Computational Biology, Virology, and Immunology – Murrell Lab

Publications

All publications from group members

• Preprint: 2025

  Time dependent loss reweighting for flow matching and diffusion models is theoretically justified

  Billera L; Nordlinder HN; Murrell B
• Preprint: 2025

  Branching Flows: Discrete, Continuous, and Manifold Flow Matching with Splits and Deletions

  Billera L; Nordlinder HN; Ryder JC; Oresten A; Stålmarck A; Björk TM; Murrell B
• Preprint: BIORXIV. 2025

  Spontaneous Emergence of Symmetry in a Generative Model of Protein Structure

  Oresten A; Sato K; Stålmarck A; Billera L; Nordlinder HN; Ryder JC; Kaduk M; Murrell B
• Article: BIOINFORMATICS. 2025;41(11):btaf576

  Detection of PCR chimeras in adaptive immune receptor repertoire sequences

  Chernyshev M; Stalmarck A; Corcoran M; Karlsson Hedestam GB; Murrell B
• Article: CELL SYSTEMS. 2025;16(9):101391

  Synthetic coevolution reveals adaptive mutational trajectories of neutralizing antibodies and SARS-CoV-2

  Ehling RA; Minot M; Overath MD; Sheward DJ; Han J; Gao B; Taft JM; Pertseva M; Weber CR; Frei L; Bikias T; Murrell B; Reddy ST
• Preprint: BIORXIV. 2025

  difFUBAR: Scalable Bayesian comparison of adaptive evolution

  Sadiq H; Truong P; Danielsson M; Kumar V; Nordlinder HN; Martin DP; Murrell B
• Preprint: BIORXIV. 2025;BIORXIV

  Detection of PCR chimeras in adaptive immune receptor repertoire sequencing using hidden Markov models.

  Chernyshev M; Stålmarck A; Corcoran M; Hedestam GBK; Murrell B
• Article: CELL REPORTS. 2025;44(1):115221

  Antigen affinity and site of immunization dictate B cell recall responses

  Termote M; Marques RC; Hyllner E; V. Guryleva M; Henskens M; Brutscher A; Baken IJL; Dopico XC; Gasull AD; Murrell B; Stamatatos L; Westerberg LS; Dosenovic P
• Letter: LANCET MICROBE. 2024;5(12):100998

  A novel SARS-CoV-2 recombinant transmitted from a patient with an acute co-infection

  Dyrdak R; Stamouli S; Aralaguppe SG; Ekman M; Safari H; Berg C; Movert E; Latorre-Margalef N; Andersson E; Gisslen M; Nederby-Ohd J; Leufven AS; Schoenmakers J; Broddesson S; Murrell B; Albert J
• Article: EBIOMEDICINE. 2024;110:105415

  Cross-sectional and longitudinal genotype to phenotype surveillance of SARS-CoV-2 variants over the fi rst four years of the COVID-19 pandemic

  Akerman A; Fichter C; Milogiannakis V; Esneau C; Silva MR; Ison T; Lopez JA; Naing Z; Caguicla J; Amatayakul-Chantler S; Roth N; Manni S; Hauser T; Barnes T; Boss T; Condylios A; Yeang M; Sato K; Bartlett NN; Darley D; Matthews G; Stark DJ; Promsri S; Rawlinson WD; Murrell B; Kelleher AD; Dwyer D; Sintchenko V; Kok J; Ellis S; Marris K; Knight E; Hoad VC; Irving DO; Gosbell I; Brilot F; Wood J; Aggarwal A; Turville SG
• Article: FRONTIERS IN PHARMACOLOGY. 2024;15:1503648

  Polyvinylalcohol-carbazate mitigates acute lung injury caused by hydrochloric acid

  Dong C; Liu J; Quaranta A; Jing X; Nie M; Wheelock CE; Murrell B; Coquet JM; Bowden TM; Engstrand T; Adner M
• 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
• 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.
• Preprint: BIORXIV. 2024

