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2022

Hassler G, Tolkoff MR, Allen WL, Ho LST, Lemey P, Suchard MA.
Inferring Phenotypic Trait Evolution on Large Trees With Many Incomplete Measurements
Journal of the American Statistical Association 117(538):678-692

Herman JD, Wang C, Burke JS, Zur Y, Compere H, Kang J, Macvicar R, Taylor S, Shin S, Frank I, Siegel D, Tebas P, Choi GH, Shaw PA, Yoon H, Pirofski LA, Julg BD, Bar KJ, Lauffenburger D, Alter G
Nucleocapsid-specific antibody function is associated with therapeutic benefits from COVID-19 convalescent plasma therapy
Cell Rep Med [Epub ahead of print]

Li H, Buck T, Zandonatti M, Yin J, Moon-Walker A, Fang J, Koval A, Heinrich ML, Rowland MM, Diaz Avalos R, Schendel SL, Parekh D, Zyla D, Enriquez A, Harkins S, Sullivan B, Smith V, Chukwudozie O, Watanabe R, Robinson JE, Garry RF, Branco LM, Hastie KM, Saphire EO
A cocktail of protective antibodies subverts the dense glycan shield of Lassa virus
Sci Transl Med 14(668)

LaSalle TJ, Gonye ALK, Freeman SS, Kaplonek P, Gushterova I, Kays KR, Manakongtreecheep K, Tantivit J, Rojas-Lopez M, Russo BC, Sharma N, Thomas MF, Lavin-Parsons KM, Lilly BM, Mckaig BN, Charland NC, Khanna HK, Lodenstein CL, Margolin JD, Blaum EM, Lirofonis PB, Revach OY, Mehta A, Sonny A, Bhattacharyya RP, Parry BA, Goldberg MB, Alter G, Filbin MR, Villani AC, Hacohen N, Sade-Feldman M
Longitudinal characterization of circulating neutrophils uncovers phenotypes associated with severity in hospitalized COVID-19 patients
Cell Rep Med 3(10):100779

Burns MD, Muir C, Atyeo C, Davis JP, Demidkin S, Akinwunmi B, Fasano A, Gray KJ, Alter G, Shook LL, Edlow AG, Yonker LM
Relationship between Anti-Spike Antibodies and Risk of SARS-CoV-2 Infection in Infants Born to COVID-19 Vaccinated Mothers
Vaccines (Basel) 10(10):169

Fisher AA, Hassler GW, Ji X, Baele G, Suchard MA, Lemey P
Scalable Bayesian phylogenetics
Philosophical Transactions of the Royal Society of London. Series B, Biol Sci 377(1861):20210242

Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Sandi JD, Goba A, Alhasan F, Grant DS, Okogbenin S, Ogbaini-Emovo E, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S
Predicting the Evolution of the Lassa virus Endemic Area and Population at Risk Over the Next Decades
Nature Communications 13(1):5596

McCrone JT, Hill V, Bajaj S, Pena RE, Lambert BC, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski AE, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O’Toole Á, Peacock TP, Twohig K, Thelwall S, Dabrera G, Myers R; COVID-19 genomics UK (COG-UK) consortium, Faria NR, Huber C, Bogoch II, Khan K, du Plessis L, Barrett JC, Aanensen DM, Barclay WS, Chand M, Connor T, Loman NJ, Suchard MA, Pybus OG, Rambaut A, Kraemer MUG
Context-specific emergence and growth of the SARS-CoV-2 Delta variant
Nature 610(7930):154-160

Dolatshahi S, Butler AL, Pou C, Henckel E, Bernhardsson AK, Gustafsson A, Bohlin K, Shin SA, Lauffenburger DA, Brodin P, Alter G
Selective transfer of maternal antibodies in preterm and fullterm children
Sci Rep 12(1):14937

Parker E, Anderson C, Zeller M, Tibi A, Havens JL, Laroche G, Benlarbi M, Ariana A, Robles-Sikisaka R, Latif AA, Watts A, Awidi A, Jaradat SA, Gangavarapu K, Ramesh K, Kurzban E, Matteson NL, Han AX, Hughes LD, McGraw M, Spencer E, Nicholson L, Khan K, Suchard MA, Wertheim JO, Wohl S, Côté M, Abdelnour A, Andersen KG, Abu-Dayyeh I
Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions
Nature Communications 13(1):4784

Chiosi JJ, Schieffelin JS, Shaffer JG, Grant DS
Evaluation of Three Clinical Prediction Tools to Predict Mortality in Hospitalized Patients with Lassa Fever
The American Journal of Tropical Medicine and Hygiene 107(4):856-862

Bartsch YC, St Denis KJ, Kaplonek P, Kang J, Lam EC, Burns MD, Farkas EJ, Davis JP, Boribong BP, Edlow AG, Fasano A, Shreffler WG, Zavadska D, Johnson M, Goldblatt D, Balazs AB, Yonker LM, Alter G
SARS-CoV-2 mRNA vaccination elicits robust antibody responses in children
Sci Transl Med [Epub ahead of print]

Worobey M, Levy JI, Serrano LM, Crits-Christoph A, Pekar JE, Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, Suchard MA, Wertheim JO, Lemey P, Robertson DL, Garry RF, Holmes EC, Rambaut A, Andersen KG
The Huanan Seafood Wholesale Market in Wuhan Was the Early Epicenter of the COVID-19 Pandemic
Science 377(6609):951-959

Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching KZY, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO
The Molecular Epidemiology of Multiple Zoonotic Origins of SARS-CoV-2
Science 377(6609):960-966

Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R
Wastewater Sequencing Reveals Early Cryptic SARS-CoV-2 Variant Transmission
Nature 609(7925):101-108

DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O’Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS
Defining the risk of SARS-CoV-2 variants on immune protection
Nature 605(7911):640-652

Kaplonek P, Cizmeci D, Fischinger S, Collier AR, Suscovich T, Linde C, Broge T, Mann C, Amanat F, Dayal D, Rhee J, de St Aubin M, Nilles EJ, Musk ER, Menon AS, Saphire EO, Krammer F, Lauffenburger DA, Barouch DH, Alter G
mRNA-1273 and BNT162b2 COVID-19 vaccines elicit antibodies with differences in Fc-mediated effector functions
Sci Transl Med 14(645)

Bartsch YC, Tong X, Kang J, Avendaño MJ, Serrano EF, García-Salum T, Pardo-Roa C, Riquelme A, Cai Y, Renzi I, Stewart-Jones G, Chen B, Medina RA, Alter G
Omicron variant Spike-specific antibody binding and Fc activity is preserved in recipients of mRNA or inactivated COVID-19 vaccines
Sci Transl Med 14(642)

Shook LL, Atyeo CG, Yonker LM, Fasano A, Gray KJ, Alter G, Edlow AG.
Durability of Anti-Spike Antibodies in Infants After Maternal COVID-19 Vaccination or Natural Infection.
JAMA 327(11):1087-1089.

