Coronavirus Disease 2019 Rebound in Nirmatrelvir Plus Ritonavir Treatment and Control Groups: A Prospective Cohort Study
November 6, 2024

Continuous vital sign monitoring of individuals with acute Lassa fever using wearable biosensor devices
August 31, 2024

Genomic Epidemiology Uncovers the Timing and Origin of the Emergence of Mpox in Humans
June 19, 2024

Molecular Epidemiology of Recurrent Zoonotic Transmission of Mpox virus in West Africa
June 19, 2024

Deep Mutational Scanning Reveals Functional Constraints and Antigenic Variability of Lassa virus Glycoprotein Complex
February 6, 2024 (Published in Immunity, July 15, 2024)

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic
September 14, 2023 (Published in Cell, September 19, 2024)

Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems
April 15, 2023 (Published in Nature Communications, November 30, 2023)

Genetic Evidence of Susceptible Wildlife in SARS-CoV-2 Positive Samples at the Huanan Wholesale Seafood Market, Wuhan: Analysis and Interpretation of Data Released by the Chinese Center for Disease Control
March 20, 2023

Genomic Surveillance Reveals Dynamic Shifts in the Connectivity of COVID-19 Epidemics
March 19, 2023 (Published in Cell, December 14, 2023)

Molecular identification of SARS-CoV-2 variants of concern at urban wastewater treatment plants across South Africa
December 16, 2022 (Published in Nature Communications, October 10, 2023)

Cryptic spread of the SARS-CoV-2 Delta variant undermined targeted travel restrictions in Iraq
November 30, 2022

Emergence and spread of two SARS-CoV-2 variants of interest in Nigeria
September 25, 2022 (Published in Nature Communications, February 13 2023)

Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021
April 16, 2022 (Published in The Journal of Infectious Diseases, 30 June, 2022)

The Huanan Market Was the Epicenter of SARS-CoV-2 Emergence
February 26, 2022 February 26, 2022 (Published in Science, July 26, 2022)

SARS-CoV-2 Emergence Very Likely Resulted From at Least Two Zoonotic Events
February 26, 2022 (Published in Science, July 26, 2022)

Genomic and Phenotypic Analyses Suggest Moderate Fitness Differences Among Zika virus Lineages
February 2, 2022 (Published in PLOS NTD, February 8, 2023)

Outbreak.info Genomic Reports: Scalable and Dynamic Surveillance of SARS-CoV-2 Variants and Mutations
January 29, 2022 (Published in Nature Methods, February 23, 2023)

Regional Connectivity Drove Bidirectional Transmission of SARS-CoV-2 in the Middle East During Travel Restrictions
January 28, 2022 (Published in Nature Communications, August 15, 2022)

Outbreak.info: A Standardized, Searchable Platform to Discover and Explore COVID-19 Resources and Data
January 21, 2022 (Published in Nature Methods, February 23, 2023)

Wastewater Sequencing Uncovers Early, Cryptic SARS-CoV-2 Variant Transmission
December 27, 2021 (Published in Nature, July 7, 2022)

Predicting the Evolution of Lassa Virus Endemic Area and Population at Risk over the Next Decades
September 22, 2021 (Published in Nature Communications, September 27, 2022)

The Origins of SARS-CoV-2: A Critical Review
July 7, 2021 (Published in Cell, August 18, 2021)

Emergence of an Early SARS-CoV-2 Epidemic in the United States
February 8, 2021 (Published in Cell, July 26, 2021)

Genomic Epidemiology Identifies Emergence and Rapid Transmission of SARS-CoV-2 B.1.1.7 in the United States
February 7, 2021 (Published in Cell, March 30, 2021)

Accommodating Individual Travel History, Global Mobility, and Unsampled Diversity in Phylogeography: a SARS-CoV-2 Case Study
June 23, 2020 (Published in Nature Communications, October 9, 2020)

International Travelers and Genomics Uncover a ‘Hidden’ Zika Outbreak
December 14, 2018 (Published in Cell, August 22, 2019)

An Amplicon-based Sequencing Framework for Accurately Measuring Intrahost Virus Diversity Using PrimalSeq and iVar
August 5, 2018 (Published in Genome Biology, Jan 9, 2019)

Common Piezo1 Allele in African Populations Causes Xerocytosis and Attenuates Plasmodium Infection
July 6, 2017 (Published in Cell, March 22, 2018)

Genetic Characterization of the Zika virus Epidemic in the US Virgin Islands
March 3, 2017

Genome Sequencing Reveals Zika virus Diversity and Spread in the Americas
February 18, 2017 (Published in Nature, May 25, 2017)

Multiple Introductions of Zika virus into the United States Revealed Through Genomic Epidemiology
February 3, 2017 (Published in Nature, May 25, 2017)

