICINE. 2023;90:104545
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
Akerman A; Milogiannakis V; Jean T; Esneau C; Silva MR; Ison T; Fichter C; Lopez JA; Chandra D; Naing Z; Caguicla J; Li D; Walker G; Amatayakul-Chantler S; Roth N; Manni S; Hauser T; Barnes T; Condylios A; Yeang M; Wong M; Foster CSP; Sato K; Lee S; Song Y; Mao L; Sigmund A; Phu A; Vande More AM; Hunt S; Douglas M; Caterson I; Britton W; Sandgren K; Bull R; Lloyd A; Triccas J; Tangye S; Bartlett NW; Darley D; Matthews G; Stark DJ; Petoumenos K; Rawlinson WD; Murrell B; Brilot F; Cunningham AL; Kelleher AD; Aggarwal A; Turville SG
Article: FRONTIERS IN VIROLOGY. 2023;3:1128253
Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses
Pushparaj P; Nicoletto A; Castro Dopico X; Sheward DJ; Kim S; Ekstrom S; Murrell B; Corcoran M; Karlsson Hedestam GB
Article: NATURE COMMUNICATIONS. 2023;14(1):1115
Phenotypic characterization of single CD4+T cells harboring genetically intact and inducible HIV genomes
Dufour C; Richard C; Pardons M; Massanella M; Ackaoui A; Murrell B; Routy B; Thomas R; Routy J-P; Fromentin R; Chomont N
Article: JCI INSIGHT. 2023;8(1):e165299
Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones
Scharf L; Axelsson H; Emmanouilidi A; Mathew NR; Sheward DJ; Leach S; Isakson P; Smirnov IV; Marklund E; Miron N; Andersson L-M; Gisslen M; Murrell B; Lundgren A; Bemark M; Angeletti D
Article: IMMUNITY. 2023;56(1):193-206.e7
Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies
Pushparaj P; Nicoletto A; Sheward DJ; Das H; Dopico XC; Vidakovics LP; Hanke L; Chernyshev M; Narang S; Kim S; Fischbach J; Ekstrom S; McInerney G; Hallberg BM; Murrell B; Corcoran M; Hedestam GBK
Article: FRONTIERS IN IMMUNOLOGY. 2023;14:941281
SARS-CoV-2 spike HexaPro formulated in aluminium hydroxide and administered in an accelerated vaccination schedule partially protects Syrian Hamsters against viral challenge despite low neutralizing antibody responses
Christensen D; Polacek C; Sheward DJ; Hanke L; McInerney G; Murrell B; Hartmann KT; Jensen HE; Zimmermann J; Jungersen G; Illigen KE; Isling LK; Fernandez-Antunez C; Ramirez S; Bukh J; Pedersen GK
Article: EBIOMEDICINE. 2022;84:104248
Protection against SARS-CoV-2 transmission by a parenteral prime-Intranasal boost vaccine strategy
Christensen D; Polacek C; Sheward DJ; Hanke L; Moliner-Morro A; McInerney G; Murrell B; Hartmann KT; Jensen HE; Jungersen G; Illigen K; Isling LK; Jensen RF; Hansen JS; Rosenkrands I; Fernandez-Antunez C; Ramirez S; Follmann F; Bukh J; Pedersen GK
Article: ALLERGY. EUROPEAN JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2022;77(10):2987-3001
Recombinant multimeric dog allergen prevents airway hyperresponsiveness in a model of asthma marked by vigorous T_H2 and T_H17 cell responses
Stark JM; Liu J; Tibbitt CA; Christian M; Ma J; Wintersand A; Dunst J; Kreslavsky T; Murrell B; Adner M; Gronlund H; Gafvelin G; Coquet JM
Article: JOURNAL OF VIROLOGY. 2022;96(14):e0032422-e00322
HIV Coinfection Provides Insights for the Design of Vaccine Cocktails to Elicit Broadly Neutralizing Antibodies
Sheward DJ; Hermanus T; Murrell B; Garrett N; Karim SSA; Morris L; Moore PL; Williamson C
Article: VIRUS EVOLUTION. 2022;8(2):veac054
