解剖学和形态学
麻醉学
听力与言语-语言病理学
行为科学
心脏和心血管系统
细胞和组织工程学
临床神经病学
危重症监护医学
牙科,口腔外科和医学
皮肤病学
急诊医学
内分泌学和新陈代谢
肠胃学和肝脏学
老人病学和老年医学
卫生保健科学和服务
血液学
免疫学
传染病
综合和补充性医学
医学伦理学
医学信息学
医学实验室技术
医学,全科和内科
医学,法律
医学,研究和试验
神经系统科学
护理
营养学和饮食学
产科医学和妇科医学
肿瘤学
眼科学
整形外科学
耳鼻喉科学
病理学
儿科学
周围血管疾病
药理学和药剂学
生理学
基本医疗保健
精神病学
公共、环境和职业卫生
放射学,核医学和医学成像
康复学
生殖生物学
呼吸系统
风湿病学
运动科学
外科学
毒理学
热带医学
泌尿学和肾脏学
病毒学
老年医学
健康政策和服务
心理学,临床
abstract::Although changes in chromatin are integral to transcriptional reprogramming during cellular differentiation, it is currently unclear how chromatin modifications are targeted to specific loci. To systematically identify transcription factors (TFs) that can direct chromatin changes during cell fate decisions, we model t...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.142661.112
更新日期:2013-01-01 00:00:00
abstract::A large fraction of the genes from sequenced organisms are of unknown function. This limits biological insight, and for pathogenic microorganisms hampers the development of new approaches to battle infections. There is thus a great need for novel strategies that link genotypes to phenotypes for microorganisms. We desc...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.137430.112
更新日期:2012-12-01 00:00:00
abstract::Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy u...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.137406.112
更新日期:2012-12-01 00:00:00
abstract::Thousands of long noncoding RNAs (lncRNAs) have been found in vertebrate animals, a few of which have known biological roles. To better understand the genomics and features of lncRNAs in invertebrates, we used available RNA-seq, poly(A)-site, and ribosome-mapping data to identify lncRNAs of Caenorhabditis elegans. We ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140475.112
更新日期:2012-12-01 00:00:00
abstract::Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.139055.112
更新日期:2012-12-01 00:00:00
abstract::Variation in the composition of the human oral microbiome in health and disease has been observed. We have characterized inter- and intra-individual variation of microbial communities of 107 individuals in one of the largest cohorts to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. We ex...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140608.112
更新日期:2012-11-01 00:00:00
abstract::Nutrient availability profoundly influences gene expression. Many animal genes encode multiple transcript isoforms, yet the effect of nutrient availability on transcript isoform expression has not been studied in genome-wide fashion. When Caenorhabditis elegans larvae hatch without food, they arrest development in the...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.133587.111
更新日期:2012-10-01 00:00:00
abstract::The genetics of aging in the yeast Saccharomyces cerevisiae has involved the manipulation of individual genes in laboratory strains. We have instituted a quantitative genetic analysis of the yeast replicative lifespan by sampling the natural genetic variation in a wild yeast isolate. Haploid segregants from a cross be...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.136549.111
更新日期:2012-10-01 00:00:00
abstract::Loss of heterozygosity (LOH) and copy number alteration (CNA) feature prominently in the somatic genomic landscape of tumors. As such, karyotypic aberrations in cancer genomes have been studied extensively to discover novel oncogenes and tumor-suppressor genes. Advances in sequencing technology have enabled the cost-e...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.137570.112
更新日期:2012-10-01 00:00:00
abstract::The regulation of gene expression is mediated at the transcriptional level by enhancer regions that are bound by sequence-specific transcription factors (TFs). Recent studies have shown that the in vivo binding sites of single TFs differ between developmental or cellular contexts. How this context-specific binding is ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.132811.111
更新日期:2012-10-01 00:00:00
abstract::The acquisition of new genes, via horizontal transfer or gene duplication/diversification, has been the dominant mechanism thus far implicated in the evolution of microbial pathogenicity. In contrast, the role of many other modes of evolution--such as changes in gene expression regulation-remains unknown. A transition...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.134080.111
更新日期:2012-10-01 00:00:00
abstract::CTCF is a ubiquitously expressed regulator of fundamental genomic processes including transcription, intra- and interchromosomal interactions, and chromatin structure. Because of its critical role in genome function, CTCF binding patterns have long been assumed to be largely invariant across different cellular environ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.136101.111
更新日期:2012-09-01 00:00:00
