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Page 1
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection.
Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau A, Dodson KW, Schreiber HL 4th, Manson AL, Hultgren SJ, Earl AM. Young MG, et al. Among authors: van dijk lr. bioRxiv [Preprint]. 2024 Jun 1:2024.02.29.582780. doi: 10.1101/2024.02.29.582780. bioRxiv. 2024. Update in: Nat Commun. 2024 Nov 2;15(1):9466. doi: 10.1038/s41467-024-53829-7 PMID: 38463963 Free PMC article. Updated. Preprint.
Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women.
Worby CJ, Schreiber HL 4th, Straub TJ, van Dijk LR, Bronson RA, Olson BS, Pinkner JS, Obernuefemann CLP, Muñoz VL, Paharik AE, Azimzadeh PN, Walker BJ, Desjardins CA, Chou WC, Bergeron K, Chapman SB, Klim A, Manson AL, Hannan TJ, Hooton TM, Kau AL, Lai HH, Dodson KW, Hultgren SJ, Earl AM. Worby CJ, et al. Among authors: van dijk lr. Nat Microbiol. 2022 May;7(5):630-639. doi: 10.1038/s41564-022-01107-x. Epub 2022 May 2. Nat Microbiol. 2022. PMID: 35505248 Free PMC article.
Strain tracking with uncertainty quantification.
Kim Y, Worby CJ, Acharya S, van Dijk LR, Alfonsetti D, Gromko Z, Azimzadeh P, Dodson K, Gerber G, Hultgren S, Earl AM, Berger B, Gibson TE. Kim Y, et al. Among authors: van dijk lr. bioRxiv [Preprint]. 2024 Jul 23:2023.01.25.525531. doi: 10.1101/2023.01.25.525531. bioRxiv. 2024. PMID: 36747646 Free PMC article. Preprint.
Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection.
Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau A, Dodson KW, Schreiber HL 4th, Manson AL, Hultgren SJ, Earl AM. Young MG, et al. Among authors: van dijk lr. Nat Commun. 2024 Nov 2;15(1):9466. doi: 10.1038/s41467-024-53829-7. Nat Commun. 2024. PMID: 39487120 Free PMC article.
Fast exact gap-affine partial order alignment with POASTA.
van Dijk LR, Manson AL, Earl AM, Garimella KV, Abeel T. van Dijk LR, et al. Bioinformatics. 2025 Jan 3:btae757. doi: 10.1093/bioinformatics/btae757. Online ahead of print. Bioinformatics. 2025. PMID: 39752324