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Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.
Lagerborg KA, Normandin E, Bauer MR, Adams G, Figueroa K, Loreth C, Gladden-Young A, Shaw BM, Pearlman LR, Berenzy D, Dewey HB, Kales S, Dobbins ST, Shenoy ES, Hooper D, Pierce VM, Zachary KC, Park DJ, MacInnis BL, Tewhey R, Lemieux JE, Sabeti PC, Reilly SK, Siddle KJ. Lagerborg KA, et al. Among authors: lemieux je. Nat Microbiol. 2022 Jan;7(1):108-119. doi: 10.1038/s41564-021-01019-2. Epub 2021 Dec 14. Nat Microbiol. 2022. PMID: 34907347 Free PMC article.
A global map of genetic diversity in Babesia microti reveals strong population structure and identifies variants associated with clinical relapse.
Lemieux JE, Tran AD, Freimark L, Schaffner SF, Goethert H, Andersen KG, Bazner S, Li A, McGrath G, Sloan L, Vannier E, Milner D, Pritt B, Rosenberg E, Telford S 3rd, Bailey JA, Sabeti PC. Lemieux JE, et al. Nat Microbiol. 2016 Jun 13;1(7):16079. doi: 10.1038/nmicrobiol.2016.79. Nat Microbiol. 2016. PMID: 27572973 Free PMC article.
Rapid Detection of Powassan Virus in a Patient With Encephalitis by Metagenomic Sequencing.
Piantadosi A, Kanjilal S, Ganesh V, Khanna A, Hyle EP, Rosand J, Bold T, Metsky HC, Lemieux J, Leone MJ, Freimark L, Matranga CB, Adams G, McGrath G, Zamirpour S, Telford S 3rd, Rosenberg E, Cho T, Frosch MP, Goldberg MB, Mukerji SS, Sabeti PC. Piantadosi A, et al. Clin Infect Dis. 2018 Feb 10;66(5):789-792. doi: 10.1093/cid/cix792. Clin Infect Dis. 2018. PMID: 29020227 Free PMC article.
Development of a SNP barcode to genotype Babesia microti infections.
Baniecki ML, Moon J, Sani K, Lemieux JE, Schaffner SF, Sabeti PC. Baniecki ML, et al. Among authors: lemieux je. PLoS Negl Trop Dis. 2019 Mar 25;13(3):e0007194. doi: 10.1371/journal.pntd.0007194. eCollection 2019 Mar. PLoS Negl Trop Dis. 2019. PMID: 30908478 Free PMC article.
Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2.
Arizti-Sanz J, Freije CA, Stanton AC, Boehm CK, Petros BA, Siddiqui S, Shaw BM, Adams G, Kosoko-Thoroddsen TF, Kemball ME, Gross R, Wronka L, Caviness K, Hensley LE, Bergman NH, MacInnis BL, Lemieux JE, Sabeti PC, Myhrvold C. Arizti-Sanz J, et al. Among authors: lemieux je. bioRxiv [Preprint]. 2020 May 28:2020.05.28.119131. doi: 10.1101/2020.05.28.119131. bioRxiv. 2020. PMID: 32511415 Free PMC article. Updated. Preprint.
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.
Yurkovetskiy L, Wang X, Pascal KE, Tomkins-Tinch C, Nyalile T, Wang Y, Baum A, Diehl WE, Dauphin A, Carbone C, Veinotte K, Egri SB, Schaffner SF, Lemieux JE, Munro J, Rafique A, Barve A, Sabeti PC, Kyratsous CA, Dudkina N, Shen K, Luban J. Yurkovetskiy L, et al. Among authors: lemieux je. bioRxiv [Preprint]. 2020 Jul 15:2020.07.04.187757. doi: 10.1101/2020.07.04.187757. bioRxiv. 2020. PMID: 32637944 Free PMC article. Updated. Preprint.
Phylogenetic analysis of SARS-CoV-2 in the Boston area highlights the role of recurrent importation and superspreading events.
Lemieux JE, Siddle KJ, Shaw BM, Loreth C, Schaffner SF, Gladden-Young A, Adams G, Fink T, Tomkins-Tinch CH, Krasilnikova LA, DeRuff KC, Rudy M, Bauer MR, Lagerborg KA, Normandin E, Chapman SB, Reilly SK, Anahtar MN, Lin AE, Carter A, Myhrvold C, Kemball ME, Chaluvadi S, Cusick C, Flowers K, Neumann A, Cerrato F, Farhat M, Slater D, Harris JB, Branda J, Hooper D, Gaeta JM, Baggett TP, O'Connell J, Gnirke A, Lieberman TD, Philippakis A, Burns M, Brown CM, Luban J, Ryan ET, Turbett SE, LaRocque RC, Hanage WP, Gallagher GR, Madoff LC, Smole S, Pierce VM, Rosenberg E, Sabeti PC, Park DJ, Maclnnis BL. Lemieux JE, et al. medRxiv [Preprint]. 2020 Aug 25:2020.08.23.20178236. doi: 10.1101/2020.08.23.20178236. medRxiv. 2020. PMID: 32869040 Free PMC article. Updated. Preprint.
Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay.
Anahtar MN, Shaw B, Slater D, Byrne E, Botti-Lodovico Y, Adams G, Schaffner S, Eversley J, McGrath G, Gogakos T, Lennerz J, Desai Marble H, Ritterhouse LL, Batten J, Georgantas NZ, Pellerin R, Signorelli S, Thierauf J, Kemball M, Happi C, Grant DS, Ndiaye D, Siddle KJ, Mehta SB, Harris J, Ryan ET, Pierce V, LaRocque R, Lemieux JE, Sabeti P, Rosenberg E, Branda J, Turbett SE. Anahtar MN, et al. Among authors: lemieux je. medRxiv [Preprint]. 2020 Sep 1:2020.08.26.20157297. doi: 10.1101/2020.08.26.20157297. medRxiv. 2020. PMID: 32909014 Free PMC article. Updated. Preprint.
Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant.
Yurkovetskiy L, Wang X, Pascal KE, Tomkins-Tinch C, Nyalile TP, Wang Y, Baum A, Diehl WE, Dauphin A, Carbone C, Veinotte K, Egri SB, Schaffner SF, Lemieux JE, Munro JB, Rafique A, Barve A, Sabeti PC, Kyratsous CA, Dudkina NV, Shen K, Luban J. Yurkovetskiy L, et al. Among authors: lemieux je. Cell. 2020 Oct 29;183(3):739-751.e8. doi: 10.1016/j.cell.2020.09.032. Epub 2020 Sep 15. Cell. 2020. PMID: 32991842 Free PMC article.
76 results