Moncla LH, Black A, DeBolt C, Lang M, Graff NR, Pérez-Osorio AC, Müller NF, Haselow D, Lindquist S, Bedford T. (2021). Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State. eLife, (10)

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. (2021). Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo. Nature medicine

Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan FL, Chemel AK, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED Jr., Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, López A, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PS. (2020). CpG-creating mutations are costly in many human viruses. Evolutionary ecology, 34(3)

Black A, MacCannell DR, Sibley TR, Bedford T. (2020). Ten recommendations for supporting open pathogen genomic analysis in public health. Nature medicine

Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Huang ML, Nalla A, Pepper G, Reinhardt A, Xie H, Shrestha L, Nguyen TN, Adler A, Brandstetter E, Cho S, Giroux D, Han PD, Fay K, Frazar CD, Ilcisin M, Lacombe K, Lee J, Kiavand A, Richardson M, Sibley TR, Truong M, Wolf CR, Nickerson DA, Rieder MJ, Englund JA, , Hadfield J, Hodcroft EB, Huddleston J, Moncla LH, Müller NF, Neher RA, Deng X, Gu W, Federman S, Chiu C, Duchin JS, Gautom R, Melly G, Hiatt B, Dykema P, Lindquist S, Queen K, Tao Y, Uehara A, Tong S, MacCannell D, Armstrong GL, Baird GS, Chu HY, Shendure J, Jerome KR. (2020). Cryptic transmission of SARS-CoV-2 in Washington state. Science (New York, N.Y.)

Huddleston J, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Whittaker L, Ermetal B, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Barr I, Subbarao K, Barrat-Charlaix P, Neher RA, Bedford T. (2020). Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution. eLife, (9)

Moncla LH, Bedford T, Dussart P, Horm SV, Rith S, Buchy P, Karlsson EA, Li L, Liu Y, Zhu H, Guan Y, Friedrich TC, Horwood PF. (2020). Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia. PLoS pathogens, 16(1)

Jackson Michael L, Hart Gregory R, McCulloch Denise J, Adler Amanda, Brandstetter Elisabeth, Fay Kairsten, Han Peter, Lacombe Kirsten, Lee Jover, Sibley Thomas, Nickerson Deborah A, Rieder Mark, Starita Lea, Englund Janet A, Bedford Trevor, Chu Helen, Famulare Michael, Investigators the Seattle Flu Study. (2020). Effects of weather-related social distancing on city-scale transmission of respiratory viruses. Cold Spring Harbor Laboratory Press

Castro LA, Bedford T, Ancel Meyers L. (2020). Early prediction of antigenic transitions for influenza A/H3N2. PLoS computational biology, 16(2)

Trevor Bedford, John Huddleston, Barney Potter, and Richard A. Neher. (2019). Seasonal influenza circulation patterns and projections for September 2019 to September 2020. bioRxiv

Soh YS, Moncla LH, Eguia R, Bedford T, Bloom JD. (2019). Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans. eLife, (8)

Black A, Moncla LH, Laiton-Donato K, Potter B, Pardo L, Rico A, Tovar C, Rojas DP, Longini IM, Halloran ME, Peláez-Carvajal D, Ramírez JD, Mercado-Reyes M, Bedford T. (2019). Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia. BMC infectious diseases, 19(1)

Bell SM, Katzelnick L, Bedford T. (2019). Dengue genetic divergence generates within-serotype antigenic variation, but serotypes dominate evolutionary dynamics. Elife, (8)

Potter BI, Kondor R, Hadfield J, Huddleston J, Barnes J, Rowe T, Guo L, Xu X, Neher RA, Bedford T, Wentworth DE. (2019). Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season. Virus evolution, 5(2)

Neher RA, Bedford T. (2018). Real-Time Analysis and Visualization of Pathogen Sequence Data. Journal of Clinical Microbiology, 56(11)

Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA. (2018). Nextstrain: real-time tracking of pathogen evolution. Bioinformatics (Oxford, England), 34(23)

Dudas G, Carvalho LM, Rambaut A, Bedford T. (2018). Correction: MERS-CoV spillover at the camel-human interface. Elife, (7)

Wen FT, Bell SM, Bedford T, Cobey S. (2018). Estimating Vaccine-Driven Selection in Seasonal Influenza. Viruses, 10(9), https://github.com/cobeylab/flu-vaccine-sieve

Dudas G, Carvalho LM, Rambaut A, Bedford T. (2018). MERS-CoV spillover at the camel-human interface. eLife, (7)

Xue KS, Moncla LH, Bedford T, Bloom JD. (2018). Within-Host Evolution of Human Influenza Virus. Trends in microbiology, 26(9)

Lee JM, Huddleston J, Doud MB, Hooper KA, Wu NC, Bedford T, Bloom JD. (2018). Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. Proceedings of the National Academy of Sciences of the United States of America, 115(35)

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. (2017). Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nature protocols, 12(6)

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. (2017). Genomic epidemiology reveals multiple introductions of Zika virus into the United States. Nature, 546(7658)