Epidemic Establishment and Cryptic Transmission of Zika virus in Brazil and the Americas
February 2, 2017 (Published in Nature, May 25, 2017)

Multiplex PCR method for MinION and Illumina Sequencing of Zika and Other Virus Genomes Directly from Clinical Samples
January 9, 2017 (Published in Nature Protocols, May 25, 2017)

Virus Genomes Reveal the Factors That Spread and Sustained the West African Ebola Epidemic
September 16, 2016 (Published in Nature, April 12, 2017)

Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Peacock TP, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KGº, Worobey Mº, Débarre Fº
Genetic Tracing of Market Wildlife and Viruses at the Epicenter of the COVID-19 Pandemic
Cell 187(19):5468-5482 [feature]
(ºco-corresponding author)

Carr CR, Crawford KHD, Murphy M, Galloway JG, Haddox HK, Matsen FA 4th, Andersen KG, King NP, Bloom JD
Deep Mutational Scanning Reveals Functional Constraints and Antibody-Escape Potential of Lassa virus Glycoprotein Complex
Immunity 57(9):2061-2076

Sandi JD, Levy JI, Tapela K, Zeller M, Yeboah JA, Saka DF, Grant DS, Awandare GA, Quashie PK, Andersen KG, Paemka L
Upper Airway Epithelial Tissue Transcriptome Analysis Reveals Immune Signatures Associated with COVID-19 Severity in Ghanaians
Journal of Immunology Research 2024:6668017

Kotliar D, Raju S, Tabrizi S, Odia I, Goba A, Momoh M, Sandi JD, Nair P, Phelan E, Tariyal R, Eromon PE, Mehta S, Robles-Sikisaka R, Siddle KJ, Stremlau M, Jalloh S, Gire SK, Winnicki S, Chak B, Schaffner SF, Pauthner M, Karlsson EK, Chapin SR, Kennedy SG, Branco LM, Kanneh L, Vitti JJ, Broodie N, Gladden-Young A, Omoniwa O, Jiang PP, Yozwiak N, Heuklom S, Moses LM, Akpede GO, Asogun DA, Rubins K, Kales S, Happi AN, Iruolagbe CO, Dic-Ijiewere M, Iraoyah K, Osazuwa OO, Okonkwo AK, Kunz S, McCormick JB, Khan SH, Honko AN, Lander ES, Oldstone MBA, Hensley L, Folarin OA, Okogbenin SA, Günther S, Ollila HM, Tewhey R, Okokhere PO, Schieffelin JS, Andersen KG, Reilly SK, Grant DS, Garry RF, Barnes KG, Happi CT, Sabeti PC
Genome-wide Association Study Identifies Human Genetic Variants Associated with Fatal Outcome from Lassa fever
Nature Microbiology 9(3):751-762

Rasmussen AL, Gronvall GK, Lowen AC, Goodrum F, Alwine J, Andersen KG, Anthony SJ, Baines J, Banerjee A, Broadbent AJ, Brooke CB, Campos SK, Caposio P, Casadevall A, Chan GC, Cliffe AR, Collins-McMillen D, Connell N, Damania B, Daugherty MD, Debbink K, Dermody TS, DiMaio D, Duprex WP, Emerman M, Galloway DA, Garry RF, Goldstein SA, Greninger AL, Hartman AL, Hogue BG, Horner SM, Hotez PJ, Jung JU, Kamil JP, Karst SM, Laimins L, Lakdawala SS, Landais I, Letko M, Lindenbach B, Liu S-L, Luftig M, McFadden G, Mehle A, Morrison J, Moscona A, Mühlberger E, Munger J, Münger K, Murphy E, Neufeldt CJ, Nikolich JZ, O’Connor CM, Pekosz A, Permar SR, Pfeiffer JK, Popescu SV, Purdy JG, Racaniello VR, Rice CM, Runstadler JA, Sapp MJ, Scott RS, Smith GA, Sorrell EM, Speranza E, Streblow D, Tibbetts SA, Toth Z, Van Doorslaer K, Weiss SR, White EA, White TM, Wobus CE, Worobey M, Yamaoka S, Yurochko A
Virology – The Path Forward
Journal of Virology 98(1):e0179123

Matteson NL*, Hassler GW*, Kurzban E**, Schwab MA**, Perkins SA**, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MAº, Andersen KGº#, Campos-Romero Aº, Wohl Sº, Zeller Mº
Genomic Surveillance Reveals Dynamic Shifts in the Connectivity of COVID-19 Epidemics
Cell 186(26):5690-5704 [feature]
(*/**equal contribution; ºco-senior author; #lead contact)

