human genome

..For the human genome, Burrows-Wheeler indexing allows Bowtie to align more than 25 million reads per CPU hour with a memory ..

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype...

..Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis...

..Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology...

..Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net...

..We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase...

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..We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male ..

..Our simple, efficient approach can easily be applied to disease studies with hundreds of thousands of markers...

..Moreover, we observe that inactive unmethylated CpG island promoters show elevated levels of dimethylation of Lys4 of histone H3, suggesting that this chromatin mark may protect DNA from methylation...

..Our data suggest that these histone modifications may act cooperatively to prepare chromatin for transcriptional activation...

..generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project...

..The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users...

..Together, these findings establish the feasibility and power of TCGA, demonstrating that it can rapidly expand knowledge of the molecular basis of cancer...

We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences...

..NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [+/-50 base pairs (bp)], which facilitated our finding ..

..over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human ..

..In addition, and unexpectedly, our analyses have uncovered detailed features of nucleosome structure...

..Taken together, our data show that single nucleotide mutational heterogeneity can be a property of low or intermediate grade primary breast cancers and that significant evolution can occur with disease progression...

..Finally, our data suggest that a miRNA can, by direct or indirect effects, tune protein synthesis from thousands of genes...

..We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap ..

..2 x 10(-16)). Our method can distinguish between different copies of highly identical genes, providing a more accurate assessment of gene content and insight into functional constraint without the limitations of array-based technology...

..The expanded molecular understanding of the basis of this disease offers promise for informed therapeutic development...

Despite our rapidly growing knowledge about the human genome, we do not know all of the genes required for some of the most basic functions of life...

..A notable future use of our method will be to boost power by combining data from genome-wide scans that use different SNP sets...

..Our results suggest an important role for mRNA stability in determining steady-state mRNA levels, and highlight the potential of eQTL mapping as a high-resolution tool for studying the determinants of gene regulation...

The elucidation of the human genome sequence has made it possible to identify genetic alterations in cancers in unprecedented detail...

..These data provide a catalog of miR genes that may have roles in cancer and argue that the full complement of miRs in a genome may be extensively involved in cancers...

..We determined the chromatin modification states in high resolution along 30 Mb of the human genome and found that active promoters are marked by trimethylation of Lys4 of histone H3 (H3K4), whereas enhancers ..

The human genome has been extensively annotated with Gene Ontology for biological functions, but minimally computationally annotated for diseases.

Cancers arise owing to mutations in a subset of genes that confer growth advantage. The availability of the human genome sequence led us to propose that systematic resequencing of cancer genomes for mutations would lead to the discovery ..

..we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel...

..This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results...

Epistatic interactions among multiple genetic variants in the human genome may be important in determining individual susceptibility to common diseases...

..The full complement of DNA mutations that are responsible for the pathogenesis of acute myeloid leukemia (AML) is not yet known...

..In this review, we discuss these epigenetic events and the molecular alterations that might cause them and/or underlie altered gene expression in cancer...

..Taken together, our results indicate that hESC differentiation has a unique DNA methylation signature that may not be indicative of in vivo differentiation...

..We show that the predictions of this model fit very well with the observed substitution patterns in the human genome. This model notably explains the positive correlation between substitution rate and recombination rate...

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..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...

..These findings illustrate the potential for next-generation sequencing to provide unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with cancer...

..Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia...

Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done...

..However, there is little or no difference in empirical power of MG and the proposed method. In any scenario, GRAMMAR is much faster than MG and enables rapid analysis of hundreds of thousands of markers...

..Here we describe mapping of 524 sites of HIV cDNA integration on the human genome sequence. Genes were found to be strongly favored as integration acceptor sites...

..To identify novel chromatin signatures in the human genome, we apply a de novo pattern-finding algorithm to genome-wide maps of histone modifications...

..This technique is highly specific and sensitive and can be applied to any biological settings to identify differentially methylated regions at the genomic scale...

..It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions...

..Understanding the molecular, cellular and clinical consequences of the newly identified loci may inform therapy and clinical care...

..We present a high-resolution genetic map of the human genome, based on statistical analyses of genetic variation data, and identify more than 25,000 recombination hotspots, ..

..Together, this analysis and annotation provides a useful resource to assist with the assessment of CNVs in the contexts of human variation, disease susceptibility, and clinical molecular diagnostics...

..The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype...

..A core network module in humans and mice was identified that is enriched for genes involved in the inflammatory and immune response and has been found to be causally associated to obesity-related traits...

..By investigating read pairs that did not align correctly with respect to each other on the reference human genome, we characterized 306 germline structural variants and 103 somatic rearrangements to the base-pair level of ..

..When combined with motif information our method outperforms previous methods for predicting locations of true binding...

..Applying this algorithm to nine chromatin marks across a 1% sampling of the human genome in HeLa cells, we recover eight clusters of distinct chromatin signatures, five of which correspond to known ..

