Sentences with phrase «using genome analysis»

Base recalibration was performed using the Genome Analysis ToolKit (GATK)[16] v1.3.

Using genome analysis tools, scientists outlined the multistage process that sperm stem cells undergo during their normal development.

Scientists use the genome analysis tool to break DNA down into smaller pieces, then sequence those and assemble those into longer pieces.

Shmulevich directs a Genome Data Analysis Center at ISB as part of The Cancer Genome Atlas project, which is using genome analyses to accelerate understanding of the molecular basis of cancer.

Not exact matches

Here's hoping that ever - cheaper genome analysis accelerates the use of genetic information.

The work carried out by Dr Casewell and his co-authors was used in the second paper outlining the analysis of the genome of the Burmese python, also published in the same edition of PNAS.

Using metabolic function analyses of identified genes, we compared our human genome with the average content of previously sequenced microbial genomes.

Using advanced sequencing technologies, University of Oklahoma anthropologists demonstrate that human DNA can be significantly enriched from dental calculus (calcified dental plaque) enabling the reconstruction of whole mitochondrial genomes for maternal ancestry analysis — an alternative to skeletal remains in ancient DNA investigations of human ancestry.

An international team of scientists from Singapore, Thailand, China and Australia has cracked the genetic code of the liver fluke parasite, Opisthorchis viverrini, using a unique DNA analysis technique developed at A * STAR's Genome Institute of Singapore (GIS).

Researchers from Boston University School of Medicine looked for new stroke genes using genome wide association as well as meta - analysis.

«In the current study, using a genome - wide analysis of DNA methylation, we identified a few PPARα target genes that underwent ligand - activated PPARα - dependent DNA demethylation during the perinatal period and whose DNA methylation status persists into adulthood,» explains a corresponding author Koshi Hashimoto.

In their work, Dr. Lessnick and his team used bioinformatics analysis of experimental data in an unbiased genome - wide approach.

Using a genome - wide association study (GWAS) that includes 1600 individuals living in Tanzania, Botswana, or Ethiopia, the authors identified regions of the genome that contribute to skin color variation and carried out a series of analyses to pinpoint the responsible genes.

To better determine the history of modern birds, we performed a genome - scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome - scale data.

This is one of the first population genomics analyses to use high - coverage whole - genome sequencing in pigs, each individual has been sequenced more than 20-fold depth with the genome coverage of 95 %.

Hvilsom noted that their comprehensive analyses of chimpanzee genomes revealed that the apes» genetic information can be used to determine from which country, and even which region, individual chimpanzees originated.

Using technologies like whole genome or whole exome (the protein - coding portion of the genome) sequencing requires specialized equipment and advanced data analysis and is still relatively expensive.

They then used genome - wide analysis to search for genes switched on by KLF4 at a late stage of reprogramming.

Given the number of genomes studied and the sophisticated analysis used, the date for when the species diverges is «the best estimate of what we've gotten so far, and it makes sense,» says Beth Shapiro, an evolutionary biologist at UC Santa Cruz, whose earlier work also suggested these bears split less than a million years ago.

«Using the genome data analysis methods developed by co-author Steve Horvath at UCLA, we have uncovered crucial gene networks and we can now predict possible future genetic disorders at the eight - cell stage.»

Each team used complex computer models and statistical analyses to interpret the population history behind the patterns of similarity and difference in the genomes.

Because Kosik's team had information on the genome sequence around the mutation, they could use something called identity - by - descent analysis to determine how the people in the study were related.

According to Paek, «Genome - wide transcriptome analysis using drought - tolerant or - susceptible variants is a promising method to reach the goal of understanding drought tolerance».

The genome analysis, which is published in the 9 May issue of Nature, also reveals blueprints for three assembly lines of hitherto unknown antibiotics, which, once identified, could be used as starting compounds in drug discovery.

Given the widespread use of the HeLa cell line, Lars Steinmetz and his colleagues at EMBL decided that conducting an extensive analysis of its genome could illustrate the changes caused by cancer — and also help researchers compare versions of the cell line that have evolved over decades of growth in labs around the world.

His group uses genome - wide and gene - specific DNA methylation analysis to identify aberrantly silenced tumor suppressor genes in B cell leukemias and lymphomas.

This HDG genome represented the most complete de novo genome assembly to date, and with other omics data resources available from this individual, the work can be used as a benchmark for developing new sequencing and assembly techniques, and for functional studies involving RNA or protein analysis.

Previous genetic studies have examined the association of aspirin, NSAIDs, or both with colorectal cancer according to a limited number of candidate genes or pathways.6 - 10 Thus, to comprehensively identify common genetic markers that characterize individuals who may obtain differential benefit from aspirin and NSAIDs, we conducted a discovery - based, genome - wide analysis of gene × environment interactions between regular use of aspirin, NSAIDs, or both and single - nucleotide polymorphisms (SNPs) in relation to risk of colorectal cancer.

