Abstract:
:A report on the Plant Genomics European Meeting (Plant-GEMS2004), Lyon, France, 22-25 September 2004.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Van de Peer Ydoi
10.1186/gb-2004-6-1-302keywords:
subject
Has Abstractpub_date
2005-01-01 00:00:00pages
302issue
1eissn
1474-7596issn
1474-760Xpii
gb-2004-6-1-302journal_volume
6pub_type
相关文献
GENOME BIOLOGY文献大全abstract::Allele-specific expression is traditionally studied by bulk RNA sequencing, which measures average expression across cells. Single-cell RNA sequencing allows the comparison of expression distribution between the two alleles of a diploid organism and the characterization of allele-specific bursting. Here, we propose SC...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1200-8
更新日期:2017-04-26 00:00:00
abstract:BACKGROUND:Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathogens amid the plethora of human sequencing reads. In cancer research, the tumorigenic ability of patho...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1819-8
更新日期:2019-10-22 00:00:00
abstract::In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-s1-s6
更新日期:2008-01-01 00:00:00
abstract::Keith Joung, Dan Voytas and Joanne Kamens share insights into how the genome editing field was advanced by early access to biological resources and the role in this process that plasmid repositories play. ...
journal_title:Genome biology
pub_type: 面试
doi:10.1186/s13059-015-0830-y
更新日期:2015-11-20 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 genetic and molecular analysis of circadian timekeeping mechanisms has accelerated as a result of the increasing volume of genomic markers and nucleotide sequence information. Completion of whole genome sequences and the use of differential gene expression technology will hasten the discovery of the clock output p...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2000-1-4-reviews1023
更新日期:2000-01-01 00:00:00
abstract::A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2012-13-12-324
更新日期:2012-12-19 00:00:00
abstract::A new study shows that genomic introgression between two Heliconius butterfly species is not solely confined to color pattern loci. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-016-0898-z
更新日期:2016-02-27 00:00:00
abstract::Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a central clock. Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2004-5-4-217
更新日期:2004-01-01 00:00:00
abstract::A recent study explores the genome content of uncultured unicellular marine eukaryotes and provides insights about interactions between uncultured eukaryotes and other biological entities. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-6-117
更新日期:2011-06-27 00:00:00
abstract:BACKGROUND:Obligate pathogenic bacteria lose more genes relative to facultative pathogens, which, in turn, lose more genes than free-living bacteria. It was suggested that the increased gene loss in obligate pathogens may be due to a reduction in the effectiveness of purifying selection. Less attention has been given t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-8-r164
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:DNA methylation and the Polycomb repression system are epigenetic mechanisms that play important roles in maintaining transcriptional repression. Recent evidence suggests that DNA methylation can attenuate the binding of Polycomb protein components to chromatin and thus plays a role in determining their geno...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-3-r25
更新日期:2013-03-25 00:00:00
abstract::Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a si...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1284-1
更新日期:2017-08-04 00:00:00
abstract::Single-cell RNA-seq in samples from the human neocortex demonstrate that long noncoding RNAs (lncRNAs) are abundantly expressed in specific individual brain cells, despite being hard to detect in bulk samples. This result suggests that the lncRNAs might have important functions in specific cell types in the brain. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-016-0933-0
更新日期:2016-04-14 00:00:00
abstract::A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2003-4-9-336
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:Genome-wide DNA methylation (DNAm) profiling has allowed for the development of molecular predictors for a multitude of traits and diseases. Such predictors may be more accurate than the self-reported phenotypes and could have clinical applications. RESULTS:Here, penalized regression models are used to deve...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1514-1
更新日期:2018-09-27 00:00:00
abstract::The accuracy of base calls produced by Illumina sequencers is adversely affected by several processes, with laser cross-talk and cluster phasing being prominent. We introduce an explicit statistical model of the sequencing process that generalizes current models of phasing and cross-talk and forms the basis of a base ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-2-r13
更新日期:2012-02-29 00:00:00
abstract:BACKGROUND:Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to s...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02192-z
更新日期:2020-11-23 00:00:00
abstract::Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction associations for entire metabolic genes in an organism, and can be simulated to predict metabolic fluxes for various systems-level metabolic studies. Since the first GEM for Haemophilus influenzae was reported in 1999, advances have be...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-019-1730-3
更新日期:2019-06-13 00:00:00
abstract::To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, we develop CICERO, a local assembly-based algorithm that integrates RNA-seq read support with extensive annotation for candidate ranking. CICERO outperforms commonly used methods, achieving a 95% detection rate for 184 independently validat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02043-x
更新日期:2020-05-28 00:00:00
abstract::Genetic studies have identified more than 150 autoimmune loci, and next-generation sequencing will identify more. Is it time to make human the model organism for autoimmune research? ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-5-212
更新日期:2010-01-01 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:The vast number of precise intercellular connections within vertebrate nervous systems is only partly explained by the comparatively few known extracellular guidance cues. Large families of neural orphan receptor proteins have been identified and are likely to contribute to these recognition processes but du...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-9-r99
更新日期:2009-01-01 00:00:00
abstract::Transposable elements (TEs) are notable drivers of genetic innovation. Over evolutionary time, TE insertions can supply new promoter, enhancer, and insulator elements to protein-coding genes and establish novel, species-specific gene regulatory networks. Conversely, ongoing TE-driven insertional mutagenesis, nonhomolo...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-016-0965-5
更新日期:2016-05-09 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:BACKGROUND:Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bay...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-12-r126
更新日期:2012-12-27 00:00:00
abstract::The subcellular localization of the entire proteome of an organism, the yeast Saccharomyces cerevisiae, has been revealed for the first time. Comparison with less comprehensive studies of mammalian cells provides insights into the localization of the mammalian proteome. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2003-4-12-240
更新日期:2003-01-01 00:00:00
abstract::Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertio...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-10-r82
更新日期:2004-01-01 00:00:00
abstract:BACKGROUND:During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-2-r11
更新日期:2012-02-20 00:00:00
abstract:BACKGROUND:Four hypervariable minisatellite loci were scored on a panel of 116 individuals of various geographical origins representing a large part of the diversity present in house mouse subspecies. Internal structures of alleles were determined by minisatellite variant repeat mapping PCR to produce maps of interming...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-5-r80
更新日期:2007-01-01 00:00:00