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Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.
Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB; Yale SARS-CoV-2 Genomic Surveillance Initiative; Hanage WP, Grubaugh ND, Peccia J, Baym M. Baaijens JA, et al. Among authors: baym m. Genome Biol. 2022 Nov 8;23(1):236. doi: 10.1186/s13059-022-02805-9. Genome Biol. 2022. PMID: 36348471 Free PMC article.
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing.
Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O'Grady J, Baym M, Hanage WP. Břinda K, et al. Among authors: baym m. Nat Microbiol. 2020 Mar;5(3):455-464. doi: 10.1038/s41564-019-0656-6. Epub 2020 Feb 10. Nat Microbiol. 2020. PMID: 32042129 Free PMC article.
Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.
Baaijens JA, Zulli A, Ott IM, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen BB; Yale SARS-CoV-2 Genomic Surveillance Initiative; Hanage WP, Grubaugh ND, Peccia J, Baym M. Baaijens JA, et al. Among authors: baym m. medRxiv [Preprint]. 2021 Sep 2:2021.08.31.21262938. doi: 10.1101/2021.08.31.21262938. medRxiv. 2021. PMID: 34494031 Free PMC article. Updated. Preprint.
Diverse and abundant phages exploit conjugative plasmids.
Quinones-Olvera N, Owen SV, McCully LM, Marin MG, Rand EA, Fan AC, Martins Dosumu OJ, Paul K, Sanchez Castaño CE, Petherbridge R, Paull JS, Baym M. Quinones-Olvera N, et al. Among authors: baym m. bioRxiv [Preprint]. 2023 Dec 21:2023.03.19.532758. doi: 10.1101/2023.03.19.532758. bioRxiv. 2023. PMID: 36993299 Free PMC article. Updated. Preprint.
The bacterial toxin colibactin triggers prophage induction.
Silpe JE, Wong JWH, Owen SV, Baym M, Balskus EP. Silpe JE, et al. Among authors: baym m. Nature. 2022 Mar;603(7900):315-320. doi: 10.1038/s41586-022-04444-3. Epub 2022 Feb 23. Nature. 2022. PMID: 35197633 Free PMC article.
Mycobacterial nucleoid-associated protein Lsr2 is required for productive mycobacteriophage infection.
Dulberger CL, Guerrero-Bustamante CA, Owen SV, Wilson S, Wuo MG, Garlena RA, Serpa LA, Russell DA, Zhu J, Braunecker BJ, Squyres GR, Baym M, Kiessling LL, Garner EC, Rubin EJ, Hatfull GF. Dulberger CL, et al. Among authors: baym m. Nat Microbiol. 2023 Apr;8(4):695-710. doi: 10.1038/s41564-023-01333-x. Epub 2023 Feb 23. Nat Microbiol. 2023. PMID: 36823286 Free PMC article.
37 results