abstract::Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the dominant technique for mapping transcription factor (TF) binding regions genome-wide. We performed an integrative analysis centered around 457 ChIP-seq data sets on 119 human TFs generated by the ENCODE Consortium. We ident...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.139105.112
更新日期:2012-09-01 00:00:00
abstract::CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in hu...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.124818.111
更新日期:2012-08-01 00:00:00
abstract::Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The 17q24.3 locus harbors the single nucleotide polymorphism (SNP) rs1859962 that is statistically associated with prostate cancer (PCa). It defines a 130-kb linkage disequilibrium (LD) block that lies in an ∼2-Mb gene d...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.135665.111
更新日期:2012-08-01 00:00:00
abstract::Phosphotyrosine (pTyr) signaling, which plays a central role in cell-cell and cell-environment interactions, has been considered to be an evolutionary innovation in multicellular metazoans. However, neither the emergence nor the evolution of the human pTyr signaling system is currently understood. Tyrosine kinase (TK)...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.128819.111
更新日期:2012-07-01 00:00:00
abstract::Short tandem repeats (STRs) have a wide range of applications, including medical genetics, forensics, and genetic genealogy. High-throughput sequencing (HTS) has the potential to profile hundreds of thousands of STR loci. However, mainstream bioinformatics pipelines are inadequate for the task. These pipelines treat S...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.135780.111
更新日期:2012-06-01 00:00:00
abstract::Aberrations of protein-coding genes are a focus of cancer genomics; however, the impact of oncogenes on expression of the ~50% of transcripts without protein-coding potential, including long noncoding RNAs (lncRNAs), has been largely uncharacterized. Activating mutations in the BRAF oncogene are present in >70% of mel...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.140061.112
更新日期:2012-06-01 00:00:00
abstract::Cross-talk between DNA methylation and histone modifications drives the establishment of composite epigenetic signatures and is traditionally studied using correlative rather than direct approaches. Here, we present sequential ChIP-bisulfite-sequencing (ChIP-BS-seq) as an approach to quantitatively assess DNA methylat...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.133728.111
更新日期:2012-06-01 00:00:00
abstract::Meiotic DNA double-stranded breaks (DSBs) initiate genetic recombination in discrete areas of the genome called recombination hotspots. DSBs can be directly mapped using chromatin immunoprecipitation followed by sequencing (ChIP-seq). Nevertheless, the genome-wide mapping of recombination hotspots in mammals is still ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.130583.111
更新日期:2012-05-01 00:00:00
abstract::Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription facto...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.130682.111
更新日期:2012-04-01 00:00:00
abstract::The Saccharomyces cerevisiae genome contains about 35 copies of dispersed retrotransposons called Ty1 elements. Ty1 elements target regions upstream of tRNA genes and other Pol III-transcribed genes when retrotransposing to new sites. We used deep sequencing of Ty1-flanking sequence amplicons to characterize Ty1 integ...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.129460.111
更新日期:2012-04-01 00:00:00
abstract::Meiotic recombination, including crossovers (COs) and gene conversions (GCs), impacts natural variation and is an important evolutionary force. COs increase genetic diversity by redistributing existing variation, whereas GCs can alter allelic frequency. Here, we sequenced Arabidopsis Landsberg erecta (Ler) and two set...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.127522.111
更新日期:2012-03-01 00:00:00
abstract::Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.128652.111
更新日期:2012-03-01 00:00:00
abstract::The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to carcinogenesis; however, the role of the microbiota is the least well understood. We have characteri...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.126573.111
更新日期:2012-02-01 00:00:00
abstract::A subset of colorectal cancers was postulated to have the CpG island methylator phenotype (CIMP), a higher propensity for CpG island DNA methylation. The validity of CIMP, its molecular basis, and its prognostic value remain highly controversial. Using MBD-isolated genome sequencing, we mapped and compared genome-wide...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122788.111
更新日期:2012-02-01 00:00:00
abstract::Microsatellites--tandem repeats of short DNA motifs--are abundant in the human genome and have high mutation rates. While microsatellite instability is implicated in numerous genetic diseases, the molecular processes involved in their emergence and disappearance are still not well understood. Microsatellites are hypot...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122937.111
