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ENCODE Project at NHGRI Publications


This page lists publications funded, at least in part, by ENCODE funds. The process of cataloging these publications is on-going, and updates to this page will be made periodically.

Updated 03 April 2012

ENCODE Consortium publications

ENCODE Project Consortium, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E et al. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.

ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40.

Recent publications of special interest on ENCODE data by ENCODE Consortium members

Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 2011 Mar;21(3):456-64.

Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009 Jun;19(6):1044-56.

Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A et al. The reality of pervasive transcription. PLoS Biol. 2011 Jul;9(7):e1000625; discussion e1001102.

Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S et al. The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet. 2011 Jul;19(7):827-31.

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9.

Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet. 2011 Aug;7(8):e1002228.

Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res. 2010 Jul;38(13):4325-36.

Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE et al. Variation in transcription factor binding among humans. Science. 2010 Apr 9;328(5975):232-5.

Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell. 2011 Nov 4;44(3):410-23.

Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010 Mar;20(3):320-31.

Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012 Jan 20;148(1-2):84-98.

McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science. 2010 Apr 9;328(5975):235-9.

Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol. 2010 May;17(5):635-40.

Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23;147(7):1628-39.

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5.

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 2011 Oct;21(10):1757-67.

Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012 Jan;40(Database issue):D930-4.

Methods and resource publications by ENCODE Consortium members


Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012;7(1):e28213.

Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23.

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S et al. Ensembl 2012. Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90.

Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H et al. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 2012 Jan;40(Database issue):D912-7.

Takahashi H, Kato S, Murata M, Carninci P. CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Methods Mol Biol. 2012;786:181-200.

Takahashi H, Lassmann T, Murata M, Carninci P. 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc. 2012 Feb 23;7(3):542-61.


Buske OJ, Hoffman MM, Ponts N, Le Roch KG, Noble WS. Exploratory analysis of genomic segmentations with Segtools. BMC Bioinformatics. 2011 Oct 26;12:415.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec;21(12):2224-41.

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82.

George AD, Tenenbaum SA Web-based tools for studying RNA structure and function. Methods Mol Biol. 2011;703:67-86.

Hubisz MJ, Lin MF, Kellis M, Siepel A Error and error mitigation in low-coverage genome assemblies. PLoS One. 2011 Feb 14;6(2):e17034.

Jain R, Devine T, George AD, Chittur SV, Baroni TE, Penalva LO, Tenenbaum SA RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63.

Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 2011 Sep;21(9):1543-51.

Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19867-72.

Lin MF, Jungreis I, Kellis M PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics. 2011 Jul 1;27(13):i275-82.

Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res. 2011 Nov;21(11):1916-28.

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM et al. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2011 Jan;39(Database issue):D871-5.

Salimullah M, Sakai M, Plessy C, Carninci P. NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harb Protoc. 2011 Jan 1;2011(1):pdb.prot5559.

Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ. Rapid empirical discovery of optimal peptides for targeted proteomics. Nat Methods. 2011 Nov 6;8(12):1041-3.


Adli M, Zhu J, Bernstein BE. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat Methods. 2010 Aug;7(8):615-8.

Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I et al. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 2010 Jan;38(3):e13.

Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics. 2010 Jun 15;26(12):i334-42.

Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25.

Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010 Jan;7(1):47-9.

Hoffman MM, Buske OJ, Noble WS. The Genomedata format for storing large-scale functional genomics data. Bioinformatics. 2010 Jun 1;26(11):1458-9.

Hung JH, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C. Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biol. 2010;11(2):R23.

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7.

Kokocinski F, Harrow J, Hubbard T. AnnoTrack--a tracking system for genome annotation. BMC Genomics. 2010 Oct 5;11:538.

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22.

Mariotti M, Guigó R. Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics. 2010 Nov 1;26(21):2656-63.

Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods. 2010 Jul;7(7):528-34.

Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9.

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5.

Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Dec;7(12):995-1001.

Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics. 2010 Sep;Chapter 11:Unit 11.5.


Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G, Hancock RE, Harrow JL. Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome. BMC Genomics. 2009 Dec 15;10:606.

Fullwood MJ, Ruan Y. ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem. 2009 May 1;107(1):30-9.

Fullwood MJ, Wei CL, Liu ET, Ruan Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32.

George AD, Tenenbaum SA. Informatic resources for identifying and annotating structural RNA motifs. Mol Biotechnol. 2009 Feb;41(2):180-93.

Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Jul;48(3):233-9.

Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 2009 Apr;6(4):283-9.

Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009 Jan;37(Database issue):D755-61.

Lajoie BR, van Berkum NL, Sanyal A, Dekker J. My5C: web tools for chromosome conformation capture studies. Nat Methods. 2009 Oct;6(10):690-1.

Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB. Pseudofam: the pseudogene families database. Nucleic Acids Res. 2009 Jan;37(Database issue):D738-43.

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 9;326(5950):289-93.