Kaplonek P, Fischinger S, Cizmeci D, Bartsch YC, Kang J, Burke JS, Shin SA, Dayal D, Martin P, Mann C, Amanat F, Julg B, Nilles EJ, Musk ER, Menon AS, Krammer F, Saphire EO, Andrea Carfi, Alter G
mRNA-1273 vaccine-induced antibodies maintain Fc effector functions across SARS-CoV-2 variants of concern
Immunity 8;55(2):355-365

Siddiqui SM, Bowman KA, Zhu AL, Fischinger S, Beger S, Maron JS, Bartsch YC, Atyeo C, Gorman MJ, Yanis A, Hultquist JF, Lorenzo-Redondo R, Ozer EA, Simons LM, Talj R, Rankin DA, Chapman L, Meade K, Steinhart J, Mullane S, Siebert S, Streeck H, Sabeti P, Halasa N, Musk ER, Barouch DH, Menon AS, Nilles EJ, Lauffenburger DA, Alter G
Serological Markers of SARS-CoV-2 Reinfection
mBio 13(1):e0214121

Quer G, Gadaleta M, Radin JM, Andersen KG, Baca-Motes K, Ramos E, Topol EJ, Steinhubl SR.
Inter-individual variation in objective measure of reactogenicity following COVID-19 vaccination via smartwatches and fitness bands.
NPJ digital medicine. 5(1):49.

Melnik LI, Garry RF.
Enterotoxigenic Escherichia coli Heat-Stable Toxin and Ebola Virus Delta Peptide: Similarities and Differences.
Pathogens 11(2):170.

Holbrook AJ, Ji X, Suchard MA
From viral evolution to spatial contagion: a biologically modulated Hawkes model
Bioinformatics 38(7):1846-1856

Melnik LI, Guha S, Ghimire J, Smither AR, Beddingfield BJ, Hoffmann AR, Sun L, Ungerleider NA, Baddoo MC, Flemington EK, Gallaher WR, Wimley WC, Garry RF
Ebola virus Delta Peptide is an Enterotoxin
Cell Reports 38(1):110172

Atyeo CG, Shook LL, Brigida S, De Guzman RM, Demidkin S, Muir C, Akinwunmi B, Baez AM, Sheehan ML, McSweeney E, Burns MD, Nayak R, Kumar MK, Patel CD, Fialkowski A, Cvrk D, Goldfarb IT, Yonker LM, Fasano A, Balazs AB, Elovitz MA, Gray KJ, Alter G, Edlow AG.
Maternal immune response and placental antibody transfer after COVID-19 vaccination across trimester and platforms.
Nature communications 13(1):3571.

Burns MD, Boribong BP, Bartsch YC, Loiselle M, St Denis KJ, Sheehan ML, Chen JW, Davis JP, Lima R, Edlow AG, Fasano A, Balazs AB, Alter G, Yonker LM.
Durability and Cross-Reactivity of SARS-CoV-2 mRNA Vaccine in Adolescent Children.
Vaccines 10(4):492.

He WT, Bollen N, Xu Y, Zhao J, Dellicour S, Yan Z, Gong W, Zhang C, Zhang L, Lu M, Lai A, Suchard MA, Ji X, Tu C, Lemey P, Baele G, Su S.
Phylogeography Reveals Association between Swine Trade and the Spread of Porcine Epidemic Diarrhea Virus in China and across the World.
Molecular biology and evolution. 39(2)

Kolls JK, Garry RF.
Role of the T cell vitamin D receptor in severe COVID-19.
Nature Immunology 23(1):5-6.

Schuemie MJ, Chen Y, Madigan D, Suchard MA.
Combining cox regressions across a heterogeneous distributed research network facing small and zero counts.
Statistical Methods in Medical Research 31(3):438-450.

2021

Kraemer M, McCrone J, Hill V, Bajaj S, Evans-Pena R, Lambert B, Inward R, Bhatt S, Volz E, Ruis C, Dellicour S, Baele G, Zarebski A, Sadilek A, Wu N, Schneider A, Ji X, Raghwani J, Jackson B, Colquhoun R, O’Toole A, Peacock T, Twohig K, Thelwall S, Dabrera G, Meyers R, Faria N, Huber C, Khan K, Bogoch I, Plessis L, Barrett J, Aanensen D, Barclay W, Chand M, Connor T, Loman N, Suchard M, Pybus O, Rambaut A.
Context-specific emergence and growth of the SARS-CoV-2 Delta variant.
Research square [Preprint] rs.3.rs-1159614.

Herman JD, Wang C, Loos C, Yoon H, Rivera J, Eugenia Dieterle M, Haslwanter D, Jangra RK, Bortz RH 3rd, Bar KJ, Julg B, Chandran K, Lauffenburger D, Pirofski LA, Alter G
Functional Convalescent Plasma Antibodies and Pre-infusion Titers Shape the Early Severe COVID-19 Immune Response
Nature Communications 12(1):6853

Borrega R, Nelson DKS, Koval AP, Bond NG, Heinrich ML, Rowland MM, Lathigra R, Bush DJ, Aimukanova I, Phinney WN, Koval SA, Hoffmann AR, Smither AR, Bell-Kareem AR, Melnik LI, Genemaras KJ, Chao K, Snarski P, Melton AB, Harrell JE, Smira AA, Elliott DH, Rouelle JA, Sabino-Santos G Jr, Drouin AC, Momoh M, Sandi JD, Goba A, Samuels RJ, Kanneh L, Gbakie M, Branco ZL, Shaffer JG, Schieffelin JS, Robinson JE, Fusco DN, Sabeti PC, Andersen KG, Grant DS, Boisen ML, Branco LM, Garry RF
Cross-Reactive Antibodies to SARS-CoV-2 and MERS-CoV in Pre-COVID-19 Blood Samples from Sierra Leoneans
Viruses 13(11):2325

Collier AY, Yu J, McMahan K, Liu J, Chandrashekar A, Maron JS, Atyeo C, Martinez DR, Ansel JL, Aguayo R, Rowe M, Jacob-Dolan C, Sellers D, Barrett J, Ahmad K, Anioke T, VanWyk H, Gardner S, Powers O, Bondzie EA, Wan H, Baric RS, Alter G, Hacker MR, Barouch DH
Differential Kinetics of Immune Responses Elicited by Covid-19 Vaccines
The New England Journal of Medicine 385(21):2010-2012

Telenti A, Arvin A, Corey L, Corti D, Diamond MS, García-Sastre A, Garry RF, Holmes EC, Pang P, Virgin HW
After the Pandemic: Perspectives on the Future Trajectory of COVID-19
Nature 596(7873):495-504

Holbrook AJ, Lemey P, Baele G, Dellicour S, Brockmann D, Rambaut A, Suchard MA
Massive Parallelization Boosts Big Bayesian Multidimensional Scaling
Journal of Computational and Graphical Statistics 30(1):11-24

Yu J, Tostanoski LH, Mercado NB, McMahan K, Liu J, Jacob-Dolan C, Chandrashekar A, Atyeo C, Martinez DR, Anioke T, Bondzie EA, Chang A, Gardner S, Giffin VM, Hope DL, Nampanya F, Nkolola J, Patel S, Sanborn O, Sellers D, Wan H, Hayes T, Bauer K, Pessaint L, Valentin D, Flinchbaugh Z, Brown R, Cook A, Bueno-Wilkerson D, Teow E, Andersen H, Lewis MG, Martinot AJ, Baric RS, Alter G, Wegmann F, Zahn R, Schuitemaker H, Barouch DH
Protective Efficacy of Ad26.COV2.S Against SARS-CoV-2 B.1.351 in Macaques
Nature 596(7872):423-427

Alter G, Yu J, Liu J, Chandrashekar A, Borducchi EN, Tostanoski LH, McMahan K, Jacob-Dolan C, Martinez DR, Chang A, Anioke T, Lifton M, Nkolola J, Stephenson KE, Atyeo C, Shin S, Fields P, Kaplan I, Robins H, Amanat F, Krammer F, Baric RS, Le Gars M, Sadoff J, de Groot AM, Heerwegh D, Struyf F, Douoguih M, van Hoof J, Schuitemaker H, Barouch DH
Immunogenicity of Ad26.COV2.S Vaccine Against SARS-CoV-2 Variants in Humans
Nature 596(7871):268-272

Nilles EJ, Siddiqui SM, Fischinger S, Bartsch YC, de St Aubin M, Zhou G, Gluck MJ, Berger S, Rhee J, Petersen E, Mormann B, Loesche M, Hu Y, Chen Z, Yu J, Gebre M, Atyeo C, Gorman MJ, Zhu AL, Burke J, Slein M, Hasdianda MA, Jambaulikar G, Boyer EW, Sabeti PC, Barouch DH, Julg B, Kucharski AJ, Musk ER, Lauffenburger DA, Alter G, Menon AS.
Epidemiological and Immunological Features of Obesity and SARS-CoV-2.
Viruses. 13(11):2235.

