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Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG
Tracking Virus Outbreaks in the Twenty-first Century
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Saphire EO, Schendel SL, Gunn BM, Milligan JC, Alter G
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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
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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
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Holmes EC, Rambaut A, Andersen KG
Pandemics: Spend on Surveillance, Not Prediction
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Suchard MA, Lemey P, Baele G, Ayres DL, Drummond AJ, Rambaut A
Bayesian Phylogenetic and Phylodynamic Data Integration using BEAST 1.10
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Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA
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Lu LL, Suscovich TJ, Fortune SM, Alter G
Beyond Binding: Antibody Effector Functions in Infectious Diseases
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Shafee T, Mietchen D, Su AI
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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
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Janes KA, Chandran PL, Ford RM, Lazzara MJ, Papin JA, Peirce SM, Saucerman JJ, Lauffenburger DA
An Engineering Design Approach to Systems Biology
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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
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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
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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
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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
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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
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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
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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
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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
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Gill MS, Lemey P, Bennett SN, Biek R, Suchard MA
Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates
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Holmes EC, Dudas G, Rambaut A, Andersen KG
The Evolution of Ebola virus: Insights from the 2013-2016 Epidemic
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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
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Boisen ML, Hartnett JN, Goba A, Vandi MA, Grant DS, Schieffelin JS, Garry RF, Branco LM
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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
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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
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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
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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
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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
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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