Results 21 to 30 of about 140,626 (267)

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

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   +9 more sources

High-throughput single nucleotide polymorphism (SNP) identification and mapping in the sesame (Sesamum indicum L.) genome with genotyping by sequencing (GBS) analysis [PDF]

Molecular Breeding, 2016
Sesame (Sesamum indicum L. syn. Sesamum orientale L.) is considered to be the first oil seed crop known to man. Despite its versatile use as an oil seed and a leafy vegetable, sesame is a neglected crop and has not been a subject of molecular genetic research until the last decade.
Ayşe Özgür Uncu, Anne Frary, Petr Karlovský, Sami Doğanlar   +3 more
openalex   +6 more sources

Targeted Amplicon Sequencing for Single-Nucleotide-Polymorphism Genotyping of Attaching and Effacing Escherichia coli O26:H11 Cattle Strains via a High-Throughput Library Preparation Technique [PDF]

Applied and Environmental Microbiology, 2015
ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) O26:H11, a serotype within Shiga toxin-producing E. coli (STEC) that causes severe human disease, has been considered to have evolved from attaching and effacing E. coli (AEEC) O26:H11 through the acquisition
Sarah A. Ison, Sabine Delannoy, Marie Bugarel, T. G. Nagaraja, David G. Renter, Henk C. den Bakker, Kendra K. Nightingale, Patrick Fach, Guy H. Loneragan   +8 more
openalex   +5 more sources

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 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

Utilization of high throughput genome sequencing technology for large scale single nucleotide polymorphism discovery in red deer and Canadian elk [PDF]

, 2015
ABSTRACTDeer farming is a significant international industry. For genetic improvement, using genomic tools, an ordered array of DNA variants and associated flanking sequence across the genome is required. This work reports a comparative assembly of the deer genome and subsequent DNA variant identification.
Rüdiger Bräuning, P. J. Fisher, Alan McCulloch, Russell J Smithies, James F Ward, Matthew J. Bixley, Cindy Lawley, Suzanne J. Rowe, John C. McEwan   +8 more
openalex   +3 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

High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses [PDF]

Genetics and Molecular Biology, 2015
The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4,
Yang, Seung Hak, Lim, Joung Soo, Khan, Modabber Ahmed, Kim, Bong Soo, Choi, Dong Yoon, Lee, Eun Young, Ahn, Hee Kwon   +6 more
openaire   +6 more sources

Optimization of conditions for in vitro modeling of subgingival normobiosis and dysbiosis

Frontiers in Microbiology, 2022
Modeling subgingival microbiome in health and disease is key to identifying the drivers of dysbiosis and to studying microbiome modulation. Here, we optimize growth conditions of our previously described in vitro subgingival microbiome model. Subgingival
Divyashri Baraniya, Thuy Do, Tsute Chen, Jasim M. Albandar, Susan M. Chialastri, Deirdre A. Devine, Philip D. Marsh, Nezar N. Al-Hebshi   +7 more
doaj   +1 more source