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The results of the ENCODE project are presented in 30 papers, published simultaneously in Nature, Genome Research and Genome Biology, and collected here. You can discover the project’s results in the conventional way, by visiting individual papers, or you can engage with the material by following ‘Threads’, each one dedicated to a theme discussed in more than one paper.View Threads

The ENCODE explorer is only available in landscape view.

News and Comment

What’s next for ENCODE?

Brendan Maher

First they sequenced it. Now they’ve surveyed its hinterlands. But no-one knows how much more information the human genome holds, or when to stop looking for it.
The Making of ENCODE

Ewan Birney

To be successful, consortia need clear management, codes of conduct and participants who are committed to working for the common good, says ENCODE lead analysis coordinator Ewan Birney.
ENCODE explained

Joseph R. Ecker

The Encyclopedia of DNA Elements (ENCODE) project dishes up a hearty banquet of data that illuminate the roles of the functional elements of the human genome. Here, six scientists describe the project and discuss how the data are influencing research directions across many fields.
A cog in the machine

Sarah Kellogg

If they remain vigilant, early-career researchers can benefit greatly from taking part in big international collaborations.

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Multimedia

Voices of ENCODE

In this video, ENCODE’s lead coordinator, Ewan Birney, and Nature editor Magdalena Skipper talk about the challenges of managing a huge genetics project and what we’ve learnt about our genomes.

ENCODE: The story of you

Ever since a monk called Mendel started breeding pea plants we’ve been learning about our genomes. The latest chapter in our story is ENCODE; an ambitious project which aims to characterise all the functional element in the human genome. This animation shows how ENCODE is the next major step along this path.

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Research papers in Nature

featured-research

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium.

Journal name:: Nature
Year Published:: (6 September 2012)

Landscape of transcription in human cells

Djebali, S., Davis, C.A. et al.

Journal name:: Nature
Year Published:: (6 September 2012)

The accessible chromatin landscape of the human genome

Thurman, R.E., Rynes, E., Humbert , R. et al.

Journal name:: Nature
Year Published:: (6 September 2012)

An expansive human regulatory lexicon encoded in transcription factor footprints

Neph, S., Vierstra, J., Stergachis, A.B., Reynolds, A.P. et al.

Journal name:: Nature
Year Published:: (6 September 2012)

Architecture of the human regulatory network derived from ENCODE data

Gerstein, M.B., Kundaje, A., Hariharan, M., Landt, S.G., Yan, K.K. et al.

Journal name:: Nature
Year Published:: (6 September 2012)

The long-range interaction landscape of gene promoters

Sanyal, A., Lajoie, B.R. et al.

Journal name:: Nature
Year Published:: (6 September 2012)

ENCODE companion papers

Analysis of variation at transcription factor binding sites in Drosophila and humans

Spivakov, M. et al.

Journal name:

Genome Biol.

Year Published:

(6 September 2012)
Annotation of functional variation in personal genomes using RegulomeDB.

Boyle, A.P. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3

Frietze, S. et al.

Journal name:

Genome Biol.

Year Published:

(6 September 2012)
ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia.

Landt, S.G. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription related factors

Yip, K.Y. et al.

Journal name:

Genome Biol.

Year Published:

(6 September 2012)
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

Howald, C. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

Tilgner, H. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Discovery of hundreds of mirtrons in mouse and human small RNA data

Ladewig, E. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Functional analysis of transcription factor binding sites in human promoters

Whitfield, T.W. et al.

Journal name:

Genome Biol.

Year Published:

(6 September 2012)
GENCODE: The reference human genome annotation for the ENCODE project

Harrow, J. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Linking disease associations with regulatory information in the human genome.

Schaub, M.A. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Long noncoding RNAs are rarely translated in two human cell lines

Bánfai, B. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Modeling gene expression using chromatin features in various cellular contexts

Dong, X. et al.

Journal name:

Genome Biol.

Year Published:

(6 September 2012)
Personal and population genomics of human regulatory variation.

Vernot, B. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Predicting cell-type–specific gene expression from regions of open chromatin.

Natarajan, A. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
RNA editing in the human ENCODE RNA-seq data

Park, E. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Sequence and chromatin determinants of cell-type–specific transcription factor binding.

Arvey, A. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Wang, J. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data

Ni et al.

Journal name:

BMC Gen.

Year Published:

(6 September 2012)
The GENCODE pseudogene resource

Pei, B. et al.

Journal name:

Genome Biol.

Year Published:

(6 September 2012)
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression.

Derrien, T. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.

Kundaje, A. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

Cheng, C. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
Widespread plasticity in CTCF occupancy linked to DNA methylation

Wang, H. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)
A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells.

Charos, A.E. et al.

Journal name:

Genome Res.

Year Published:

(6 September 2012)

Additional Research Papers

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

Ezkurdia, I. et al.

Journal name:: Mol. Biol. Evol. 29, 2265-2283 (2012)

An Atlas of the Epstein-Barr Virus Transcriptome and Epigenome Reveals Host-Virus Regulatory Interactions

Arvey, A. et al.

Journal name:: Cell Host Microbe 12, 233-245 (2012)

The Chromatin Fingerprint of Gene Enhancer Elements

Zentner, G.E. & Scacheri, P.C.

Journal name:: J. Biol. Chem. 287, 30888-30896 (2012)

Genome-wide studies of CTCF and cohesin provide insight into chromatin structure and regulation

Lee, B.K. & Iyer, V.R.

Journal name:: J. Biol. Chem. 287, 30906-30913 (2012)

Transcription factor mediated epigenetic reprogramming

Sindu, C. et al.

Journal name:: J. Biol. Chem. 287, 30922-30931 (2012)

SWI/SNF Chromatin Remodeling Factors: Multiscale Analyses and Diverse Functions

Euskirchen, G. et al.

Journal name:: J. Biol. Chem. 287, 30897-30905 (2012)

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