PureCLIP: capturing target-specific protein-RNA interaction footprints from single-nucleotide CLIP-seq data.


: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.


Genome Biol


Genome biology


Krakau S,Richard H,Marsico A




Has Abstract


2017-12-28 00:00:00














  • Using orthologous and paralogous proteins to identify specificity determining residues.

    abstract:BACKGROUND:Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which de...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Mirny LA,Gelfand MS

    更新日期:2002-01-01 00:00:00

  • A Keystone for ncRNA.

    abstract::A report on the Keystone symposium 'Non-coding RNAs' held at Snowbird, Utah, USA, 31 March to 5 April 2012. ...

    journal_title:Genome biology



    authors: Hacisuleyman E,Cabili MN,Rinn JL

    更新日期:2012-05-25 00:00:00

  • EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.

    abstract::The EpiGRAPH web service http://epigraph.mpi-inf.mpg.de/ enables biologists to uncover hidden associations in vertebrate genome and epigenome datasets. Users can upload sets of genomic regions and EpiGRAPH will test multiple attributes (including DNA sequence, chromatin structure, epigenetic modifications and evolutio...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Bock C,Halachev K,Büch J,Lengauer T

    更新日期:2009-02-10 00:00:00

  • MicroPro: using metagenomic unmapped reads to provide insights into human microbiota and disease associations.

    abstract::We develop a metagenomic data analysis pipeline, MicroPro, that takes into account all reads from known and unknown microbial organisms and associates viruses with complex diseases. We utilize MicroPro to analyze four metagenomic datasets relating to colorectal cancer, type 2 diabetes, and liver cirrhosis and show tha...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Zhu Z,Ren J,Michail S,Sun F

    更新日期:2019-08-06 00:00:00

  • Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia.

    abstract:BACKGROUND:Although aberrant DNA methylation has been observed previously in acute lymphoblastic leukemia (ALL), the patterns of differential methylation have not been comprehensively determined in all subtypes of ALL on a genome-wide scale. The relationship between DNA methylation, cytogenetic background, drug resista...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Nordlund J,Bäcklin CL,Wahlberg P,Busche S,Berglund EC,Eloranta ML,Flaegstad T,Forestier E,Frost BM,Harila-Saari A,Heyman M,Jónsson OG,Larsson R,Palle J,Rönnblom L,Schmiegelow K,Sinnett D,Söderhäll S,Pastinen T,Gusta

    更新日期:2013-09-24 00:00:00

  • Network security and data integrity in academia: an assessment and a proposal for large-scale archiving.

    abstract::A direct impediment to the optimal use of online databases is the increasing prevalence, severity, and toll of computer and network security incidents. Funding agencies should set up working groups that can provide essential services such as universal backup, archival storage, and mirroring of community resources, con...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Smith A,Greenbaum D,Douglas SM,Long M,Gerstein M

    更新日期:2005-01-01 00:00:00

  • The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading.

    abstract:BACKGROUND:The RNA-binding protein Argonaute 2 (AGO2) is a key effector of RNA-silencing pathways It exerts a pivotal role in microRNA maturation and activity and can modulate chromatin remodeling, transcriptional gene regulation and RNA splicing. Estrogen receptor beta (ERβ) is endowed with oncosuppressive activities,...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Tarallo R,Giurato G,Bruno G,Ravo M,Rizzo F,Salvati A,Ricciardi L,Marchese G,Cordella A,Rocco T,Gigantino V,Pierri B,Cimmino G,Milanesi L,Ambrosino C,Nyman TA,Nassa G,Weisz A

    更新日期:2017-10-06 00:00:00

  • Use of high-density tiling microarrays to identify mutations globally and elucidate mechanisms of drug resistance in Plasmodium falciparum.

    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


    authors: Dharia NV,Sidhu AB,Cassera MB,Westenberger SJ,Bopp SE,Eastman RT,Plouffe D,Batalov S,Park DJ,Volkman SK,Wirth DF,Zhou Y,Fidock DA,Winzeler EA

    更新日期:2009-02-13 00:00:00

  • Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia.

    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


    authors: Xia X,Kung AL

    更新日期:2009-01-01 00:00:00

  • Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca.

    abstract:BACKGROUND:Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alp...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Fan R,Gu Z,Guang X,Marín JC,Varas V,González BA,Wheeler JC,Hu Y,Li E,Sun X,Yang X,Zhang C,Gao W,He J,Munch K,Corbett-Detig R,Barbato M,Pan S,Zhan X,Bruford MW,Dong C

    更新日期:2020-07-02 00:00:00

  • Transcriptional response to alcohol exposure in Drosophila melanogaster.

    abstract:BACKGROUND:Alcoholism presents widespread social and human health problems. Alcohol sensitivity, the development of tolerance to alcohol and susceptibility to addiction vary in the population. Genetic factors that predispose to alcoholism remain largely unknown due to extensive genetic and environmental variation in hu...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Morozova TV,Anholt RR,Mackay TF

    更新日期:2006-01-01 00:00:00

  • Genomic parasites and genome evolution.

    abstract::A report of the Second International Conference/Workshop on the Genomic Impact of Eukaryotic Transposable Elements, Pacific Grove, USA, 6-10 February 2009. ...

    journal_title:Genome biology



    authors: Ivics Z

    更新日期:2009-01-01 00:00:00

  • Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.