Barnes KG, Levy JI, Gauld J, Rigby J, Kanjerwa O, Uzzell CB, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana MG, Ashton PM, Jere KC, Meschke JS, Diggle P, Cornick J, Chilima B, Jambo K, Andersen KG, Kawalazira G, Paterson S, Nyirenda TS, Feasey N
Utilizing River and Wastewater as a SARS-CoV-2 Surveillance Tool in Settings with Limited Formal Sewage Systems
Nature Communications 14(1):7883

Hastie KM, Melnik LI, Cross RW, Klitting RM, Andersen KG, Saphire EO, Garry RF
The Arenaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens
The Journal of Infectious Diseases 228(Supplement_6):S359-S375

Yousif M, Rachida S, Taukobong S, Ndlovu N, Iwu-Jaja C, Howard W, Moonsamy S, Mhlambi N, Gwala S, Levy JI, Andersen KG, Scheepers C, von Gottberg A, Wolter N, Bhiman JN, Amoako DG, Ismail A, Suchard M, McCarthy K
SARS-CoV-2 Genomic Surveillance in Wastewater as a Model For Monitoring Evolution of Endemic Viruses
Nature Communications 14(1):6325

Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S; GISAID Core and Curation Team; Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD
Outbreak.info Genomic Reports: Scalable and Dynamic Surveillance of SARS-CoV-2 Variants and Mutations
Nature Methods 20(4):512-522 [feature]

Tsueng G, Mullen JL, Alkuzweny M, Cano M, Rush B, Haag E, Lin J, Welzel DJ, Zhou X, Qian Z, Latif AA, Hufbauer E, Zeller M, Andersen KG, Wu C, Su AI, Gangavarapu K, Hughes LD
Outbreak.info Research Library: A Standardized, Searchable Platform To Discover and Explore COVID-19 Resources
Nature Methods 20(4):536-540

Oluniyi PE*, Oguzie JU*, Uwanibe JN*, Kayode TA*, Olumade TJ*, Ajogbasile FV*, Parker E*, Eromon PE, Abechi P, Sobajo TA, Ugwu CA, George UE, Ayoade F, Akano K, Oyejide NE, Nosamiefan I, Fred-Akintunwa I, Adedotun-Sulaiman K, Brimmo FB, Adegboyega BB, Philip C, Adeleke RA, Chukwu GC, Ahmed MI, Ope-Ewe OO, Otitoola SG, Ogunsanya OA, Saibu MF, Sijuwola AE, Ezekiel GO, John OG, Akin-John JO, Akinlo OO, Fayemi OO, Ipaye TO, Nwodo DC, Omoniyi AE, Omwanghe IB, Terkuma CA, Okolie J, Ayo-Ale O, Ikponmwosa O, Benevolence E, Naregose GO, Patience AE, Blessing O, Micheal A, Jacqueline A, Aiyepada JO, Ebhodaghe P, Racheal O, Rita E, Rosemary GE, Solomon E, Anieno E, Edna Y, Chris AO, Donatus AI, Ogbaini-Emovon E, Tatfeng MY, Omunakwe HE, Bob-Manuel M, Ahmed RA, Onwuamah CK, Shaibu JO, Okwuraiwe A, Ataga AE, Bock-Oruma A, Daramola F, Yusuf IF, Fajola A, Ntia NA, Ekpo JJ, Moses AE, Moore-Igwe BW, Fakayode OE, Akinola M, Kida IM, Oderinde BS, Wudiri ZW, Adeyemi OO, Akanbi OA, Ahumibe A, Akinpelu A, Ayansola O, Babatunde O, Omoare AA, Chukwu C, Mba NG, Omoruyi EC, Olisa O, Akande OK, Nwafor IE, Ekeh MA, Ndoma E, Ewah RL, Duruihuoma RO, Abu A, Odeh E, Onyia V, Ojide CK, Okoro S, Igwe D, Ogah EO, Khan K, Ajayi NA, Ugwu CN, Ukwaja KN, Ugwu NI, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Isamotu RO, Gadzama G, Petros BA, Siddle KJ, Schaffner SF, Akpede G, Erameh CO, Baba MM, Oladiji F, Audu R, Ndodo N, Fowotade A, Okogbenin S, Okokhere PO, Park DJ, Mcannis BL, Adetifa IM, Ihekweazu C, Salako BL, Tomori O, Happi AN, Folarin OA, Andersen KG, Sabeti PC, Happi CT
Emergence and Spread of Two SARS-CoV-2 Variants of Interest in Nigeria
Nature Communications 14(1):811
(*equal contribution)

