Abstract:
:A report of the Wellcome Trust Functional Genomics and Systems Biology Conference, Hinxton, UK, 29 November to 1 December 2011.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Bakal Cdoi
10.1186/gb-2012-13-1-312subject
Has Abstractpub_date
2012-01-30 00:00:00pages
312issue
1eissn
1474-7596issn
1474-760Xpii
gb-2012-13-1-312journal_volume
13pub_type
相关文献
GENOME BIOLOGY文献大全abstract::Prediction of the diagnostic category of a tissue sample from its gene-expression profile and selection of relevant genes for class prediction have important applications in cancer research. We have developed the uncorrelated shrunken centroid (USC) and error-weighted, uncorrelated shrunken centroid (EWUSC) algorithms...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-12-r83
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:In microarray data analysis, the comparison of gene-expression profiles with respect to different conditions and the selection of biologically interesting genes are crucial tasks. Multivariate statistical methods have been applied to analyze these large datasets. Less work has been published concerning the a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-4-research0019
更新日期:2002-01-01 00:00:00
abstract::Recent genomic studies showing abnormalities in the fibroblast growth factor system in the postmortem brains of people with major depressive disorder support previous indications of a role for growth factors in mood disorders. Similar molecular pathways, volumetric changes, and the effects of exercise on mood suggest ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2005-6-4-215
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become usefu...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1368-y
更新日期:2017-12-20 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:Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or activ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-3-r45
更新日期:2014-03-03 00:00:00
abstract::Two landmark studies of cell signaling, by RNA interference and phosphoproteomics, provide complementary global views of the pathways downstream of receptor kinases, including those regulated by Erks. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-1-202
更新日期:2007-01-01 00:00:00
abstract::A recent study in Genome Biology has characterized the evolution of candidate hominoid-specific liver enhancers by using massively parallel reporter assays (MPRAs). ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1502-5
更新日期:2018-08-14 00:00:00
abstract::The spectrum of mutations discovered in cancer genomes can be explained by the activity of a few elementary mutational processes. We present a novel probabilistic method, EMu, to infer the mutational signatures of these processes from a collection of sequenced tumors. EMu naturally incorporates the tumor-specific oppo...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-4-r39
更新日期:2013-04-29 00:00:00
abstract::We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by journal_title:Genome biology pub_type: 杂志文章 doi:10.1186/gb-2010-11-3-r34 更新日期:2010-01-01 00:00:00
abstract::A subset of X-linked genes escapes silencing by X inactivation and is expressed from both X chromosomes in mammalian females. Species-specific differences in the identity of these genes have recently been discovered, suggesting a role in the evolution of sex differences. Chromatin analyses have aimed to discover how g...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2010-11-6-213
更新日期:2010-01-01 00:00:00
abstract:BACKGROUND:Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-8-r75
更新日期:2012-08-28 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::Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output signaling mechanisms. Over the past few years the first three-dimensional structures of phytochrome light-sensi...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2008-9-8-230
更新日期:2008-01-01 00:00:00
abstract::ELXR (Exon Locator and Extractor for Resequencing) streamlines the process of determining exon/intron boundaries and designing PCR and sequencing primers for high-throughput resequencing of exons. We have pre-computed ELXR primer sets for all exons identified from the human, mouse, and rat mRNA reference sequence (Ref...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-5-r36
更新日期:2004-01-01 00:00:00
abstract:BACKGROUND:Chronic psychological stress is associated with accelerated aging and increased risk for aging-related diseases, but the underlying molecular mechanisms are unclear. RESULTS:We examined the effect of lifetime stressors on a DNA methylation-based age predictor, epigenetic clock. After controlling for blood c...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0828-5
更新日期:2015-12-17 00:00:00
abstract::Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1642-2
更新日期:2019-02-26 00:00:00
abstract:BACKGROUND:Despite decades of research, the agent responsible for transmitting spongiform encephalopathies (TSEs) has not been identified. The Prion hypothesis, which dominates the field, supposes that modified host PrP protein, termed PrPSc, acts as the transmissible agent. This model fits the observation that TSE dis...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2001-2-7-preprint0006
更新日期:2001-01-01 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::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::We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple-species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surpris...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-9-r96
更新日期:2010-01-01 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::We propose a novel approach for finding a list of features that are commonly perturbed in two or more experiments, quantifying the evidence of dependence between the experiments by a ratio. We present a Bayesian analysis of this ratio, which leads us to suggest two rules for choosing a cut-off on the ranked list of p ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-4-r54
更新日期:2007-01-01 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::The functional annotation of proteins identified in genome sequencing projects is based on similarities to homologs in the databases. As a result of the possible strategies for divergent evolution, homologous enzymes frequently do not catalyze the same reaction, and we conclude that assignment of function from sequenc...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2000-1-5-reviews0005
更新日期:2000-01-01 00:00:00
abstract:BACKGROUND:Cultivable archaeal species are assigned to two phyla -- the Crenarchaeota and the Euryarchaeota -- by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. The recently described hyperthermophile Nanoarchaeum equitans, harboring the smallest cellul...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-5-r42
更新日期:2005-01-01 00:00:00
abstract::Abhay Sharma brings two arguments in favor of transgenerational epigenetic inheritance (TGEI) in mammals when criticizing our work. He uses probability calculations and finds that the probability of obtaining the number of common changes in the in utero-exposed prospermatogonia and the same cells in the next generatio...
journal_title:Genome biology
pub_type: 评论,信件
doi:10.1186/s13059-016-0978-0
更新日期:2016-05-16 00:00:00
abstract::The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1138-2
更新日期:2017-01-18 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:BACKGROUND:Polydnaviruses, double-stranded DNA viruses with segmented genomes, have evolved as obligate endosymbionts of parasitoid wasps. Virus particles are replication deficient and produced by female wasps from proviral sequences integrated into the wasp genome. These particles are co-injected with eggs into caterp...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-12-r183
更新日期:2008-01-01 00:00:00