    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


    authors: Frankl-Vilches C,Kuhl H,Werber M,Klages S,Kerick M,Bakker A,de Oliveira EH,Reusch C,Capuano F,Vowinckel J,Leitner S,Ralser M,Timmermann B,Gahr M

    更新日期:2015-01-29 00:00:00

  • Butterfly gene flow goes berserk.

    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


    authors: Ffrench-Constant RH

    更新日期:2016-02-27 00:00:00

  • Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.

    abstract:BACKGROUND:Transcription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has b...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Gordân R,Murphy KF,McCord RP,Zhu C,Vedenko A,Bulyk ML

    更新日期:2011-12-21 00:00:00

  • A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.

    abstract::Improving the quality and coverage of the protein interactome is of tantamount importance for biomedical research, particularly given the various sources of uncertainty in high-throughput techniques. We introduce a structure-based framework, Coev2Net, for computing a single confidence score that addresses both false-p...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Hosur R,Peng J,Vinayagam A,Stelzl U,Xu J,Perrimon N,Bienkowska J,Berger B

    更新日期:2012-08-31 00:00:00

  • Chemical genomics in yeast.

    abstract::Many drugs have unknown, controversial or multiple mechanisms of action. Four recent 'chemical genomic' studies, using genome-scale collections of yeast gene deletions that were either arrayed or barcoded, have presented complementary approaches to identifying gene-drug and pathway-drug interactions. ...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Brenner C

    更新日期:2004-01-01 00:00:00

  • Predicting the effects of frameshifting indels.

    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


    authors: Hu J,Ng PC

    更新日期:2012-02-09 00:00:00

  • Comparative genomics of gene-family size in closely related bacteria.

    abstract:BACKGROUND:The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. RESULTS:The relative content o...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Pushker R,Mira A,Rodríguez-Valera F

    更新日期:2004-01-01 00:00:00

  • An improved method for detecting and delineating genomic regions with altered gene expression in cancer.

    abstract::Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method c...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Nilsson B,Johansson M,Heyden A,Nelander S,Fioretos T

    更新日期:2008-01-21 00:00:00

  • The sequence of human chromosome 21 and implications for research into Down syndrome.

    abstract::The recent completion of the DNA sequence of human chromosome 21 has provided the first look at the 225 genes that are candidates for involvement in Down syndrome (trisomy 21). A broad functional classification of these genes, their expression data and evolutionary conservation, and comparison with the gene content of...

    journal_title:Genome biology

    pub_type: 杂志文章,评审


    authors: Gardiner K,Davisson M

    更新日期:2000-01-01 00:00:00

  • Global orchestration of gene expression by the biological clock of cyanobacteria.

    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


    authors: Johnson CH

    更新日期:2004-01-01 00:00:00

  • Conserved rules govern genetic interaction degree across species.

    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


    authors: Koch EN,Costanzo M,Bellay J,Deshpande R,Chatfield-Reed K,Chua G,D'Urso G,Andrews BJ,Boone C,Myers CL

    更新日期:2012-07-02 00:00:00

  • Current status and applications of genome-scale metabolic models.

    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


    authors: Gu C,Kim GB,Kim WJ,Kim HU,Lee SY

    更新日期:2019-06-13 00:00:00

  • A genomic and evolutionary approach reveals non-genetic drug resistance in malaria.

    abstract:BACKGROUND:Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis with other resistance mechanisms has not yet been elucidated. RESULTS:We previously described two mut...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Herman JD,Rice DP,Ribacke U,Silterra J,Deik AA,Moss EL,Broadbent KM,Neafsey DE,Desai MM,Clish CB,Mazitschek R,Wirth DF

    更新日期:2014-01-01 00:00:00

  • Consensus clustering and functional interpretation of gene-expression data.

    abstract::Microarray analysis using clustering algorithms can suffer from lack of inter-method consistency in assigning related gene-expression profiles to clusters. Obtaining a consensus set of clusters from a number of clustering methods should improve confidence in gene-expression analysis. Here we introduce consensus cluste...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Swift S,Tucker A,Vinciotti V,Martin N,Orengo C,Liu X,Kellam P

    更新日期:2004-01-01 00:00:00

  • Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation.

    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


    authors: Dueck H,Khaladkar M,Kim TK,Spaethling JM,Francis C,Suresh S,Fisher SA,Seale P,Beck SG,Bartfai T,Kuhn B,Eberwine J,Kim J

    更新日期:2015-06-09 00:00:00

  • Mechanisms of aging in senescence-accelerated mice.

    abstract:BACKGROUND:Progressive neurological dysfunction is a key aspect of human aging. Because of underlying differences in the aging of mice and humans, useful mouse models have been difficult to obtain and study. We have used gene-expression analysis and polymorphism screening to study molecular senescence of the retina and...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Carter TA,Greenhall JA,Yoshida S,Fuchs S,Helton R,Swaroop A,Lockhart DJ,Barlow C

    更新日期:2005-01-01 00:00:00

  • Repression of chimeric transcripts emanating from endogenous retrotransposons by a sequence-specific transcription factor.

    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


    authors: Mak KS,Burdach J,Norton LJ,Pearson RC,Crossley M,Funnell AP

    更新日期:2014-04-30 00:00:00

  • A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems.

    abstract:BACKGROUND:We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. RESULTS:We outline here a conceptual basis for designing such a language and describe Bio...

    journal_title:Genome biology

    pub_type: 杂志文章


    authors: Cook DL,Farley JF,Tapscott SJ

    更新日期:2001-01-01 00:00:00