Oliveira G, Vogels CBF, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, P Leon K, Ontiveros CO, Agarwal R, Tsetsarkin KA, Harris E, Ebel GD, Wohl S, Grubaugh NDº, Andersen KGº
Genomic and Phenotypic Analyses Suggest Moderate Fitness Differences Among Zika virus Lineages
PLoS Negl Trop Dis 17(2):e0011055
( ºco-corresponding author)

Levy JIº, Andersen KGº, Knight R, Karthikeyan S
Wastewater Surveillance for Public Health
Science 379(6627):26-27
( ºco-corresponding author)

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

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 KGº, Abu-Dayyeh Iº
Regional Connectivity Drove Bidirectional Transmission Of SARS-CoV-2 In The Middle East During Travel Restrictions
Nature Communications 13(1):4784
(*equal contribution; ºco-senior author)

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 [feature]

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 MAº, Andersen KGº, Worobey Mº, Wertheim JOº
The Molecular Epidemiology of Multiple Zoonotic Origins of SARS-CoV-2
Science 377(6609):960-966 [feature]
(ºco-senior author)

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 KGº, Knight Rº
Wastewater Sequencing Reveals Early Cryptic SARS-CoV-2 Variant Transmission
Nature 609(7925):101–108 [feature]
(*equal contribution; ºco-senior author)

Vasylyeva TI, Fang CE, Su M, Havens JL, Parker E, Wang JC, Zeller M, Yakovleva A, Hassler GW, Chowdhury MA, Andersen KG, Hughes S, Wertheim JO
Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021
The Journal of Infectious Diseases 226(12):2142-2149

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

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

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
Viruses 13(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 [feature]

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 [feature]

Arze CA, Springer S, Dudas G, Patel S, Bhattacharyya A, Swaminathan H, Brugnara C, Delagrave S, Ong T, Kahvejian A, Echelard Y, Weinstein EG, Hajjar RJ, Andersen KG, Yozwiak NL
Global Genome Analysis Reveals a Vast and Dynamic Anellovirus Landscape Within The Human Virome
Cell Host Microbe 29(8):1305-1315

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)

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 13(7):1202

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 Wº, Andersen KGº
Emergence and Rapid Transmission of SARS-CoV-2 B.1.1.7 in the United States
Cell 184(10):2587-2594  [feature]
(*equal contribution; ºco-senior author)

Landeras-Bueno S*, Wasserman H*, Oliveira G*, VanAernum ZL, Busch F, Salie ZL, Wysocki VH, Andersen Kº, Saphire EOº
Cellular mRNA Triggers Structural Transformation of Ebola virus Matrix Protein VP40 to Its Essential Regulatory Form
Cell Reports 35(2):108986
(*equal contribution; ºco-senior author)

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

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

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 NJº, Bedford Tº, Andersen KGº, Wiley MRº, Ahuka-Mundeke Sº, Muyembe Tamfum JJº
Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease
The New England Journal of Medicine 384(13):1240-1247 [feature]
(*equal contribution; ºco-senior author)

Cantrell K, Fedarko MW, Rahman G, McDonald D, Yang Y, Zaw T, Gonzalez A, Janssen S, Estaki M, Haiminen N, Beck KL, Zhu Q, Sayyari E, Morton JT, Armstrong G, Tripathi A, Gauglitz JM, Marotz C, Matteson NL, Martino C, Sanders JG, Carrieri AP, Song SJ, Swafford AD, Dorrestein PC, Andersen KG, Parida L, Kim HC, Vázquez-Baeza Y, Knight R
EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets
mSystems 16;6(2):e01216-20

Mina MJ, Andersen KG
COVID-19 testing: One Size Does Not Fit All
Science 371(6525):126-127

Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P
Epidemiological Hypothesis Testing Using a Phylogeographic and Phylodynamic Framework
Nature Communications 11(1):5110

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

Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Martin CS, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Van Rompay KKA, Coffey LL
Two Sides of a Coin: A Zika virus Mutation Selected in Pregnant Rhesus Macaques Promotes Fetal Infection in Mice but at a Cost of Reduced Fitness in Nonpregnant Macaques and Diminished Transmissibility by Vectors
Journal of Virology 94(24):e01605-20

Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria N, Wang C, Yu G, Bushnell B, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Chu HY, Shendure J, Jerome KR, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen KG, MacCannell D, Paden CR, Li Y, Zhang J, Tong S, Armstrong G, Morrow S, Willis M, Matyas BT, Mase S, Kasirye O, Park M, Masinde G, Chan C, Yu AT, Chai SJ, Villarino E, Bonin B, Wadford DA, Chiu CY
Genomic Surveillance Reveals Multiple Introductions of SARS-CoV-2 Into Northern California
Science 369(6503):582-587

