student

John Huddleston

Computational Biology (Area Director)

Genetics, Genomics & Evolution

Microbiology, Infection & Immunity

Entry Quarter: Autumn 2016
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Publications

The following publications were retrieved from PubMed:

Cryptic transmission of SARS-CoV-2 in Washington State.

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 J, 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.

medRxiv. 2020 Apr 6;

A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo.

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.

Nat Genet. 2020 Feb; 2(52)146-159

Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants.

Lee JM, Huddleston J, Doud MB, Hooper KA, Wu NC, Bedford T, Bloom JD.

Proc Natl Acad Sci U S A. 2018 Aug 28; 35(115)E8276-E8285

Nextstrain: real-time tracking of pathogen evolution.

Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, Sagulenko P, Bedford T, Neher RA.

Bioinformatics. 2018 Dec 1; 23(34)4121-4123

Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (<i>CFH</i>) gene family.

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.

Proc Natl Acad Sci U S A. 2018 May 8; 19(115)E4433-E4442



Publications Link

Research Summary

Accurate prediction of seasonal influenza evolution depends on a comprehensive integration of biologically relevant viral characteristics. My research seeks to integrate influenza genome sequences, experimental assays, and patterns of geographic distribution into a novel unified predictive model. The predictions from this model will directly inform vaccine strain recommendations made to the CDC and WHO for all four seasonal influenza subtypes.

Lab Information

Advisor: Trevor Bedford