Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples.

Autor: James B Pettengill, Arthur W Pightling, Joseph D Baugher, Hugh Rand, Errol Strain

Publikováno v: PLoS ONE, Vol 11, Iss 11, p e0166162 (2016)

The adoption of whole-genome sequencing within the public health realm for molecular characterization of bacterial pathogens has been followed by an increased emphasis on real-time detection of emerging outbreaks (e.g., food-borne Salmonellosis). In

Externí odkaz: https://doaj.org/article/059b7dcaabce4f2686d04df5f0f6dcbe

An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis.

Autor: Shehre-Banoo Malik, Arthur W Pightling, Lauren M Stefaniak, Andrew M Schurko, John M Logsdon

Publikováno v: PLoS ONE, Vol 3, Iss 8, p e2879 (2007)

Meiosis is a defining feature of eukaryotes but its phylogenetic distribution has not been broadly determined, especially among eukaryotic microorganisms (i.e. protists)-which represent the majority of eukaryotic 'supergroups'. We surveyed genomes of

Externí odkaz: https://doaj.org/article/8e9b2dbdb2604fb0945e766cfbd64158

Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Autor: Arthur W. Pightling, James B. Pettengill, Yu Wang, Hugh Rand, Errol Strain

Publikováno v: Genome Biology, Vol 20, Iss 1, Pp 1-6 (2019)

Abstract Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogenetics, and multi-locus sequencing

Externí odkaz: https://doaj.org/article/2f919a58db87418dae5e7640757dc58a

A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing

Autor: Marco Fabbri, Valentina Paracchini, Henrik Westh, Mauro Petrillo, Paul Hammer, Barbara Raffael, Guy Van den Eede, Alexandre Angers-Loustau, Derya Aytan-Aktug, Alessandro Cestaro, Alice C. McHardy, Maddalena Querci, Christoph Endrullat, Catherine D. Carrillo, Silke Peter, Jean-Yves Madec, Erik Alm, John W. A. Rossen, Ivo Gut, Dafni-Maria Kagkli, Gemma L. Kay, Alison E. Mather, T. M. Coque, Kevin Vanneste, Thierry Naas, Kok-Gan Chan, Etienne Ruppé, Lukas M. Weber, Salvador Capella-Gutierrez, Robert Schlaberg, Arthur W. Pightling

Publikováno v: F1000Research, 10:80. F1000Research
Petrillo, M, Fabbri, M, Kagkli, D M, Querci, M, Van den Eede, G, Alm, E, Aytan, D, Capella-Gutierrez, S, Carrillo, C, Cestaro, A, Chan, K-G, Coque, T, Endrullat, C, Gut, I, Hammer, P, Kay, G L, Madec, J-Y, Mather, A E, McHardy, A C, Naas, T, Paracchini, V, Peter, S, Pightling, A, Raffael, B, Rossen, J, Ruppé, E, Schlaberg, R, Vanneste, K, Weber, L, Westh, H & Angers-Loustau, A 2021, ' A roadmap for the generation of benchmarking resources for antimicrobial resistance detection using next generation sequencing ', F1000Research, vol. 10, 80 . https://doi.org/10.12688/f1000research.39214.1

Next Generation Sequencing technologies significantly impact the field of Antimicrobial Resistance (AMR) detection and monitoring, with immediate uses in diagnosis and risk assessment. For this application and in general, considerable challenges rema

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::50c7dcf2caf2baa7d65a72af15dd1e82
https://research.rug.nl/en/publications/7fb855b6-5a63-4351-87fe-0fc0bc129525

Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Autor: Errol Strain, James B. Pettengill, Arthur W. Pightling, Yu Wang, Hugh Rand

Publikováno v: Genome Biology, Vol 20, Iss 1, Pp 1-6 (2019)
Genome Biology

Although it is assumed that contamination in bacterial whole-genome sequencing causes errors, the influences of contamination on clustering analyses, such as single-nucleotide polymorphism discovery, phylogenetics, and multi-locus sequencing typing,

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ddcb9d0450df29dfb9bda82231a436fb
https://doaj.org/article/2f919a58db87418dae5e7640757dc58a