Klitting R, Mehta SB, Oguzie JU, Oluniyi PE, Pauthner MG, Siddle KJ, Andersen KG, Happi CT, Sabeti PC
Lassa Virus Genetics
Current Topics in Microbiology and Immunology 440:23-65

Andersen KG, Rambaut A, Lipkin WA, Holmes EC, Garry RF
The Proximal Origin of SARS-CoV-2
Nature Medicine 26(4):450-452 [feature]

Sakabe S, Hartnett JN, Ngo N, Goba A, Momoh M, Demby Sandi J, Kanneh L, Cubitt B, Garcia SD, Ware BC, Kotliar D, Robles-Sikisaka R, Gangavarapu K, Branco LM, Eromon P, Odia I, Ogbaini-Emovon E, Folarin O, Okogbenin S, Okokhere PO, Happi C, Sabeti PC, Andersen KG, Garry RF, de la Torre JC, Grant DS, Schieffelin JS, Oldstone MBA, Sullivan BM
Identification of Common CD8+ T cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone
Journal of Virology 94(12):e00153-20

Sullivan BM, Sakabe S, Hartnett JN, Ngo N, Goba A, Momoh M, Demby Sandi J, Kanneh L, Cubitt B, Garcia SD, Ware BC, Kotliar D, Robles-Sikisaka R, Gangavarapu K, Branco L, Eromon P, Odia I, Ogbaini-Emovon E, Folarin O, Okogbenin S, Okokhere PO, Happi C, de la Torre JC, Sabeti PC, Andersen KG, Garry RF, Grant DS, Schieffelin JS, Oldstone MBA
High Crossreactivity of Human T Cell Responses Between Lassa virus Lineages
PLOS Pathogens 16(3):e1008352

Lin AE, Diehl WE, Cai Y, Finch CL, Akusobi C, Kirchdoerfer RN, Bollinger L, Schaffner SF, Brown EA, Saphire EO, Andersen KG, Kuhn JH, Luban J, Sabeti PC
Reporter Assays for Ebola virus Nucleoprotein Oligomerization, Virion-Like Particle Budding, and Minigenome Activity Reveal the Importance of Nucleoprotein Amino Acid Position 111
Viruses 15;12(1). pii: E105

Hadfield J, Brito AF, Swetnam DM, Vogels CBF, 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 31;15(10):e1008042

Grubaugh ND*º, 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*º, Andersen KG*º
Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic
Cell 178(5):1057-1071 [feature]
(*equal contribution; ºco-corresponding authors)

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

Ladner JT, Grubaugh ND, Pybus OG, Andersen KG
Precision Epidemiology for Infectious Disease Control
Nature Medicine 25(2):206-211 [feature]

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 [feature]

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 [feature]

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
The New England Journal of Medicine 379(18):1745-1753

Saphire EOº, 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 GPº, Andersen KGº, Kawaoka Yº, Alter Gº, Chandran Kº, Dye JMº
Systematic Analysis of Monoclonal Antibodies against Ebola virus GP Defines Features that Contribute to Protection
Cell 174(4):938-952 [feature]
(*equal contribution; ºco-corresponding authors)

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

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
Proceedings of the National Academy of Sciences of the USA 115(32):E7578-E7586

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

Magnani DM, Rogers TF, Maness NJ, Grubaugh ND, Beutler N, Bailey VK, Gonzalez-Nieto L, Gutman MJ, Pedreño-Lopez N, Kwal JM, Ricciardi MJ, Myers TA, Julander JG, Bohm RP, Gilbert MH, Schiro F, Aye PP, Blair RV, Martins MA, Falkenstein KP, Kaur A, Curry CL, Kallas EG, Desrosiers RC, Goldschmidt-Clermont PJ, Whitehead SS, Andersen KG, Bonaldo MC, Lackner AA, Panganiban AT, Burton DR, Watkins DI
Fetal Demise and Failed Antibody Therapy During Zika virus Infection of Pregnant Macaque
Nature Communications 9(1):1624

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 fever
Scientific Reports 8(1):5939

Mark Zeller, Andersen KG
Backbone of RNA viruses Uncovered
Nature 556(7700):182-183

Ma S, Cahalan S, LaMonte G, Grubaugh ND, Zeng W, Murthy SE, Paytas E, Gamini R, Lukacs V, Whitwam T, Loud M, Lohia R, Berry L, Khan SM, Janse CJ, Bandell M, Schmedt C, Wengelnik K, Su AI, Honore E, Winzeler EA, Andersen KG, Patapoutian A
Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium Infection
Cell 173(2):443-455 [feature]

Grubaugh ND, Faria NR, Andersen KGº, Pybus OGº
Genomic Insights into Zika virus Emergence and Spread
Cell 172(6):1160-1162 [feature]
(ºco-corresponding authors)