Conserved recombination patterns across coronavirus subgenera
de Klerk A; Swanepoel P; Lourens R; Zondo M; Abodunran I; Lytras S; MacLean OA; Robertson D; Kosakovsky Pond SL; Zehr JD; Kumar V; Stanhope MJ; Harkins G; Murrell B; Martin DP
Article: THE LANCET INFECTIOUS DISEASES. 2022;22(6):813-820
Neutralisation sensitivity of the SARS-CoV-2 omicron (B.1.1.529) variant: a cross-sectional study
Sheward DJ; Kim C; Ehling RA; Pankow A; Dopico XC; Dyrdak R; Martin DP; Reddy ST; Dillner J; Hedestam GBK; Albert J; Murrell B
Article: MOLECULAR BIOLOGY AND EVOLUTION (MBE). 2022;39(4):msac061
Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function
Martin DP; Lytras S; Lucaci AG; Maier W; Gruening B; Shank SD; Weaver S; MacLean OA; Orton RJ; Lemey P; Boni MF; Tegally H; Harkins GW; Scheepers C; Bhiman JN; Everatt J; Amoako DG; San JE; Giandhari J; Sigal A; Williamson C; Hsiao N-Y; von Gottberg A; De Klerk A; Shafer RW; Robertson DL; Wilkinson RJ; Sewell BT; Lessells R; Nekrutenko A; Greaney AJ; Starr TN; Bloom JD; Murrell B; Wilkinson E; Gupta RK; de Oliveira T; Kosakovsky Pond SL
Article: SCIENCE ADVANCES. 2022;8(12):eabm0220
Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies
Hanke L; Sheward DJ; Pankow A; Vidakovics LP; Karl V; Kim C; Urgard E; Smith NL; Astorga-Wells J; Ekstrom S; Coquet JM; McInerney GM; Murrell B
Article: CELL REPORTS. 2022;38(3):110242
SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display
Ehling RA; Weber CR; Mason DM; Friedensohn S; Wagner B; Bieberich F; Kapetanovic E; Vazquez-Lombardi R; Di Roberto RB; Hong K-L; Wagner C; Pataia M; Overath MD; Sheward DJ; Murrell B; Yermanos A; Cuny AP; Savic M; Rudolf F; Reddy ST
Article: NATURE COMMUNICATIONS. 2022;13(1):155
A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo
Hanke L; Das H; Sheward DJ; Vidakovics LP; Urgard E; Moliner-Morro A; Kim C; Karl V; Pankow A; Smith NL; Porebski B; Fernandez-Capetillo O; Sezgin E; Pedersen GK; Coquet JM; Hallberg BM; Murrell B; McInerney GM
Article: FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY. 2022;10:1083232
Silver nanoparticles with excellent biocompatibility block pseudotyped SARS-CoV-2 in the presence of lung surfactant
Gupta G; Hamawandi B; Sheward DJ; Murrell B; Hanke L; McInerney G; Blosi M; Costa AL; Toprak MS; Fadeel B
Article: CLINICAL & TRANSLATIONAL IMMUNOLOGY. 2022;11(3):e1379
Probabilistic classification of anti-SARS-CoV-2 antibody responses improves seroprevalence estimates
Dopico XC; Muschiol S; Grinberg NF; Aleman S; Sheward DJ; Hanke L; Ahl M; Vikstrom L; Forsell M; Coquet JM; McInerney G; Dillner J; Bogdanovic G; Murrell B; Albert J; Wallace C; Hedestam GBK
Article: CELL REPORTS MEDICINE. 2021;2(11):100450
Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models
Sheward DJ; Mandolesi M; Urgard E; Kim C; Hanke L; Vidakovics LP; Pankow A; Smith NL; Dopico XC; McInerney GM; Coquet JM; Hedestam GBK; Murrell B
Article: CELL. 2021;184(20):5189-5200.e7
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages
Martin DP; Weaver S; Tegally H; San JE; Shank SD; Wilkinson E; Lucaci AG; Giandhari J; Naidoo S; Pillay Y; Singh L; Lessells RJ; Gupta RK; Wertheim JO; Nekturenko A; Murrell B; Harkins GW; Lemey P; MacLean OA; Robertson DL; de Oliveira T; Pond SLK
