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2004 1
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Consistency of Mycobacterium tuberculosis Complex Spoligotyping between the Membrane-Based Method and In Silico Approach.
Genestet C, Hodille E, Bernard A, Vallée M, Lina G, Le Meur A, Refrégier G, Dumitrescua O; Lyon TB study group. Genestet C, et al. Microbiol Spectr. 2022 Jun 29;10(3):e0022322. doi: 10.1128/spectrum.00223-22. Epub 2022 Apr 25. Microbiol Spectr. 2022. PMID: 35467406 Free PMC article.
Previous genotyping approaches, such as spoligotyping consisting of an initial PCR step followed by reverse dot hybridization, are currently being replaced by WGS. Several pipelines have been developed to extract a spoligotype from WGS data (in silico spoligotyping) allowi …
Previous genotyping approaches, such as spoligotyping consisting of an initial PCR step followed by reverse dot hybridization, are currently …
Development, Evaluation, and Implementation of a House-Made Targeted Next-Generation Sequencing Spoligotyping in a French Laboratory.
Genestet C, Baffert Y, Vallée M, Bernard A, Benito Y, Lina G, Hodille E, Dumitrescu O; Lyon TB Study Group. Genestet C, et al. Int J Mol Sci. 2022 Sep 25;23(19):11302. doi: 10.3390/ijms231911302. Int J Mol Sci. 2022. PMID: 36232601 Free PMC article.
The tNGS spoligotyping, whose thresholds were finely-tuned during a careful bioinformatics pipeline development process, appears be a technique that is reliable, inexpensive, free of handling errors, and automatable through automatic transfer into the laboratory computer s …
The tNGS spoligotyping, whose thresholds were finely-tuned during a careful bioinformatics pipeline development process, appears be a …
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation.
Charre C, Ginevra C, Sabatier M, Regue H, Destras G, Brun S, Burfin G, Scholtes C, Morfin F, Valette M, Lina B, Bal A, Josset L. Charre C, et al. Virus Evol. 2020 Oct 5;6(2):veaa075. doi: 10.1093/ve/veaa075. eCollection 2020 Jul. Virus Evol. 2020. PMID: 33318859 Free PMC article.
Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setting a high threshold to call SNP compared to reference sequence. ...
Just one mismatch in three samples was observed in CleanPlex vs the other methods, due to the dedicated bioinformatics pipeline setti …
Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.
Sreedharan VT, Schultheiss SJ, Jean G, Kahles A, Bohnert R, Drewe P, Mudrakarta P, Görnitz N, Zeller G, Rätsch G. Sreedharan VT, et al. Bioinformatics. 2014 May 1;30(9):1300-1. doi: 10.1093/bioinformatics/btt731. Epub 2014 Jan 11. Bioinformatics. 2014. PMID: 24413671 Free PMC article.
Its distinguishing features include customizable computational workflows and a modular pipeline architecture that facilitates comparative assessment of tool and data quality. ...
Its distinguishing features include customizable computational workflows and a modular pipeline architecture that facilitates compara …
Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort.
Xu J, Zhou P, Liu J, Zhao L, Fu H, Han Q, Wang L, Wu W, Ou Q, Ma Y, He J. Xu J, et al. Infect Dis Ther. 2023 Apr;12(4):1175-1187. doi: 10.1007/s40121-023-00790-5. Epub 2023 Mar 29. Infect Dis Ther. 2023. PMID: 36988865 Free PMC article.
CONCLUSION: Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort and strongly supports the notion that in clinical practice, mNGS represents a valuable supplementary tool to CTs to rapidly determine etiolo …
CONCLUSION: Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort …
The Swiss-Prot variant page and the ModSNP database: a resource for sequence and structure information on human protein variants.
Yip YL, Scheib H, Diemand AV, Gattiker A, Famiglietti LM, Gasteiger E, Bairoch A. Yip YL, et al. Hum Mutat. 2004 May;23(5):464-70. doi: 10.1002/humu.20021. Hum Mutat. 2004. PMID: 15108278
In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structures via an automatic homology modeling pipeline. Currently, among the 16,566 human SAPs recorded in the Swiss-Prot knowledgebase (relea …
In particular, the ModSNP database was set up to store information related to SAPs and to manage the modeling of SAPs onto protein structure …