Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

Search Page

Filters

My NCBI Filters

Text availability

Article attribute

Article type

Publication date

Search Results

289 results

Filters applied: . Clear all
Results are displayed in a computed author sort order. The Results By Year timeline is not available.
Page 1
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. Hadfield J, et al. Bioinformatics. 2018 Dec 1;34(23):4121-4123. doi: 10.1093/bioinformatics/bty407. Bioinformatics. 2018. PMID: 29790939 Free PMC article.
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens.
Huddleston J, Hadfield J, Sibley TR, Lee J, Fay K, Ilcisin M, Harkins E, Bedford T, Neher RA, Hodcroft EB. Huddleston J, et al. Among authors: hadfield j. J Open Source Softw. 2021;6(57):2906. doi: 10.21105/joss.02906. Epub 2021 Jan 7. J Open Source Softw. 2021. PMID: 34189396 Free PMC article.
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; Seattle Flu Study Investigators; 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. Bedford T, et al. Among authors: hadfield j. Science. 2020 Oct 30;370(6516):571-575. doi: 10.1126/science.abc0523. Epub 2020 Sep 10. Science. 2020. PMID: 32913002 Free PMC article.
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; Seattle Flu Study Investigators; 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. Bedford T, et al. Among authors: hadfield j. medRxiv [Preprint]. 2020 Apr 6:2020.04.02.20051417. doi: 10.1101/2020.04.02.20051417. medRxiv. 2020. PMID: 32511596 Free PMC article. Updated. Preprint.
Characterising the epidemic spread of influenza A/H3N2 within a city through phylogenetics.
Müller NF, Wüthrich D, Goldman N, Sailer N, Saalfrank C, Brunner M, Augustin N, Seth-Smith HM, Hollenstein Y, Syedbasha M, Lang D, Neher RA, Dubuis O, Naegele M, Buser A, Nickel CH, Ritz N, Zeller A, Lang BM, Hadfield J, Bedford T, Battegay M, Schneider-Sliwa R, Egli A, Stadler T. Müller NF, et al. Among authors: hadfield j. PLoS Pathog. 2020 Nov 19;16(11):e1008984. doi: 10.1371/journal.ppat.1008984. eCollection 2020 Nov. PLoS Pathog. 2020. PMID: 33211775 Free PMC article.
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable.
Mavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M. Mavian C, et al. Among authors: hadfield j. Proc Natl Acad Sci U S A. 2020 Jun 9;117(23):12522-12523. doi: 10.1073/pnas.2007295117. Epub 2020 May 7. Proc Natl Acad Sci U S A. 2020. PMID: 32381734 Free PMC article. No abstract available.
Integration of genomic sequencing into the response to the Ebola virus outbreak in Nord Kivu, Democratic Republic of the Congo.
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. Kinganda-Lusamaki E, et al. Among authors: hadfield j. Nat Med. 2021 Apr;27(4):710-716. doi: 10.1038/s41591-021-01302-z. Epub 2021 Apr 12. Nat Med. 2021. PMID: 33846610 Free PMC article.
The Seattle Flu Study: a multiarm community-based prospective study protocol for assessing influenza prevalence, transmission and genomic epidemiology.
Chu HY, Boeckh M, Englund JA, Famulare M, Lutz B, Nickerson DA, Rieder M, Starita LM, Adler A, Brandstetter E, Frazer CD, Han PD, Gulati RK, Hadfield J, Jackson M, Kiavand A, Kimball LE, Lacombe K, Newman K, Sibley TR, Logue JK, Lyon VR, Wolf CR, Zigman Suchsland M, Shendure J, Bedford T. Chu HY, et al. Among authors: hadfield j. BMJ Open. 2020 Oct 7;10(10):e037295. doi: 10.1136/bmjopen-2020-037295. BMJ Open. 2020. PMID: 33033018 Free PMC article.
289 results