Abstract:
:We used scaled factorial moments to search for intermittency in the log expression ratios (LERs) for thousands of genes spotted on cDNA microarrays (gene chips). Results indicate varying levels of intermittency in gene expression. The observation of intermittency in the data analyzed provides a complimentary handle on moderately expressed genes, generally not tackled by conventional techniques.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Peterson LE,Lau Kdoi
10.1186/gb-2002-3-7-preprint0005keywords:
subject
Has Abstractpub_date
2002-05-29 00:00:00pages
PREPRINT0005issue
7eissn
1474-7596issn
1474-760Xjournal_volume
3pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract::Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb4030
更新日期:2012-07-17 00:00:00
abstract::Searching for similarities between biological sequences is the principal means by which bioinformatics contributes to our understanding of biology. Of the various informatics tools developed to accomplish this task, the most widely used is BLAST, the basic local alignment search tool. This article discusses the princi...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2001-2-10-reviews2002
更新日期:2001-01-01 00:00:00
abstract::Normalization is an essential step in the analysis of high-throughput data. Multi-sample global normalization methods, such as quantile normalization, have been successfully used to remove technical variation. However, these methods rely on the assumption that observed global changes across samples are due to unwanted...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0679-0
更新日期:2015-06-04 00:00:00
abstract::Field pathogenomics adds highly informative data to surveillance surveys by enabling rapid evaluation of pathogen variability, population structure and host genotype. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0615-3
更新日期:2015-03-02 00:00:00
abstract::Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably e...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-5-r86
更新日期:2008-01-01 00:00:00
abstract::Advances in sequencing technology have led to a sharp decrease in the cost of 'data generation'. But is this sufficient to ensure cost-effective and efficient 'knowledge generation'? ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-8-125
更新日期:2011-08-25 00:00:00
abstract:BACKGROUND:Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample. RESULTS:Application of decon...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-0893-4
更新日期:2016-02-22 00:00:00
abstract:BACKGROUND:Immunolabeling of metaphase chromosome spreads can map components of the human epigenome at the single cell level. Previously, there has been no systematic attempt to explore the potential of this approach for epigenomic mapping and thereby to complement approaches based on chromatin immunoprecipitation (ChI...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-11-r110
更新日期:2010-01-01 00:00:00
abstract::Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of communit...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1643-1
更新日期:2019-02-26 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::An exciting recent study examining the methylation profile of human brain tissue implicates early-life epigenetic disruption in the neurodevelopmental origin of schizophrenia. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-014-0495-y
更新日期:2014-10-29 00:00:00
abstract:BACKGROUND:Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in gr...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-6-r54
更新日期:2013-06-07 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:BACKGROUND:Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chromosome 13 is the chromosome with the highest number of neocentromeres. We reconstructed the mammali...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-10-r91
更新日期:2006-01-01 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::MiRNAs play important roles in many diseases including cancers. However computational prediction of miRNA target genes is challenging and the accuracies of existing methods remain poor. We report mirMark, a new machine learning-based method of miRNA target prediction at the site and UTR levels. This method uses experi...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0500-5
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:The functional impact of genetic variation has been extensively surveyed, revealing that genetic changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific genetic changes to gene expression, DNA methylation, and histone marks but these investigations have ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1173-7
更新日期:2017-03-10 00:00:00
abstract:BACKGROUND:The history of African indigenous cattle and their adaptation to environmental and human selection pressure is at the root of their remarkable diversity. Characterization of this diversity is an essential step towards understanding the genomic basis of productivity and adaptation to survival under African fa...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1153-y
更新日期:2017-02-20 00:00:00
abstract:BACKGROUND:Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-11-r167
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Differentiation of metazoan cells requires execution of different gene expression programs but recent single-cell transcriptome profiling has revealed considerable variation within cells of seeming identical phenotype. This brings into question the relationship between transcriptome states and cell phenotype...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0683-4
更新日期:2015-06-09 00:00:00
abstract:BACKGROUND:The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-10-r152
更新日期:2008-10-14 00:00:00
abstract:BACKGROUND:Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred dur...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1275-2
更新日期:2017-07-21 00:00:00
abstract:BACKGROUND:DNA methylation is a key epigenetic mechanism for driving and stabilizing cell-fate decisions. Local deposition and removal of DNA methylation are tightly coupled with transcription factor binding, although the relationship varies with the specific differentiation process. Conversion of monocytes to osteocla...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-9-r99
更新日期:2013-01-01 00:00:00
abstract::How the mechanisms of dosage compensation distinguish the sex chromosomes from the autosomes has been something of a mystery. A recent study in Caenorhabditis elegans has identified clusters of two common DNA motifs as a cis-acting code for the recruitment of the DCC, the protein complex that mediates dosage compensat...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2007-8-2-204
更新日期:2007-01-01 00:00:00
abstract::Two recent studies have added microarrays to the toolkit used to analyze the origins of replication in yeast chromosomes, providing a fuller picture of how genomic DNA replication is organized. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2002-3-6-reviews1016
更新日期:2002-01-01 00:00:00
abstract::PIWI proteins, a subfamily of PAZ/PIWI Domain family RNA-binding proteins, are best known for their function in silencing transposons and germline development by partnering with small noncoding RNAs called PIWI-interacting RNAs (piRNAs). However, recent studies have revealed multifaceted roles of the PIWI-piRNA pathwa...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/s13059-020-02221-x
更新日期:2021-01-08 00:00:00
abstract::A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2005-6-8-336
更新日期:2005-01-01 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:BACKGROUND:Two distinct classes of regulators have been implicated in regulating neuronal gene expression and mediating neuronal identity: transcription factors such as REST/NRSF (RE1 silencing transcription factor) and CREB (cAMP response element-binding protein), and microRNAs (miRNAs). How these two classes of regul...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-9-r85
更新日期:2006-01-01 00:00:00
abstract::Each human has approximately 50 to 280 frameshifting indels, yet their implications are unknown. We created SIFT Indel, a prediction method for frameshifting indels that has 84% accuracy. The percentage of human frameshifting indels predicted to be gene-damaging is negatively correlated with allele frequency. We also ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-2-r9
更新日期:2012-02-09 00:00:00