Article: JOURNAL OF INTERNAL MEDICINE. 2021;290(3):666-676
Seropositivity in blood donors and pregnant women during the first year of SARS-CoV-2 transmission in Stockholm, Sweden
Castro Dopico X; Muschiol S; Christian M; Hanke L; Sheward DJ; Grinberg NF; Rorbach J; Bogdanovic G; Mcinerney GM; Allander T; Wallace C; Murrell B; Albert J; Karlsson Hedestam GB
Article: SCIENCE IMMUNOLOGY. 2021;6(62):eabg6356
Single-cell analysis pinpoints distinct populations of cytotoxic CD4⁺ T cells and an IL-10⁺CD109⁺ T_H2 cell population in nasal polyps
Ma J; Tibbitt CA; Georen SK; Christian M; Murrell B; Cardell L-O; Bachert C; Coquet JM
Article: NATURE COMMUNICATIONS. 2021;12(1):3695
Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2
Roxhed N; Bendes A; Dale M; Mattsson C; Hanke L; Dodig-Crnkovic T; Christian M; Meineke B; Elsasser S; Andrell J; Havervall S; Thalin C; Eklund C; Dillner J; Beck O; Thomas CE; McInerney G; Hong M-G; Murrell B; Fredolini C; Schwenk JM
Article: CELL REPORTS MEDICINE. 2021;2(4):100252
SARS-CoV-2 protein subunit vaccination of mice and rhesus macaques elicits potent and durable neutralizing antibody responses
Mandolesi M; Sheward DJ; Hanke L; Ma J; Pushparaj P; Vidakovics LP; Kim C; Adori M; Lenart K; Lore K; Dopico XC; Coquet JM; McInerney GM; Hedestam GBK; Murrell B
Article: IMMUNITY. 2021;54(2):355-366.e4
Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles
Bernat NV; Corcoran M; Nowak I; Kaduk M; Dopico XC; Narang S; Maisonasse P; Dereuddre-Bosquet N; Murrell B; Hedestam GBK
Article: SCIENTIFIC REPORTS. 2021;11(1):3125
DNA-launched RNA replicon vaccines induce potent anti-SARS-CoV-2 immune responses in mice
Szurgot I; Hanke L; Sheward DJ; Vidakovics LP; Murrell B; McInerney GM; Liljestrom P
Article: IMMUNOLOGY AND CELL BIOLOGY. 2021;99(2):234-243
GPR43 regulates marginal zone B-cell responses to foreign and endogenous antigens
Rohrbeck L; Adori M; Wang S; He C; Tibbitt CA; Chernyshev M; Sirel M; Ribacke U; Murrell B; Bohlooly-Y M; Karlsson MCI; Karlsson Hedestam GB; Coquet JM
Article: VIRUS EVOLUTION. 2021;7(1):veaa087
RDP5: a computer program for analyzing recombination in, and removing signals of recombination from, nucleotide sequence datasets
Martin DP; Varsani A; Roumagnac P; Botha G; Maslamoney S; Schwab T; Kelz Z; Kumar V; Murrell B
Article: CLINICAL & TRANSLATIONAL IMMUNOLOGY. 2021;10(7):e1312
Systematic evaluation of SARS-CoV-2 antigens enables a highly specific and sensitive multiplex serological COVID-19 assay
Hober S; Hellstrom C; Olofsson J; Andersson E; Bergstrom S; Jernbom Falk A; Bayati S; Mravinacova S; Sjoberg R; Yousef J; Skoglund L; Kanje S; Berling A; Svensson A-S; Jensen G; Enstedt H; Afshari D; Xu LL; Zwahlen M; von Feilitzen K; Hanke L; Murrell B; McInerney G; Karlsson Hedestam GB; Lendel C; Roth RG; Skoog I; Svenungsson E; Olsson T; Fogdell-Hahn A; Lindroth Y; Lundgren M; Maleki KT; Lagerqvist N; Klingstrom J; Da Silva Rodrigues R; Muschiol S; Bogdanovic G; Arroyo Muhr LS; Eklund C; Lagheden C; Dillner J; Sivertsson A; Havervall S; Thalin C; Tegel H; Pin E; Manberg A; Hedhammar M; Nilsson P
Article: EBIOMEDICINE. 2021;63:103197
Adjuvanted SARS-CoV-2 spike protein elicits neutralizing antibodies and CD4 T cell responses after a single immunization in mice
Worzner K; Sheward DJ; Schmidt ST; Hanke L; Zimmermann J; McInerney G; Hedestam GBK; Murrell B; Christensen D; Pedersen GK
Article: BIOMOLECULES. 2020;10(12):E1661-1661
Picomolar SARS-CoV-2 Neutralization Using Multi-Arm PEG Nanobody Constructs
Moliner-Morro A; J. Sheward D; Karl V; Perez Vidakovics L; Murrell B; McInerney GM; Hanke L
Article: NATURE COMMUNICATIONS. 2020;11(1):5850
Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells
Huang D; Tran JT; Olson A; Vollbrecht T; Tenuta M; Guryleva MV; Fuller RP; Schiffner T; Abadejos JR; Couvrette L; Blane TR; Saye K; Li W; Landais E; Gonzalez-Martin A; Schief W; Murrell B; Burton DR; Nemazee D; Voss JE
Article: NATURE COMMUNICATIONS. 2020;11(1):5588
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2
Custodio TF; Das H; Sheward DJ; Hanke L; Pazicky S; Pieprzyk J; Sorgenfrei M; Schroer MA; Gruzinov AY; Jeffries CM; Graewert MA; Svergun DI; Dobrev N; Remans K; Seeger MA; McInerney GM; Murrell B; Haellberg BM; Loew C
Article: NATURE COMMUNICATIONS. 2020;11(1):5064
SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden
Rudberg A-S; Havervall S; Manberg A; Jernbom Falk A; Aguilera K; Ng H; Gabrielsson L; Salomonsson A-C; Hanke L; Murrell B; McInerney G; Olofsson J; Andersson E; Hellstrom C; Bayati S; Bergstrom S; Pin E; Sjoberg R; Tegel H; Hedhammar M; Phillipson M; Nilsson P; Hober S; Thalin C
Article: NATURE COMMUNICATIONS. 2020;11(1):4420
An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction
Hanke L; Perez LV; Sheward DJ; Das H; Schulte T; Moliner-Morro A; Corcoran M; Achour A; Hedestam GBK; Haellberg BM; Murrell B; McInerney GM
Article: JOURNAL OF EXPERIMENTAL MEDICINE (JEM). 2020;217(2):e20191155
Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses
Phad GE; Pushparaj P; Tran K; Dubrovskaya V; Adori M; Martinez-Murillo P; Bernat NV; Singh S; Dionne G; O'Dell S; Bhullar K; Narang S; Sorini C; Villablanca EJ; Sundling C; Murrell B; Mascola JR; Shapiro L; Pancera M; Martin M; Corcoran M; Wyatt RT; Hedestam GBK
Article: MOLECULAR BIOLOGY AND EVOLUTION (MBE). 2020;37(2):576-592
Evolutionary Analyses of Base-Pairing Interactions in DNA and RNA Secondary Structures
Golden M; Murrell B; Martin D; Pybus OG; Hein J
Article: MOLECULAR BIOLOGY AND EVOLUTION (MBE). 2020;37(1):295-299
HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies
Pond SLK; 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
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2019;116(51):25891-25899
Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors
Patro SC; Brandt LD; Bale MJ; Halvas EK; Joseph KW; Shao W; Wu X; Guo S; Murrell B; Wiegand A; Spindler J; Raley C; Hautman C; Sobolewski M; Fennessey CM; Hu W-S; Luke B; Hasson JM; Niyongabo A; Capoferri AA; Keele BF; Milush J; Hoh R; Deeks SG; Maldarelli F; Hughes SH; Coffin JM; Rausch JW; Mellors JW; Kearney MF
Article: NATURE COMMUNICATIONS. 2019;10(1):5389
An MPER antibody neutralizes HIV-1 using germline features shared among donors
