(Q33815482)

29 July 2017

title

Detection and removal of biases in the analysis of next-generation sequencing reads (English)

1 reference

29 July 2017

1 reference

1

Schraga Schwartz

0 references

Ram Oren

series ordinal

2

object named as

Ram Oren

1 reference

29 July 2017

Gil Ast

3

1 reference

29 July 2017

language of work or name

English

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publication date

31 January 2011

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29 July 2017

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29 July 2017

volume

6

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29 July 2017

issue

1

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29 July 2017

page(s)

e16685

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Creative Commons Attribution 4.0 International

29 July 2017

copyright license

start time

31 January 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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4 July 2018

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A map of open chromatin in human pancreatic islets

4 July 2018

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The organization of nucleosomes around splice sites

4 July 2018

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RNA-Seq gene expression estimation with read mapping uncertainty

4 July 2018

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RNA processing and its regulation: global insights into biological networks

4 July 2018

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Sequencing technologies - the next generation

4 July 2018

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Discovery and annotation of functional chromatin signatures in the human genome

4 July 2018

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Biased chromatin signatures around polyadenylation sites and exons

4 July 2018

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Sense from sequence reads: methods for alignment and assembly

4 July 2018

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Computation for ChIP-seq and RNA-seq studies

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Computational methods for discovering structural variation with next-generation sequencing

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Human DNA methylomes at base resolution show widespread epigenomic differences

4 July 2018

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Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing

4 July 2018

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Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

4 July 2018

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Characterizing natural variation using next-generation sequencing technologies.

4 July 2018

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Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Nucleosomes are well positioned in exons and carry characteristic histone modifications

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Improved base calling for the Illumina Genome Analyzer using machine learning strategies

4 July 2018

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High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

4 July 2018

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Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

4 July 2018

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Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing.

4 July 2018

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Differential chromatin marking of introns and expressed exons by H3K36me3.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Patterns of exon-intron architecture variation of genes in eukaryotic genomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Divergent transcription from active promoters

4 July 2018

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RNA-Seq: a revolutionary tool for transcriptomics

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Alternative isoform regulation in human tissue transcriptomes

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

4 July 2018

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4 July 2018

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Intronic noncoding RNAs and splicing.

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

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

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

High-resolution mapping and characterization of open chromatin across the genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

RNA polymerase is poised for activation across the genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

High-resolution profiling of histone methylations in the human genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

SnoRNP biogenesis meets Pre-mRNA splicing

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

miRBase: microRNA sequences, targets and gene nomenclature

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

A high-resolution map of active promoters in the human genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

New human and mouse microRNA genes found by homology search

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Biogenesis of small nuclear RNPs

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

4 July 2018

The microRNA Registry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

A slow RNA polymerase II affects alternative splicing in vivo

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Biogenesis of small nucleolar ribonucleoproteins

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Whole-genome sequencing and variant discovery in C. elegans.

4 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016685

Transposable elements have rewired the core regulatory network of human embryonic stem cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016685

Chromatin organization marks exon-intron structure

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016685

Nucleosome positioning as a determinant of exon recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016685

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0016685

Small nucleolar RNAs: an abundant group of noncoding RNAs with diverse cellular functions

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3031631

Chromatin, transcript elongation and alternative splicing

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21304912

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Cotranscriptional coupling of splicing factor recruitment and precursor messenger RNA splicing in mammalian cells

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21304912

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0016685

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference