Zobrazeno 1 - 10
of 145
pro vyhledávání: '"Christina Boucher"'
Publikováno v:
Algorithms for Molecular Biology, Vol 19, Iss 1, Pp 1-14 (2024)
Abstract FM-indexes are crucial data structures in DNA alignment, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer [1] observed in 2007 that word-based indexes often use fewer
Externí odkaz:
https://doaj.org/article/5d545f4b58b649eaad33789914714512
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-15 (2023)
Abstract Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-class classification using a novel
Externí odkaz:
https://doaj.org/article/beed168329644a80b28abeb68de43d92
Autor:
Ilya B. Slizovskiy, Marco Oliva, Jonathen K. Settle, Lidiya V. Zyskina, Mattia Prosperi, Christina Boucher, Noelle R. Noyes
Publikováno v:
Microbiome, Vol 10, Iss 1, Pp 1-24 (2022)
Abstract Background Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full geno
Externí odkaz:
https://doaj.org/article/d5dfa1529441450bbc40f8fc1d41287b
Publikováno v:
Frontiers in Microbiology, Vol 14 (2023)
Characterization of antibiotic resistance genes (ARGs) from high-throughput sequencing data of metagenomics and cultured bacterial samples is a challenging task, with the need to account for both computational (e.g., string algorithms) and biological
Externí odkaz:
https://doaj.org/article/b8d723e56d6d4f91a59ba0acf7f7e4d9
Autor:
Sarah Morrison-Smith, Christina Boucher, Aleksandra Sarcevic, Noelle Noyes, Catherine O’Brien, Nazaret Cuadros, Jaime Ruiz
Publikováno v:
Humanities & Social Sciences Communications, Vol 9, Iss 1, Pp 1-9 (2022)
Abstract Biological and biomedical research is increasingly conducted in large, interdisciplinary collaborations to address problems with significant societal impact, such as reducing antibiotic resistance, identifying disease sub-types, and identify
Externí odkaz:
https://doaj.org/article/e02d1ced804d4ea5ae42125e5a804d37
Autor:
Gowri Nayar, Ignacio Terrizzano, Ed Seabolt, Akshay Agarwal, Christina Boucher, Jaime Ruiz, Ilya B. Slizovskiy, James H. Kaufman, Noelle R. Noyes
Publikováno v:
Frontiers in Genetics, Vol 13 (2022)
Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of c
Externí odkaz:
https://doaj.org/article/e92efee6dede40778680f04fcac97b5b
Publikováno v:
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-10 (2021)
Abstract Background Identification of motifs and quantification of their occurrences are important for the study of genetic diseases, gene evolution, transcription sites, and other biological mechanisms. Exact formulae for estimating count distributi
Externí odkaz:
https://doaj.org/article/94c2fa9f8f344d28bca92966ce920c5a
Publikováno v:
Frontiers in Bioengineering and Biotechnology, Vol 10 (2022)
Nanopore technology enables portable, real-time sequencing of microbial populations from clinical and ecological samples. An emerging healthcare application for Nanopore includes point-of-care, timely identification of antibiotic resistance genes (AR
Externí odkaz:
https://doaj.org/article/e4e07e6697954b70b571a3d2df17b96e
Publikováno v:
Algorithms for Molecular Biology, Vol 16, Iss 1, Pp 1-13 (2021)
Abstract Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately
Externí odkaz:
https://doaj.org/article/80b0f04e524b408baa746d115960e3ca
Publikováno v:
Computational and Structural Biotechnology Journal, Vol 19, Iss , Pp 4067-4078 (2021)
Motivation: The de Bruijn graph has become a ubiquitous graph model for biological data ever since its initial introduction in the late 1990s. It has been used for a variety of purposes including genome assembly (Zerbino and Birney, 2008; Bankevich e
Externí odkaz:
https://doaj.org/article/d09103a281304b56a7b353dbcea9853d