Zhang L; Irimia A; He L; Landais E; Rantalainen K; Leaman DP; Vollbrecht T; Stano A; Sands DI; Kim AS; Poignard P; Burton DR; Murrell B; Ward AB; Zhu J; Wilson IA; Zwick MB; Miiro G; Serwanga J; Pozniak A; McPhee D; Manigart O; Mwananyanda L; Karita E; Inwoley A; Jaoko W; DeHovitz J; Bekker L-G; Pitisuttithum P; Paris R; Allen S
Article: CELL REPORTS. 2019;29(7):1756-1766.e8
Rapid Germinal Center and Antibody Responses in Non-human Primates after a Single Nanoparticle Vaccine Immunization
Havenar-Daughton C; Carnathan DG; Boopathy AV; Upadhyay AA; Murrell B; Reiss SM; Enemuo CA; Gebru EH; Choe Y; Dhadvai P; Viviano F; Kaushik K; Bhiman JN; Briney B; Burton DR; Bosinger SE; Schief WR; Irvine DJ; Silvestri G; Crotty S
Article: NUCLEIC ACIDS RESEARCH (NAR). 2019;47(18):e104
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
Article: IMMUNITY. 2019;51(1):141-154.e6
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; Poignard P; Schief WR; Burton DR; Murrell B; Moore PL; Briney B; Sok D; Landais E
Article: VIRUS EVOLUTION. 2019;5(2):vez041
Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage
Hostager R; Ragonnet-Cronin M; Murrell B; Hedskog C; Osinusi A; Susser S; Sarrazin C; Svarovskaia E; Wertheim JO
Article: CELL. 2019;177(5):1153-1171.e28
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
Article: ELIFE. 2019;8:e42995
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
Article: IMMUNITY. 2019;50(1):241-252.e6
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; Prevost 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
Article: PLOS COMPUTATIONAL BIOLOGY. 2018;14(12):e1006498
Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons
Eren K; Weaver S; Ketteringham R; Valentyn M; Smith ML; Kumar V; Mohan S; Pond SLK; Murrell B
Article: BIOINFORMATICS. 2018;34(22):3817-3824
RIFRAF: a frame-resolving consensus algorithm
Eren K; Murrell B
Article: JOURNAL OF INFECTIOUS DISEASES. 2018;218(12):1943-1953
Growth of HIV-1 Molecular Transmission Clusters in New York City
Wertheim JO; Murrell B; Mehta SR; Forgione LA; Pond SLK; Smith DM; Torian LV
Article: CELL HOST AND MICROBE. 2018;24(4):593-599.e3
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; Karim QA; Karim SSA; Morris L; Moore PL; Williamson C
Article: VIRUS EVOLUTION. 2018;4(2):vey030
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
Article: PLOS PATHOGENS. 2018;14(5):e1007024
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; Ramisch S; Menis S; Schief WR; Doria-Rose N; Haynes B; Murrell B; Cale EM; Pegu A; Mascola JR; Vidarsson G; Binley JM
Article: JOURNAL OF VIRAL HEPATITIS. 2018;25(4):344-353
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
Article: IMMUNITY. 2017;47(5):990-1003.e9
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 P-Y; Karita E; Ward AB; Wilson IA; Burton DR; Smith D; Pond SLK; Poignard P
Article: PLOS PATHOGENS. 2017;13(2):e1006235
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
Article: NATURE MEDICINE. 2017;23(2):185-191
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; Kuemmerle T; Wyen C; Levin R; Witmer-Pack M; Eren K; Ignacio C; Kiss S; West APJ; Mouquet H; Zingman BS; Gulick RM; Keler T; Bjorkman PJ; Seaman MS; Hahn BH; Faetkenheuer G; Schlesinger SJ; Nussenzweig MC; Klein F
Article: METHODS IN MOLECULAR BIOLOGY. 2017;1525:433-460
Detecting and Analyzing Genetic Recombination Using RDP4.
