Abstract:
:Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Sibley CR,Attig J,Ule Jdoi
10.1186/gb4030subject
Has Abstractpub_date
2012-07-17 00:00:00pages
163issue
7eissn
1474-7596issn
1474-760Xpii
gb-2012-13-7-163journal_volume
13pub_type
相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications mus...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02190-1
更新日期:2020-11-25 00:00:00
abstract:BACKGROUND:The current bovine genomic reference sequence was assembled from a Hereford cow. The resulting linear assembly lacks diversity because it does not contain allelic variation, a drawback of linear references that causes reference allele bias. High nucleotide diversity and the separation of individuals by hundr...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02105-0
更新日期:2020-07-27 00:00:00
abstract:BACKGROUND:The variation in the sizes of the genomes of distinct life forms remains somewhat puzzling. The organization of proteins into domains and the different mechanisms that regulate gene expression are two factors that potentially increase the capacity of genomes to create more complex systems. High-throughput pr...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-5-r94
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Nuclear factor I-A (NFI-A), a phylogenetically conserved transcription/replication protein, plays a crucial role in mouse brain development. Previous studies have shown that disruption of the Nfia gene in mice leads to perinatal lethality, corpus callosum agenesis, and hydrocephalus. RESULTS:To identify pot...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-5-r72
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Epigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesize that using a generic reference could lead to incorrectly mapped reads and bias ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02038-8
更新日期:2020-05-25 00:00:00
abstract:BACKGROUND:Microarray technology is increasingly being applied in biological and medical research to address a wide range of problems, such as the classification of tumors. An important statistical problem associated with tumor classification is the identification of new tumor classes using gene-expression profiles. Tw...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-7-research0036
更新日期:2002-06-25 00:00:00
abstract:BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1078-x
更新日期:2016-11-01 00:00:00
abstract:BACKGROUND:Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-s2-s9
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:The identification of genetic changes that confer drug resistance or other phenotypic changes in pathogens can help optimize treatment strategies, support the development of new therapeutic agents, and provide information about the likely function of genes. Elucidating mechanisms of phenotypic drug resistanc...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-2-r21
更新日期:2009-02-13 00:00:00
abstract::An elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors has been developed by Rhee and Pugh. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-1-139
更新日期:2012-01-27 00:00:00
abstract::Droplet-based single-cell RNA sequencing protocols have dramatically increased the throughput of single-cell transcriptomics studies. A key computational challenge when processing these data is to distinguish libraries for real cells from empty droplets. Here, we describe a new statistical method for calling cells fro...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1662-y
更新日期:2019-03-22 00:00:00
abstract::The ability to quantitatively measure the expression of all genes in a given tissue or cell with a single assay is an exciting promise of gene-expression profiling technology. An in situ-synthesized 60-mer oligonucleotide microarray designed to detect transcripts from all mouse genes was validated, as well as a set of...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-7-r61
更新日期:2005-01-01 00:00:00
abstract::A combined approach of whole genome shotgun sequencing and ultra-high density linkage mapping using skim sequencing of a segregating population is effective for assembling allopolyploid genomes. ...
journal_title:Genome biology
pub_type: 信件
doi:10.1186/s13059-015-0585-5
更新日期:2015-01-31 00:00:00
abstract::Toxin/antitoxin (TA) systems, viewed as essential regulators of growth arrest and programmed cell death, are widespread among prokaryotes, but remain sparsely annotated. We present RASTA-Bacteria, an automated method allowing quick and reliable identification of TA loci in sequenced prokaryotic genomes, whether they a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-8-r155
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Epigenetic mechanisms such as chromatin accessibility impact transcription factor binding to DNA and transcriptional specificity. The androgen receptor (AR), a master regulator of the male phenotype and prostate cancer pathogenesis, acts primarily through ligand-activated transcription of target genes. Altho...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-10-r88
更新日期:2012-10-03 00:00:00
abstract:BACKGROUND:Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, b...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-9-r84
更新日期:2011-09-14 00:00:00
abstract::We describe domain pair exclusion analysis (DPEA), a method for inferring domain interactions from databases of interacting proteins. DPEA features a log odds score, Eij, reflecting confidence that domains i and j interact. We analyzed 177,233 potential domain interactions underlying 26,032 protein interactions. In to...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-10-r89
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:In eukaryotic cells, oxidative phosphorylation (OXPHOS) uses the products of both nuclear and mitochondrial genes to generate cellular ATP. Interspecies comparative analysis of these genes, which appear to be under strong functional constraints, may shed light on the evolutionary mechanisms that act on a set...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-2-r11
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:The identification of signatures of natural selection has long been used as an approach to understanding the unique features of any given species. Genes within segmental duplications are overlooked in most studies of selection due to the limitations of draft nonhuman genome assemblies and to the methodologic...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-1-r9
更新日期:2013-01-29 00:00:00
abstract:BACKGROUND:Hypoxia-inducible factor 1 (HIF-1) plays a key role in cellular adaptation to hypoxia. To better understand the determinants of HIF-1 binding and transactivation, we used ChIP-chip and gene expression profiling to define the relationship between the epigenetic landscape, sites of HIF-1 binding, and genes tra...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-10-r113
更新日期:2009-01-01 00:00:00
abstract::The discovery of several new structured non-coding RNAs in bacterial and archaeal genomes and metagenomes raises burning questions about their biological and biochemical functions. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2010-11-3-108
更新日期:2010-01-01 00:00:00
abstract::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 we announce Avianbase, a resource for bird genomics, which provides access to data released ...
journal_title:Genome biology
pub_type: 信件
doi:10.1186/s13059-015-0588-2
更新日期:2015-01-29 00:00:00
abstract::The mouse is an important model of human genetic disease. Describing phenotypes of mutant mice in a standard, structured manner that will facilitate data mining is a major challenge for bioinformatics. Here we describe a novel, compositional approach to this problem which combines core ontologies from a variety of sou...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-6-1-r8
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Population genetic theory predicts that rapid adaptation is largely driven by complex traits encoded by many loci of small effect. Because large-effect loci are quickly fixed in natural populations, they should not contribute much to rapid adaptation. RESULTS:To investigate the genetic architecture of therm...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1503-4
更新日期:2018-08-20 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenc...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-6-r96
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:The function of the non-coding portion of the human genome remains one of the most important questions of our time. Its vast complexity is exemplified by the recent identification of an unusual and notable component of the transcriptome - very long intergenic non-coding RNAs, termed vlincRNAs. RESULTS:Here ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-7-r73
更新日期:2013-07-22 00:00:00
abstract:BACKGROUND:Despite the biological and economic significance of scleractinian reef-building corals, the lack of large molecular datasets for a representative range of species limits understanding of many aspects of their biology. Within the Scleractinia, based on molecular evidence, it is generally recognised that there...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1552-8
更新日期:2018-11-02 00:00:00
abstract::The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-11-r111
更新日期:2006-01-01 00:00:00
abstract::From worms to humans, recognizing and modifying a specific chromosome is essential for dosage compensation, the mechanism by which equal X-linked gene expression in males and females is achieved. Recent molecular genetic and biochemical studies have provided new insights into how regulatory factors in Drosophila are r...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2000-1-6-reviews1030
更新日期:2000-01-01 00:00:00
abstract:BACKGROUND:Pre-mRNA splicing is an essential step in gene expression that occurs co-transcriptionally in the cell nucleus, involving a large number of RNA binding protein splicing factors, in addition to core spliceosome components. Several of these proteins are required for the recognition of intronic sequence element...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-11-r113
更新日期:2006-01-01 00:00:00