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    Archived pages: 7 . Archive date: 2013-06.

  • Title: Center for Genomic Epidemiology
    Descriptive info: .. Services.. Multi Locus Sequence Typing (MLST) from an assembled genome or from set of reads.. MLST typing.. Identifcation of acquired antibiotic resistance genes from a file with sequence reads.. ResFinder.. SNPs phylogenetic tree from assembled genomes or sets of reads.. snpTree.. Reads2Type gives a fast and dirty prediction of bacterial taxonomy.. Reads2Type.. Organization.. Project.. Publications.. Contact.. Welcome to the Center for Genomic Epidemiology.. The cost of sequencing a bacterial genome is $50 and is expected to decrease further in the near future and the equipment needed cost less than $150 000.. Thus, within a few years all clinical microbiological laboratories will have a sequencer in use on a daily basis.. The price of genome sequencing is already so low that whole genome sequencing will also find worldwide application in human and veterinary practices as well as many other places where bacteria are handled.. In Denmark alone this equals more than 1 million isolates annually in 15-20 laboratories and globally up to 1-2 billion isolates per year.. The limiting factor will therefore in the future not be the cost of the sequencing, but how to assemble, process and handle the large amount of data in a standardized way that will make the information useful, especially for diagnostic and surveillance.. The aim  ...   Genomic Epidemiology took place at DTU on March 1st.. Global Microbial Identifier.. December 2012.. The initiative 'Global Microbial Identifier' focuses on the use of genome sequencing techniques in a global system for microbiological identification and epidemiological surveillance.. Visit the homepage for further information.. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes.. The use of whole genome sequencing will make it possible to eliminate, or at least reduce, the need for several typing steps used in traditional epidemiology.. Link to article.. Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response.. October 2012.. Publications in the center.. Identification of acquired antimicrobial resistance genes.. August 2012.. We here present ResFinder, a web server that uses WGS data for identifying acquired antimicrobial resistance genes in bacteria.. The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.. May 2012.. Combining three RNA-sequencing techniques and two sequencing platforms to generate transcriptional map of SL1344 advances our understanding of S.. Typhimurium, arguably the most important bacterial infection model.. Copyright DTU 2011 / All rights reserved.. Center for Genomic Epidemiology, DTU, Kemitorvet, Building 204, 2800 Kgs.. Lyngby, Denmark.. Contact: Vibeke Dybdahl Hammer, Telephone: +45 3588 6420, E-mail: vdha@food.. dtu.. dk.. Funded by: The Danish Council for Strategic Research..

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  • Title: Center for Genomic Epidemiology
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  • Title: Center for Genomic Epidemiology
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    Descriptive info: You should be reffered to Center for Genomic Epidemiology, if not? click.. here..

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  • Title: Center for Genomic Epidemiology
    Descriptive info: For more information please contact the administrative coordinator.. Vibeke Dybdahl Hammer..

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  • Title: Center for Genomic Epidemiology
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  • Title: Center for Genomic Epidemiology
    Descriptive info: Center for Genomic Epidemiology.. Home.. Search.. February 2013.. The annual advisory board meeting in the Center for Genomic Epidemiology will take place at DTU on March 1st.. At the meeting we will discuss the progress in the center.. GMI focuses on the use of genome sequencing techniques in a global system for microbiological identification and epidemiological surveillance.. The vision is to develop a global system to aggregate, share, mine and use microbiological genomic data to address global public health and clinical challenges, a high impact area in need of focused effort.. Visit the homepage for further info.. Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes.. (e-published ahead of print).. Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response.. Maj 2012.. Typhimurium, arguably the most important bacterial infection model.. Genomic variation in Salmonella enterica core genes for epidemiological typing.. March 2012.. The variation within core genome is useful for investigating evolution and providing candidate genes from bacterial genome typing.. Staphylococcus aureus CC398.. Host Adaptation and Emergence of Methicillin Resistance in Livestock.. February 2012.. Comparative Genomics of Bifidobacterium, Lactobacillus and Related Probiotic Genera.. January 2012.. Genome diversity within a set of 'good bacteria' have been examined by a team from the CGE.. Multilocus Sequence Typing of Total Genome Sequenced Bacteria.. Characterization of Salmonella enterica serovar Stanley isolates; a serovar endemic to Asia and associated with travel.. December 2011.. The CGE is quoted in the Science article: Outbreak Detectives Embrace The Genome Era.. September 2011.. Doctors could soon be sequencing bacterial samples from virtually every patient.. The avalanche of data will help fight disease outbreaks.. Read more.. Denmark leads the way in the global battle against infectious diseases.. DTU organized an expert meeting on microbiological genomic identification systems in September in Bruxelles.. Please find more information and download the presentations from the meeting.. Information and presentations.. Population Genetics of Vibrio cholerae from Nepal in 2010: Evidence on  ...   or even the globe.. Whether this is due to a fitness advantage or simply due to stochastic opportunities isn't always clear, but these populations are highly clonal and highly homogeneous.. The analytical challenges include the identification of rare genetic variation to discriminate among isolates and the subsequent genotyping of large sample sets to track the disease.. Whole genome sequencing can now identify nucleotide differences, even if vanishingly rare.. Genotyping assay development and implementation strategies are many, but need to fit particular applications in expense, speed, and sensitivity.. Dr.. Keim will discuss the state of this science and give examples from bioterrorism (anthrax), laboratory safety (plague) and public health (cholera).. For further information please contact:.. David Ussery.. Molecular characterization and antimicrobial susceptibility testing of Escherichia coli isolates from patients with urinary tract infections in 20 Chinese hospitals.. July 2011.. New paper is published about the Salmonella enterica Pan-genome.. June 2011.. We have compared 45 sequenced S.. enterica genomes that are publicly available (22 complete and 23 draft genome sequences) along with two Escherichia coli strains and estimated the core and pan-genome of Salmonella to be around 2,800 and 10,000 gene clusters, respectively.. Pan-genomic dendrograms suggest that gene content is often, but not uniformly correlated to serotype.. Any given Salmonella strain has a large stable core, which is extended with an abundance of variable accessory genes, typically localized in specific flexible genomic regions or islands, such as transposable elements, phages, and integrated plasmid DNA.. These islands were typically well conserved in some, but not all, isolates - a difference which could have implications in, e.. g.. , host specificity.. CGE supercomputer becomes operational.. February 25, 2011.. The new CGE supercomputer today became operational.. The computer has 512 cores and will be used to analyse bacterial genomes.. The computer will also act as server for CGE's webservices.. CGE reserchers publish paper about predicting bacterial pathogenecity.. October 10, 2010.. Center for genomic Epidemiology officially opens.. April 1, 2010.. Report problems..

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  • Archived pages: 7