This page lists papers that use ENCODE data, by authors not funded by ENCODE. The ENCODE project tracks these papers in part to assess impact of the resource. Please contact Mike Pazin at NHGRI to suggest publications to add to this list. The lists below are non-overlapping; each paper is only assigned to one list.

• Human disease publications
• Basic biology publications
• Tools, methods, databases and review/commentary publications
• Publications using modENCODE data, without modENCODE authors

Updated 19 October 2012

Adrianto I, Wen F, Templeton A, Wiley G, King JB, Lessard CJ, Bates JS, Hu Y, Kelly JA, Kaufman KM et al. Association of a functional variant downstream of TNFAIP3 with systemic lupus erythematosus. Nat Genet. 2011 Mar;43(3):253-8.
ENCODE DNase, TF ChIP, histone modification ChIP presented in Figure S5; other resources also used

Akhtar-Zaidi B, Cowper-Sal-lari R, Corradin O, Saiakhova A, Bartels CF, Balasubramanian D, Myeroff L, Lutterbaugh J, Jarrar A, Kalady MF et al. Epigenomic enhancer profiling defines a signature of colon cancer. Science. 2012 May 11;336(6082):736-9.
ENCODE TF ChIP, Histone modification ChIP; Fig 2a, S2, S6, S7

Bekris LM, Lutz F, Yu CE. Functional analysis of APOE locus genetic variation implicates regional enhancers in the regulation of both TOMM40 and APOE. J Hum Genet. 2012 Jan;57(1):18-25.
ENCODE histone modification ChIP, TF ChIP in Figure 2a

Berlivet S, Moussette S, Ouimet M, Verlaan DJ, Koka V, Al Tuwaijri A, Kwan T, Sinnett D, Pastinen T, Naumova AK. Interaction between genetic and epigenetic variation defines gene expression patterns at the asthma-associated locus 17q12-q21 in lymphoblastoid cell lines. Hum Genet. 2012 Jul;131(7):1161-71.
ENCODE TF ChIP, histone modification ChIP, Fig 1S

Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2011 Nov 27;44(1):40-6.
ENCODE TF ChIP, histone modification ChIP, DNase, RNA, chromatin states, Fig 2B, S6, S8, S16

Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet. 2010 Dec 2;6(12):e1001233.
ENCODE RNA, Fig 2B and results

Calva D, Dahdaleh FS, Woodfield G, Weigel RJ, Carr JC, Chinnathambi S, Howe JR. Discovery of SMAD4 promoters, transcription factor binding sites and deletions in juvenile polyposis patients. Nucleic Acids Res. 2011 Jul;39(13):5369-78.
ENCODE TF ChIP, DNase, Figure 6

Carvajal-Carmona LG, Cazier JB, Jones AM, Howarth K, Broderick P, Pittman A, Dobbins S, Tenesa A, Farrington S, Prendergast J et al. Fine-mapping of colorectal cancer susceptibility loci at 8q23.3, 16q22.1 and 19q13.11: refinement of association signals and use of in silico analysis to suggest functional variation and unexpected candidate target genes. Hum Mol Genet. 2011 Jul 15;20(14):2879-88.
ENCODE DNase, histone modification ChIP, TF ChIP (Table 1)

Crapoulet N, O'Brien P, Ouellette RJ, Robichaud GA. Coordinated expression of Pax-5 and FAK1 in metastasis. Anticancer Agents Med Chem. 2011 Sep;11(7):643-9.
ENCODE data in Figure 1, text

Davison LJ, Wallace C, Cooper JD, Cope NF, Wilson NK, Smyth DJ, Howson JM, Saleh N, Al-Jeffery A, Angus KL et al. Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene. Hum Mol Genet. 2012 Jan 15;21(2):322-33.
ENCODE histone modification ChIP, DNase, TF ChIP, data in Figure 3, and S3A; found enhancer in one gene that regulates distal, neighboring gene

