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ENCODE publication plans

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This page is for ENCODE investigators to share updates on the status of planned/submitted/in press publications. The purpose of sharing plans is to encourage communication between groups about the analysis of datasets and to foster an openness about ENCODE publications.

Please add information for your publication to the table below, with the Title formatted as a wiki link. For plain text or HTML abstracts, click through the link and paste the abstract to the new page. For .doc or other formats, upload the file to the wiki, and reference the upload from the link.

Planned publications should be added to this page no later than one month before submission.

For additional information on acknowledgment of NIH grant support and the ENCODE program in upcoming publications, please consult the NIH Grant Policy Statment:

See also companion paper proposals.

Planned ENCODE, modENCODE and Mouse ENCODE Integrative Analysis Publications

Planned Human/Fly/Worm Integrative Analysis Papers

ENCODE Publications

Authors Title Status Date Updated
The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Published, June 2007 Nature N/A
Rozowsky et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls Published, Jan 2009 Nature Biotech N/A
Frietze et al.; (Farnham lab) GENOMIC TARGETS OF THE KRAB AND SCAN DOMAIN-CONTAINING ZINC FINGER PROTEIN ZNF263 Published J. Biol. Chem. 285:1393-403, 2009 January 29, 2010
Auerbach and Euskirchen et al.; (Snyder lab) Mapping accessible chromatin regions using Sono-Seq Published. PNAS, 106:35 14926-14931 (2009).September 10, 2009
Hoffman et al. Unsupervised pattern discovery in human chromatin structure through genomic segmentationPublished. Nature Methods (2012). doi:10.1038/nmeth.1937March 19, 2012
Affymetrix/Cold Spring Harbor Laboratory ENCODE Transcriptome Project Post-transcriptional processing generates a diversity of 5'-modified long and short RNAsPublished, Nature 457:1028-1032 (2009) N/A
ENCODE Transcriptome Project .; (Farnham lab) Evidence for RNA NetworksIn Preparation
Fujiwara et al.;(Gingeras and Hannon labs) Discovering Hematopoietic Mechanisms Through Genome-Wide Analysis of GATA Factor Chromatin Occupancy Published, Molecular Cell. 36:667-681, 2009January 29, 2010
Gingeras,T. R. Implications of chimeric non-collinear transcripts Published, Nature 2009 Sep 10;461(7261):206-11. April 13,2010
Raha et al. Mapping of Pol III binding sites in K562 and GM12878 genome In preparation
Hoffman, Buske, Noble The Genomedata format for storing large-scale functional genomics dataPublished, Bioinformatics.
Reddy et al. Glucocorticoid Receptor Binding and Gene Expression Response to DexamethasonePublished, Genome Research, Early access on October 2, 2009
Lajoie, van Berkum, Sanyal and Dekker My5C: web tools for chromosome conformation capture studies.Nat. Methods, 6: 690-691 (2009)5 March 2010
Blahnik et al.; (Farnham lab) Sole-search: an intergrated analysis program for ChIP-seq data Published. Nucleic Acids Res. 2010 Jan;38(3):e13. Epub 2009 Nov 11.
Dekker lab and Stamatoyannopoulos lab Long-range gene regulatory architecture of human chromosome 21 In preparation
Gaulton et al.; Mohlke, Lieb, and Ferrer labs (Lieb group) A map of open chromatin in human pancreatic islets Published, Nature Genetics August 7, 2009
Stitzel et al (Crawford and Furey group)Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci Published, Cell Metab. 2010 Nov 3;12(5):443-55.December 7, 2010
Dobin, A.,Gingeras,T. R., et al. Comparative analyses of transcriptomes by tiling arrays and RNA sequencing In preparation
McDaniell et al.; (Birney, Iyer, Furey, Lieb & Crawford labs)Heritable individual-specific and allele-specific chromatin signatures in humansPublished online March 18 2010; 10.1126/science.1184655 (Science Express Reports)
Boyle et al.; (Crawford/Furey lab) High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Published, Genome Res. 2010 Nov 24. [Epub ahead of print] December 7, 2010
Song et al.; (Crawford/Iyer/Birney/Lieb/Furey Groups) Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Published. Genome Res. 2011 Oct;21(10):1757-67. November 3, 2011
Gheldof et al.; (Dekker lab)Cell type specific long-range looping interactions identify distant regulatory elements of the CFTR gene Nucleic Acids Res. (2010), 38 (13): 4325-4336 5 March 2010
Bau et al.; (Dekker lab)The three-dimensional folding of the alpha-globin domain reveals formation of chromatin globulesNat. Struct. Mol. Biol. (2011), 18(1): 107-1145 March 2010
Plessy et al; (Carninci, Hayashizaki, Gingeras labs)Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan Published Nat Methods. 2010 Jul;7(7):528-34.
Jin, V; (Farnham lab) W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high throughput data Published. . Bioinformatics. 25:3191-3193, 2009.January 29, 2010
Moqtaderi, Z.,; (Struhl lab) Genome-wide binding profiles of functional distinct RNA polymerase III transcription complexes in human cells Submitted January 29, 2010
Kokocinski, F.; (Hubbard group) AnnoTrack - a tracking system for genome annotation Published, BMC Genomics 2010, 11:538October 12, 2010
Frietze, S.; (Farnham group) ZNF274 recruits the histone methyltransferase SETDB1 to the human genome In press October, 2010
Gingeras,T. R. Pervasive and interleaved transcriptionPublished, Nature Rev Genet 10: No 11 (Poster) April 13,2010
Trojer et al.; (Farnham group) L3MBTL2 protein acts in concert with PcG protein mediated monoubiquitation of H2A to establish a repressive chromatin structure In Press, Molecular Cell May 5, 2010
O'Geen,H. et al.; (Farnham group) Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in RNA metabolism In Press October 12, 2010
Ernst et al.; (Kellis, Bernstein groups)Mapping and analysis of chromatin state dynamics in nine human cell lines. Published Nature 473: 43-49, 2011.June 17, 2011
Blahnik, K. et al.; (Farnham lab) Characterization of the contradictory chromatin signatures at the 3�� exons of zinc finger genes Accepted in PLOS One January 20, 2011
Linnemann, O'Geen, Keles, Farnham, and Bresnick; (Farnham lab) Genetic framework for GATA factor function in Vascular Biology PNAS In Press October, 2010
Karczewski, KJ et al.; (Snyder lab) Discovering Cooperative Transcription Factor Interactions using Binding Variation Information and the ALPHABIT Pipeline Submitted Feb 24, 2011
Rozowsky, Abyzov et al.; (Gerstein lab) AlleleSeq: Analysis of Coordination of Allele-Specific Expression and Binding Published: Molecular Systems Biology 7:522 (2011) July 2, 2011
Zhu, Adli, Zou et al.; (Bernstein lab) Chromatin landscapes for phenotypically-diverse human cells and tissues (primarily Roadmap data) In preparation Oct 15, 2010
Reddy TE, et al. (Myers lab) Effects of sequence variation on differential allelic transcription factor occupancy and gene expression Submitted Nov 1, 2010
Reddy TE, et al. (Myers lab) Glucocorticoid Receptor Drives PER1 in Response to Low Doses of Corticosteroids In preparation Nov 1, 2010
Gertz, J et al.; (Myers lab) Genome-wide binding of estrogen receptor �� in response to environmental estrogen exposure is cell-type specific In preparation Nov 4, 2010
Gertz, J et al.; (Myers lab) Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation Published: PLoS Genet. 2011 Aug;7(8):e1002228. Nov 4, 2010
Varley, KE et al.; (Myers lab) Genome-wide DNA methylation differences across human tissues and cell lines In preparation Nov 19, 2010
Iyengar S. et al.; (Farnham lab) Functional analysis of KAP1 genomic recruitment In Press, in MCB Feb, 2011
John S et al.; (Stamatoyannopoulos lab) Chromatin accessibility pre-determines glucocorticoid receptor binding patterns [MouseENCODE] In press December, 2010
Mortazavi & Pepke et al.; (Wold lab) Self-organizing maps for analysis and mining of functional genomic data Submitted January 12, 2011
Ram, Goren et al.; (Bernstein lab) Genome-wide mapping reveals diverse patterns of chromatin regulator protein localization In preparation Jan 17, 2011
Nielsen et al.; (Farnham lab) Spark: A Tool for Interactive Visual Exploration of Genome-Scale Data Submitted Jan 15, 2011
Lee B-K. et al.; (Iyer lab, Crawford DNase group) Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells In press, Genome Research October 18, 2011
Cao, A. et al.; (Farnham lab) Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome JBC, In Press February 10, 2011
Yu et al.; (Chen/Giddings collaboration) A novel integrated approach of GELFrEE, FASP and microwave digestion for membrane proteome analysis In preparation, to be submitted to MCP in February 2011 February 10, 2011
Khatun et al. (Giddings lab)Proteogenomic mapping for

