(Q33999125)

30 July 2017

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title

Computation for ChIP-seq and RNA-seq studies (English)

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30 July 2017

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2

Barbara Wold

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30 July 2017

Shirley Pepke

1

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PubMed ID

19844228

30 July 2017

Ali Mortazavi

series ordinal

3

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30 July 2017

1 November 2009

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30 July 2017

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30 July 2017

6

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30 July 2017

S22-32

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30 July 2017

11 Suppl

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https://scigraph.springernature.com/pub.10.1038/nmeth.1371

30 July 2017

0 references

cites work

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Extracting transcription factor targets from ChIP-Seq data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

De novo transcriptome assembly with ABySS.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Detection of single nucleotide variations in expressed exons of the human genome using RNA-Seq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

How to map billions of short reads onto genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Transcript length bias in RNA-seq data confounds systems biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

TopHat: discovering splice junctions with RNA-Seq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

RNA Pol II accumulates at promoters of growth genes during developmental arrest.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Statistical inferences for isoform expression in RNA-Seq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Annotating genomes with massive-scale RNA sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

An integrated software system for analyzing ChIP-chip and ChIP-seq data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Model-based analysis of ChIP-Seq (MACS)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

F-Seq: a feature density estimator for high-throughput sequence tags

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Optimal spliced alignments of short sequence reads

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Stem cell transcriptome profiling via massive-scale mRNA sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Mapping and quantifying mammalian transcriptomes by RNA-Seq

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

The transcriptional landscape of the yeast genome defined by RNA sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

SOAP: short oligonucleotide alignment program

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Sequence census methods for functional genomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Genome-wide maps of chromatin state in pluripotent and lineage-committed cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Genome-wide mapping of in vivo protein-DNA interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

Comparative analysis of processed pseudogenes in the mouse and human genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

High-resolution profiling of histone methylations in the human genome

28 July 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1371

Design and analysis of ChIP-seq experiments for DNA-binding proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1371

Alternative isoform regulation in human tissue transcriptomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1371

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1371

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1371

RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4121056

29 October 2018

Identifiers

DOI

10.1038/NMETH.1371

1 reference

PubMed ID

19844228

Dimensions Publication ID

30 July 2017

0 references

1 reference

30 July 2017

1 reference

PubMed ID

19844228