  The Continuous Language of Protein Structure

  Billera L; Oresten A; Stålmarck A; Sato K; Kaduk M; Murrell B
• 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: 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
• Preprint: RESEARCH SQUARE. 2024

  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; Dopico XC; Fischbach J; Kim S; Guryleva M; Adori M; Chernyshev M; Stålmarck A; Hanke L; McInerney G; Sheward D; Corcoran M; Hällberg M; Murrell B; Hedestam GK
• 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
• Letter: 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
• 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
• 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
• Preprint: BIORXIV. 2023

  Sensitivity of BA.2.86 to prevailing neutralising antibody responses

  Sheward D; Yang Y; Westerberg M; Öling S; Muschiol S; Sato K; Peacock T; Karlsson Hedestam G; Albert J; Murrell B
• 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: 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

  Vikstrom L; Fjallstrom P; Gwon Y-D; Sheward DJ; Wigren-Bystrom J; Evander M; Bladh O; Widerstrom M; Molnar C; Rasmussen G; Bennet L; Aberg M; Bjork J; Tevell S; Thalin C; Blom K; Klingstrom 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: 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: 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: 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: 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
• Preprint: RESEARCH SQUARE. 2022

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

  Chernyshev M; Sakharkar M; Connor R; Dugan H; Sheward D; Rappazzo G; Stålmarck A; Forsell M; Wright P; Corcoran M; Murrell B; Walker L; Hedestam GK
• Letter: 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
• Article: ALLERGY. 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: 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
• Letter: 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
• 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: 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. 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
• 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
• 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: 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
• 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
• 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
• Corrigendum: NATURE COMMUNICATIONS. 2020;11(1):6360

  Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells (vol 11, 5850, 2020)

  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):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. 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. 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
• 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
• Article: MOLECULAR BIOLOGY AND EVOLUTION. 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. 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 & 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: 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: 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: 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: METHODS IN MOLECULAR BIOLOGY. 2017;1525:433-460

  Detecting and Analyzing Genetic Recombination Using RDP4.

  Martin DP; Murrell B; Khoosal A; Muhire B
• 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 ONE. 2016;11(3):e0151551

  Discovering General Multidimensional Associations

  Murrell B; Murrell D; Murrell H
• 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
• 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. 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: 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 B-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. 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. 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. 2015;32(3):820-832

  RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

  Wertheim JO; Murrell B; Smith MD; Pond SLK; Scheffler K
• 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
• 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
• Article: PLOS ONE. 2014;9(4):e94534

  On the Validity of Evolutionary Models with Site-Specific Parameters

  Scheffler K; Murrell B; 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: 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. 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
• 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
• 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
• 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
• 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: 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
• Article: MOLECULAR BIOLOGY AND EVOLUTION. 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
• Other:

  Geometrically Aware Markov Chain Monte Carlo

  Nordlinder H
• Show more

Staff and contact

Group leader

• 

  Benjamin Sylvester Murrell

  Principal Researcher

  E-mail benjamin.murrell@ki.se

All members of the group

• Lukas Billera

  Teaching Assistant

  E-mail lukas.billera@ki.se
• Theodor Björk

  Teaching Assistant

  E-mail theodor.mosetti.bjork@ki.se
• Willó Corry

  Teaching Assistant

  E-mail willo.corry@ki.se
• Maximilian Danielsson

  Teaching Assistant

  E-mail maximilian.danielsson@ki.se
• Hedwig Nordlinder

  Teaching Assistant

  E-mail hedwig.nordlinder@ki.se
• Tove Nordmark

  Teaching Assistant

  E-mail tove.nordmark@ki.se
• Anton Oresten

  Bioinformatician

  E-mail anton.oresten@ki.se
• Jack Elliot Ryder

  Teaching Assistant

  E-mail jack.collier.ryder@ki.se
• Aron Stålmarck

  Teaching Assistant

  E-mail aron.stalmarck@ki.se
• Yue Xu

  Phd Student

  E-mail yue.xu@ki.se