Abstract:
:A method has been developed to identify proteins required for the biogenesis of non-coding RNA in yeast, using a microarray to screen for aberrant patterns of RNA processing in mutant strains, and new proteins involved in the processing of ribosomal and non-coding RNAs have been found.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Granneman S,Baserga SJdoi
10.1186/gb-2003-4-10-229keywords:
subject
Has Abstractpub_date
2003-01-01 00:00:00pages
229issue
10eissn
1474-7596issn
1474-760Xjournal_volume
4pub_type
杂志文章,评审相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:The role played by microRNAs (miRs) as common regulators in physiologic processes such as development and various disease states was recently highlighted. Retinitis pigmentosa (RP) linked to RHO (which encodes rhodopsin) is the most frequent form of inherited retinal degeneration that leads to blindness, for...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-11-r248
更新日期:2007-01-01 00:00:00
abstract::Our knowledge on tissue- and disease-specific functions of human genes is rather limited and highly context-specific. Here, we have developed a method for the comparison of mRNA expression levels of most human genes across 9,783 Affymetrix gene expression array experiments representing 43 normal human tissue types, 68...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-9-r139
更新日期:2008-01-01 00:00:00
abstract::A report on the Cold Spring Harbor Asia conference on Genome Assisted Biology of Crops and Model Plant Systems Meeting, held in Suzhou, China, April 21-25, 2014. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb4176
更新日期:2014-05-23 00:00:00
abstract::Bisulfite sequencing (BS-seq) is the gold standard for studying genome-wide DNA methylation. We developed MOABS to increase the speed, accuracy, statistical power and biological relevance of BS-seq data analysis. MOABS detects differential methylation with 10-fold coverage at single-CpG resolution based on a Beta-Bino...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-2-r38
更新日期:2014-02-24 00:00:00
abstract:BACKGROUND:Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patient...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0677-2
更新日期:2015-05-30 00:00:00
abstract:BACKGROUND:The time of locus replication during S-phase is tightly regulated and correlates with chromatin state. Embryonic stem (ES) cells have an unusual chromatin profile where many developmental regulator genes that are not yet expressed are marked by both active and repressive histone modifications. This poised or...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-8-r169
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...
journal_title:Genome biology
pub_type: 杂志文章,随机对照试验
doi:10.1186/gb-2013-14-4-r34
更新日期:2013-04-29 00:00:00
abstract:BACKGROUND:Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1633-3
更新日期:2019-01-31 00:00:00
abstract:BACKGROUND:Hemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms u...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-6-r65
更新日期:2010-01-01 00:00:00
abstract::Normalization is critical for removing systematic variation from microarray data. For two-color microarray platforms, intensity-dependent lowess normalization is commonly used to correct relative gene expression values for biases. Here we outline a normalization method for use when the assumptions of lowess normalizat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-1-r2
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes. RESULTS:Using publicly available milk proteome data and mammary expressed sequence tags, 197 milk protein genes and over 6,000 mammary genes were identified in the bovine genome...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-4-r43
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Recent advancements in next-generation sequencing have rapidly improved our ability to study genomic material at an unprecedented scale. Despite substantial improvements in sequencing technologies, errors present in the data still risk confounding downstream analysis and limiting the applicability of sequenc...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01988-3
更新日期:2020-03-17 00:00:00
abstract:BACKGROUND:Gene duplications have a major role in the evolution of new biological functions. Theoretical studies often assume that a duplication per se is selectively neutral and that, following a duplication, one of the gene copies is freed from purifying (stabilizing) selection, which creates the potential for evolut...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-2-research0008
更新日期:2002-01-01 00:00:00
abstract::Short hairpin RNAs can provide stable gene silencing via RNA interference. Recent studies have shown toxicity in vivo that appears to be related to saturation of the endogenous microRNA pathway. Will these findings limit the therapeutic use of such hairpins? ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-8-231
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Dictyostelium discoideum is a eukaryote with a simple lifestyle and a relatively small genome whose sequence has been fully determined. It is widely used for studies on cell signaling, movement and multicellular development. Ras guanine-nucleotide exchange factors (RasGEFs) are the proteins that activate Ras...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-8-r68