ENCODE cell lines: revealing new genes and splice variants (working

revised version submitted April 11, 2012
Buske et al. (Noble lab)Exploratory analysis of genomic segmentations with SegtoolsSubmitted.
Euskirchen and Auerbach et al. (Snyder lab)Diverse roles and interactions of the SWI/SNF chromatin-remodeling complex revealed using global approaches Published. PLoS Genetics (2011) 7(3): e1002008. doi:10.1371/journal.pgen.1002008 March 6, 2011
Sanyal et al.; (Dekker lab)Long-range interaction networks involved in gene regulation in the ENCODE pilot regionsin preparationMarch 17, 2011
Ram, Goren et al.; (Bernstein lab) Genome-wide mapping reveals diverse patterns of chromatin regulator protein localization Submitted March 22, 2011
Whitfield et al. (Weng lab) Functional analysis of transcription factor binding sites in human promoters Submitted March 1, 2011
Hoffman et al.Pattern discovery in RNA-seq and CAGE dataIn preparationMarch, 30 2011
Zhu, Adli, Zou et al.; (Bernstein lab) Chromatin landscapes for phenotypically-diverse human cells and tissues (primarily Roadmap data) Submitted Jun 13, 2011
Li, Ruan, and Auerbach, et al. (Ruan and Snyder Labs) Extensive Promoter-centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation Cell (2012), 148, 84-98June, 2012
Takahashi H, Murata M, Lassmann T and Carninci P (Carninci Lab) 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing Nat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005 March 22, 2012
Ezkurdia I, et al. (Valencia Lab) Comparative proteomics reveals a significant bias towards alternative protein isoforms with conserved structure and function Published Mol. Biol. Evol. Mar 2012
Rodriguez JM, et al. (Valencia Lab) APPRIS: analysis of functional annotations for alternative splice formsIn review process Mar 2012