National Institutes of Health, National Institute of Allergy and Infectious Diseases
People: John Huddleston
2022 – 2028 Continue Reading Forecasting influenza evolution on a heterogeneous immune landscape
National Institutes of Health, National Institute of Allergy and Infectious Diseases
People: John Huddleston
2019 – 2020 Continue Reading Integrative prediction of seasonal influenza evolution by genotype, phenotype, and geography
National Institutes of Health, National Institute of General Medical Sciences
People: Trevor Bedford, John Huddleston
2014 – 2020 Continue Reading Understanding Transmission with Integrated Genetic and Epidemiologic Inference
Loes AN, Tarabi RAL, Li SH, Atkinson RK, Huddleston J, Kikawa C, Griffiths T, Drapeau EM, Wong S-S, Cheng SMS, Leung NHL, Cobey S, Cowling BJ, Bedford T, Hensley SE, Bloom JD. (2026). Strain-specific differences in the response to egg-derived versus recombinant protein influenza vaccines. Journal of virology, 100(6)
Neher RA, Huddleston J, Bedford T, Lewis NS, Harvey R, Galiano M, Byrne AMP, James S, Smith D, Łuksza M, Ruchnewitz D, Laessig M, Fujisaki S, Watanabe S, Hasegawa H, Hassell N, Wentworth DE, Kondor R, Deng YM, Dapat C, Subbarao K, Barr I. (2026). Nomenclature for Tracking of Genetic Variation of Seasonal Influenza Viruses. Influenza and other respiratory viruses, 20(2)
Perofsky AC, Huddleston J, Hansen CL, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Lewis N, Whittaker L, Ermetal B, Harvey R, Galiano M, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Sullivan SG, Barr IG, Subbarao K, Krammer F, Bedford T, Viboud C. (2024). Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. eLife, (13)
Loes AN, Tarabi RAL, Huddleston J, Touyon L, Wong SS, Cheng SMS, Leung NHL, Hannon WW, Bedford T, Cobey S, Cowling BJ, Bloom JD. (2024). High-throughput sequencing-based neutralization assay reveals how repeated vaccinations impact titers to recent human H1N1 influenza strains. Journal of virology
Welsh FC, Eguia RT, Lee JM, Haddox HK, Galloway J, Van Vinh Chau N, Loes AN, Huddleston J, Yu TC, Quynh Le M, Nhat NTD, Thi Le Thanh N, Greninger AL, Chu HY, Englund JA, Bedford T, Matsen FA 4th., Boni MF, Bloom JD. (2024). Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. Cell host & microbe
Kistler KE, Huddleston J, Bedford T. (2022). Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2. Cell host & microbe
Wraith S, Balmaseda A, Carrillo FAB, Kuan G, Huddleston J, Kubale J, Lopez R, Ojeda S, Schiller A, Lopez B, Sanchez N, Webby R, Nelson MI, Harris E, Gordon A. (2022). Homotypic protection against influenza in a pediatric cohort in Managua, Nicaragua. Nature communications, 13(1)
Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB. (2021). Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. Journal of open source software, 6(57)
Barrat-Charlaix P, Huddleston J, Bedford T, Neher RA. (2021). Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses. Molecular biology and evolution
Nakamori M, Panigrahi GB, Lanni S, Gall-Duncan T, Hayakawa H, Tanaka H, Luo J, Otabe T, Li J, Sakata A, Caron MC, Joshi N, Prasolava T, Chiang K, Masson JY, Wold MS, Wang X, Lee MYWT, Huddleston J, Munson KM, Davidson S, Layeghifard M, Edward LM, Gallon R, Santibanez-Koref M, Murata A, Takahashi MP, Eichler EE, Shlien A, Nakatani K, Mochizuki H, Pearson CE. (2020). A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo. Nature genetics, 52(2)
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.)