..Here we report the use of single-molecule methods to sequence an individual human genome. We aligned billions of 24- to 70-bp reads (32 bp average) to approximately 90% of the National Center for ..

Understanding the prevailing mutational mechanisms responsible for human genome structural variation requires uniformity in the discovery of allelic variants and precision in terms of breakpoint delineation...

..Our results demonstrate that H3K27me3 modifications change during early differentiation, both relieving existing repressive domains and imparting new ones, and that colocalization with H3K4me3 is not restricted to pluripotent cells...

..variation in a sample of 3,000 European individuals genotyped at over half a million variable DNA sites in the human genome. Despite low average levels of genetic differentiation among Europeans, we find a close correspondence between ..

A plethora of epigenetic modifications have been described in the human genome and shown to play diverse roles in gene regulation, cellular differentiation and the onset of disease...

..This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas...

..This resulted in the selection of 331 polymorphisms located in 112 different candidate genes out of an initial set of 23,300 SNPs...

..At 50% relative efficacy, the commercial marker sets cover between 19 and 68% of the human genome, depending upon the population under study...

Array-based technologies have been used to detect chromosomal copy number changes (aneuploidies) in the human genome. Recent studies identified numerous copy number variants (CNV) and some are common polymorphisms that may contribute to ..

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..It provides a relatively fast and fairly good tool for screening and limiting the candidate SNPs for further more complex computational modeling task...

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..Crohn's disease (CD) and sarcoidosis (SA) are chronic inflammatory barrier diseases that share several clinical and immunological features, including the occurrence of granulomas...

..Thus, although the truth of the common disease / common variant hypothesis remains undecided, recent successes suggest that there are many more common genetic disease-associated variants, requiring larger studies to be identified...

..to provide an accurate description of gene functions to a set of 1737 highly curated disease genes in the human genome. This analysis is the first attempt on in silico identification of druggable domains within disease genes...

..The regions identified underscore the importance of pathways influencing pancreatic beta cell development and function in the etiology of type 2 diabetes...

..Thus, we recommend to use MAX-rank for genome-wide scans. After the top-ranked SNPs are identified, their P-values based on MAX can be calculated and compared with the significance level...

..The server is freely available and can be accessed at the URL http://bioinformoodics.jhmi.edu/quickSNP.pl...

..However, the formidable size of the diploid human genome, approximately 6 gigabases, has prevented the routine application of sequencing methods to deciphering complete ..

Knowledge about structural variation in the human genome has grown tremendously in the past few years. However, inversions represent a class of structural variation that remains difficult to detect...

..The issues we explore are important not only to these types of studies, but also to studies that select tSNPs based on (external) HapMap phase II data, and those that use genome-wide markers...

..We demonstrate that this approach can be effectively applied to the truly genomewide Affymetrix GeneChip Mapping 500 K Array...

..In particular, the ratio of substitution to indel rates between human and mouse appears to be around gamma = 8, rather than the currently accepted value of about gamma = 14...

..32 (rs11083846, PRKD2; P = 3.96 x 10(-9)). These data provide the first evidence for the existence of common, low-penetrance susceptibility to a hematological malignancy and new insights into disease causation in CLL...

..The principles developed in this work will help to make epigenetic profiling of the entire human genome a routine procedure.

..The region on chromosome 13q14-32 has previously been implicated in other bipolar and schizophrenia cohorts. Our results provide further support for the existence of a susceptibility locus on chromosome 13q14...

Limited comparative studies suggest that the human genome is particularly enriched for recent segmental duplications...

..These data illustrate the power of comparative genomic analysis for the study of human disease and identifies a novel BBS gene...

Identifying regions of the human genome that have been targets of natural selection will provide important insights into human evolutionary history and may facilitate the identification of complex disease genes...

..Thus, we measured the fixation rate of NUMTs in the human genome. Six such NUMTs show insertion polymorphism and provide a useful set of DNA markers for human population ..

..The corresponding region of the human genome is particularly gene rich, containing genes involved in development, metabolism, and cancer that are likely to ..

..We obtained clones representing 70% of genes on human chromosome 22, whereas searching available cDNA clone collections found at best 48% from a single collection and 60% for all collections combined...

..These results show that the theoretical benefits of genome-wide association studies are at last realizable...

..A useful preliminary investigation of datasets of this type is provided by counting the numbers of distinct multi-locus genotypes in windows of a few markers...

..Our system is applicable to any genetic study of complex disease, of either large or small scale...

..mechanism by which physiological knowledge obtained in model systems such as the rat can be projected onto the human genome to further the research on human disease...

..Our results demonstrate the potential of combining sequence and expression data for improving functional gene annotation and expanding our understanding of how gene expression and diversity evolved...

..The SNP500Cancer Database is freely accessible via the web page at http://snp500cancer.nci.nih.gov/...