Delgado-Vega AM, Dozmorov MG, Quirós MB, Wu YY, Martínez-García B, Kozyrev SV, Frostegård J, Truedsson L, de Ramón E, González-Escribano MF et al. Fine mapping and conditional analysis identify a new mutation in the autoimmunity susceptibility gene BLK that leads to reduced half-life of the BLK protein. Ann Rheum Dis. 2012 Jul;71(7):1219-26.
ENCODE TF ChIP, Histone modification ChIP, Fig 1, S2, Table S3

Farrell JJ, Sherva RM, Chen ZY, Luo HY, Chu BF, Ha SY, Li CK, Lee AC, Li RC, Li CK et al. A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression. Blood. 2011 May 5;117(18):4935-45.
ENCODE TF ChIP, Histone modification ChIP, DNase, RNA in Figure 6

Feenstra B, Geller F, Krogh C, Hollegaard MV, Gørtz S, Boyd HA, Murray JC, Hougaard DM, Melbye M. Common variants near MBNL1 and NKX2-5 are associated with infantile hypertrophic pyloric stenosis. Nat Genet. 2012 Feb 5;44(3):334-7.
ENCODE histone modification ChIP, described in results

Fu YP, Kohaar I, Rothman N, Earl J, Figueroa JD, Ye Y, Malats N, Tang W, Liu L, Garcia-Closas M et al. Common genetic variants in the PSCA gene influence gene expression and bladder cancer risk. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4974-9.
ENCODE histone modification ChIP, Figure 2

Ghedira K, Hornischer K, Konovalova T, Jenhani AZ, Benkahla A, Kel A. Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis. Infect Genet Evol. 2011 Jun;11(4):769-77.
ENCODE TF ChIP, Fig 3B, Table S3, S4

Gijselinck I, Van Langenhove T, van der Zee J, Sleegers K, Philtjens S, Kleinberger G, Janssens J, Bettens K, Van Cauwenberghe C, Pereson S et al. A C9orf72 promoter repeat expansion in a Flanders-Belgian cohort with disorders of the frontotemporal lobar degeneration-amyotrophic lateral sclerosis spectrum: a gene identification study. Lancet Neurol. 2012 Jan;11(1):54-65.
ENCODE Histone modification ChIP, TF ChIP, DNase, Figure S4

Glinskii AB, Ma S, Ma J, Grant D, Lim CU, Guest I, Sell S, Buttyan R, Glinsky GV. Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders. Cell Cycle. 2011 Oct 15;10(20):3571-97.
ENCODE TF ChIP, histone modification ChIP, DNase, Fig 4A, 4D, S4, S10

Han J, Park SG, Bae JB, Choi J, Lyu JM, Park SH, Kim HS, Kim YJ, Kim S, Kim TY. The characteristics of genome-wide DNA methylation in naïve CD4+ T cells of patients with psoriasis or atopic dermatitis. Biochem Biophys Res Commun. 2012 May 25;422(1):157-63.
ENCODE Txn, His, DNase, and TF composite tracks, Figure 1, S1-S6

Harismendy O, Bansal V, Bhatia G, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Sipe JC, Murray SS et al. Population sequencing of two endocannabinoid metabolic genes identifies rare and common regulatory variants associated with extreme obesity and metabolite level. Genome Biol. 2010;11(11):R118.
ENCODE histone modifications, Fig 5C, TFs, Fig 5D

Harismendy O, Notani D, Song X, Rahim NG, Tanasa B, Heintzman N, Ren B, Fu XD, Topol EJ, Rosenfeld MG et al. 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature. 2011 Feb 10;470(7333):264-8.
ENCODE histone modification ChIP, TF ChIP, Figure 1

Higareda-Almaraz JC, Enríquez-Gasca Mdel R, Hernández-Ortiz M, Resendis-Antonio O, Encarnación-Guevara S. Proteomic patterns of cervical cancer cell lines, a network perspective. BMC Syst Biol. 2011 Jun 22;5:96.
ENCODE TF ChIP, GENCODE, Figure 1, table 4

