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Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences.
Tran-Kiem C, Paredes MI, Perofsky AC, Frisbie LA, Xie H, Kong K, Weixler A, Greninger AL, Roychoudhury P, Peterson JM, Delgado A, Halstead H, MacKellar D, Dykema P, Gamboa L, Frazar CD, Ryke E, Stone J, Reinhart D, Starita L, Thibodeau A, Yun C, Aragona F, Black A, Viboud C, Bedford T. Tran-Kiem C, et al. Among authors: xie h. medRxiv [Preprint]. 2024 Nov 7:2024.05.24.24307811. doi: 10.1101/2024.05.24.24307811. medRxiv. 2024. PMID: 38826243 Free PMC article. Preprint.
Phylogenetic estimates of SARS-CoV-2 introductions into Washington State.
Tordoff DM, Greninger AL, Roychoudhury P, Shrestha L, Xie H, Jerome KR, Breit N, Huang ML, Famulare M, Herbeck JT. Tordoff DM, et al. Among authors: xie h. medRxiv [Preprint]. 2021 Apr 7:2021.04.05.21254924. doi: 10.1101/2021.04.05.21254924. medRxiv. 2021. Update in: Lancet Reg Health Am. 2021 Sep;1:100018. doi: 10.1016/j.lana.2021.100018 PMID: 33855313 Free PMC article. Updated. Preprint.
Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State.
Müller NF, Wagner C, Frazar CD, Roychoudhury P, Lee J, Moncla LH, Pelle B, Richardson M, Ryke E, Xie H, Shrestha L, Addetia A, Rachleff VM, Lieberman NAP, Huang ML, Gautom R, Melly G, Hiatt B, Dykema P, Adler A, Brandstetter E, Han PD, Fay K, Ilcisin M, Lacombe K, Sibley TR, Truong M, Wolf CR, Boeckh M, Englund JA, Famulare M, Lutz BR, Rieder MJ, Thompson M, Duchin JS, Starita LM, Chu HY, Shendure J, Jerome KR, Lindquist S, Greninger AL, Nickerson DA, Bedford T. Müller NF, et al. Among authors: xie h. Sci Transl Med. 2021 May 26;13(595):eabf0202. doi: 10.1126/scitranslmed.abf0202. Epub 2021 May 3. Sci Transl Med. 2021. PMID: 33941621 Free PMC article.
Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study.
Paredes MI, Lunn SM, Famulare M, Frisbie LA, Painter I, Burstein R, Roychoudhury P, Xie H, Mohamed Bakhash SA, Perez R, Lukes M, Ellis S, Sathees S, Mathias PC, Greninger A, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, McDermot E, Truong M, Nickerson DA, Bates DL, Hartman ME, Haugen E, Nguyen TN, Richards JD, Rodriguez JL, Stamatoyannopoulos JA, Thorland E, Melly G, Dykema PE, MacKellar DC, Gray HK, Singh A, Peterson JM, Russell D, Torres LM, Lindquist S, Bedford T, Allen KJ, Oltean HN. Paredes MI, et al. Among authors: xie h. medRxiv [Preprint]. 2022 Feb 16:2021.09.29.21264272. doi: 10.1101/2021.09.29.21264272. medRxiv. 2022. Update in: Clin Infect Dis. 2022 Aug 24;75(1):e536-e544. doi: 10.1093/cid/ciac279 PMID: 34729567 Free PMC article. Updated. Preprint.
Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat.
Hannon WW, Roychoudhury P, Xie H, Shrestha L, Addetia A, Jerome KR, Greninger AL, Bloom JD. Hannon WW, et al. Among authors: xie h. bioRxiv [Preprint]. 2022 Feb 9:2022.02.09.479546. doi: 10.1101/2022.02.09.479546. bioRxiv. 2022. Update in: Virus Evol. 2022 Jun 16;8(2):veac052. doi: 10.1093/ve/veac052 PMID: 35169803 Free PMC article. Updated. Preprint.
Genomic Analysis of Early Monkeypox Virus Outbreak Strains, Washington, USA.
Roychoudhury P, Sereewit J, Xie H, Nunley E, Bakhash SM, Lieberman NAP, Greninger AL. Roychoudhury P, et al. Among authors: xie h. Emerg Infect Dis. 2023 Mar;29(3):644-646. doi: 10.3201/eid2903.221446. Epub 2023 Feb 2. Emerg Infect Dis. 2023. PMID: 36732066 Free PMC article.
Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county.
Paredes MI, Perofsky AC, Frisbie L, Moncla LH, Roychoudhury P, Xie H, Bakhash SAM, Kong K, Arnould I, Nguyen TV, Wendm ST, Hajian P, Ellis S, Mathias PC, Greninger AL, Starita LM, Frazar CD, Ryke E, Zhong W, Gamboa L, Threlkeld M, Lee J, Stone J, McDermot E, Truong M, Shendure J, Oltean HN, Viboud C, Chu H, Müller NF, Bedford T. Paredes MI, et al. Among authors: xie h. PLoS Pathog. 2024 Mar 26;20(3):e1012117. doi: 10.1371/journal.ppat.1012117. eCollection 2024 Mar. PLoS Pathog. 2024. PMID: 38530853 Free PMC article.
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