Browsing Genetics by Subject "Whole genome sequencing (WGS)"

Now showing items 1-12 of 12

The benefits of whole genome sequencing for foodborne outbreak investigation from the perspective of a National Reference laboratory in a smaller country

Nouws, Stephanie; Bogaerts, Bert; Verhaegen, Bavo; Denayer, Sarah; Crombe, Florence; De Rauw, Klara; Pierard, Denis; Marchal, Kathleen; Vanneste, Kevin; Roosens, Nancy H.C.; De Keersmaecker, Sigrid C.J. (MDPI, 2020-08-01)

Gradually, conventional methods for foodborne pathogen typing are replaced by whole genome sequencing (WGS). Despite studies describing the overall benefits, National Reference Laboratories of smaller countries often ...
Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:-

Saltykova, Assia; Wuyts, Veronique; Mattheus, Wesley; Bertrand, Sophie; Roosens, Nancy H.C.; Marchal, Kathleen; De Keersmaecker, Sigrid C.J. (Public Library of Science, 2018-02-06)

Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable ...
Complete genome sequence and epigenetic profile of Bacillus velezensis UCMB5140 used for plant and crop protection in comparison with other plant-associated Bacillus strains

Reva, Oleg N.; Larisa, Safronova A.; Mwakilili, Aneth D.; Tibuhwa, Donatha; Lyantagaye, Sylvester; Chan, Wai Yin; Lutz, Stefanie; Ahrens, Christian H.; Vater, Joachim; Borriss, Rainer (Springer, 2020-09)

The application of biocontrol biopesticides based on plant growth–promoting rhizobacteria (PGPR), particularly members of the genus Bacillus, is considered a promising perspective to make agricultural practices sustainable ...
A de novo 2.2 Mb recurrent 17q23.1q23.2 deletion unmasks novel putative regulatory non-coding SNVs associated with lethal lung hypoplasia and pulmonary hypertension : a case report

Karolak, Justyna A.; Gambin, Tomasz; Honey, Engela M.; Slavik, Tomas; Popek, Edwina; Stankiewicz, Paweł (BioMed Central, 2020-03-06)

BACKGROUND : Application of whole genome sequencing (WGS) enables identification of non-coding variants that play a phenotype-modifying role and are undetectable by exome sequencing. Recently, non-coding regulatory single ...
Genome and metabolome ms-based mining of a marine strain of Aspergillus affinis

Gonçalves, Micael F. M.; Hilario, Sandra; Tacao, Marta; Van de Peer, Yves; Alves, Artur; Esteves, Ana C. (MDPI, 2021-12)

Aspergillus section Circumdati encompasses several species that express both beneficial (e.g., biochemical transformation of steroids and alkaloids, enzymes and metabolites) and harmful compounds (e.g., production of ...
Genomic and metabolomic analyses of the marine fungus Emericellopsis cladophorae: insights into saltwater adaptability mechanisms and its biosynthetic potential

Goncalves, Micael; Hilario, Sandra; Van de Peer, Yves; Esteves, Ana; Alves, Artur (MDPI, 2022-01)

The genus Emericellopsis is found in terrestrial, but mainly in marine, environments with a worldwide distribution. Although Emericellopsis has been recognized as an important source of bioactive compounds, the range of ...
Impact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin‑producing Escherichia coli isolates

Nouws, Stephanie; Bogaerts, Bert; Verhaegen, Bavo; Denayer, Sarah; Pierard, Denis; Marchal, Kathleen; Roosens, Nancy H.C.; Vanneste, Kevin; De Keersmaecker, Sigrid C.J. (Nature Publishing Group, 2020-09-04)

Whole genome sequencing (WGS) has proven to be the ultimate tool for bacterial isolate characterization and relatedness determination. However, standardized and harmonized workflows, e.g. for DNA extraction, are required ...
Phylogenomic structure of Bacillus anthracis isolates in the Northern Cape Province, South Africa revealed novel single nucleotide polymorphisms

Lekota, Kgaugelo Edward; Hassim, Ayesha; Madoroba, Evelyn; Hefer, Charles A.; Van Heerden, Henriette (Elsevier, 2020-06)

Bacillus anthracis, the aetiological agent of anthrax, is regarded as a highly monomorphic pathogen that presents a low genetic diversity using standard molecular techniques. Whole genome sequencing and single nucleotide ...
A practical method to implement strain-level metagenomics-based foodborne outbreak investigation and source tracking in routine

Buytaers, Florence E.; Saltykova, Assia; Denayer, Sarah; Verhaegen, Bavo; Vanneste, Kevin; Roosens, Nancy H.C.; Pierard, Denis; Marchal, Kathleen; De Keersmaecker, Sigrid C.J. (MDPI, 2020-08-05)

The management of a foodborne outbreak depends on the rapid and accurate identification of the responsible food source. Conventional methods based on isolation of the pathogen from the food matrix and target-specific ...
Resistance sniffer : an online tool for prediction of drug resistance patterns of Mycobacterium tuberculosis isolates using next generation sequencing data

Muzondiwa, Dillon; Mutshembele, Awelani; Pierneef, Rian Ewald; Reva, Oleg N. (Elsevier, 2020-02)

The effective control of multidrug resistant tuberculosis (MDR-TB) relies upon the timely diagnosis and correct treatment of all tuberculosis cases. Whole genome sequencing (WGS) has great potential as a method for ...
syntenet : an R/Bioconductor package for the inference and analysis of synteny networks

Almeida-Silva, Fabricio; Zhao, Tao; Ullrich, Kristian K.; Schranz, M. Eric; Van de Peer, Yves (Oxford University Press, 2023-01)

Interpreting and visualizing synteny relationships across several genomes is a challenging task. We previously proposed a network-based approach for better visualization and interpretation of large-scale microsynteny ...
Virulence and antimicrobial resistance genes are enriched in the plasmidome of clinical Escherichia coli isolates compared with wastewater isolates from western Kenya

Wawire, Sifuna Anthony; Reva, Oleg N.; O'Brien, Thomas J.; Figueroa, Wendy; Dinda, Victor; Shivoga, William A.; Welch, Martin (Elsevier, 2021-07)

Many low-middle income countries in Africa have poorly-developed infectious disease monitoring systems. Here, we employed whole genome sequencing (WGS) to investigate the presence/absence of antimicrobial resistance (AMR) ...

Now showing items 1-12 of 12

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Browsing Genetics by Subject "Whole genome sequencing (WGS)"

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