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Methylation of nucleotides, notably in the forms of 5-methylcytosine (5mC) in DNA and N6-methyladenosine (m6A) in mRNA, carries important information for gene regulation. 5mC has been elucidated to participate in the regulation of fruit ripening, whereas the function of m6A in this process and the interplay ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1771-7
更新日期:2019-08-06 00:00:00
abstract:BACKGROUND:CRISPR-Cas systems have been broadly embraced as effective tools for genome engineering applications, with most studies to date utilizing the Streptococcus pyogenes Cas9. Here we characterize and manipulate the smaller, 1053 amino acid nuclease Staphylococcus aureus Cas9. RESULTS:We find that the S. aureus ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0817-8
更新日期:2015-11-24 00:00:00
abstract::Next-generation massively parallel sequencing technology provides a powerful new means of assessing rates and regulation of translation across an entire transcriptome. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2009-10-4-215
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Piwi-interacting RNAs (piRNAs) are a class of short (~26-31-nucleotide) non-protein-coding RNAs expressed in the metazoan germline. The piRNA pathway in arthropods is best understood in the ovary of Drosophila melanogaster, where it acts to silence active transposable elements (TEs). Maternal loading of piRN...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1304-1
更新日期:2017-09-26 00:00:00
abstract:BACKGROUND:Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-3-r48
更新日期:2008-01-01 00:00:00
abstract::A report of the recent EMBO Conference 'From Functional Genomics to Systems Biology' held at the EMBL Advanced Training Centre, Heidelberg, Germany, 13-16 November 2010. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2011-12-1-302
更新日期:2011-01-01 00:00:00
abstract:BACKGROUND:Retroviral elements are pervasively transcribed and dynamically regulated during development. While multiple histone- and DNA-modifying enzymes have broadly been associated with their global silencing, little is known about how the many diverse retroviral families are each selectively recognized. RESULTS:He...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-4-r58
更新日期:2014-04-30 00:00:00
abstract:BACKGROUND:While large-scale cancer genomic projects are comprehensively characterizing the mutational spectrum of various cancers, so far little attention has been devoted to either define the antigenicity of these mutations or to characterize the immune responses they elicit. Here we present a strategy to characteriz...
journal_title:Genome biology
pub_type: 杂志文章,meta分析
doi:10.1186/s13059-015-0620-6
更新日期:2015-03-31 00:00:00
abstract:BACKGROUND:Protein synthesis is tightly regulated and alterations to translation are characteristic of many cancers.Translation regulation is largely exerted at initiation through the eukaryotic translation initiation factor 4 F (eIF4F). eIF4F is pivotal for oncogenic signaling as it integrates mitogenic signals to amp...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0476-1
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Synthetic genetic interactions have recently been mapped on a genome scale in the budding yeast Saccharomyces cerevisiae, providing a functional view of the central processes of eukaryotic life. Currently, comprehensive genetic interaction networks have not been determined for other species, and we therefore...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-7-r57
更新日期:2012-07-02 00:00:00
abstract::Microarrays have been used in a wide variety of experimental systems, but realizing their full potential is contingent on sophisticated and rigorous experimental design and data analysis. This article highlights what is needed to get the most out of microarrays in terms of accurately and effectively revealing differen...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-2-105
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target gene...
journal_title:Genome biology
pub_type: 杂志文章,meta分析
doi:10.1186/gb-2004-5-9-r66
更新日期:2004-01-01 00:00:00
abstract::A novel in vivo screening approach has identified KLF17 as a key metastasis suppressor gene that acts through regulation of Id1 transcription factor-dependent induction of the epithelial-to-mesenchymal transition. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2009-10-11-244
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Transposable elements (TEs) are major components of large plant genomes and main drivers of genome evolution. The most recent assembly of hexaploid bread wheat recovered the highly repetitive TE space in an almost complete chromosomal context and enabled a detailed view into the dynamics of TEs in the A, B, ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1479-0
更新日期:2018-08-17 00:00:00
abstract::Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-1941-7
更新日期:2020-02-12 00:00:00