Browsing by Subject "Databases, Genetic"
Now showing items 1-16 of 16
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Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
(Nature, 2002-12-05)Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure ... -
Analysis of the mouse transcriptome for genes involved in the function of the nervous system.
(Genome Res, 2003-06)We analyzed the mouse Representative Transcript and Protein Set for molecules involved in brain function. We found full-length cDNAs of many known brain genes and discovered new members of known brain gene families, including ... -
Application of a rank-based genetic association test to age-at-onset data from the Collaborative Study on the Genetics of Alcoholism study.
(BMC Genet, 2005-12-30)Association studies of quantitative traits have often relied on methods in which a normal distribution of the trait is assumed. However, quantitative phenotypes from complex human diseases are often censored, highly skewed, ... -
Avianbase: a community resource for bird genomics.
(Genome Biol, 2015-01-29)Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore ... -
Characterization of the standard and recommended CODIS markers.
(Journal of forensic sciences, 2013-01)As U.S. courts grapple with constitutional challenges to DNA identification applications, judges are resting legal decisions on the fingerprint analogy, questioning whether the information from a DNA profile could, in light ... -
Detecting local haplotype sharing and haplotype association.
(Genetics, 2014-07)A novel haplotype association method is presented, and its power is demonstrated. Relying on a statistical model for linkage disequilibrium (LD), the method first infers ancestral haplotypes and their loadings at each marker ... -
Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.
(PLoS One, 2010-05-20)BACKGROUND: The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely ... -
Genome-wide association study of acute kidney injury after coronary bypass graft surgery identifies susceptibility loci.
(Kidney Int, 2015-10)Acute kidney injury (AKI) is a common, serious complication of cardiac surgery. Since prior studies have supported a genetic basis for postoperative AKI, we conducted a genome-wide association study (GWAS) for AKI following ... -
GREAT improves functional interpretation of cis-regulatory regions.
(Nature biotechnology, 2010-05-02)We developed the Genomic Regions Enrichment of Annotations Tool (GREAT) to analyze the functional significance of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. ... -
Inter-chromosomal level of genome organization and longevity-related phenotypes in humans.
(Age (Dordr), 2013-04)Studies focusing on unraveling the genetic origin of health span in humans assume that polygenic, aging-related phenotypes are inherited through Mendelian mechanisms of inheritance of individual genes. We use the Framingham ... -
Latent factor analysis to discover pathway-associated putative segmental aneuploidies in human cancers.
(PLoS Comput Biol, 2010-09-02)Tumor microenvironmental stresses, such as hypoxia and lactic acidosis, play important roles in tumor progression. Although gene signatures reflecting the influence of these stresses are powerful approaches to link expression ... -
Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.
(Genome Biol, 2010)BACKGROUND: There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, ... -
SNPpy--database management for SNP data from genome wide association studies.
(PLoS One, 2011)BACKGROUND: We describe SNPpy, a hybrid script database system using the Python SQLAlchemy library coupled with the PostgreSQL database to manage genotype data from Genome-Wide Association Studies (GWAS). This system makes ... -
SplicerAV: a tool for mining microarray expression data for changes in RNA processing.
(BMC Bioinformatics, 2010-02-25)BACKGROUND: Over the past two decades more than fifty thousand unique clinical and biological samples have been assayed using the Affymetrix HG-U133 and HG-U95 GeneChip microarray platforms. This substantial repository has ... -
The characterization of twenty sequenced human genomes.
(PLoS Genet, 2010-09-09)We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten "case" genomes from individuals ... -
Whole genome sequencing identifies circulating Beijing-lineage Mycobacterium tuberculosis strains in Guatemala and an associated urban outbreak.
(Tuberculosis (Edinb), 2015-12)Limited data are available regarding the molecular epidemiology of Mycobacterium tuberculosis (Mtb) strains circulating in Guatemala. Beijing-lineage Mtb strains have gained prevalence worldwide and are associated with increased ...
