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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. Nat Commun. 2024 Apr 12;15(1):3197. doi: 10.1038/s41467-024-47416-z. Nat Commun. 2024. PMID: 38609370 Free PMC article.
Analysis of the limited M. tuberculosis accessory genome reveals potential pitfalls of pan-genome analysis approaches.
Marin MG, Wippel C, Quinones-Olvera N, Behruznia M, Jeffrey BM, Harris M, Mann BC, Rosenthal A, Jacobson KR, Warren RM, Li H, Meehan CJ, Farhat MR. Marin MG, et al. Among authors: quinones olvera n. bioRxiv [Preprint]. 2024 May 4:2024.03.21.586149. doi: 10.1101/2024.03.21.586149. bioRxiv. 2024. PMID: 38585972 Free PMC article. Preprint.
Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.
Břinda K, Lima L, Pignotti S, Quinones-Olvera N, Salikhov K, Chikhi R, Kucherov G, Iqbal Z, Baym M. Břinda K, et al. Among authors: quinones olvera n. bioRxiv [Preprint]. 2023 Apr 18:2023.04.15.536996. doi: 10.1101/2023.04.15.536996. bioRxiv. 2023. PMID: 37131636 Free PMC article. 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. 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.
Prophages encode phage-defense systems with cognate self-immunity.
Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Owen SV, et al. Among authors: quinones olvera n. Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8. doi: 10.1016/j.chom.2021.09.002. Epub 2021 Sep 30. Cell Host Microbe. 2021. PMID: 34597593 Free PMC article.
Non-Coding RNA Analysis Using the Rfam Database.
Kalvari I, Nawrocki EP, Argasinska J, Quinones-Olvera N, Finn RD, Bateman A, Petrov AI. Kalvari I, et al. Among authors: quinones olvera n. Curr Protoc Bioinformatics. 2018 Jun;62(1):e51. doi: 10.1002/cpbi.51. Epub 2018 Jun 5. Curr Protoc Bioinformatics. 2018. PMID: 29927072 Free PMC article.
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families.
Kalvari I, Argasinska J, Quinones-Olvera N, Nawrocki EP, Rivas E, Eddy SR, Bateman A, Finn RD, Petrov AI. Kalvari I, et al. Among authors: quinones olvera n. Nucleic Acids Res. 2018 Jan 4;46(D1):D335-D342. doi: 10.1093/nar/gkx1038. Nucleic Acids Res. 2018. PMID: 29112718 Free PMC article.