Abstract:
:The iCLIP and eCLIP techniques facilitate the detection of protein-RNA interaction sites at high resolution, based on diagnostic events at crosslink sites. However, previous methods do not explicitly model the specifics of iCLIP and eCLIP truncation patterns and possible biases. We developed PureCLIP ( https://github.com/skrakau/PureCLIP ), a hidden Markov model based approach, which simultaneously performs peak-calling and individual crosslink site detection. It explicitly incorporates a non-specific background signal and, for the first time, non-specific sequence biases. On both simulated and real data, PureCLIP is more accurate in calling crosslink sites than other state-of-the-art methods and has a higher agreement across replicates.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Krakau S,Richard H,Marsico Adoi
10.1186/s13059-017-1364-2subject
Has Abstractpub_date
2017-12-28 00:00:00pages
240issue
1eissn
1474-7596issn
1474-760Xpii
10.1186/s13059-017-1364-2journal_volume
18pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases an...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1147-9
更新日期:2017-01-30 00:00:00
abstract:BACKGROUND:Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram-positive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-6-r69
更新日期:2009-01-01 00:00:00
abstract::A report on the Cold Spring Harbor Laboratory meeting on the Evolution of Developmental Diversity, Cold Spring Harbor, NY, USA, 17-21 April 2002. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2002-3-8-reports4023
更新日期:2002-07-15 00:00:00
abstract::The protein folding game Foldit shows that games are an effective way to recruit, engage and organize ordinary citizens to help solve difficult scientific problems. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-12-135
更新日期:2011-12-28 00:00:00
abstract::Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronom...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2002-3-5-reviews1013
更新日期:2002-01-01 00:00:00
abstract::A recent study has used serial analysis of gene expression to compare mouse forelimb and hindlimb gene-expression profiles. The method successfully identified known regulators of limb identity and has generated a candidate set of differentially expressed genes that may regulate limb identity. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2002-3-3-reviews1007
更新日期:2002-01-01 00:00:00
abstract:BACKGROUND:Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-6-r102
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. RESULTS...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1894-x
更新日期:2020-01-07 00:00:00
abstract::Two recent studies demonstrate the power of integrating tumor genotype information with epigenetic and proteomic studies to discover potential therapeutic targets in breast cancer. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1238-7
更新日期:2017-05-22 00:00:00
abstract::Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. Based on this, we introduce a new computational strategy...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-2-r23
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:Trypanosoma brucei is the causative agent of human sleeping sickness and animal trypanosomiasis in sub-Saharan Africa, and it has been subdivided into three subspecies: Trypanosoma brucei gambiense and Trypanosoma brucei rhodesiense, which cause sleeping sickness in humans, and the nonhuman infective Trypano...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-6-r103
更新日期:2008-01-01 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::An intriguing recent study examines the role of miR-1202, a glutamate receptor regulating microRNA, in regulating major depressive disorder. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0421-3
更新日期:2014-07-26 00:00:00
abstract:BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0578-9
更新日期:2015-01-29 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:Metastatic progress is the primary cause of death in most cancers, yet the regulatory dynamics driving the cellular changes necessary for metastasis remain poorly understood. Multi-omics approaches hold great promise for addressing this challenge; however, current analysis tools have limited capabilities to ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02213-x
更新日期:2021-01-07 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::We develop PIRCh-seq, a method which enables a comprehensive survey of chromatin-associated RNAs in a histone modification-specific manner. We identify hundreds of chromatin-associated RNAs in several cell types with substantially less contamination by nascent transcripts. Non-coding RNAs are found enriched on chromat...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1880-3
更新日期:2019-12-20 00:00:00
abstract:BACKGROUND:Comparisons between C3 and C4 grasses often utilize C3 species from the subfamilies Ehrhartoideae or Pooideae and C4 species from the subfamily Panicoideae, two clades that diverged over 50 million years ago. The divergence of the C3 panicoid grass Dichanthelium oligosanthes from the independent C4 lineages ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1080-3
更新日期:2016-10-28 00:00:00
abstract::Genome editing holds remarkable promise to transform human medicine as new therapies that can directly address the genetic causes of disease. However, concerns remain about possible undesired biological consequences of genome editors, particularly the introduction of unintended 'off-target' mutations. Here, we discuss...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1610-2
更新日期:2018-12-22 00:00:00
abstract::Two recent publications have demonstrated how delivering CRISPR nucleases provides a promising solution to the growing problem of bacterial antibiotic resistance. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/s13059-014-0516-x
更新日期:2014-11-08 00:00:00
abstract:BACKGROUND:Gynecologic malignancy is one of the leading causes of mortality in female adults worldwide. Comprehensive genomic analysis has revealed a list of molecular aberrations that are essential to tumorigenesis, progression, and metastasis of gynecologic tumors. However, targeting such alterations has frequently l...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1848-3
更新日期:2019-11-26 00:00:00
abstract::A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases....
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2005-6-6-113
更新日期:2005-01-01 00:00:00
abstract::Ancient DNA research is revealing a human history far more complex than that inferred from parsimonious models based on modern DNA. Here, we review some of the key events in the peopling of the world in the light of the findings of work on ancient DNA. ...
journal_title:Genome biology
pub_type: 历史文章,杂志文章,评审
doi:10.1186/s13059-015-0866-z
更新日期:2016-01-11 00:00:00
abstract:BACKGROUND:RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-6-r79
更新日期:2014-06-19 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::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: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:BACKGROUND:Short-term laboratory evolution of bacteria followed by genomic sequencing provides insight into the mechanism of adaptive evolution, such as the number of mutations needed for adaptation, genotype-phenotype relationships, and the reproducibility of adaptive outcomes. RESULTS:In the present study, we descri...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-10-r118
更新日期:2009-01-01 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