Chen RE, Gorman MJ, Zhu DY, Carreño JM, Yuan D, VanBlargan LA, Burdess S, Lauffenburger DA, Kim W, Turner JS, Droit L, Handley SA, Chahin S, Deepak P, O’Halloran JA, Paley MA, Presti RM, Wu GF, Krammer F, Alter G, Ellebedy AH, Kim AHJ, Diamond MS.
Reduced antibody activity against SARS-CoV-2 B.1.617.2 delta virus in serum of mRNA-vaccinated individuals receiving tumor necrosis factor-α inhibitors.
Med (N Y). 2(12):1327-1341.e4.

Pullen KM, Atyeo C, Collier AY, Gray KJ, Belfort MB, Lauffenburger DA, Edlow AG, Alter G.
Selective functional antibody transfer into the breastmilk after SARS-CoV-2 infection.
Cell reports. 37(6):109959.

Bordt EA, Shook LL, Atyeo C, Pullen KM, De Guzman RM, Meinsohn MC, Chauvin M, Fischinger S, Yockey LJ, James K, Lima R, Yonker LM, Fasano A, Brigida S, Bebell LM, Roberts DJ, Pépin D, Huh JR, Bilbo SD, Li JZ, Kaimal A, Schust D, Gray KJ, Lauffenburger D, Alter G, Edlow AG
Maternal SARS-CoV-2 Infection Elicits Sexually Dimorphic Placental Immune Responses
Science Translational Medicine 13(617):eabi7428

Atyeo C, DeRiso EA, Davis C, Bordt EA, De Guzman RM, Shook LL, Yonker LM, Fasano A, Akinwunmi B, Lauffenburger DA, Elovitz MA, Gray KJ, Edlow AG, Alter G
COVID-19 mRNA Vaccines Drive Differential Antibody Fc-functional Profiles in Pregnant, Lactating, and Non-pregnant Women
Science Translational Medicine 13(617):eabi8631

Kaplonek P, Wang C, Bartsch Y, Fischinger S, Gorman MJ, Bowman K, Kang J, Dayal D, Martin P, Nowak RP, Villani AC, Hsieh CL, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilley BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Sade-Feldman M, Feldman J, Julg B, Nilles EJ, Musk ER, Menon AS, Fischer ES, McLellan JS, Schmidt A, Goldberg MB, Filbin MR, Hacohen N, Lauffenburger DA, Alter G
Early Cross-coronavirus Reactive Signatures of Humoral Immunity Against COVID-19
Science Immunology 6(64):eabj2901

Beddingfield BJ, Hartnett JN, Wilson RB, Kulakosky PC, Andersen KG, Robles-Sikisaka R, Grubaugh ND, Aybar A, Nunez MZ, Fermin CD, Garry RF.
Zika Virus Non-Structural Protein 1 Antigen-Capture Immunoassay.
Viruses13(9), 1771.

Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G Jr, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG
Emergence of an Early SARS-CoV-2 Epidemic in the United States
Cell 184(19):4939-4952

Gorman MJ, Patel N, Guebre-Xabier M, Zhu AL, Atyeo C, Pullen KM, Loos C, Goez-Gazi Y, Carrion R Jr, Tian JH, Yuan D, Bowman KA, Zhou B, Maciejewski S, McGrath ME, Logue J, Frieman MB, Montefiori D, Mann C, Schendel S, Amanat F, Krammer F, Saphire EO, Lauffenburger DA, Greene AM, Portnoff AD, Massare MJ, Ellingsworth L, Glenn G, Smith G, Alter G.
Fab and Fc contribute to maximal protection against SARS-CoV-2 following NVX-CoV2373 subunit vaccine with Matrix-M vaccination.
Cell reports. Medicine 2(9):100405

Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang X, Leibowitz JL, Neil SJD, Skern T, Weiss SR, Worobey M, Andersen KG, Garry RF, Rambaut A
The Origins of SARS-CoV-2: A Critical Review
Cell 184(19):4848-4856

Meyer M, Gunn BM, Malherbe DC, Gangavarapu K, Yoshida A, Pietzsch C, Kuzmina NA, Saphire EO, Collins PL, Crowe JE Jr, Zhu JJ, Suchard MA, Brining DL, Mire CE, Cross RW, Geisbert JB, Samal SK, Andersen KG, Alter G, Geisbert TW, Bukreyev A
Ebola Vaccine-Induced Protection In Nonhuman Primates Correlates With Antibody Specificity and Fc-Mediated Effects
Science Translational Medicine 13(602)

Koch MR, Kanneh L, Wise PH, Kurina LM, Alhasan F, Garry RF, Schieffelin JS, Shaffer JG, Grant DS.
Health seeking behavior after the 2013-16 Ebola epidemic: Lassa fever as a metric of persistent changes in Kenema District, Sierra Leone.
PLoS Neglected Tropical Diseases. 15(7):e0009576.

Drouin AC, Theberge MW, Liu SY, Smither AR, Flaherty SM, Zeller M, Geba GP, Reynaud P, Rothwell WB, Luk AP, Tian D, Boisen ML, Branco LM, Andersen KG, Robinson JE, Garry RF, Fusco DN.
Successful Clearance of 300 Day SARS-CoV-2 Infection in a Subject with B-Cell Depletion Associated Prolonged (B-DEAP) COVID by REGEN-COV Anti-Spike Monoclonal Antibody Cocktail. 
Viruses. 2021; 13(7):1202.

Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Oude Munnink BB, Koopmans M, Sadilek A, Lai S, Tatem AJ, Baele G, Suchard MA, Dellicour S
Untangling Introductions and Persistence in COVID-19 Resurgence in Europe
Nature 595(7869):713-717

Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Schiabor Barrett KM, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM 3rd, Rivera-Garcia C, Sandoval E, Wang X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, Deng X, Wang C, Servellita V, Valentine H, De Hoff P, Seaver P, Sathe S, Gietzen K, Sickler B, Antico J, Hoon K, Liu J, Harding A, Bakhtar O, Basler T, Austin B, MacCannell D, Isaksson M, Febbo PG, Becker D, Laurent M, McDonald E, Yeo GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu CY, Suchard MA, Lu JT, Lee W, Andersen KG
Emergence and Rapid Transmission of SARS-CoV-2 B.1.1.7 in the United States
Cell 184(10):2587-2594.e7

Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FCS, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MUG, Gaburo N Jr, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, Ferreira ACS, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Proença-Modena JL, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Prete CA Jr, Nascimento VH, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC
Genomics and Epidemiology of the P.1 SARS-CoV-2 Lineage in Manaus, Brazil
Science 372(6544):815-821

Landeras-Bueno S, Wasserman H, Oliveira G, VanAernum ZL, Busch F, Salie ZL, Wysocki VH, Andersen K, Saphire EO
Cellular mRNA Triggers Structural Transformation of Ebola virus Matrix Protein VP40 to Its Essential Regulatory Form
Cell Reports 35(2):108986

Gunn BM, Lu R, Slein MD, Ilinykh PA, Huang K, Atyeo C, Schendel SL, Kim J, Cain C, Roy V, Suscovich TJ, Takada A, Halfmann PJ, Kawaoka Y, Pauthner MG, Momoh M, Goba A, Kanneh L, Andersen KG, Schieffelin JS, Grant D, Garry RF, Saphire EO, Bukreyev A, Alter G
A Fc Engineering Approach to Define Functional Humoral Correlates of Immunity Against Ebola virus
Immunity 54(4):815-828.e5

Bond NG, Grant DS, Himmelfarb ST, Engel EJ, Al-Hasan F, Gbakie M, Kamara F, Kanneh L, Mustapha I, Okoli A, Fischer W, Wohl D, Garry RF, Samuels R, Shaffer JG, Schieffelin JS
Post-Ebola Syndrome Presents With Multiple Overlapping Symptom Clusters: Evidence From an Ongoing Cohort Study in Eastern Sierra Leone
Clinical Infectious Diseases 73(6):1046-1054

Kinganda-Lusamaki E, Black A, Mukadi DB, Hadfield J, Mbala-Kingebeni P, Pratt CB, Aziza A, Diagne MM, White B, Bisento N, Nsunda B, Akonga M, Faye M, Faye O, Edidi-Atani F, Matondo-Kuamfumu M, Mambu-Mbika F, Bulabula J, Di Paola N, Pauthner MG, Andersen KG, Palacios G, Delaporte E, Sall AA, Peeters M, Wiley MR, Ahuka-Mundeke S, Bedford T, Tamfum JM
Integration of Genomic Sequencing Into the Response to the Ebola virus Outbreak in Nord Kivu, Democratic Republic of the Congo
Nature Medicine 27(4):710-716

Hong SL, Lemey P, Suchard MA, Baele G.
Bayesian Phylogeographic Analysis Incorporating Predictors and Individual Travel Histories in BEAST. 
Curr Protoc. 2021;1(4):e98.

Mbala-Kingebeni P, Pratt C, Mutafali-Ruffin M, Pauthner MG, Bile F, Nkuba-Ndaye A, Black A, Kinganda-Lusamaki E, Faye M, Aziza A, Diagne MM, Mukadi D, White B, Hadfield J, Gangavarapu K, Bisento N, Kazadi D, Nsunda B, Akonga M, Tshiani O, Misasi J, Ploquin A, Epaso V, Sana-Paka E, N’kasar YTT, Mambu F, Edidi F, Matondo M, Bula Bula J, Diallo B, Keita M, Belizaire MRD, Fall IS, Yam A, Mulangu S, Rimion AW, Salfati E, Torkamani A, Suchard MA, Crozier I, Hensley L, Rambaut A, Faye O, Sall A, Sullivan NJ, Bedford T, Andersen KG, Wiley MR, Ahuka-Mundeke S, Muyembe Tamfum JJ
Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease
The New England Journal of Medicine 384(13):1240-1247

Watson GL, Xiong D, Zhang L, Zoller JA, Shamshoian J, Sundin P, Bufford T, Rimoin AW, Suchard MA, Ramirez CM.
Pandemic velocity: Forecasting COVID-19 in the US with a machine learning & Bayesian time series compartmental model.
PLoS Comput Biol. 2021;17(3):e1008837.

Bartsch YC, Wang C, Zohar T, Fischinger S, Atyeo C, Burke JS, Kang J, Edlow AG, Fasano A, Baden LR, Nilles EJ, Woolley AE, Karlson EW, Hopke AR, Irimia D, Fischer ES, Ryan ET, Charles RC, Julg BD, Lauffenburger DA, Yonker LM, Alter G
Humoral Signatures of Protective and Pathological SARS-CoV-2 Infection in Children
Nature Medicine 27(3):454-462

Bartsch YC, Fischinger S, Siddiqui SM, Chen Z, Yu J, Gebre M, Atyeo C, Gorman MJ, Zhu AL, Kang J, Burke JS, Slein M, Gluck MJ, Beger S, Hu Y, Rhee J, Petersen E, Mormann B, Aubin MS, Hasdianda MA, Jambaulikar G, Boyer EW, Sabeti PC, Barouch DH, Julg BD, Musk ER, Menon AS, Lauffenburger DA, Nilles EJ, Alter G
Discrete SARS-CoV-2 Antibody Titers Track With Functional Humoral Stability
Nature Communications 12(1):1018

Atyeo C, Pullen KM, Bordt EA, Fischinger S, Burke J, Michell A, Slein MD, Loos C, Shook LL, Boatin AA, Yockey LJ, Pepin D, Meinsohn MC, Nguyen NMP, Chauvin M, Roberts D, Goldfarb IT, Matute JD, James KE, Yonker LM, Bebell LM, Kaimal AJ, Gray KJ, Lauffenburger D, Edlow AG, Alter G
Compromised SARS-CoV-2-Specific Placental Antibody Transfer
Cell S0092-8674(20)31749-9

2020

McMahan K, Yu J, Mercado NB, Loos C, Tostanoski LH, Chandrashekar A, Liu J, Peter L, Atyeo C, Zhu A, Bondzie EA, Dagotto G, Gebre MS, Jacob-Dolan C, Li Z, Nampanya F, Patel S, Pessaint L, Van Ry A, Blade K, Yalley-Ogunro J, Cabus M, Brown R, Cook A, Teow E, Andersen H, Lewis MG, Lauffenburger DA, Alter G, Barouch DH
Correlates of Protection Against SARS-CoV-2 in Rhesus Macaques
Nature 590(7847):630-634.

Samuels RJ, Moon TD, Starnes JR, Alhasan F, Gbakie M, Goba A, Koroma V, Momoh M, Sandi JD, Garry RF, Engel EJ, Shaffer JG, Schieffelin JS, Grant DS
Lassa Fever among Children in Eastern Province, Sierra Leone: A 7-year Retrospective Analysis (2012-2018)
The American Journal of Tropical Medicine and Hygiene 104(2):585-592.

Gale TV, Schieffelin JS, Branco LM, Garry RF, Grant DS
Elevated L-threonine is a biomarker for Lassa fever and Ebola
Virology Journal 17(1):188.

Zohar T, Loos C, Fischinger S, Atyeo C, Wang C, Slein MD, Burke J, Yu J, Feldman J, Hauser BM, Caradonna T, Schmidt AG, Cai Y, Streeck H, Ryan ET, Barouch DH, Charles RC, Lauffenburger DA, Alter G
Compromised Humoral Functional Evolution Tracks with SARS-CoV-2 Mortality
Cell S0092-8674(20)31459-8.

