(Q28274448)

16

0 references

Serafim Batzoglou

6

0 references

Aleksandar Milosavljevic

29

0 references

Lijia Ma

28

0 references

Katherine I Fisher-Aylor

Katherine I Fisher-Aylor

14

0 references

Tao Liu

Tao Liu

26

0 references

Michael M. Hoffman

Michael M Hoffman

19

0 references

Michael J. Pazin

Michael J Pazin

32

0 references

Anshul Kundaje

Anshul Kundaje

3

0 references

Joel Rozowsky

Joel Rozowsky

36

0 references

Peggy Farnham

Peggy J Farnham

44

0 references

Georgi K Marinov

Georgi K Marinov

2

0 references

Jason Gertz

Jason Gertz

17

0 references

Manolis Kellis

23

Manolis Kellis

0 references

John Stamatoyannopoulos

40

John A Stamatoyannopoulos

0 references

Peter V Kharchenko

24

Peter V Kharchenko

0 references

Barbara J. Wold

46

Barbara J Wold

0 references

Michael P. Snyder

47

Michael Snyder

0 references

Alexander J Hartemink

18

Alexander J Hartemink

0 references

Jason D Lieb

45

Jason D Lieb

0 references

Bradley Bernstein

7

Bradley E Bernstein

0 references

Richard M. Myers

30

Richard M Myers

0 references

Pouya Kheradpour

4

Pouya Kheradpour

0 references

Philip Cayting

10

Philip Cayting

0 references

Matthew Slattery

39

Matthew Slattery

0 references

Peter J. Bickel

8

Peter Bickel

0 references

author name string

Stephen G Landt

1

0 references

Florencia Pauli

5

0 references

James B Brown

9

0 references

Yiwen Chen

11

0 references

Gilberto DeSalvo

12

0 references

Charles Epstein

13

0 references

Ghia Euskirchen

15

0 references

Vishwanath R Iyer

20

0 references

Youngsook L Jung

21

0 references

Subhradip Karmakar

22

0 references

Qunhua Li

25

0 references

X Shirley Liu

27

0 references

Peter J Park

31

0 references

Marc D Perry

33

0 references

Debasish Raha

34

0 references

Timothy E Reddy

35

0 references

Noam Shoresh

37

0 references

Arend Sidow

38

0 references

Michael Y Tolstorukov

41

0 references

Kevin P White

42

0 references

Simon Xi

A user's guide to the encyclopedia of DNA elements (ENCODE)

43

0 references

language of work or name

English

0 references

publication date

September 2012

0 references

published in

Genome Research

0 references

volume

22

0 references

page(s)

1813-31

0 references

issue

9

0 references

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Model-based analysis of ChIP-Seq (MACS)

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Combinatorial patterns of histone acetylations and methylations in the human genome

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

High-resolution profiling of histone methylations in the human genome

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Genomic targets of the human c-Myc protein

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Genome-wide location and function of DNA binding proteins

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Mapping and analysis of chromatin state dynamics in nine human cell types

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Genome-wide mapping of in vivo protein-DNA interactions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

The ENCODE (ENCyclopedia Of DNA Elements) Project

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Discovery and characterization of chromatin states for systematic annotation of the human genome

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

ChIP-seq: advantages and challenges of a maturing technology

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Identification of functional elements and regulatory circuits by Drosophila modENCODE

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

modMine: flexible access to modENCODE data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

ENCODE whole-genome data in the UCSC Genome Browser: update 2012.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Genome-wide analysis of simultaneous GATA1/2, RUNX1, FLI1, and SCL binding in megakaryocytes identifies hematopoietic regulators.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

An assessment of histone-modification antibody quality

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Close association of RNA polymerase II and many transcription factors with Pol III genes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Computation for ChIP-seq and RNA-seq studies

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Mapping accessible chromatin regions using Sono-Seq

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Genomic antagonism between retinoic acid and estrogen signaling in breast cancer.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Unlocking the secrets of the genome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Suz12 binds to silenced regions of the genome in a cell-type-specific manner

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

ChIP-chip: a genomic approach for identifying transcription factor binding sites

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

Regulation of B lymphocyte and macrophage development by graded expression of PU.1.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3431496

27 November 2018

Identifiers

DOI

10.1101/GR.136184.111

1 reference

275301

275301

1 reference

1 reference

1 reference