Ricciardi MJ, Magnani DM, Grifoni A, Kwon YC, Gutman MJ, Grubaugh ND, Gangavarapu K, Sharkey M, Silveira CGT, Bailey VK, Pedreño-Lopez N, Gonzalez-Nieto L, Maxwell HS, Domingues A, Martins MA, Pham J, Weiskopf D, Altman J, Kallas EG, Andersen KG, Stevenson M, Lichtenberger P, Choe H, Whitehead SS, Sette A, Watkins DI
Ontogeny of the B- and T-cell Response in a Primary Zika virus Infection of a Dengue-naïve Individual During the 2016 Outbreak in Miami, FL
PLOS Neglected Tropical Diseases 11(12):e0006000

Torkamani A, Andersen KG, Steinhubl SR, Topol EJ
High-Definition Medicine
Cell 170(5):828-843

Grubaugh NDª, Ladner JTª, Kraemer MUGª, Dudas Gª, Tan ALª, Gangavarapu Kª, Wiley MRª, White Sª, Thézé Jª, 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*º, Andersen KG*º
Genomic Epidemiology Reveals Multiple Introductions of Zika virus into the United States
Nature 546(7658):401-405 [feature]
(ªco-first authors; *co-senior authors; ºco-corresponding authors)

Faria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Raghwani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, França RF, Magalhães T, Marques ET Jr, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman NJ, Pybus OG
Establishment and Cryptic Transmission of Zika virus in Brazil and the Americas
Nature 546(7658):406-410

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 [feature]
(*co-senior authors)

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

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, [PI alphabetical] 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

Grubaugh ND, Andersen KG
Experimental Evolution to Study Virus Emergence
Cell 169(1):1-3

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

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 KGº, Sabeti PCº, Luban Jº
Ebola virus Glycoprotein with Increased Infectivity Dominated the 2013-2016 Epidemic
Cell 167(4):1088-1098 [feature]
(*co-first authors; ºco-corresponding authors)

Radin JM, Topol EJ, Andersen KG, Steinhubl SR
A Laboratory in Your Pocket
Lancet 388(10054):1875

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

Grubaugh ND, Andersen KG
Navigating the Zika Panic
F1000 Research 5:1914

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

Pallesen J, Murin CD, de Val N, Cottrell CA, Hastie KM, Turner HL, Fusco ML, Flyak AI, Zeitlin L, Crowe JE, Andersen KG, Saphire EO, Ward AB
Structures of Ebola virus GP and sGP in Complex with Therapeutic Antibodies
Nature Microbiology 1:16128

Lemieux JE, Tran AD, Freimark L, Schaffner SF, Goethert H, Andersen KG, Bazner S, Li A, McGrath G, Sloan L, Vannier E, Milner D, Pritt B, Rosenberg E, Telford S, Bailey JA, Sabeti PC
A Global Map of Genetic Diversity in Babesia microti Reveals Strong Population Structure and Identifies Variants Associated with Clinical Relapse
Nature Microbiology 1:16079

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

Folarin OA, Ehichioya D, Schaffner SF, Winnicki SM, Wohl S, Eromon P, West KL, Gladden-Young A, Oyejide NE, Matranga CB, Deme AB, James A, Tomkins-Tinch C, Onyewurunwa K, Ladner JT, Palacios G, Nosamiefan I, Andersen KG, Omilabu S, Park DJ, Yozwiak NL, Nasidi A, Garry RF, Tomori O, Sabeti PC, Happi CT
Ebola virus Epidemiology and Evolution in Nigeria
Journal of Infectious Diseases 214(suppl 3):S102-S109

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 [feature]

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC
Direct Identification of Hundreds of Expression-modulating Variants Using a Multiplexed Reporter Assay
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

Andersen KG*º, 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 CTº, Garry RF, Sabeti PCº
Clinical Sequencing Uncovers Origins and Evolution of Lassa virus
Cell 162(4):738-50 [feature]
(*co-first authors; ºco-corresponding authors)

Xie X, Stubbington MJ, Nissen JK, Andersen KG, Hebenstreit D, Teichmann SA, Betz AG
The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression Through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding
PLOS Genetics 11(5):e1005251

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 [feature]

Andersen KG
Cases of Ebola virus Disease Predicted to Rise from Hundreds to Thousands per Week Unless Control Measures Improve
Evidence Based Nursing ebnurs-2014-102031