Martin DP; Murrell B; Khoosal A; Muhire B
Article: PLOS PATHOGENS. 2017;13(1):e1006000
Social and Genetic Networks of HIV-1 Transmission in New York City
Wertheim JO; Pond SLK; Forgione LA; Mehta SR; Murrell B; Shah S; Smith DM; Scheffler K; Torian LV
Article: JOURNAL OF VIROLOGY. 2016;90(18):8085-8089
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
Article: VIRUS EVOLUTION. 2016;2(2):vew018
Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples
Smith ML; Murrell B; Eren K; Ignacio C; Landais E; Weaver S; Pham P; Ludka C; Hepler L; Caballero G; Pollner T; Guo Y; Richman D; Poignard P; Paxinos EE; Pond SLK; Smith DM
Article: CLINICAL INFECTIOUS DISEASES. 2016;63(1):101-107
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; Pond SLK; Wertheim JO; Young JA; Freitas L; Richman DD; Mathews WC; Scheffler K; Little SJ; Smith DM
Article: IMMUNITY. 2016;44(5):1215-1226
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 C-H; Ramos A; Bian CB; Wickramasinghe L; Kong L; Eren K; Wu C-Y; Wong C-H; Pond SLK; Wilson IA; Burton DR; Poignard P
Article: JOURNAL OF NEUROVIROLOGY. 2016;22(2):191-200
Cell-free mitochondrial DNA in CSF is associated with early viral rebound, inflammation, and severity of neurocognitive deficits in HIV infection
Perez-Santiago J; Schrier RD; de Oliveira MF; Gianella S; Var SR; Day TRC; Ramirez-Gaona M; Suben JD; Murrell B; Massanella M; Cherner M; Smith DM; Ellis RJ; Letendre SL; Mehta SR
Article: PLOS PATHOGENS. 2016;12(1):e1005369
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 L-G; Tang J; Gilmour J; Kosakovsky-Pond SL; Pham P; Wrin T; Crotty S; Godzik A; Poignard P
Article: PLOS ONE. 2016;11(3):e0151551
Discovering General Multidimensional Associations
Murrell B; Murrell D; Murrell H
Article: EBIOMEDICINE. 2015;2(10):1456-1463
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
Article: PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON. BIOLOGICAL SCIENCES. 2015;370(1676):20140240
Assigning and visualizing germline genes in antibody repertoires
Frost SDW; Murrell B; Hossain ASMM; Silverman GJ; Pond SLK
Article: MOLECULAR BIOLOGY AND EVOLUTION (MBE). 2015;32(5):1365-1371
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; Pond SLK
Article: MOLECULAR BIOLOGY AND EVOLUTION (MBE). 2015;32(5):1342-1353
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; Pond SLK
Article: VIRUS EVOLUTION. 2015;1(1):vev003
RDP4: Detection and analysis of recombination patterns in virus genomes.
Martin DP; Murrell B; Golden M; Khoosal A; Muhire B
Article: VIRUS EVOLUTION. 2015;1(1):vev002
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
Article: MOLECULAR BIOLOGY AND EVOLUTION (MBE). 2015;32(3):820-832
RELAX: Detecting Relaxed Selection in a Phylogenetic Framework
Wertheim JO; Murrell B; Smith MD; Pond SLK; Scheffler K
Article: PLOS ONE. 2015;10(11):e0140936
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
Article: JOURNAL OF CLINICAL VIROLOGY. 2015;62:48-53
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; Pond SLK; Van Zyl GU
Article: PLOS COMPUTATIONAL BIOLOGY. 2014;10(9):e1003842
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; Pond SLK
Article: JOURNAL OF VIROLOGY. 2014;88(4):1972-1989
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 J-M; Gray A; Poon AYF; Ngandu NK; Semegni Y; Tanov EP; Monjane AL; Harkins GW; Varsani A; Shepherd DN; Martin DP
Article: PLOS ONE. 2014;9(4):e94534
On the Validity of Evolutionary Models with Site-Specific Parameters
Scheffler K; Murrell B; Pond SLK
Article: VIROLOGY JOURNAL. 2013;10:347
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 SSA; Mascola JR; Korber BTM; Montefiori DC; Morris L; Williamson C; Seoighe C
Article: MOLECULAR BIOLOGY AND EVOLUTION (MBE). 2013;30(5):1196-1205
FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection
Murrell B; Moola S; Mabona A; Weighill T; Sheward D; Pond SLK; Scheffler K
Article: JOURNAL OF VIROLOGY. 2012;86(11):6231-6237
Deep Sequencing Reveals Minor Protease Resistance Mutations in Patients Failing a Protease Inhibitor Regimen
Fisher R; van Zyl GU; Travers SAA; Pond SLK; Engelbrech S; Murrell B; Scheffler K; Smith D
Article: PLOS GENETICS. 2012;8(7):e1002764
Detecting Individual Sites Subject to Episodic Diversifying Selection
Murrell B; Wertheim JO; Moola S; Weighill T; Scheffler K; Pond SLK
Article: PLOS COMPUTATIONAL BIOLOGY. 2012;8(5):e1002507
Modeling HIV-1 Drug Resistance as Episodic Directional Selection
Murrell B; de Oliveira T; Seebregts C; Pond SLK; Scheffler K
Article: MOLECULAR BIOLOGY AND EVOLUTION (MBE). 2011;28(11):3033-3043
A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection
Pond SLK; Murrell B; Fourment M; Frost SDW; Delport W; Scheffler K
Article: PLOS ONE. 2011;6(12):e28898
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
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Corrigendum: VIRUS EVOLUTION. 2024;10(1):veae038
Correction to: Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations-Application to HIV-1 quasispecies.
