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Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.
Meisel JS, Nasko DJ, Brubach B, Cepeda-Espinoza V, Chopyk J, Corrada-Bravo H, Fedarko M, Ghurye J, Javkar K, Olson ND, Shah N, Allard SM, Bazinet AL, Bergman NH, Brown A, Caporaso JG, Conlan S, DiRuggiero J, Forry SP, Hasan NA, Kralj J, Luethy PM, Milton DK, Ondov BD, Preheim S, Ratnayake S, Rogers SM, Rosovitz MJ, Sakowski EG, Schliebs NO, Sommer DD, Ternus KL, Uritskiy G, Zhang SX, Pop M, Treangen TJ. Meisel JS, et al. Among authors: treangen tj. Microbiome. 2018 Nov 5;6(1):197. doi: 10.1186/s40168-018-0582-5. Microbiome. 2018. PMID: 30396371 Free PMC article.
Ultra-high throughput mapping of genetic design space.
O'Connell RW, Rai K, Piepergerdes TC, Wang Y, Samra KD, Wilson JA, Lin S, Zhang TH, Ramos E, Sun A, Kille B, Curry KD, Rocks JW, Treangen TJ, Mehta P, Bashor CJ. O'Connell RW, et al. Among authors: treangen tj. bioRxiv [Preprint]. 2023 Jul 6:2023.03.16.532704. doi: 10.1101/2023.03.16.532704. bioRxiv. 2023. PMID: 36993481 Free PMC article. Preprint.
Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.
Curry KD, Yu FB, Vance SE, Segarra S, Bhaya D, Chikhi R, Rocha EPC, Treangen TJ. Curry KD, et al. Among authors: treangen tj. bioRxiv [Preprint]. 2024 Jan 30:2024.01.25.577285. doi: 10.1101/2024.01.25.577285. bioRxiv. 2024. Update in: Bioinformatics. 2024 Jun 28;40(Suppl 1):i58-i67. doi: 10.1093/bioinformatics/btae224 PMID: 38352454 Free PMC article. Updated. Preprint.
Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta.
Trovao NS, Pan V, Goel C, Gallego-García P, Liu Y, Barbara C, Borg R, Briffa M, Cilia C, Grech L, Vassallo M, Treangen TJ, Posada D, Beheshti A, Borg J, Zahra G. Trovao NS, et al. Among authors: treangen tj. Microbiol Spectr. 2023 Dec 12;11(6):e0153923. doi: 10.1128/spectrum.01539-23. Epub 2023 Oct 6. Microbiol Spectr. 2023. PMID: 37800925 Free PMC article.
The Great Deceiver: miR-2392's Hidden Role in Driving SARS-CoV-2 Infection.
McDonald JT, Enguita FJ, Taylor D, Griffin RJ, Priebe W, Emmett MR, Sajadi MM, Harris AD, Clement J, Dybas JM, Aykin-Burns N, Guarnieri JW, Singh LN, Grabham P, Baylin SB, Yousey A, Pearson AN, Corry PM, Saravia-Butler A, Aunins TR, Sharma S, Nagpal P, Meydan C, Foox J, Mozsary C, Cerqueira B, Zaksas V, Singh U, Wurtele ES, Costes SV, Davanzo GG, Galeano D, Paccanaro A, Meinig SL, Hagan RS, Bowman NM; UNC COVID-19 Pathobiology Consortium; Wolfgang MC, Altinok S, Sapoval N, Treangen TJ, Moraes-Vieira PM, Vanderburg C, Wallace DC, Schisler J, Mason CE, Chatterjee A, Meller R, Beheshti A. McDonald JT, et al. Among authors: treangen tj. bioRxiv [Preprint]. 2021 Aug 18:2021.04.23.441024. doi: 10.1101/2021.04.23.441024. bioRxiv. 2021. Update in: Cell Rep. 2021 Oct 19;37(3):109839. doi: 10.1016/j.celrep.2021.109839 PMID: 33948587 Free PMC article. Updated. Preprint.
Next generation sequence assembly with AMOS.
Treangen TJ, Sommer DD, Angly FE, Koren S, Pop M. Treangen TJ, et al. Curr Protoc Bioinformatics. 2011 Mar;Chapter 11:Unit 11.8. doi: 10.1002/0471250953.bi1108s33. Curr Protoc Bioinformatics. 2011. PMID: 21400694 Free PMC article.
Bambus 2: scaffolding metagenomes.
Koren S, Treangen TJ, Pop M. Koren S, et al. Among authors: treangen tj. Bioinformatics. 2011 Nov 1;27(21):2964-71. doi: 10.1093/bioinformatics/btr520. Epub 2011 Sep 16. Bioinformatics. 2011. PMID: 21926123 Free PMC article.
100 results