Stremlau MH*º, Andersen KG*º, Folarin OA, Grove JN, Odia I, Ehiane PE, Omoniwa O, Omoregie O, Jiang PP, Yozwiak NL, Matranga CB, Yang X, Gire SK, Winnicki S, Tariyal R, Schaffner SF, Okokhere PO, Okogbenin S, Akpede GO, Asogun DA, Agbonlahor DE, Walker PJ, Tesh RB, Levin JZ, Garry RF, Sabeti PCº, Happi CTº
Discovery of Novel Rhabdoviruses in the Blood of Healthy Individuals from West Africa
PLOS Neglected Tropical Diseases 17;9(3):e0003631
(*co-first authors; ºco-corresponding authors)

Boisen ML, Schieffelin JS, Goba A, Oottamasathien D, Jones AB, Shaffer JG, Hastie KM, Hartnett JN, Momoh M, Fullah M, Gabiki M, Safa S, Zandonatti M, Fusco M, Bornholdt Z, Abelson D, Gire SK, Andersen KG, Tariyal R, Stremlau M, Cross RW, Geisbert JB, Pitts KR, Geisbert TW, Kulakoski P, Wilson RB, Henderson L, Sabeti PC, Grant DS, Garry RF, Saphire EO, Branco LM, Khan SH
Multiple Circulating Infections Can Mimic the Early Stages of Viral Hemorrhagic Fevers and Possible Human Exposure to Filoviruses in Sierra Leone Prior to the 2014 Outbreak
Viral Immunology 28(1):19-31

Lauck M, Bailey A, Andersen KG, Goldberg TL, Sabeti PC, O’Connor D
GB virus C Co-infections in West African Ebola Patients
Journal of Virology 15;89(4):2425-9

Kugelman J, Sanchez-Lockhart M, Andersen KG, Gire S, Park DJ, Sealfon R, Lin A, Wohl S, Sabeti P, Kuhn JH
Evaluation of the Potential Impact of Ebola virus Genomic Drift on the Efficacy of Sequence-based Candidate Therapeutics
mBio 20;6(1). pii:e02227-14

Kuhn JH, [alphabetical] Andersen KG, Baize S, Bào Y, Bavari S, Berthet N, Blinkova O, Brister JR, Clawson AN, Fair J, Gabriel M, Garry RF, Gire SK, Goba A, Gonzalez JP, Günther S, Happi CT, Jahrling PB, Kapetshi J, Kobinger G, Kugelman JR, Leroy EM, Maganga GD, Mbala PK, Moses LM, Muyembe-Tamfum JJ, N’Faly M, Nichol ST, Omilabu SA, Palacios G, Park DJ, Paweska JT, Radoshitzky SR, Rossi CA, Sabeti PC, Schieffelin JS, Schoepp RJ, Sealfon R, Swanepoel R, Towner JS, Wada J, Wauquier N, Yozwiak NL, Formenty P
Nomenclature- and Database-compatible Names for the Two Ebola virus Variants That Emerged in Guinea and the Democratic Republic of the Congo in 2014
Viruses 6(11):4760-4799

Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC
Enhanced Methods for Unbiased Deep Sequencing of Lassa and Ebola RNA Viruses in Clinical and Biological Samples
Genome Biology 15(11):519

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
The New England Journal of Medicine 371(22):2092-100

Kuhn JH, [alphabetical] Andersen KG, Bào Y, Bavari S, Becker S, Bennett RS, Bergman NH, Blinkova O, Bradfute S, Brister JR, Bukreyev A, Chandran K, Chepurnov AA, Davey RA, Dietzgen RG, Doggett NA, Dolnik O, Dye JM, Enterlein S, Fenimore PW, Formenty P, Freiberg AN, Garry RF, Garza NL, Gire SK, Gonzalez JP, Griffiths A, Happi CT, Hensley LE, Herbert AS, Hevey MC, Hoenen T, Honko AN, Ignatyev GM, Jahrling PB, Johnson JC, Johnson KM, Kindrachuk J, Klenk HD, Kobinger G, Kochel TJ, Lackemeyer MG, Lackner DF, Leroy EM, Lever MS, Mühlberger E, Netesov SV, Olinger GG, Omilabu SA, Palacios G, Panchal RG, Park DJ, Patterson JL, Paweska JT, Peters CJ, Pettitt J, Pitt L, Radoshitzky SR, Ryabchikova EI, Saphire EO, Sabeti PC, Sealfon R, Shestopalov AM, Smither SJ, Sullivan NJ, Swanepoel R, Takada A, Towner JS, van der Groen G, Volchkov VE, Volchkova VA, Wahl-Jensen V, Warren TK, Warfield KL, Weidmann M, Nichol ST
Filovirus RefSeq Entries: Evaluation and Selection of Filovirus Type Variants, Type Sequences, and Names
Viruses 6(9):3663-3682

Gire SK*, Goba A*, Andersen KG*º, 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 PCº
Genomic Surveillance Elucidates Ebola virus Origin and Transmission During the 2014 Outbreak
Science 345(6202):1369-72 [feature]
(*co-first authors; ºco-corresponding authors)