Chen Y, Zuiani A, Fischinger S, Mullur J, Atyeo C, Travers M, Lelis FJN, Pullen KM, Martin H, Tong P, Gautam A, Habibi S, Bensko J, Gakpo D, Feldman J, Hauser BM, Caradonna TM, Cai Y, Burke JS, Lin J, Lederer JA, Lam EC, Lavine CL, Seaman MS, Chen B, Schmidt AG, Balazs AB, Lauffenburger DA, Alter G, Wesemann DR
Quick COVID-19 Healers Sustain Anti-SARS-CoV-2 Antibody Production
Cell S0092-8674(20)31458-6.

Fajnzylber J, Regan J, Coxen K, Corry H, Wong C, Rosenthal A, Worrall D, Giguel F, Piechocka-Trocha A, Atyeo C, Fischinger S, Chan A, Flaherty KT, Hall K, Dougan M, Ryan ET, Gillespie E, Chishti R, Li Y, Jilg N, Hanidziar D, Baron RM, Baden L, Tsibris AM, Armstrong KA, Kuritzkes DR, Alter G, Walker BD, Yu X, Li JZ
SARS-CoV-2 Viral Load is Associated with Increased Disease Severity and Mortality
Nature Communications 11(1):5493.

Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O’Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA
Accommodating Individual Travel History and Unsampled Diversity in Bayesian Phylogeographic Inference of SARS-CoV-2
Nature Communications 11(1):5110.

Worobey M, Pearm J, Larsen B, Nelson M, Hill V, Joy J, Rambaut A, Suchard M, Wertheim J and Lemey P.
The emergence of SARS-CoV-2 in Europe and North America
Science 370(6516):564-570

Atyeo C, Fischinger S, Zohar T, Slein MD, Burke J, Loos C, McCulloch DJ, Newman KL, Wolf C, Yu J, Shuey K, Feldman J, Hauser BM, Caradonna T, Schmidt A, Suscovich TJ, Linde C, Cai Y, Barouch D, Ryan ET, Charles RC, Lauffenburger D, Chu H, Alter G.
Distinct early serological signatures track with SARS-CoV-2 survival
Immunity 53(3): 524–532.e4.

Loos C, Lauffenburger D A, & Alter G.
Dissecting the antibody-OME: past, present, and future
Current Opinion in Immunology, 65, 89–96.

Düx A, Lequime S, Patrono LV, Vrancken B, Boral S, Gogarten JF, Hilbig A, Horst D, Merkel K, Prepoint B, Santibanez S, Schlotterbeck J, Suchard MA, Ulrich M, Widulin N, Mankertz A, Leendertz FH, Harper K, Schnalke T, Lemey P, Calvignac-Spencer S
Measles virus and rinderpest virus divergence dated to the sixth century BCE
Science 368(6497):1367-1370.

Rogers TF, Zhao F, Huang D, Beutler N, Burns A, He WT, Limbo O, Smith C, Song G, Woehl J, Yang L, Abbott RK, Callaghan S, Garcia E, Hurtado J, Parren M, Peng L, Ramirez S, Ricketts J, Ricciardi MJ, Rawlings SA, Wu NC, Yuan M, Smith DM, Nemazee D, Teijaro JR, Voss JE, Wilson IA, Andrabi R, Briney B, Landais E, Sok D, Jardine JG, Burton DR.
Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model
Science, 369(6506):956-963

Baele G, Gill MS, Lemey P, Suchard MA
Hamiltonian Monte Carlo sampling to estimate past population dynamics using the skygrid coalescent model in a Bayesian phylogenetics framework.
Wellcome Open Research 2020, 5:53

Baele G, Gill MS, Bastide P, Lemey P,  Suchard MA
Markov-modulated continuous-time Markov chains to identify site- and branch-specific evolutionary variation in BEAST.
Systematic Biology 70(1):181-189

He WT, Ji X, He W, Dellicour S, Wang S, Li G, Zhang L, Gilbert M, Zhu H, Xing G, Veit M, Huang Z, Han G Z, Huang Y, Suchard MA, Baele G, Lemey P,  Su S
Genomic epidemiology, evolution, and transmission dynamics of porcine deltacoronavirus
Molecular Biology and Evolution, 37(9):2641-2654

Sun J, He WT, Wang L, Lai A, Ji X, Zhai X, Li G, Suchard MA, Tian J, Zhou J, Veit M, Su S
COVID-19: Epidemiology, Evolution, and Cross-Disciplinary Perspectives
Trends in Molecular Medicine 26(5):483-495.

Andersen, K. G., Rambaut, A., Lipkin, W. I., Holmes, E. C., & Garry, R. F.
The proximal origin of SARS-CoV-2
Nature Medicine, 26(4), 450–452.

Yang Q, Zhao X, Lemey P, Suchard MA, Bi Y, Shi W, Liu D, Qi W, Zhang G, Stenseth NC, Pybus OG, Tian H
Assessing the role of live poultry trade in community-structured transmission of avian influenza in China
Proc Natl Acad Sci U S A 117(11):5949-5954

Garry CE,  Garry RF
Proteomics Computational Analyses Suggest That the Envelope Glycoproteins of Segmented Jingmen Flavi-Like Viruses are Class II Viral Fusion Proteins (b-Penetrenes) with Mucin-Like Domains
Viruses, 12(3), 260

Gill MS, Lemey P, Suchard MA, Rambaut A,  Baele G
Online Bayesian Phylodynamic Inference in BEAST with Application to Epidemic Reconstruction.
Molecular Biology and Evolution 37(6), 1832–1842

Joyce C, Burton DR, Briney B
Comparisons of the antibody repertoires of a humanized rodent and humans by high throughput sequencing
Scientific Reports 10(1):1120

2019

Hadfield J, Brito AF, Swetnam DM, Vogels C, Tokarz RE, Andersen KG, Smith RC, Bedford T,  Grubaugh ND
Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain
PLoS Pathogens 15(10), e1008042

Suchard MA, Schuemie MJ, Krumholz HM, You SC, Chen R, Pratt N, Reich CG, Duke J, Madigan D, Hripcsak G, Ryan PB
Comprehensive Comparative Effectiveness and Safety of First-line Antihypertensive Drug Classes: a Systematic, Multinational, Large-scale Analysis
Lancet pii: S0140-6736(19)32317-7

Grubaugh ND, Saraf S, Gangavarapu K, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW 4th, Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH; GeoSentinel Surveillance Network, Gardner LM, Perkins TA, Baele G, Khan K, Morrison A, Isern S, Michael SF, Andersen KG
Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic
Cell 178(5):1057-1071

Hastie KM, Cross RW, Harkins SS, Zandonatti MA, Koval AP, Heinrich ML, Rowland MM, Robinson JE, Geisbert TW, Garry RF, Branco LM, Saphire EO
Convergent Structures Illuminate Features for Germline Antibody Binding and Pan-Lassa Virus Neutralization
Cell 178(4):1004-1015

Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P
Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates
Molecular Biology and Evolution 36(8):1793-1803

Fischinger S, Fallon JK, Michell AR, Broge T, Suscovich TJ, Streeck H, Alter G
A High-throughput, Bead-based, Antigen-specific Assay to Assess the Ability of Antibodies to Induce Complement Activation
Journal of Immunological Methods 473:112630

Gunn BM, Roy V, Karim MM, Hartnett JN, Suscovich TJ, Goba A, Momoh M, Sandi JD, Kanneh L, Andersen KG, Shaffer JG, Schieffelin JS, Garry RF, Grant DS, Alter G
Survivors of Ebola virus Disease Develop Polyfunctional Antibody Responses
The Journal of Infectious Diseases 221(1):156-161

Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA
BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics
Systematic Biology 68(6):1052-1061

Shaffer JG, Schieffelin JS, Gbakie M, Alhasan F, Roberts NB, Goba A, Randazzo J, Momoh M, Moon TD, Kanneh L, Levy DC, Podgorski RM, Hartnett JN, Boisen ML, Branco LM, Samuels R, Grant DS, Garry RF; Viral Hemorrhagic Fever Consortium
A Medical Records and Data Capture and Management System for Lassa fever in Sierra Leone: Approach, Implementation, and Challenges
PLoS One 14(3):e0214284

Briney B, Inderbitzin A, Joyce C, Burton DR
Commonality Despite Exceptional Diversity in the Baseline Human Antibody Repertoire
Nature 566(7744):393-397

Grubaugh ND, Gangavarapu K, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG
An Amplicon-based Sequencing Framework for Accurately Measuring Intrahost Virus Diversity using PrimalSeq and iVar
Genome Biology 20(1):8

Kafetzopoulou LE, Pullan ST, Lemey P, Suchard MA, Ehichioya DU, Pahlmann M, Thielebein A, Hinzmann J, Oestereich L, Wozniak DM, Efthymiadis K, Schachten D, Koenig F, Matjeschk J, Lorenzen S, Lumley S, Ighodalo Y, Adomeh DI, Olokor T, Omomoh E, Omiunu R, Agbukor J, Ebo B, Aiyepada J, Ebhodaghe P, Osiemi B, Ehikhametalor S, Akhilomen P, Airende M, Esumeh R, Muoebonam E, Giwa R, Ekanem A, Igenegbale G, Odigie G, Okonofua G, Enigbe R, Oyakhilome J, Yerumoh EO, Odia I, Aire C, Okonofua M, Atafo R, Tobin E, Asogun D, Akpede N, Okokhere PO, Rafiu MO, Iraoyah KO, Iruolagbe CO, Akhideno P, Erameh C, Akpede G, Isibor E, Naidoo D, Hewson R, Hiscox JA, Vipond R, Carroll MW, Ihekweazu C, Formenty P, Okogbenin S, Ogbaini-Emovon E, Günther S, Duraffour S
Metagenomic Sequencing at the Epicenter of the Nigeria 2018 Lassa fever Outbreak
Science 363(6422):74-77

Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG
Tracking Virus Outbreaks in the Twenty-first Century
Nature Microbiology 4(1):10-19

2018

Saphire EO, Schendel SL, Gunn BM, Milligan JC, Alter G
Antibody-mediated Protection against Ebola virus
Nature Immunology 19(11):1169-1178

Siddle KJ, Eromon P, Barnes KG, Mehta S, Oguzie JU, Odia I, Schaffner SF, Winnicki SM, Shah RR, Qu J, Wohl S, Brehio P, Iruolagbe C, Aiyepada J, Uyigue E, Akhilomen P, Okonofua G, Ye S, Kayode T, Ajogbasile F, Uwanibe J, Gaye A, Momoh M, Chak B, Kotliar D, Carter A, Gladden-Young A, Freije CA, Omoregie O, Osiemi B, Muoebonam EB, Airende M, Enigbe R, Ebo B, Nosamiefan I, Oluniyi P, Nekoui M, Ogbaini-Emovon E, Garry RF, Andersen KG, Park DJ, Yozwiak NL, Akpede G, Ihekweazu C, Tomori O, Okogbenin S, Folarin OA, Okokhere PO, MacInnis BL, Sabeti PC, Happi CT
Genomic Analysis of Lassa virus during an Increase in Cases in Nigeria in 2018
New England Journal of Medicine 379(18):1745-1753

Saphire EO, Schendel SL, Fusco ML, Gangavarapu K, Gunn BM, Wec AZ, Halfmann PJ, Brannan JM, Herbert AS, Qiu X, Wagh K, He S, Giorgi EE, Theiler J, Pommert KBJ, Krause TB, Turner HL, Murin CD, Pallesen J, Davidson E, Ahmed R, Aman MJ, Bukreyev A, Burton DR, Crowe JE Jr, Davis CW, Georgiou G, Krammer F, Kyratsous CA, Lai JR, Nykiforuk C, Pauly MH, Rijal P, Takada A, Townsend AR, Volchkov V, Walker LM, Wang CI, Zeitlin L, Doranz BJ, Ward AB, Korber B, Kobinger GP, Andersen KG, Kawaoka Y, Alter G, Chandran K, Dye JM
Systematic Analysis of Monoclonal Antibodies against Ebola virus GP Defines Features that Contribute to Protection
Cell 174(4):938-952

Gunn BM, Yu WH, Karim MM, Brannan JM, Herbert AS, Wec AZ, Halfmann PJ, Fusco ML, Schendel SL, Gangavarapu K, Krause T, Qiu X, He S, Das J, Suscovich TJ, Lai J, Chandran K, Zeitlin L, Crowe JE Jr, Lauffenburger D, Kawaoka Y, Kobinger GP, Andersen KG, Dye JM, Saphire EO, Alter G
A Role for Fc Function in Therapeutic Monoclonal Antibody-Mediated Protection Against Ebola virus
Cell Host & Microbe 24(2):221-233

Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA
Posterior Summarisation in Bayesian Phylogenetics using Tracer 1.7
Systematic Biology 67(5):901-904

Sakabe S, Sullivan BM, Hartnett JN, Robles-Sikisaka R, Gangavarapu K, Cubitt B, Ware BC, Kotliar D, Branco LM, Goba A, Momoh M, Sandi JD, Kanneh L, Grant DS, Garry RF, Andersen KG, de la Torre JC, Sabeti PC, Schieffelin JS, Oldstone MBA
Analysis of CD8+ T Cell Response During the 2013-2016 Ebola Epidemic in West Africa
Proc Natl Acad Sci U S A 115(32):E7578-E7586

Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A
Bayesian Phylogenetic and Phylodynamic Data Integration using BEAST 1.10
Virus Evolution 4(1):vey016

Holmes EC, Rambaut A, Andersen KG
Pandemics: Spend on Surveillance, Not Prediction
Nature 558(7709):180-182

Boisen ML, Hartnett JN, Shaffer JG, Goba A, Momoh M, Sandi JD, Fullah M, Nelson DKS, Bush DJ, Rowland MM, Heinrich ML, Koval AP, Cross RW, Barnes KG, Lachenauer AE, Lin AE, Nekoui M, Kotliar D, Winnicki SM, Siddle KJ, Gbakie M, Fonnie M, Koroma VJ, Kanneh L, Kulakosky PC, Hastie KM, Wilson RB, Andersen KG, Folarin OO, Happi CT, Sabeti PC, Geisbert TW, Saphire EO, Khan SH, Grant DS, Schieffelin JS, Branco LM, Garry RF
Field validation of Recombinant Antigen Immunoassays for Diagnosis of Lassa Lever
Scientific Reports 8(1):5939

2017

Lu LL, Suscovich TJ, Fortune SM, Alter G
Beyond Binding: Antibody Effector Functions in Infectious Diseases
Nature Reviews Immunology 18(1):46-61

Shafee T, Mietchen D, Su AI
Academics Can Help Shape Wikipedia
Science 357(6351):557-558