Cantsilieris S, Sunkin SM, Johnson ME, Anaclerio F, Huddleston J, Baker C, Dougherty ML, Underwood JG, Sulovari A, Hsieh P, Mao Y, Catacchio CR, Malig M, Welch AE, Sorensen M, Munson KM, Jiang W, Girirajan S, Ventura M, Lamb BT, Conlon RA, Eichler EE. (2020). An evolutionary driver of interspersed segmental duplications in primates. Genome biology, 21(1)
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)
Greaney AJ, Starr TN, Gilchuk P, Zost SJ, Binshtein E, Loes AN, Hilton SK, Huddleston J, Eguia R, Crawford KHD, Dingens AS, Nargi RS, Sutton RE, Suryadevara N, Rothlauf PW, Liu Z, Whelan SPJ, Carnahan RH, Crowe JE Jr., Bloom JD. (2021). Complete Mapping of Mutations to the SARS-CoV-2 Spike Receptor-Binding Domain that Escape Antibody Recognition. Cell host & microbe, 29(1)
Hilton SK, Huddleston J, Black A, North K, Dingens AS, Bedford T, Bloom JD. (2020). dms-view: Interactive visualization tool for deep mutational scanning data. Journal of open source software, 5(52)
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)
Trevor Bedford, John Huddleston, Barney Potter, and Richard A. Neher. (2019). Seasonal influenza circulation patterns and projections for September 2019 to September 2020. bioRxiv
Cantsilieris S, Nelson BJ, Huddleston J, Baker C, Harshman L, Penewit K, Munson KM, Sorensen M, Welch AE, Dang V, Grassmann F, Richardson AJ, Guymer RH, Graves-Lindsay TA, Wilson RK, Weber BHF, Baird PN, Allikmets R, Eichler EE. (2018). Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (CFH) gene family. Proceedings of the National Academy of Sciences of the United States of America, 115(19)
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)
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)
Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE. (2017). Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome research, 28(1)
Kuderna LFK, Tomlinson C, Hillier LW, Tran A, Fiddes IT, Armstrong J, Laayouni H, Gordon D, Huddleston J, Garcia Perez R, Povolotskaya I, Serres Armero A, Gómez Garrido J, Ho D, Ribeca P, Alioto T, Green RE, Paten B, Navarro A, Betranpetit J, Herrero J, Eichler EE, Sharp AJ, Feuk L, Warren WC, Marques-Bonet T. (2017). A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0). GigaScience, 6(11)
Alexandre CM, Urton JR, Jean-Baptiste K, Huddleston J, Dorrity MW, Cuperus JT, Sullivan AM, Bemm F, Jolic D, Arsovski AA, Thompson A, Nemhauser JL, Fields S, Weigel D, Bubb KL, Queitsch C. (2018). Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana. Molecular biology and evolution, 35(4)
Dennis MY, Harshman L, Nelson BJ, Penn O, Cantsilieris S, Huddleston J, Antonacci F, Penewit K, Denman L, Raja A, Baker C, Mark K, Malig M, Janke N, Espinoza C, Stessman HAF, Nuttle X, Hoekzema K, Lindsay-Graves TA, Wilson RK, Eichler EE. (2017). The evolution and population diversity of human-specific segmental duplications. Nature ecology & evolution, 1(3)
Dougherty ML, Nuttle X, Penn O, Nelson BJ, Huddleston J, Baker C, Harshman L, Duyzend MH, Ventura M, Antonacci F, Sandstrom R, Dennis MY, Eichler EE. (2017). The birth of a human-specific neural gene by incomplete duplication and gene fusion. Genome biology, 18(1)
Tolomeo D, Capozzi O, Stanyon RR, Archidiacono N, D'Addabbo P, Catacchio CR, Purgato S, Perini G, Schempp W, Huddleston J, Malig M, Eichler EE, Rocchi M. (2017). Epigenetic origin of evolutionary novel centromeres. Scientific reports, (7)
Mohajeri K, Cantsilieris S, Huddleston J, Nelson BJ, Coe BP, Campbell CD, Baker C, Harshman L, Munson KM, Kronenberg ZN, Kremitzki M, Raja A, Catacchio CR, Graves TA, Wilson RK, Ventura M, Eichler EE. (2016). Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region. Genome research, 26(11)
Huddleston J, Eichler EE. (2016). An Incomplete Understanding of Human Genetic Variation. Genetics, 202(4)
Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE. (2017). Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome research, 27(5)
Turner TN, Yi Q, Krumm N, Huddleston J, Hoekzema K, F Stessman HA, Doebley AL, Bernier RA, Nickerson DA, Eichler EE. (2017). denovo-db: a compendium of human de novo variants. Nucleic acids research, 45(D1)
Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE. (2014). Reconstructing complex regions of genomes using long-read sequencing technology. Genome research, 24(4)
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