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

Grossman SR*, Andersen KG*, Shlyakhter I*, Tabrizi S*, Winnicki S, Yen A, Park DJ, Griesemer D, Karlsson EK, Wong SH, Cabili M, Adegbola RA, Bamezai RNK, Hill AVS, Vannberg FO, Rinn JL, 1000 Genomes Project, Lander ES, Schaffner SF, Sabeti PC
Identifying Recent Adaptations in Large-scale Genomic Data
Cell 152(4):703-713
(*co-first authors)

Gire SK, Stremlau M, Andersen KG, Schaffner SF, Bjornson Z, Rubins K, Hensley L, McCormick JB, Lander ES, Garry RF, Happi C, Sabeti PC
Emerging Disease or Emerging Diagnosis?
Science 338(6108):750-2

Regateiro FS, Ye Chen Y, Kendal AR, Hilbrands R, Adams E, Cobbold SP, Ma J, Andersen KG, Betz AG, Zhang M, Madhiwalla S, Roberts B, Waldmann H, Nolan KF, Howie D
Foxp3 Expression Is Required for the Induction of Therapeutic Tissue Tolerance
Journal of Immunology 189(8):3947-56

Chen Y, Adams E, Regateiro FS, Vaux DJ, Betz AG, Andersen KG, Waldmann H, Howie D
Activation Rather than Foxp3 Expression Determines That TGF-b-induced Regulatory T Cells Out-compete Naïve T Cells in Dendritic Cell Clustering
European Journal of Immunology 42(6):1436-48

Andersen KGº, Nissen JK, Betz AGº
Comparative Genomics Reveals Key Gain-of-Function Events in Foxp3 During Regulatory T Cell Evolution
Frontiers Immunology 3:113
(ºco-corresponding authors)

Andersen KGº, Shylakhter I, Tabrizi S, Grossman SR, Happi CT, Sabeti PCº
Genome-wide Scans Provide Evidence for Positive Selection of Genes Implicated in Lassa Fever
Philosophical Transactions of the Royal Society B 367(1590):868-77
(ºco-corresponding authors)

Asogun DA, Adomeh DI, Ehimuan J, Odia I, Hass M, Gabriel M, Olschläger S, Becker-Ziaja B, Folarin O, Phelan E, Ehiane PE, Ifeh VE, Uyigue EA, Oladapo YT, Muoebonam EB, Osunde O, Dongo A, Okokhere PO, Okogbenin SA, Momoh M, Alikah SO, Akhuemokhan OC, Imomeh P, Odike MA, Gire S, Andersen K, Sabeti PC, Happi CT, Akpede GO, Günther S
Molecular Diagnostics for Lassa Fever at Irrua Specialist Teaching Hospital, Nigeria: Lessons Learnt from Two Years of Laboratory Operation
PLOS Neglected Tropical Diseases 6(9):e1839

Branco LM, Boisen ML, Andersen KG, Grove JN, Moses LM, Muncy IJ, Henderson LA, Schieffellin JS, Robinson JE, Bangura JJ, Grant DS, Raabe VN, Fonnie M, Sabeti PC, Garry RF
Lassa Hemorrhagic Fever in a Late Term Pregnancy from Northern Sierra Leone with a Positive Maternal Outcome: Case Report
Virology Journal 8:404

Loizou L*, Andersen KG*, Betz AG
Foxp3 Interacts with c-Rel to Mediate NF-kappaB Repression
PLOS One 6(4):e18670
(*co-first authors)

Betz AG, Andersen KG
Methods of Switching the Phenotype of T Cells by Transgenic Lineage Factor Foxp3
Patent application #20100203068

Andersen KG, Butcher T, Betz AG
Specific Immunosuppression with Inducible Foxp3-transduced Polyclonal T Cells
PLOS Biology 6(11):e276

Hebenstreit D, Giaisi M, Treiber MK, Zhang XB, Mi HF, Horejs-Hoeck J, Andersen KG, Duschl A, Li-Weber M
LEF-1 Negatively Controls Interleukin-4 Expression Through a Proximal Promoter Regulatory Element
Journal of Biological Chemistry 283(33):22490-7

Sarris M, Andersen KG, Randow F, Mayr L, Betz AG
Neuropilin-1 Expression on Regulatory T Cells Enhances Their Interactions with Dendritic Cells During Antigen Recognition
Immunity 28(3):402-13

Kallikourdis M, Andersen KG, Welch KA, Betz AG
Alloantigen-enhanced Accumulation of CCR5+ ‘effector’ Regulatory T Cells in the Gravid Uterus
Proceedings of the National Academy of Sciences of the USA 1104(2):594-9