更新日期:2011-12-01 00:00:00
abstract::Drug development efforts against cancer are often hampered by the complex properties of signaling networks. Here we combined the results of an RNAi screen targeting the cellular signaling machinery, with graph theoretical analysis to extract the core modules that process both mitogenic and oncogenic signals to drive c...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.116145.110
更新日期:2011-12-01 00:00:00
abstract::Disturbance of DNA methylation leading to aberrant gene expression has been implicated in the etiology of many diseases. Whereas variation at the genetic level has been studied extensively, less is known about the extent and function of epigenetic variation. To explore variation and heritability of DNA methylation, we...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.119685.110
更新日期:2011-11-01 00:00:00
abstract::Dictyostelium discoideum (DD), an extensively studied model organism for cell and developmental biology, belongs to the most derived group 4 of social amoebas, a clade of altruistic multicellular organisms. To understand genome evolution over long time periods and the genetic basis of social evolution, we sequenced th...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.121137.111
更新日期:2011-11-01 00:00:00
abstract::Translocations are a common class of chromosomal aberrations and can cause disease by physically disrupting genes or altering their regulatory environment. Some translocations, apparently balanced at the microscopic level, include deletions, duplications, insertions, or inversions at the molecular level. Traditionally...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.122986.111
更新日期:2011-10-01 00:00:00
abstract::High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs with various lengths, and GC content covering a 2(20) concentration ra...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.121095.111
更新日期:2011-09-01 00:00:00
abstract::Genome-wide association studies (GWAS) have consistently implicated noncoding variation within the TCF7L2 locus with type 2 diabetes (T2D) risk. While this locus represents the strongest genetic determinant for T2D risk in humans, it remains unclear how these noncoding variants affect disease etiology. To test the hyp...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.123745.111
更新日期:2011-09-01 00:00:00
abstract::The Collaborative Cross (CC) is a mouse recombinant inbred strain panel that is being developed as a resource for mammalian systems genetics. Here we describe an experiment that uses partially inbred CC lines to evaluate the genetic properties and utility of this emerging resource. Genome-wide analysis of the incipien...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.111310.110
更新日期:2011-08-01 00:00:00
abstract::All individuals in a finite population are related if traced back long enough and will, therefore, share regions of their genomes identical by descent (IBD). Detection of such regions has several important applications-from answering questions about human evolution to locating regions in the human genome containing di...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.115360.110
更新日期:2011-07-01 00:00:00
abstract::Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functi...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.119016.110
更新日期:2011-07-01 00:00:00
abstract::We report the development of a simplified cap analysis of gene expression (CAGE) protocol adapted for single-molecule sequencers that avoids second strand synthesis, ligation, digestion, and PCR. HeliScopeCAGE directly sequences the 3' end of cap trapped first-strand cDNAs. As with previous versions of CAGE, we better...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.115469.110
更新日期:2011-07-01 00:00:00
abstract::Network "guilt by association" (GBA) is a proven approach for identifying novel disease genes based on the observation that similar mutational phenotypes arise from functionally related genes. In principle, this approach could account even for nonadditive genetic interactions, which underlie the synergistic combinatio...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.118992.110
更新日期:2011-07-01 00:00:00
abstract::Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulator...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.113381.110
更新日期:2011-05-01 00:00:00
abstract::Aberrant DNA methylation (DNAm) was first linked to cancer over 25 yr ago. Since then, many studies have associated hypermethylation of tumor suppressor genes and hypomethylation of oncogenes to the tumorigenic process. However, most of these studies have been limited to the analysis of promoters and CpG islands (CGIs...
journal_title:Genome research
pub_type: 杂志文章
doi:10.1101/gr.109678.110
更新日期:2011-04-01 00:00:00