..In addition, we provide BLAST results for each protein sequence, InParanoid orthologs and 'In-Paralogs' data, previously established paralogy data, and, to compare vertebrates and Drosophila, orthology data...

..Because the classification power is very high, the SOM is an efficient and fundamental bioinformatic strategy for extracting a wide range of genomic information from a vast amount of sequences...

Retrotransposons comprise almost half of the human genome and substantial fractions of other metazoan genomes. Nonetheless, the mechanisms and localization of retrotransposon assembly are poorly understood...

..result of rapid progress in defining the landscape of genetic organization and cataloging variation across the human genome. This proposal builds on the availability of second generation, high-quality genome-wide association results ..

..PUBLIC HEALTH RELEVANCE: In 2003, Human Genome Project (HGP) released a working draft of the human genome sequence...

..processes as well as the etiology of many human diseases However, in contrast to rapid advances in human genome sequencing, it is still impractical to characterize the methylation status of every single CpG in the human ..

..processes as well as the etiology of many human diseases However, in contrast to rapid advances in human genome sequencing, it is still impractical to characterize the methylation status of every single CpG in the human ..

..processes as well as the etiology of many human diseases However, in contrast to rapid advances in human genome sequencing, it is still impractical to characterize the methylation status of every single CpG in the human ..

The information content of the human genome is expanded by the covalent methylation of cytosine residues, which introduces approximately 3 X 10(7) residues of 5-methylcytosine per haploid genome...

..in post genomic biomedical research is to translate the information encoded in genes and gene products of the human genome into an understanding of their functions in cellular physiology and patho- physiology, and into new approaches ..

..in post genomic biomedical research is to translate the information encoded in genes and gene products of the human genome into an understanding of their functions in cellular physiology and patho- physiology, and into new approaches ..

Our ability to identify the majority of exons in the human genome has been dramatically facilitated by the availability of extensive experimental data (EST, cDNA, and protein sequences) thereby providing training sets for the development ..

Our ability to identify the majority of exons in the human genome has been dramatically facilitated by the availability of extensive experimental data (EST, cDNA, and protein sequences) thereby providing training sets for the ..

..The completion of the human genome project and genetic screenings of several hundreds of human cancers over the last years, have led to the ..

..replicator as a replication origin are the same at its endogenous chromosomal site and at ectopic sites in the human genome. In this application, the c-myc replicator will be used as a model mammalian replication origin to study the ..

The repetitive DNA structure of the human genome The recent completion of the human genome project gives today's scientists the privileged opportunity to provide, for the first and only time, a detailed comprehensive description of ..

The repetitive DNA structure of the human genome The recent completion of the human genome project gives today's scientists the privileged opportunity to provide, for the first and only time, a detailed comprehensive description of the ..

..We aim to (1) identify and classify all DNA sequences in human genome that resemble native recombination target for Flp, FRT; (2) evolve Flp variants that can recombine the ..

..We aim to (1) identify and classify all DNA sequences in human genome that resemble native recombination target for Flp, FRT;(2) evolve Flp variants that can recombine the ..

..For example, at least 40% of the human genome is composed of these reverse transcripts...

..For example, at least 40% of the human genome is composed of these reverse transcripts...

..The overwhelming majority of L1s can no longer move (i.e., retrotranspose). However, the average human genome contains ~80-100 retrotransposition-competent L1s (RC-L1s) and their mobility, in both germ line and somatic ..

..The overwhelming majority of L1s can no longer move (i.e., retrotranspose). However, the average human genome contains ~80-100 retrotransposition-competent L1s (RC-L1s) and their mobility, in both germ line and somatic ..

..and ACTH respond and interact differently before and after challenge in some children with AD and (3) the Human Genome Project has provided ahead of schedule a dense map of the human genome including about half of the expressed ..

..this renewal application is to identify and define the in vivo activities of a sizeable set of enhancers in the human genome to serve as a springboard for broad community access...

One of the next major goals of the Human Genome Project is to identify the function of all the genes it encodes...

One of the major accomplishments in biology of the last century has been the sequencing of the human genome. This has brought about a revolution, allowing researchers to gain information on cellular proteins, function, and human health ..

One of the major accomplishments in biology of the last century has been the sequencing of the human genome. This has brought about a revolution, allowing researchers to gain information on cellular proteins, function, and human health ..

DESCRIPTION: (Adapted from the investigator's abstract) The Human Genome Project (HGP) promises to deliver a complete human genome sequence by the year 2005...

..duplication and/or deletion, termed as copy number variation (CNV), has been shown to frequently occur in the human genome. CNVs account for more nucleotide variation than SNPs and they may be an unrecognized source of breast cancer ..

..duplication and/or deletion, termed as copy number variation (CNV), has been shown to frequently occur in the human genome. CNVs account for more nucleotide variation than SNPs and they may be an unrecognized source of breast cancer ..