Widespread misinterpretable ChIP-seq bias in yeast (Q35071005)

6 August 2017

title

Widespread misinterpretable ChIP-seq bias in yeast (English)

1 reference

6 August 2017

1 reference

Daechan Park

1

0 references

author name string

Yaelim Lee

series ordinal

2

1 reference

6 August 2017

Gurvani Bhupindersingh

series ordinal

3

1 reference

6 August 2017

Vishwanath R Iyer

series ordinal

4

1 reference

6 August 2017

language of work or name

English

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publication date

9 December 2013

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6 August 2017

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6 August 2017

volume

8

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6 August 2017

issue

12

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6 August 2017

page(s)

e83506

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Creative Commons Attribution 4.0 International

6 August 2017

copyright license

start time

9 December 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

limma

object named as

Bioconductor limma

2 references

22 June 2022

https://europepmc.org/article/PMC/3857294

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

ISWI and CHD chromatin remodelers bind promoters but act in gene bodies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

The accessible chromatin landscape of the human genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

An integrated encyclopedia of DNA elements in the human genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Genome-wide nucleosome specificity and directionality of chromatin remodelers.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

The NIH Roadmap Epigenomics Program data resource

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Computational Analysis of Protein–DNA Interactions from ChIP-seq Data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

ChIP-Seq: technical considerations for obtaining high-quality data

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Stable and dynamic nucleosome states during a meiotic developmental process

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

A comprehensive genomic binding map of gene and chromatin regulatory proteins in Saccharomyces

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Identification of functional elements and regulatory circuits by Drosophila modENCODE

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Evaluation of algorithm performance in ChIP-seq peak detection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

The telomere-binding protein Tbf1 demarcates snoRNA gene promoters in Saccharomyces cerevisiae.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

ChIP-seq: advantages and challenges of a maturing technology

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Mapping accessible chromatin regions using Sono-Seq

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Fast and accurate short read alignment with Burrows-Wheeler transform

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Where does mediator bind in vivo?

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Model-based analysis of ChIP-Seq (MACS)

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

A systems approach to mapping DNA damage response pathways

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Transcriptional regulatory code of a eukaryotic genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Genome-wide analysis of the biology of stress responses through heat shock transcription factor

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Global analysis of protein expression in yeast

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

The human genome browser at UCSC

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Turning genes off by Ssn6-Tup1: a conserved system of transcriptional repression in eukaryotes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Dissecting the regulatory circuitry of a eukaryotic genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Absolute mRNA levels and transcriptional initiation rates in Saccharomyces cerevisiae

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3857294

Matplotlib: A 2D Graphics Environment

8 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0083506

Micrococcal nuclease analysis of chromatin structure.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0083506

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371/JOURNAL.PONE.0083506

Recovery of the yeast cell cycle from heat shock-induced G(1) arrest involves a positive regulation of G(1) cyclin expression by the S phase cyclin Clb5

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24349523

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0083506

1 reference

6 August 2017

0 references

1 reference

6 August 2017

1 reference