A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly

scientific article

A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1101/GR.5578007
P3181OpenCitations bibliographic resource ID1800150
P932PMC publication ID1891355
P698PubMed publication ID17568012
P5875ResearchGate publication ID6269169

P50authorWebb MillerQ12061804
Ross HardisonQ27063030
Anton NekrutenkoQ30004030
James TaylorQ30362443
Daniel BlankenbergQ47451229
Istvan AlbertQ80058787
P2093author name stringJianbin He
Yi Zhang
Narayanan Veeraraghavan
Kateryna D Makova
Matthew Ghent
Ian Schenck
P2860cites workGenome sequence, comparative analysis and haplotype structure of the domestic dogQ22122465
Initial sequence of the chimpanzee genome and comparison with the human genomeQ22122468
Genome sequence of the Brown Norway rat yields insights into mammalian evolutionQ22122498
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomesQ24534193
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22Q24594479
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolutionQ28241731
HyPhy: hypothesis testing using phylogeniesQ29013475
The ENCODE (ENCyclopedia Of DNA Elements) ProjectQ29547219
Galaxy: a platform for interactive large-scale genome analysisQ29547494
The general stochastic model of nucleotide substitutionQ29617428
Conservation and functional significance of gene topology in the genome of Caenorhabditis elegansQ33239533
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequencesQ33910867
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolutionQ35024015
Combining phylogenetic and hidden Markov models in biosequence analysisQ35851929
Male-biased mutation rate and divergence in autosomal, z-linked and w-linked introns of chicken and TurkeyQ48191094
Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimationQ57079033
P433issue6
P407language of work or nameEnglishQ1860
P921main subjectcollaborationQ1145523
data collaborationQ96060107
P304page(s)960-4
P577publication date2007-06-01
P1433published inGenome ResearchQ5533485
P1476titleA framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly
P478volume17

Reverse relations

cites work (P2860)
Q2875659628-way vertebrate alignment and conservation track in the UCSC Genome Browser
Q35095378A generalized topological entropy for analyzing the complexity of DNA sequences
Q33302934A macaque's-eye view of human insertions and deletions: differences in mechanisms
Q33594385A quick guide to large-scale genomic data mining
Q57002885A reference model for deploying applications in virtualized environments
Q33953905An integrated ChIP-seq analysis platform with customizable workflows
Q45043815An integrative approach to detect subtle trophic niche differentiation in the sympatric trawling bat species Myotis dasycneme and Myotis daubentonii
Q89810966Antifreeze protein complements cryoprotective dehydration in the freeze-avoiding springtail Megaphorura arctica
Q37112503Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes
Q21267236Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend
Q53071822Biology Needs Evolutionary Software Tools: Let's Build Them Right.
Q35946185Cancer therapeutic approach based on conformational stabilization of mutant p53 protein by small peptides.
Q36922980CloudLCA: finding the lowest common ancestor in metagenome analysis using cloud computing.
Q35195937Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes
Q35057220Complete Genome Sequence of Sphingobacterium sp. Strain ML3W, Isolated from Wings of Myotis lucifugus Infected with White Nose Syndrome
Q34715061Computational epigenetics
Q30049175DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES
Q90639239Design of Bacterial Strain-Specific qPCR Assays Using NGS Data and Publicly Available Resources and Its Application to Track Biocontrol Strains
Q42006359Diet of the insectivorous bat Pipistrellus nathusii during autumn migration and summer residence
Q28243453Dissemination of scientific software with Galaxy ToolShed
Q91651449Diversity of tryptophan halogenases in sponges of the genus Aplysina
Q42068405Does base-pairing strength play a role in microRNA repression?
Q30580514Dynamic estrogen receptor interactomes control estrogen-responsive trefoil Factor (TFF) locus cell-specific activities
Q41888953Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.
Q35557723Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study
Q33408033EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data
Q37961980Epigenetic biomarker development
Q28752380Evolution and survival on eutherian sex chromosomes
Q35056061Fine-mapping of colorectal cancer susceptibility loci at 8q23.3, 16q22.1 and 19q13.11: refinement of association signals and use of in silico analysis to suggest functional variation and unexpected candidate target genes
Q46261370First Insights into the Diverse Human Archaeome: Specific Detection of Archaea in the Gastrointestinal Tract, Lung, and Nose and on Skin.
Q21092859Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
Q31151459GeneTrack--a genomic data processing and visualization framework.
Q21092268Genome and phylogenetic analyses of trypanosoma evansi reveal extensive similarity to T. brucei and multiple independent origins for dyskinetoplasty
Q35384578Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.
Q37634409Genome-wide approaches to determining origin distribution
Q46614925Genome-wide detection and characterization of mating asymmetry in human populations
Q36948921Genome-wide studies highlight indirect links between human replication origins and gene regulation.
Q46056377Genomics made easier: an introductory tutorial to genome datamining
Q33520389GonadSAGE: a comprehensive SAGE database for transcript discovery on male embryonic gonad development
Q28743765Gramene database in 2010: updates and extensions
Q46247262Identification and Expression Profile of CYPome in Perennial Ryegrass and Tall Fescue in Response to Temperature Stress
Q31097599Integrated Systems for NGS Data Management and Analysis: Open Issues and Available Solutions
Q64910666Integrated entropy-based approach for analyzing exons and introns in DNA sequences.
Q28236549Integrating diverse databases into an unified analysis framework: a Galaxy approach
Q33761996MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks.
Q28243703Making whole genome multiple alignments usable for biologists
Q28285724Manipulation of FASTQ data with Galaxy
Q41965853MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays
Q44087548Mitochondrial genomics in Orthoptera using MOSAS.
Q57091933Multi-omic analyses of extensively decayed reveal expression of diverse array of lignocellulose degrading enzymes
Q34130760Mutation biases and mutation rate variation around very short human microsatellites revealed by human-chimpanzee-orangutan genomic sequence alignments
Q33833646NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs
Q28730711Next-generation genomics: an integrative approach
Q33791123Nucleosome regulatory dynamics in response to TGFβ
Q33651603PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.
Q33801716PileLine: a toolbox to handle genome position information in next-generation sequencing studies
Q33844997Preparing DNA libraries for multiplexed paired-end deep sequencing for Illumina GA sequencers
Q33699592Processing and analyzing ChIP-seq data: from short reads to regulatory interactions
Q36142497Profiling of adhesive-related genes in the freshwater cnidarian Hydra magnipapillata by transcriptomics and proteomics
Q28602497REPRODUCIBLE RESEARCH WORKFLOW IN R FOR THE ANALYSIS OF PERSONALIZED HUMAN MICROBIOME DATA
Q57525485RNA-Seq Read Alignments with PALMapper
Q34588437Regulation of alternative splicing by the core spliceosomal machinery
Q33857647Rice-Map: a new-generation rice genome browser
Q37247028Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
Q31037902S-MART, a software toolbox to aid RNA-Seq data analysis
Q104495240Serum amyloid A is a positive acute phase protein in Russian sturgeon challenged with Aeromonas hydrophila
Q37428432Strong heterogeneity in mutation rate causes misleading hallmarks of natural selection on indel mutations in the human genome
Q24673501Structured RNAs in the ENCODE selected regions of the human genome
Q35145517Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
Q33812545The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important
Q33698635The ETS family member GABPα modulates androgen receptor signalling and mediates an aggressive phenotype in prostate cancer
Q55518659The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.
Q39538459The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis
Q33691022The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites
Q110698159Transcriptional identification of genes light-interacting in the extraretinal photoreceptors of the crayfish Procambarus clarkii
Q37293358Transcriptome of embryonic and neonatal mouse cortex by high-throughput RNA sequencing.
Q36333534Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts.
Q34304668Using Galaxy to perform large-scale interactive data analyses
Q28277397Using galaxy to perform large-scale interactive data analyses
Q33541911Web-based analysis of (Epi-) genome data using EpiGRAPH and Galaxy
Q30488526WebLab: a data-centric, knowledge-sharing bioinformatic platform.
Q33920255ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence
Q33777909seqMINER: an integrated ChIP-seq data interpretation platform
Q28508449ΔNp63 is an ectodermal gatekeeper of epidermal morphogenesis

Search more.