Hofer T, Foll M, Excoffier L. Evolutionary forces shaping genomic islands of population differentiation in humans. BMC Genomics. 2012 Mar 22;13:107.
ENCODE TF ChIP, described in text and methods

Jaeger E, Leedham S, Lewis A, Segditsas S, Becker M, Cuadrado PR, Davis H, Kaur K, Heinimann K, Howarth K et al. Hereditary mixed polyposis syndrome is caused by a 40-kb upstream duplication that leads to increased and ectopic expression of the BMP antagonist GREM1. Nat Genet. 2012 May 6;44(6):699-703.
ENCODE Histone modification ChIP, TF ChIP, DNase, Fig S3

Jones AM, Beggs AD, Carvajal-Carmona L, Farrington S, Tenesa A, Walker M, Howarth K, Ballereau S, Hodgson SV, Zauber A et al. TERC polymorphisms are associated both with susceptibility to colorectal cancer and with longer telomeres. Gut. 2012 Feb;61(2):248-54.
ENCODE DNase, Histone modification ChIP, TF ChIP, described in results

Lamina C, Coassin S, Illig T, Kronenberg F. Look beyond one's own nose: combination of information from publicly available sources reveals an association of GATA4 polymorphisms with plasma triglycerides. Atherosclerosis. 2011 Dec;219(2):698-703.
ENCODE histone modification ChIP, TF ChIP, DNase, figure 2, S1, S2

Lessard CJ, Adrianto I, Kelly JA, Kaufman KM, Grundahl KM, Adler A, Williams AH, Gallant CJ, Marta E. Alarcón-Riquelme on behalf of the BIOLUPUS and GENLES Networks, Anaya JM et al. Identification of a systemic lupus erythematosus susceptibility locus at 11p13 between PDHX and CD44 in a multiethnic study. Am J Hum Genet. 2011 Jan 7;88(1):83-91.
ENCODE TF ChIP, histone modification ChIP, Figure 2C, text

Li YJ, Minear MA, Rimmler J, Zhao B, Balajonda E, Hauser MA, Allingham RR, Eghrari AO, Riazuddin SA, Katsanis N et al. Replication of TCF4 through association and linkage studies in late-onset Fuchs endothelial corneal dystrophy. PLoS One. 2011 Apr 20;6(4):e18044.
ENCODE data mentioned in text

Liu JZ, Almarri MA, Gaffney DJ, Mells GF, Jostins L, Cordell HJ, Ducker SJ, Day DB, Heneghan MA, Neuberger JM et al. Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis. Nat Genet. 2012 Sep 9;44(10):1137-1141.
ENCODE DNase, FAIRE, Table 1, S7, S9, Figure 2, S9

Lu Y, Zhang Z, Yu H, Zheng SL, Isaacs WB, Xu J, Sun J. Functional annotation of risk loci identified through genome-wide association studies for prostate cancer. Prostate. 2011 Jun 15;71(9):955-63.
ENCODE TF ChIP, histone modification ChIP, Table 1, 2, 3

Lubbe SJ, Pittman AM, Olver B, Lloyd A, Vijayakrishnan J, Naranjo S, Dobbins S, Broderick P, Gómez-Skarmeta JL, Houlston RS. The 14q22.2 colorectal cancer variant rs4444235 shows cis-acting regulation of BMP4. Oncogene. 2012 Aug 16;31(33):3777-84.
ENCODE histone modification ChIP, DNase, Fig 2

Maruo S, Zhao B, Johannsen E, Kieff E, Zou J, Takada K. Epstein-Barr virus nuclear antigens 3C and 3A maintain lymphoblastoid cell growth by repressing p16INK4A and p14ARF expression. Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1919-24.
ENCODE histone modification ChIP, TF ChIP, figure S2

Middelberg RP, Benyamin B, de Moor MH, Warrington NM, Gordon S, Henders AK, Medland SE, Nyholt DR, de Geus EJ, Hottenga JJ et al. Loci affecting gamma-glutamyl transferase in adults and adolescents show age × SNP interaction and cardiometabolic disease associations. Hum Mol Genet. 2012 Jan 15;21(2):446-55.
ENCODE TF ChIP, histone modification ChIP, described in discussion