Lu DV, Brown RH, Arumugam M, Brent MR. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. Bioinformatics. 2009 Jul 1;25(13):1587-93.

Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009 Nov;6(11 Suppl):S22-32.

Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009 Jan;27(1):66-75.


Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8.

Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR et al. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods. 2008 Jul;5(7):629-35.

Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 2008 Jan;36(Database issue):D773-9.

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8.

Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J et al. Determination and validation of principal gene products. Bioinformatics. 2008 Jan 1;24(1):11-7.

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods. 2008 Sep;5(9):829-34.

Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL. The vertebrate genome annotation (Vega) database. Nucleic Acids Res. 2008 Jan;36(Database issue):D753-60.


Day N, Hemmaplardh A, Thurman RE, Stamatoyannopoulos JA, Noble WS. Unsupervised segmentation of continuous genomic data. Bioinformatics. 2007 Jun 1;23(11):1424-6.

Review and commentary publications by ENCODE Consortium members

Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Gene inactivation and its implications for annotation in the era of personal genomics. Genes Dev. 2011 Jan 1;25(1):1-10.

Boyle AP, Furey TS. High-resolution mapping studies of chromatin and gene regulatory elements. Epigenomics. 2009 Dec 1;1(2):319-329.

Cline MS, Karchin R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. 2011 Feb 15;27(4):441-8.

Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009 Sep;10(9):605-16.

Faulkner GJ, Carninci P. Altruistic functions for selfish DNA. Cell Cycle. 2009 Sep 15;8(18):2895-900.

Forrest AR, Abdelhamid RF, Carninci P. Annotating non-coding transcription using functional genomics strategies. Brief Funct Genomic Proteomic. 2009 Nov;8(6):437-43.

Gingeras TR. Implications of chimaeric non-co-linear transcripts. Nature. 2009 Sep 10;461(7261):206-11.

Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R. Identifying protein-coding genes in genomic sequences. Genome Biol. 2009;10(1):201.

Mendenhall EM, Bernstein BE. Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev. 2008 Apr;18(2):109-15.

Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA et al. The human mitochondrial transcriptome. Cell. 2011 Aug 19;146(4):645-58.

Saxena A, Carninci P. Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays. 2011 Nov;33(11):830-9.

Washington NL, Stinson EO, Perry MD, Ruzanov P, Contrino S, Smith R, Zha Z, Lyne R, Carr A, Lloyd P et al. The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details. Database (Oxford). 2011;2011:bar023.

Biological findings publications by ENCODE Consortium members


Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol. 2012 Jan;32(1):226-39.

Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS et al. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res. 2012 Jan;22(1):9-24.


Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J, Gerstein M. Gene inactivation and its implications for annotation in the era of personal genomics. Genes Dev. 2011 Jan 1;25(1):1-10.

Cline MS, Karchin R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. 2011 Feb 15;27(4):441-8.

Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR et al. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011 Oct 23;43(12):1179-85.

Karczewski KJ, Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M. Cooperative transcription factor associations discovered using regulatory variation. Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13353-8.

Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13641-6.

Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res. 2011 Nov;21(11):1833-40.


Aiden AP, Rivera MN, Rheinbay E, Ku M, Coffman EJ, Truong TT, Vargas SO, Lander ES, Haber DA, Bernstein BE. Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Cell Stem Cell. 2010 Jun 4;6(6):591-602.

Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Allele-specific and heritable chromatin signatures in humans. Hum Mol Genet. 2010 Oct 15;19(R2):R204-9.

Frietze S, Lan X, Jin VX, Farnham PJ. Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem. 2010 Jan 8;285(2):1393-403.

Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ. ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One. 2010 Dec 8;5(12):e15082.

Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D et al. A map of open chromatin in human pancreatic islets. Nat Genet. 2010 Mar;42(3):255-9.

Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44.

O'Geen H, Lin YH, Xu X, Echipare L, Komashko VM, He D, Frietze S, Tanabe O, Shi L, Sartor MA et al. Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. BMC Genomics. 2010 Dec 2;11:689.

Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T et al. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet. 2010 Jul 15;6(7):e1001023.

Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ et al. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metab. 2010 Nov 3;12(5):443-55.

Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol. 2010;11(3):R26.

Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q et al. Long noncoding RNAs with enhancer-like function in human cells. Cell. 2010 Oct 1;143(1):46-58.


Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature. 2009 Feb 19;457(7232):1028-32.

Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol. 2009;10(1):R2.

Boyle AP, Furey TS. High-resolution mapping studies of chromatin and gene regulatory elements. Epigenomics. 2009 Dec 1;1(2):319-329.

Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009 Sep;10(9):605-16.

Faulkner GJ, Carninci P. Altruistic functions for selfish DNA. Cell Cycle. 2009 Sep 15;8(18):2895-900.

Forrest AR, Abdelhamid RF, Carninci P. Annotating non-coding transcription using functional genomics strategies. Brief Funct Genomic Proteomic. 2009 Nov;8(6):437-43.

Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell. 2009 Nov 25;36(4):667-81.

Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009 Nov 5;462(7269):58-64.

Gingeras TR. Implications of chimaeric non-co-linear transcripts. Nature. 2009 Sep 10;461(7261):206-11.

Guo X, Zhang Z, Gerstein MB, Zheng D. Small RNAs originated from pseudogenes: cis- or trans-acting?. PLoS Comput Biol. 2009 Jul;5(7):e1000449.

Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R. Identifying protein-coding genes in genomic sequences. Genome Biol. 2009;10(1):201.

Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB. Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics. 2009 Oct 16;10:480.

Reddy TE, Pauli F, Sprouse RO, Neff NF, Newberry KM, Garabedian MJ, Myers RM. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res. 2009 Dec;19(12):2163-71.

Sekimata M, Pérez-Melgosa M, Miller SA, Weinmann AS, Sabo PJ, Sandstrom R, Dorschner MO, Stamatoyannopoulos JA, Wilson CB. CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity. 2009 Oct 16;31(4):551-64.

Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. Human mutation rate associated with DNA replication timing. Nat Genet. 2009 Apr;41(4):393-5.


Cotterman R, Jin VX, Krig SR, Lemen JM, Wey A, Farnham PJ, Knoepfler PS. N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Res. 2008 Dec 1;68(23):9654-62.

Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R et al. An endogenous small interfering RNA pathway in Drosophila. Nature. 2008 Jun 5;453(7196):798-802.

Fu Y, Sinha M, Peterson CL, Weng Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 2008 Jul 25;4(7):e1000138.

Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JG, Halls K, Harrow JL et al. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics. 2008 Jan;60(1):1-18.

Mendenhall EM, Bernstein BE. Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev. 2008 Apr;18(2):109-15.

Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG, Harrow JL. Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. Genome Biol. 2008;9(5):R91.

Stoecklin G, Tenenbaum SA, Mayo T, Chittur SV, George AD, Baroni TE, Blackshear PJ, Anderson P. Genome-wide analysis identifies interleukin-10 mRNA as target of tristetraprolin. J Biol Chem. 2008 Apr 25;283(17):11689-99.

Zhang ZD, Cayting P, Weinstock G, Gerstein M. Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories. Mol Biol Evol. 2008 Jan;25(1):131-43.

ENCODE pilot project publications

Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 Jun;17(6):910-6.

Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD et al. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4.

Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res. 2007 Jun;17(6):928-39.

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007 Jun;17(6):746-59.

Elnitski LL, Shah P, Moreland RT, Umayam L, Wolfsberg TG, Baxevanis AD. The ENCODEdb portal: simplified access to ENCODE Consortium data. Genome Res. 2007 Jun;17(6):954-9.

Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M et al. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res. 2007 Jun;17(6):886-97.

Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909.

Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007 Jun;17(6):669-81.

Gingeras TR. Origin of phenotypes: genes and transcripts. Genome Res. 2007 Jun;17(6):682-90.

Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 Jun;17(6):877-85.

Greenbaum JA, Pang B, Tullius TD. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res. 2007 Jun;17(6):947-53.

Greenbaum JA, Parker SC, Tullius TD. Detection of DNA structural motifs in functional genomic elements. Genome Res. 2007 Jun;17(6):940-6.

Jin VX, O'Geen H, Iyengar S, Green R, Farnham PJ. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res. 2007 Jun;17(6):807-17.

Karnani N, Taylor C, Malhotra A, Dutta A. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res. 2007 Jun;17(6):865-76.

King DC, Taylor J, Zhang Y, Cheng Y, Lawson HA, Martin J, ENCODE groups for Transcriptional Regulation and Multispecies Sequence Analysis, Chiaromonte F, Miller W, Hardison RC. Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res. 2007 Jun;17(6):775-86.

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P et al. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res. 2007 Jun;17(6):691-707.

Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z. Transcription factor binding and modified histones in human bidirectional promoters. Genome Res. 2007 Jun;17(6):818-27.

Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 Jun;17(6):760-74.

Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF et al. Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes. Genome Res. 2007 Jun;17(6):708-19.

Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R et al. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res. 2007 Jun;17(6):732-45.

Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P et al. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 2007 Jun;17(6):828-38.

Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J et al. The ENCODE Project at UC Santa Cruz. Nucleic Acids Res. 2007 Jan;35(Database issue):D663-7.

Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA. Identification of higher-order functional domains in the human ENCODE regions. Genome Res. 2007 Jun;17(6):917-27.

Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M et al. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res. 2007 Jun;17(6):720-31.

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007 Jun;17(6):852-64.

Xi H, Yu Y, Fu Y, Foley J, Halees A, Weng Z. Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res. 2007 Jun;17(6):798-806.

Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res. 2007 Jun;17(6):787-97.

Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 2007 Jun;17(6):839-51.