Zobrazeno 1 - 10
of 18
pro vyhledávání: '"Karel Břinda"'
Publikováno v:
Microbiome, Vol 10, Iss 1, Pp 1-16 (2022)
Abstract Background Our interconnected world and the ability of bacteria to quickly swap antibiotic resistance genes (ARGs) make it particularly important to establish the epidemiological links of multidrug resistance (MDR) transfer between wastewate
Externí odkaz:
https://doaj.org/article/2107f4be71c8489da55d8128fe74c506
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-24 (2021)
Abstract de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable representation, and ProphAsm, a fast algorithm for their comput
Externí odkaz:
https://doaj.org/article/d577f3a473874b568592374e10d3cd10
Autor:
Karel Břinda
Publikováno v:
Electronic Proceedings in Theoretical Computer Science, Vol 151, Iss Proc. AFL 2014, Pp 139-150 (2014)
Several algorithms for similarity search employ seeding techniques to quickly discard very dissimilar regions. In this paper, we study theoretical properties of lossless seeds, i.e., spaced seeds having full sensitivity. We prove that lossless seeds
Externí odkaz:
https://doaj.org/article/ddc87189fccc48a0b6b03e4d029e2a95
Autor:
Karel Břinda, Leandro Lima, Simone Pignotti, Natalia Quinones-Olvera, Kamil Salikhov, Rayan Chikhi, Gregory Kucherov, Zamin Iqbal, Michael Baym
Publikováno v:
bioRxiv
Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections makes it effectively impossible to search these data using tools such as
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0bc0ba595790ea10d788f64e03734f2d
https://europepmc.org/articles/PMC10153118/
https://europepmc.org/articles/PMC10153118/
The popularity ofk-mer-based methods has recently led to the development of compactk-mer-set representations, such as simplitigs/Spectrum-Preserving String Sets (SPSS), matchtigs, and eulertigs. These aim to representk-mer sets via strings that conta
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b506f4311ab0fbf42efc8fd87d8e3c91
https://doi.org/10.1101/2023.02.01.526717
https://doi.org/10.1101/2023.02.01.526717
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-24 (2021)
Genome Biology
Genome Biology, BioMed Central, 2021, 22 (96), ⟨10.1101/2020.01.12.903443⟩
Genome Biology
Genome Biology, BioMed Central, 2021, 22 (96), ⟨10.1101/2020.01.12.903443⟩
Motivation: De Bruijn graphs play an essential role in computational biology, facilitating rapid alignment-free comparison of genomic datasets as well as reconstruction of underlying genomic sequences. Subsequently, an important question is how to ef
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0907443d111fdd111fe4ca5bab4734e3
https://doaj.org/article/d577f3a473874b568592374e10d3cd10
https://doaj.org/article/d577f3a473874b568592374e10d3cd10
Publikováno v:
Proc Natl Acad Sci U S A
We thank Liam Shaw for his letter (1), “Null models for gene enrichment in plasmids,” and appreciate the detailed simulation regarding the enrichment analysis of AMR genes on different types of plasmids, which confirms our original conclusions th
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3af9c2d184782aaff04286aed3eaf6e0
https://pubmed.ncbi.nlm.nih.gov/33975907
https://pubmed.ncbi.nlm.nih.gov/33975907
Publikováno v:
Proc Natl Acad Sci U S A
It is well established that plasmids play an important role in the dissemination of antimicrobial resistance (AMR) genes; however, little is known about the role of the underlying interactions between different plasmid categories and other mobile gen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::056c6caf2d9d74894a649174f8ec2698
https://doi.org/10.1073/pnas.2008731118
https://doi.org/10.1073/pnas.2008731118
Autor:
Marc Lipsitch, Samira Mubareka, Roberto G. Melano, Karel Břinda, Derek R. MacFadden, William P. Hanage, Allison McGeer, Nick Daneman, Antoine Corbeil, Robyn S Lee, Bryan Coburn, David N. Fisman
Publikováno v:
Antimicrobial Agents and Chemotherapy
The rising rates of antibiotic resistance increasingly compromise empirical treatment. Knowing the antibiotic susceptibility of a pathogen’s close genetic relative(s) may improve empirical antibiotic selection. Using genomic and phenotypic data for
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::778c6ab54058c59a9a40ab885a0f411e
http://europepmc.org/articles/PMC7179619
http://europepmc.org/articles/PMC7179619
Autor:
Robyn S Lee, Gregory Kucherov, Kevin C. Ma, Derek R. MacFadden, Themoula Charalampous, Karel Břinda, Michael H. Baym, Crista B. Wadsworth, Lauren A. Cowley, William P. Hanage, Yonatan H. Grad, Justin O'Grady, Alanna Callendrello
Publikováno v:
Nature Microbiology
Nature Microbiology, Nature Publishing Group, 2020, ⟨10.1038/s41564-019-0656-6⟩
Nature Microbiology, Nature Publishing Group, 2020, ⟨10.1038/s41564-019-0656-6⟩
Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::625bcf0e63186572ea763c0ce5f0fcdf
https://hal.archives-ouvertes.fr/hal-02416034/document
https://hal.archives-ouvertes.fr/hal-02416034/document