Scientists for years have looked for the biological roots of the problem using tools such as genome - wide association studies and gene - linkage analysis, which crunch genetic and health data from thousands of people in an effort to pinpoint disease - causing genetic variants.

Detailed phylogenetic analyses of several virus genes, some of which used complete CDV genomes, revealed that strains from lions and hyenas during the 1993/1994 epidemic were strongly distinct from those in domestic dogs and wild canids.

NORMAN — Using advanced sequencing technologies, University of Oklahoma anthropologists demonstrate that human DNA can be significantly enriched from dental calculus (calcified dental plaque) enabling the reconstruction of whole mitochondrial genomes for maternal ancestry analysis — an alternative to skeletal remains in ancient DNA investigations of human ancestry.

We aim to build a novel liquid biopsy platform for the cases with a low burden in plasma using a sensitive whole genome, whole methylome and epigenetics analyses.

Association testing was performed using the PLINK whole genome analysis [36].

Firstly, both species have well characterised genomes with highly accurate and well annotated assemblies [5, 17] and have both been used frequently in comparative genomic analyses resulting in many easily accessible pairwise alignment datasets available on the UCSC genome browser [18].

To study these pathways, we use a range of in vitro and in vivo approaches, including manipulating genes in mice and leveraging genome - wide analyses and chemical biology.

• Mouse whole genome scanning The unit offers microsatellite and SNP based Genome Scanning Services for gene identification projects, based on linkage analysis, offering coverage for a number of mouse strains (i.e. C57BL6, DBA2J, CBA, 129S6, 129P2), as well as bioinformatic analysis using suitable mouse genetic sofgenome scanning The unit offers microsatellite and SNP based Genome Scanning Services for gene identification projects, based on linkage analysis, offering coverage for a number of mouse strains (i.e. C57BL6, DBA2J, CBA, 129S6, 129P2), as well as bioinformatic analysis using suitable mouse genetic sofGenome Scanning Services for gene identification projects, based on linkage analysis, offering coverage for a number of mouse strains (i.e. C57BL6, DBA2J, CBA, 129S6, 129P2), as well as bioinformatic analysis using suitable mouse genetic software.

Taking advantage of this relevant cell model, we provided, by using a whole - genome transcriptional analysis, a list of DM1 specific biomarkers that could be considered as a robust DM1 signature.

We will take the user from a beginner level understanding to one that can analysis multiple whole human genomes and derive meaningful clinical results using the latest methodologies.

A large variety of methods is used including genetic, molecular and cytogenetic techniques, fluorescence in situ hybridisation and DNA «combing», as well as high throughput sequencing approaches such as DNA - seq for mutation landscape analyses, RNA - seq for transcriptome analyses and ChIP - seq mapping of chromatin - associated proteins and their genome - wide modulation in response to DNA damages.

The Cancer, Ageing and Somatic Mutation Programme encompasses three Projects that respectively cover the genomics of human cancers; functional analysis of the cancer genome using a range of in vitro and in vivo model systems; and the characterisation of somatic mutations in development and adult homeostasis in health and disease.

It was identified using a genome - wide linkage analysis of patients who suffered from stroke, using a broad but rigorous definition of the disease.

The authors of this scientific report explain further that comparing aligned sequences relative to their respective genomes using BowTie version 0.12.7 served two purposes: (i) To obtain unaligned reads for further analysis; and (ii) to observe variation in the numbers of both aligned and unaligned reads across different runs, experiments and organisms.

Parallel whole - genome microarray analysis was used to determine the transcriptome in matched samples.

For enrichment analysis, both the scaffolds in which the carotenoid - associated SNPs were located and the total of SNPs located in these scaffolds were determined by aligning the catalog tags with the draft genome using GMAP (version 2015-09-29).

Using deCODE's proprietary analysis tool for complex traits, the deCODE Clinical Genome Miner ™, the researchers were able to correlate a wide range of clinical, behavioral, and genotypic data, and gained important new insights into the heritability of different aspects of obesity, as well as into the complex interplay between obesity and diabetes, stroke, heart disease, and hyperlipidemia.

As a part of VIOLIN, we have developed Vaxign, the first web - based publically available vaccine target design tool based on bioinformatics analysis of genome sequences using the strategy of reverse vaccinology.

A key program of VIOLIN is Vaxign, the first web - based publically available vaccine target design tool based on bioinformatics analysis of genome sequences using the strategy of reverse vaccinology.

Variants were called using both the Genome Analysis Tool Kit (GATK)- HaplotypeCaller and Atlas V2pipelines.

We applied gene set enrichment analysis (GSEA)(23) to expression array data using KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways.

«Analysis of the bread wheat genome using whole genome shotgun sequencing» is published online in Nature on November 29, 2012.