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, Di Caro A, 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 MVT, 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 MPG, 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. (2017). Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature, 544(7650)

Morris DH, Gostic KM, Pompei S, Bedford T, Łuksza M, Neher RA, Grenfell BT, Lässig M, McCauley JW. (2018). Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology. Trends in microbiology, 26(2)

Bell SM, Bedford T. (2017). Modern-day SIV viral diversity generated by extensive recombination and cross-species transmission. PLoS Pathogens, 13(7)

Langat P, Raghwani J, Dudas G, Bowden TA, Edwards S, Gall A, Bedford T, Rambaut A, Daniels RS, Russell CA, Pybus OG, McCauley J, Kellam P, Watson SJ. (2017). Genome-wide evolutionary dynamics of influenza B viruses on a global scale. PLoS pathogens, 13(12)

Lorenzo-Redondo R, Fryer HR, Bedford T, Kim EY, Archer J, Pond SLK, Chung YS, Penugonda S, Chipman J, Fletcher CV, Schacker TW, Malim MH, Rambaut A, Haase AT, McLean AR, Wolinsky SM. (2016). Persistent HIV-1 replication maintains the tissue reservoir during therapy. Nature, 530(7588)

Wen F, Bedford T, Cobey S. (2016). Explaining the geographical origins of seasonal influenza A (H3N2). Proceedings. Biological sciences, 283(1838)

Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. (2016). Viral factors in influenza pandemic risk assessment. Elife, (5)

Neher RA, Bedford T, Daniels RS, Russell CA, Shraiman BI. (2016). Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses. Proceedings of the National Academy of Sciences of the United States of America, 113(12)

Bedford T, Malik HS. (2016). Did a Single Amino Acid Change Make Ebola Virus More Virulent. Cell, 167(4)

Karcher MD, Palacios JA, Bedford T, Suchard MA, Minin VN. (2016). Quantifying and Mitigating the Effect of Preferential Sampling on Phylodynamic Inference. PLoS computational biology, 12(3)

Harvey WT, Benton DJ, Gregory V, Hall JP, Daniels RS, Bedford T, Haydon DT, Hay AJ, McCauley JW, Reeve R. (2016). Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses. PLoS pathogens, 12(4)

Black A, Breyta R, Bedford T, Kurath G. (2016). Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus. Virus evolution, 2(2)

Neher RA, Bedford T. (2015). nextflu: real-time tracking of seasonal influenza virus evolution in humans. Bioinformatics (Oxford, England), 31(21)

Machkovech HM, Bedford T, Suchard MA, Bloom JD. (2015). Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages. Journal of virology, 89(22)

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. (2015). Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone. Cell, 161(7)

Bedford T, Riley S, Barr IG, Broor S, Chadha M, Cox NJ, Daniels RS, Gunasekaran CP, Hurt AC, Kelso A, Klimov A, Lewis NS, Li X, McCauley JW, Odagiri T, Potdar V, Rambaut A, Shu Y, Skepner E, Smith DJ, Suchard MA, Tashiro M, Wang D, Xu X, Lemey P, Russell CA. (2015). Global circulation patterns of seasonal influenza viruses vary with antigenic drift. Nature, 523(7559)

Frost SD, Pybus OG, Gog JR, Viboud C, Bonhoeffer S, Bedford T. (2015). Eight challenges in phylodynamic inference. Epidemics, (10)

Bedford T, Suchard MA, Lemey P, Dudas G, Gregory V, Hay AJ, McCauley JW, Russell CA, Smith DJ, Rambaut A. (2014). Integrating influenza antigenic dynamics with molecular evolution. Elife, (3)

Roche B, Drake JM, Brown J, Stallknecht DE, Bedford T, Rohani P. (2014). Adaptive evolution and environmental durability jointly structure phylodynamic patterns in avian influenza viruses. PLoS biology, 12(8)

Volz EM, Koelle K, Bedford T. (2013). Viral phylodynamics. PLoS computational biology, 9(3)

Landis MJ, Bedford T. (2014). Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. Bioinformatics (Oxford, England), 30(1)

Bedford T, Rambaut A, Pascual M. (2012). Canalization of the evolutionary trajectory of the human influenza virus. BMC biology, (10)

Bedford T, Cobey S, Pascual M. (2011). Strength and tempo of selection revealed in viral gene genealogies. BMC evolutionary biology, (11)

Bedford T, Cobey S, Beerli P, Pascual M. (2010). Global migration dynamics underlie evolution and persistence of human influenza A (H3N2). PLoS pathogens, 6(5)

Bedford T, Hartl DL. (2009). Optimization of gene expression by natural selection. Proceedings of the National Academy of Sciences of the United States of America, 106(4)

Bedford T, Wapinski I, Hartl DL. (2008). Overdispersion of the molecular clock varies between yeast, Drosophila and mammals. Genetics, 179(2)

Bedford T, Hartl DL. (2008). Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila. Molecular biology and evolution, 25(8)