Mire CE, Cross RW, Geisbert JB, Borisevich V, Agans KN, Deer DJ, Heinrich ML, Rowland MM, Goba A, Momoh M, Boisen ML, Grant DS, Fullah M, Khan SH, Fenton KA, Robinson JE, Branco LM, Garry RF, Geisbert TW
Human-monoclonal-antibody Therapy Protects Nonhuman Primates Against Advanced Lassa Fever
Nature Medicine (10):1146-1149

Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA
An Engineering Design Approach to Systems Biology
Integrative Biology: Quantitative Biosciences from Nano to Macro 17;9(7):574-583

Hastie KM, Zandonatti MA, Kleinfelter LM, Heinrich ML, Rowland MM, Chandran K, Branco LM, Robinson JE, Garry RF, Saphire EO
Structural Basis for Antibody-mediated Neutralization of Lassa virus
Science 356(6341):923-928

Grubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Luo C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC Jr, Lichtenberger PN, Ricciardi MJ, Bailey VK, Watkins DI, Cone MR, Kopp EW 4th, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG
Genomic Epidemiology Reveals Multiple Introductions of Zika virus into the United States
Nature 546(7658):401-405

Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC
Zika virus Evolution and Spread in the Americas
Nature 546(7658):411-415

Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC Jr, Sabino EC, Baylis SA, Faria NR, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ
Multiplex PCR method for MinION and Illumina Sequencing of Zika and Other Virus Genomes Directly from Clinical Samples
Nature Protocols 12(6):1261-1276

Gill MS, Tung Ho LS, Baele G, Lemey P, Suchard MA
A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution
Systematic Biology 66(3):299-319

Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, Caro AD, Diclaro JW, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MV, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll MW, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MP, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A
Virus Genomes Reveal Factors That Spread and Sustained the Ebola Epidemic
Nature 544(7650):309-315

Saphire EO, Chandran K, Alter G, Aman MJ, Andersen KG, Branco LM, Doranz BJ, Feldmann H, Fusco ML, Garry RF, Geisbert TW, Halfmann PJ, Hensley LE, Kawaoka Y, Kobinger GP, Lai JR, Lobel L, Lutwama JJ, Olinger GG, Qiu X, Robinson JE, Sprecher A, Takada A, Ward AB, Whaley K, Zeitlin L, Chandran K, Dye JM
How to Turn Competitors into Collaborators
Nature 541(7637):283-285

2016

Diehl WE, Lin AE, Grubaugh ND, Carvalho LM, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Rambaut A, Garber M, Andersen KG, Sabeti PC, Luban J
Ebola virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic
Cell 167(4):1088-1098

Tsueng G, Good BM, Ping P, Golemis E, Hanukoglu I, van Wijnen AJ, Su AI
Gene Wiki Reviews-raising the Quality and Accessibility of Information about the Human Genome
Gene 592(2):235-8

Gill MS, Lemey P, Bennett SN, Biek R, Suchard MA
Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates
Systematic Biology 65(6):1041-1056

Holmes EC, Dudas G, Rambaut A, Andersen KG
The Evolution of Ebola virus: Insights from the 2013-2016 Epidemic
Nature 538(7624):193-200

Lu LL, Chung AW, Rosebrock TR, Ghebremichael M, Yu WH, Grace PS, Schoen MK, Tafesse F, Martin C, Leung V, Mahan AE, Sips M, Kumar MP, Tedesco J, Robinson H, Tkachenko E, Draghi M, Freedberg KJ, Streeck H, Suscovich TJ, Lauffenburger DA, Restrepo BI, Day C, Fortune SM, Alter G
A Functional Role for Antibodies in Tuberculosis
Cell 167(2):433-443

Boisen ML, Hartnett JN, Goba A, Vandi MA, Grant DS, Schieffelin JS, Garry RF, Branco LM
Epidemiology and Management of the 2013-16 West African Ebola Outbreak
Annual Review Virology 3(1):147-171

Briney B, Sok D, Jardine JG, Kulp DW, Skog P, Menis S, Jacak R, Kalyuzhniy O, de Val N, Sesterhenn F, Le KM, Ramos A, Jones M, Saye-Francisco KL, Blane TR, Spencer S, Georgeson E, Hu X, Ozorowski G, Adachi Y, Kubitz M, Sarkar A, Wilson IA, Ward AB, Nemazee D, Burton DR, Schief WR
Tailored Immunogens Direct Affinity Maturation Toward HIV Neutralizing Antibodies
Cell 166(6):1459-1470

Sok D, Briney B, Jardine JG, Kulp DW, Menis S, Pauthner M, Wood A, Lee EC, Le KM, Jones M, Ramos A, Kalyuzhniy O, Adachi Y, Kubitz M, MacPherson S, Bradley A, Friedrich GA, Schief WR, Burton DR
Priming HIV-1 Broadly Neutralizing Antibody Precursors in Human Ig Loci Transgenic Mice
Science 353(6307):1557-1560

Rambaut A, Dudas G, de Carvalho LM, Park DJ, Yozwiak NL, Holmes EC, Andersen KG
Comment on “Mutation Rate and Genotype Variation of Ebola virus from Mali Case Sequences”
Science 353(6300):658

Goba A, Khan SH, Fonnie M, Fullah M, Moigboi A, Kovoma A, Sinnah V, Yoko N, Rogers H, Safai S, Momoh M, Koroma V, Kamara FK, Konowu E, Yillah M, French I, Mustapha I, Kanneh F, Foday M, McCarthy H, Kallon T, Kallon M, Naiebu J, Sellu J, Jalloh AA, Gbakie M, Kanneh L, Massaly JL, Kargbo D, Kargbo B, Vandi M, Gbetuwa M, Gevao SM, Sandi JD, Jalloh SC, Grant DS, Blyden SO, Crozier I, Schieffelin JS, McLellan SL, Jacob ST, Boisen ML, Hartnett JN, Cross RW, Branco LM, Andersen KG, Yozwiak NL, Gire SK, Tariyal R, Park DJ, Haislip AM, Bishop CM, Melnik LI, Gallaher WR, Wimley WC, He J, Shaffer JG, Sullivan BM, Grillo S, Oman S, Garry CE, Edwards DR, McCormick SJ, Elliott DH, Rouelle JA, Kannadka CB, Reyna AA, Bradley BT, Yu H, Yenni RE, Hastie KM, Geisbert JB, Kulakosky PC, Wilson RB, Oldstone MB, Pitts KR, Henderson LA, Robinson JE, Geisbert TW, Saphire EO, Happi CT, Asogun DA, Sabeti PC, Garry RF
An Outbreak of Ebola virus Disease in the Lassa Fever Zone
Journal of Infectious Diseases 214(suppl 3):S110-S121

Yozwiak NL, Happi CT, Grant DS, Schieffelin JS, Garry RF, Sabeti PC, Andersen KG
Roots, Not Parachutes: Research Collaborations Combat Outbreaks
Cell 165(6):1519-29

Robinson JE, Hastie KM, Cross RW, Yenni RE, Elliott DH, Rouelle JA, Kannadka CB, Smira AA, Garry CE, Bradley BT, Yu H, Shaffer JG, Boisen ML, Hartnett JN, Zandonatti MA, Rowland MM, Heinrich ML, Martínez-Sobrido L, Cheng B, de la Torre JC, Andersen KG, Goba A, Momoh M, Fullah M, Gbakie M, Kanneh L, Koroma VJ, Fonnie R, Jalloh SC, Kargbo B, Vandi MA, Gbetuwa M, Ikponmwosa O, Asogun DA, Okokhere PO, Follarin OA, Schieffelin JS, Pitts KR, Geisbert JB, Kulakoski PC, Wilson RB, Happi CT, Sabeti PC, Gevao SM, Khan SH, Grant DS, Geisbert TW, Saphire EO, Branco LM, Garry RF
Most Neutralizing Human Monoclonal Antibodies Target Novel Epitopes Requiring Both Lassa virus Glycoprotein Subunits
Nature Communications 7:11544

