Results 21 to 30 of about 273,042 (329)

Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies [PDF]

PeerJ, 2023
Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area.
Johan Rollin, Rachelle Bester, Yves Brostaux, Kadriye Çağlayan, Kris De Jonghe, Aleš Eichmeier, Yoika Foucart, Annelies Haegeman, Igor Koloniuk, Petr Komínek, Hans J. Maree, Serkan Önder, Susana Posada-Céspedes, Vahid Roumi, Dana Šafářová, Olivier Schumpp, Çiğdem Ulubaş Serçe, Merike Sõmera, Lucie Tamisier, Eeva J. Vainio, R.A.A. van der Vlugt, Sébastien Massart   +21 more
openalex   +11 more sources

Rapid, High-Throughput Identification of Anthrax-Causing and Emetic Bacillus cereus Group Genome Assemblies via BTyper, a Computational Tool for Virulence-Based Classification of Bacillus cereus Group Isolates by Using Nucleotide Sequencing Data

Applied and Environmental Microbiology, 2017
The Bacillus cereus group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, but it can be particularly challenging ...
Laura M. Carroll, Jasna Kovač, Rachel A. Miller, Martin Wiedmann   +3 more
openalex   +2 more sources

Evaluation of a High-Throughput Dense Single-Nucleotide Polymorphism PCR Multiplex Next Generation Sequencing Application for Human Remains Identification

Forensic Genomics, 2023
Sarah Radecke, Joana Antunes, June Snedecor, Clare Zlatkov, Laurence Devesse, Gothami Padmabandu, Kathryn M. Stephens   +6 more
openalex   +2 more sources

A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations [PDF]

Viruses, 2020
High-throughput sequencing such as those provided by Illumina are an efficient way to understand sequence variation within viral populations. However, challenges exist in distinguishing process-introduced error from biological variance, which significantly impacts our ability to identify sub-consensus single-nucleotide variants (SNVs).
David J. King, Graham Freimanis, Lidia Lasecka‐Dykes, Amin S. Asfor, Paolo Ribeca, Ryan Waters, Donald P. King, Emma Laing   +7 more
openalex   +5 more sources

High, clustered, nucleotide diversity in the genome of Anopheles gambiae revealed through pooled-template sequencing: implications for high-throughput genotyping protocols [PDF]

BMC Genomics, 2009
Association mapping approaches are dependent upon discovery and validation of single nucleotide polymorphisms (SNPs). To further association studies in Anopheles gambiae we conducted a major resequencing programme, primarily targeting regions within or close to candidate genes for insecticide resistance.Using two pools of mosquito template DNA we ...
Craig S. Wilding, David Weetman, Keith Steen, Martin J. Donnelly   +3 more
openalex   +6 more sources

Microbiome Analysis Using Next-Generation Sequencing in Urinary Tract Infections [PDF]

Urogenital Tract Infection, 2022
In recent decades, the understanding of the genetic information of microbes and hosts has advanced considerably with the development of next-generation sequencing (NGS).
Hyunho Han, Joo Yong Lee
doaj   +1 more source

Selection of optimal bioinformatic tools and proper reference for reducing the alignment error in targeted sequencing data

Journal of Medical Signals and Sensors, 2021
Background: Careful design in the primary steps of a next-generation sequencing study is critical for obtaining successful results in downstream analysis.
Hannane Mohammadi Nodehi, Mohammad Amin Tabatabaiefar, Mohammadreza Sehhati   +2 more
doaj   +1 more source

Microbiome profiling by Illumina sequencing of combinatorial sequence-tagged PCR products [PDF]

, 2010
We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region.
A Chao, A Chao, A Mortazavi, A Nocker, AF Andersson, Andrew D. Fernandes, B Efron, C Camacho, C Quince, CL Lauber, DA Benson, DJG Lahr, DN Frank, DR Bentley, DR Smith, EP Smith, Frank R. DeLeo, Gregor Reid, Gregory B. Gloor, J Oksanen, J Pawlowski, J Ravel, J Reeder, J Schellenberg, Jean M. Macklaim, JF Petrosino, JG Caporaso, JR Cole, LA Amaral-Zettler, M Hamady, N Whiteford, PJA Cock, PN Polymenakou, R Colwell, R Hummelen, Roderick MacPhee, Ruben Hummelen, Russell J. Dickson, S Hurlbert, S Rodrigue, S Srinivasan, SF Altschul, SF Altschul, SM Huse, V Laurikari, WR Engels, Y Shi, Y Wang   +47 more
core   +13 more sources

Gene expression profile of Scardovia spp. in the metatranscriptome of root caries [PDF]

Brazilian Oral Research, 2020
A few investigations of caries biofilms have identified Scardovia spp.; however, little is known about its involvement in caries pathogenesis. The purpose of this study was to assess the gene expression profile of Scardovia spp.
Naile DAMÉ-TEIXEIRA, Clarissa Cavalcanti Fatturi PAROLO, Marisa MALZ, Deirdre Ann DEVINE, Thuy DO   +4 more
doaj   +2 more sources

Analytical Tools and Databases for Metagenomics in the Next-Generation Sequencing Era [PDF]

Genomics & Informatics, 2013
Metagenomics has become one of the indispensable tools in microbial ecology for the last few decades, and a new revolution in metagenomic studies is now about to begin, with the help of recent advances of sequencing techniques.
Mincheol Kim, Ki-Hyun Lee, Seok-Whan Yoon, Bong-Soo Kim, Jongsik Chun, Hana Yi   +5 more
doaj   +1 more source