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Table representation of search results timeline featuring number of search results per year.

Year Number of Results
1988 1
1989 1
1993 1
1995 1
1996 2
1997 2
1998 1
1999 5
2000 4
2001 10
2002 21
2003 23
2004 27
2005 47
2006 56
2007 56
2008 65
2009 57
2010 59
2011 94
2012 114
2013 120
2014 154
2015 193
2016 237
2017 244
2018 284
2019 350
2020 342
2021 33
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2,346 results
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PlasmidFinder and In Silico pMLST: Identification and Typing of Plasmid Replicons in Whole-Genome Sequencing (WGS).
Carattoli A, Hasman H. Carattoli A, et al. Methods Mol Biol. 2020;2075:285-294. doi: 10.1007/978-1-4939-9877-7_20. Methods Mol Biol. 2020. PMID: 31584170
PlasmidFinder and in silico plasmid multiLocus sequence typing (pMLST) are two easy-to-use web tools for detection and characterization of plasmid sequences in whole-genome sequencing (WGS) data from Enterobacteriaceae. ...PlasmidFinder i …
PlasmidFinder and in silico plasmid multiLocus sequence typing (pMLST) are two easy-to-use web tools for detection and charact …
In Silico Serotyping Based on Whole-Genome Sequencing Improves the Accuracy of Shigella Identification.
Wu Y, Lau HK, Lee T, Lau DK, Payne J. Wu Y, et al. Appl Environ Microbiol. 2019 Mar 22;85(7):e00165-19. doi: 10.1128/AEM.00165-19. Print 2019 Apr 1. Appl Environ Microbiol. 2019. PMID: 30709819 Free PMC article.
Using this information, we developed ShigaTyper, an automated workflow that utilizes limited computational resources to accurately and rapidly determine 59 Shigella serotypes using Illumina paired-end whole-genome sequencing (WGS) reads. Shigella serotype det …
Using this information, we developed ShigaTyper, an automated workflow that utilizes limited computational resources to accurately and rapid …
Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.
Tagini F, Greub G. Tagini F, et al. Eur J Clin Microbiol Infect Dis. 2017 Nov;36(11):2007-2020. doi: 10.1007/s10096-017-3024-6. Epub 2017 Jun 21. Eur J Clin Microbiol Infect Dis. 2017. PMID: 28639162 Free PMC article. Review.
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. ...For each pathogen group, we focused on five different aspects: the genome characteristics, the most common …
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise c …
Whole genome and in-silico analyses of G1P[8] rotavirus strains from pre- and post-vaccination periods in Rwanda.
Rasebotsa S, Mwangi PN, Mogotsi MT, Sabiu S, Magagula NB, Rakau K, Uwimana J, Mutesa L, Muganga N, Murenzi D, Tuyisenge L, Jaimes J, Esona MD, Bowen MD, Mphahlele MJ, Seheri ML, Mwenda JM, Nyaga MM. Rasebotsa S, et al. Sci Rep. 2020 Aug 10;10(1):13460. doi: 10.1038/s41598-020-69973-1. Sci Rep. 2020. PMID: 32778711 Free PMC article.
To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre- and post-vaccine introduction, rotavirus positive fecal samples collected between 2011 and 2016 from children under the age of 5 years as part of ongoing surveillance were genotyped wit …
To gain insights into the overall genetic make-up and evolution of Rwandan G1P[8] strains pre- and post-vaccine introduction, rotavirus posi …
Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates.
Laczny CC, Galata V, Plum A, Posch AE, Keller A. Laczny CC, et al. Brief Bioinform. 2019 May 21;20(3):857-865. doi: 10.1093/bib/bbx162. Brief Bioinform. 2019. PMID: 29220507
Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based …
Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identificat …
Performance and Accuracy of Four Open-Source Tools for In Silico Serotyping of Salmonella spp. Based on Whole-Genome Short-Read Sequencing Data.
Uelze L, Borowiak M, Deneke C, Szabó I, Fischer J, Tausch SH, Malorny B. Uelze L, et al. Appl Environ Microbiol. 2020 Feb 18;86(5):e02265-19. doi: 10.1128/AEM.02265-19. Print 2020 Feb 18. Appl Environ Microbiol. 2020. PMID: 31862714 Free PMC article.
We compared the performance of four open-source in silico Salmonella typing tools (SeqSero, SeqSero2, Salmonella In Silico Typing Resource [SISTR], and Metric Oriented Sequence Typer [MOST]) to assess their potential for replacing laboratory serological testi …
We compared the performance of four open-source in silico Salmonella typing tools (SeqSero, SeqSero2, Salmonella In Silico Typ …
Proteogenomics: From next-generation sequencing (NGS) and mass spectrometry-based proteomics to precision medicine.
Ang MY, Low TY, Lee PY, Wan Mohamad Nazarie WF, Guryev V, Jamal R. Ang MY, et al. Clin Chim Acta. 2019 Nov;498:38-46. doi: 10.1016/j.cca.2019.08.010. Epub 2019 Aug 14. Clin Chim Acta. 2019. PMID: 31421119 Review.
One of the best-established area within multi-omics is proteogenomics, whereby the underpinning technologies are next-generation sequencing (NGS) and mass spectrometry (MS). Proteogenomics has contributed significantly to genome (re)-annotation, whereby novel coding …
One of the best-established area within multi-omics is proteogenomics, whereby the underpinning technologies are next-generation sequenci …
Comprehensive assessment of the quality of Salmonella whole genome sequence data available in public sequence databases using the Salmonella in silico Typing Resource (SISTR).
Robertson J, Yoshida C, Kruczkiewicz P, Nadon C, Nichani A, Taboada EN, Nash JHE. Robertson J, et al. Microb Genom. 2018 Feb;4(2):e000151. doi: 10.1099/mgen.0.000151. Epub 2018 Jan 17. Microb Genom. 2018. PMID: 29338812 Free PMC article.
Public health and food safety institutions around the world are adopting whole genome sequencing (WGS) to replace conventional methods for characterizing Salmonella for use in surveillance and outbreak response. ...These data were used to compare the concorda …
Public health and food safety institutions around the world are adopting whole genome sequencing (WGS) to replace conve …
Comparative Genomics of 86 Whole-Genome Sequences in the Six Species of the Elizabethkingia Genus Reveals Intraspecific and Interspecific Divergence.
Liang CY, Yang CH, Lai CH, Huang YH, Lin JN. Liang CY, et al. Sci Rep. 2019 Dec 16;9(1):19167. doi: 10.1038/s41598-019-55795-3. Sci Rep. 2019. PMID: 31844108 Free PMC article.
In silico DNA-DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed, and clusters of orthologous groups were evaluated. Of the 86 …
In silico DNA-DNA hybridization, whole-genome sequence-based phylogeny, pan genome analysis, and K …
Comparative analyses of whole-genome protein sequences from multiple organisms.
Yokono M, Satoh S, Tanaka A. Yokono M, et al. Sci Rep. 2018 May 1;8(1):6800. doi: 10.1038/s41598-018-25090-8. Sci Rep. 2018. PMID: 29717164 Free PMC article.
Average sequence similarity methods are different than most other whole-genome methods, because they are based on local alignments. However, previous average similarity methods fail to reconstruct a correct phylogeny when compared against other whole- …
Average sequence similarity methods are different than most other whole-genome methods, because they are based on local …
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