Baele G, Lemey P, Suchard MA
Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty
Systematic Biology 65(2):250-64

2015

Chung AW, Kumar MP, Arnold KB, Yu WH, Schoen MK, Dunphy LJ, Suscovich TJ, Frahm N, Linde C, Mahan AE, Hoffner M, Streeck H, Ackerman ME, McElrath MJ, Schuitemaker H, Pau MG, Baden LR, Kim JH, Michael NL, Barouch DH, Lauffenburger DA, Alter G
Dissecting Polyclonal Vaccine-Induced Humoral Immunity against HIV Using Systems Serology
Cell 163(4):988-98

Andersen KG, Shapiro BJ, Matranga CB, Sealfon R, Lin AE, Moses LM, Folarin OA, Goba A, Odia I, Ehiane PE, Momoh M, England EM, Winnicki S, Branco LM, Gire SK, Phelan E, Tariyal R, Tewhey R, Omoniwa O, Fullah M, Fonnie R, Fonnie M, Kanneh L, Jalloh S, Gbakie M, Saffa S, Karbo K, Gladden AD, Qu J, Stremlau M, Nekoui M, Finucane HK, Tabrizi S, Vitti JJ, Birren B, Fitzgerald M, McCowan C, Ireland A, Berlin AM, Bochicchio J, Tazon-Vega B, Lennon NJ, Ryan EM, Bjornson Z, Milner DA Jr, Lukens AK, Broodie N, Rowland M, Heinrich M, Akdag M, Schieffelin JS, Levy D, Akpan H, Bausch DG, Rubins K, McCormick JB, Lander ES, Günther S, Hensley L, Okogbenin S; Viral Hemorrhagic Fever Consortium, Schaffner SF, Okokhere PO, Khan SH, Grant DS, Akpede GO, Asogun DA, Gnirke A, Levin JZ, Happi CT, Garry RF, Sabeti PC
Clinical Sequencing Uncovers Origins and Evolution of Lassa virus
Cell 162(4):738-50

Park DJ, Dudas G, Wohl S, Goba A, Whitmer SL, Andersen KG, Sealfon RS, Ladner JT, Kugelman JR, Matranga CB, Winnicki SM, Qu J, Gire SK, Gladden-Young A, Jalloh S, Nosamiefan D, Yozwiak NL, Moses LM, Jiang PP, Lin AE, Schaffner SF, Bird B, Towner J, Mamoh M, Gbakie M, Kanneh L, Kargbo D, Massally JL, Kamara FK, Konuwa E, Sellu J, Jalloh AA, Mustapha I, Foday M, Yillah M, Erickson BR, Sealy T, Blau D, Paddock C, Brault A, Amman B, Basile J, Bearden S, Belser J, Bergeron E, Campbell S, Chakrabarti A, Dodd K, Flint M, Gibbons A, Goodman C, Klena J, McMullan L, Morgan L, Russell B, Salzer J, Sanchez A, Wang D, Jungreis I, Tomkins-Tinch C, Kislyuk A, Lin MF, Chapman S, MacInnis B, Matthews A, Bochicchio J, Hensley LE, Kuhn JH, Nusbaum C, Schieffelin JS, Birren BW, Forget M, Nichol ST, Palacios GF, Ndiaye D, Happi C, Gevao SM, Vandi MA, Kargbo B, Holmes EC, Bedford T, Gnirke A, Ströher U, Rambaut A, Garry RF, Sabeti PC
Ebola virus Epidemiology, Transmission, and Evolution During Seven Months in Sierra Leone
Cell 161(7):1516-26

Fisch KM, Meißner T, Gioia L, Ducom JC, Carland TM, Loguercio S, Su AI
OmicsPipe: A Community-based Framework for Reproducible Multi-omics Data Analysis
Bioinformatics 31(11):1724-8

2014

Schieffelin JS, Shaffer JG, Goba A, Gbakie M, Gire SK, Colubri A, Sealfon RSG, Kanneh L, Moigboi A, Momoh M, Fullah M, Moses LM, Brown BL, Andersen KG, Winnicki S, Schaffner SF, Park DJ, Yozwiak NL, Jiang PP, Kargbo D, Jalloh S, Fonnie M, Sinnah V, French I, Kovoma A, Kamara FK, Tucker V, Konuwa E, Sellu J, Mustapha I, Foday M, Yillah M, Kanneh F, Saffa S, Massally JL, Boisen ML, Branco LM, Vandi MA, Grant DS, Happi C, Gevao SM, Fletcher TE, Fowler RA, Bausch DG, Sabeti PC, Khan SH, Garry RF for the KGH Lassa Fever Program, the Viral Hemorrhagic Fever Consortium and the WHO Clinical Response Team
Clinical Illness and Outcomes in Patients with Ebola in Sierra Leone
New England Journal of Medicine 371(22):2092-100

Gire SK, Goba A, Andersen KG, Sealfon RSG, Park DJ, Kanneh L, Jalloh S, Momoh M, Fullah M, Dudas G, Wohl S, Moses LM, Yozwiak NL, Winnicki S, Matranga CB, Malboeuf CM, Qu J, Gladden AD, Schaffner SF, Yang X, Jiang PP, Nekoui M, Colubri A, Coomber MR, Fonnie M, Moigboi A, Gbakie M, Kamara FK, Tucker V, Konuwa E, Saffa S, Sellu J, Jalloh AA, Kovoma A, Koninga J, Mustapha I, Kargbo K, Foday M, Yillah M, Kanneh F, Robert W, Massally JL, Chapman SB, Bochicchio J, Murphy C, Nusbaum C, Young S, Birren BW, Grant DS, Scheiffelin JS, Lander ES, Happi C, Gevao SM, Gnirke A, Rambaut A, Garry RF, Khan SH, Sabeti PC
Genomic Surveillance Elucidates Ebola virus Origin and Transmission During the 2014 Outbreak
Science 345(6202):1369-72

The H3Africa Consortium
Research Capacity: Enabling the Genomic Revolution in Africa
Science 344(6190):1346-8

Shaffer JG, Grant DS, Schieffelin JS, Boisen ML, Goba A, Hartnett JN, Levy DC, Yenni RE, Moses LM, Fullah M, Momoh M, Fonnie M, Fonnie R, Kanneh L, Koroma VJ, Kargbo K, Ottomassathien D, Muncy IJ, Jones AB, Illick MM, Kulakosky PC, Haislip AM, Bishop CM, Elliot DH, Brown BL, Zhu H, Hastie KM, Andersen KG, Gire SK, Tabrizi S, Tariyal R, Stremlau M, Matschiner A, Sampey DB, Spence JS, Cross RW, Geisbert JB, Folarin OA, Happi CT, Pitts KR, Geske FJ, Geisbert TW, Saphire EO, Robinson JE, Wilson RB, Sabeti PC, Henderson LA, Khan SH, Bausch DG, Branco LM, Garry RF, the Viral Hemorrhagic Fever Consortium
Lassa Fever in Post-conflict Sierra Leone
PLOS Neglected Tropical Diseases 8(3):e2748