Review: NATURE MICROBIOLOGY. 2023;8(11):1952-1959
SARS-CoV-2 evolution in the Omicron era
Roemer C; Sheward DJ; Hisner R; Gueli F; Sakaguchi H; Frohberg N; Schoenmakers J; Sato K; O'Toole A; Rambaut A; Pybus OG; Ruis C; Murrell B; Peacock TP
Letter: THE LANCET INFECTIOUS DISEASES. 2023;23(11):e462-e463
Sensitivity of the SARS-CoV-2 BA.2.86 variant to prevailing neutralising antibody responses
Sheward DJ; Yang Y; Westerberg M; Oling S; Muschiol S; Sato K; Peacock TP; Hedestam GBK; Albert J; Murrell B
Letter: THE LANCET INFECTIOUS DISEASES. 2022;22(11):1538-1540
Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies
Sheward DJ; Kim C; Fischbach J; Sato K; Muschiol S; Ehling RA; Bjorkstrom NK; Hedestam GBK; Reddy ST; Albert J; Peacock TP; Murrell B
Letter: THE LANCET INFECTIOUS DISEASES. 2022;22(10):1421-1422
Evasion of neutralising antibodies by omicron sublineage BA.2.75
Sheward DJ; Kim C; Fischbach J; Muschiol S; Ehling RA; Bjorkstrom NK; Hedestam GBK; Reddy ST; Albert J; Peacock TP; Murrell B
Preprint: BIORXIV. 2022;BIORXIV
Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Martin DP; Lytras S; Lucaci AG; Maier W; Grüning B; Shank SD; Weaver S; MacLean OA; Orton RJ; Lemey P; Boni MF; Tegally H; Harkins G; Scheepers C; Bhiman JN; Everatt J; Amoako DG; San JE; Giandhari J; Sigal A; NGS-SA; Williamson C; Hsiao N-Y; von Gottberg A; De Klerk A; Shafer RW; Robertson DL; Wilkinson RJ; Sewell BT; Lessells R; Nekrutenko A; Greaney AJ; Starr TN; Bloom JD; Murrell B; Wilkinson E; Gupta RK; de Oliveira T; Kosakovsky Pond SL
Preprint: MEDRXIV. 2021;MEDRXIV
The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.
Martin DP; Weaver S; Tegally H; San EJ; Shank SD; Wilkinson E; Lucaci AG; Giandhari J; Naidoo S; Pillay Y; Singh L; Lessells RJ; NGS-SA; COVID-19 Genomics UK (COG-UK); Gupta RK; Wertheim JO; Nekturenko A; Murrell B; Harkins GW; Lemey P; MacLean OA; Robertson DL; de Oliveira T; Kosakovsky Pond SL
Corrigendum: NATURE COMMUNICATIONS. 2020;11(1):6360
Author Correction: Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells.
Huang D; Tran JT; Olson A; Vollbrecht T; Tenuta M; Guryleva MV; Fuller RP; Schiffner T; Abadejos JR; Couvrette L; Blane TR; Saye K; Li W; Landais E; Gonzalez-Martin A; Schief W; Murrell B; Burton DR; Nemazee D; Voss JE
Corrigendum: CELL. 2020;180(1):206
Slow Delivery Immunization Enhances HIV Neutralizing Antibody and Germinal Center Responses via Modulation of Immunodominance (vol 177, pg 1153, 2019)
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
Corrigendum: SCIENTIFIC REPORTS. 2016;6:19387
Circulating HIV DNA Correlates With Neurocognitive Impairment in Older HIV-infected Adults on Suppressive ART (vol 5, 17094, 2015)
de Oliveira MF; Murrell B; Perez-Santiago J; Vargas M; Ellis RJ; Letendre S; Grant I; Smith DM; Woods SP; Gianella S
Letter: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2014;111(21):E2160
R²-equitability is satisfiable
Murrell B; Murrell D; Murrell H
Letter: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2012;109(21):E1330
Degenerate Primer IDs and the Birthday Problem
Sheward DJ; Murrell B; Williamson C
Review: METHODS IN MOLECULAR BIOLOGY. 2012;856:239-272
Evolution of viral genomes: interplay between selection, recombination, and other forces.
Pond SLK; Murrell B; Poon AFY

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