Ramagopalan SV, Heger A, Berlanga AJ, Maugeri NJ, Lincoln MR, Burrell A, Handunnetthi L, Handel AE, Disanto G, Orton SM et al. A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome Res. 2010 Oct;20(10):1352-60.
ENCODE DNase, Histone modification ChIP, TF ChIP, Fig 5, S1, S3

Rushefski M, Aplenc R, Meyer N, Li M, Feng R, Lanken PN, Gallop R, Bellamy S, Localio AR, Feinstein SI et al. Novel variants in the PRDX6 Gene and the risk of Acute Lung Injury following major trauma. BMC Med Genet. 2011 May 31;12:77.
ENCODE TF ChIP used, negative result

Sankaran VG, Menne TF, Šćepanović D, Vergilio JA, Ji P, Kim J, Thiru P, Orkin SH, Lander ES, Lodish HF. MicroRNA-15a and -16-1 act via MYB to elevate fetal hemoglobin expression in human trisomy 13. Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1519-24.
ENCODE histone modification ChIP in Table S2, S3

Spain SL, Carvajal-Carmona LG, Howarth KM, Jones AM, Su Z, Cazier JB, Williams J, Aaltonen LA, Pharoah P, Kerr DJ et al. Refinement of the associations between risk of colorectal cancer and polymorphisms on chromosomes 1q41 and 12q13.13. Hum Mol Genet. 2012 Feb 15;21(4):934-46.
ENCODE DNase, Histone modification ChIP, TF ChIP, in results and discussion

Szymanski M, Wang R, Bassett SS, Avramopoulos D. Alzheimer's risk variants in the clusterin gene are associated with alternative splicing. Transl Psychiatry. 2011 Jul 5;1:e18.
ENCODE DNase, TF ChIP, Methyl-seq, Figure 1b

Thakur RK, Yadav VK, Kumar P, Chowdhury S. Mechanisms of non-metastatic 2 (NME2)-mediated control of metastasis across tumor types. Naunyn Schmiedebergs Arch Pharmacol. 2011 Oct;384(4-5):397-406.
ENCODE TF ChIP, Figure 3

Tomlinson IP, Carvajal-Carmona LG, Dobbins SE, Tenesa A, Jones AM, Howarth K, Palles C, Broderick P, Jaeger EE, Farrington S et al. Multiple common susceptibility variants near BMP pathway loci GREM1, BMP4, and BMP2 explain part of the missing heritability of colorectal cancer. PLoS Genet. 2011 Jun;7(6):e1002105.
ENCODE DNase, Histone modification ChIP, results

Trynka G, Hunt KA, Bockett NA, Romanos J, Mistry V, Szperl A, Bakker SF, Bardella MT, Bhaw-Rosun L, Castillejo G et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat Genet. 2011 Nov 6;43(12):1193-201.
ENCODE TF ChIP, Table S2, discussion

Verlaan DJ, Berlivet S, Hunninghake GM, Madore AM, Larivière M, Moussette S, Grundberg E, Kwan T, Ouimet M, Ge B et al. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease. Am J Hum Genet. 2009 Sep;85(3):377-93.
ENCODE TF ChIP, figure S4

Visser M, Kayser M, Palstra RJ. HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome Res. 2012 Mar;22(3):446-55.
ENCODE histone modification ChIP, DNase, Figure S4b

Zhang X, Cowper-Sal Lari R, Bailey SD, Moore JH, Lupien M. Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus. Genome Res. 2012 Aug;22(8):1437-46.
ENCODE Histone modification ChIP, DNase, Fig 1

Zhu Q, Ge D, Maia JM, Zhu M, Petrovski S, Dickson SP, Heinzen EL, Shianna KV, Goldstein DB. A genome-wide comparison of the functional properties of rare and common genetic variants in humans. Am J Hum Genet. 2011 Apr 8;88(4):458-68.
ENCODE histone modification ChIP, TF ChIP, FAIRE, Figure 3B, 4B, Table 3, 4

Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y. Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res. 2008 Feb;18(2):310-23.
ENCODE Pilot DNase, GENCODE genes, described in results

Bailey TL, Machanick P. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res. 2012 Sep 1;40(17):e128.
ENCODE TF ChIP, Fig S7, Table S3

Baker A, Audit B, Chen CL, Moindrot B, Leleu A, Guilbaud G, Rappailles A, Vaillant C, Goldar A, Mongelard F et al. Replication fork polarity gradients revealed by megabase-sized U-shaped replication timing domains in human cell lines. PLoS Comput Biol. 2012;8(4):e1002443.
ENCODE DNase, TF ChIP, HiC, Fig 3, 4, 5, S10, S11, S13

Barkess G, Postnikov Y, Campos CD, Mishra S, Mohan G, Verma S, Bustin M, West KL. The chromatin-binding protein HMGN3 stimulates histone acetylation and transcription across the Glyt1 gene. Biochem J. 2012 Mar 15;442(3):495-505.
Mouse ENCODE DNase, TF ChIP, histone modification ChIP in figure 4

Begum G, Stevens A, Smith EB, Connor K, Challis JR, Bloomfield F, White A. Epigenetic changes in fetal hypothalamic energy regulating pathways are associated with maternal undernutrition and twinning. FASEB J. 2012 Apr;26(4):1694-703.
ENCODE histone modification ChIP, TF ChIP in Figure 1, Figure S1

Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011;12(1):R10.
ENCODE histone modification ChIP, figure 5e, S5

Bieberstein NI, Oesterreich FC, Straube K, Neugebauer KM. First exon length controls active chromatin signatures and transcription. Cell Rep. 2012 Jul 26;2(1):62-8.
ENCODE RNA, histone modification ChIP, TF ChIP, nucleosomes, mouse TF ChIP, Fig 1, 4, S1, S2, S3, S5, Table S3

Birnbaum RY, Clowney EJ, Agamy O, Kim MJ, Zhao J, Yamanaka T, Pappalardo Z, Clarke SL, Wenger AM, Nguyen L et al. Coding exons function as tissue-specific enhancers of nearby genes. Genome Res. 2012 Jun;22(6):1059-68.
ENCODE histone modification ChIP, TF ChIP, Table S1

Bock C, Halachev K, Büch J, Lengauer T. EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol. 2009 Feb 10;10(2):R14.
ENCODE Pilot hydroxyl radical cleavage (ORChiD), text, supplement

Böhlig L, Friedrich M, Engeland K. p53 activates the PANK1/miRNA-107 gene leading to downregulation of CDK6 and p130 cell cycle proteins. Nucleic Acids Res. 2011 Jan;39(2):440-53.
ENCODE histone modification ChIP, DNase, TF ChIP in Figure 7

Bolotin E, Chellappa K, Hwang-Verslues W, Schnabl JM, Yang C, Sladek FM. Nuclear receptor HNF4α binding sequences are widespread in Alu repeats. BMC Genomics. 2011 Nov 15;12:560.
ENCODE DNase, TF ChIP, used in text, Fig 7

Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011 Sep 15;25(18):1915-27.
ENCODE histone modification ChIP, GENCODE, Figure 1, S2, S4, S5, S6

Chen H, Tian Y, Shu W, Bo X, Wang S. Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PLoS One. 2012;7(7):e41374.
ENCODE TF ChIP, DNase, FAIRE, histone modification ChIP used throughout

Chen W, Feng P, Lin H. Prediction of replication origins by calculating DNA structural properties. FEBS Lett. 2012 Mar 23;586(6):934-8.
ENCODE Pilot hydroxyl radical cleavage (ORChiD), Fig 2, 3B

Chorley BN, Campbell MR, Wang X, Karaca M, Sambandan D, Bangura F, Xue P, Pi J, Kleeberger SR, Bell DA. Identification of novel NRF2-regulated genes by ChIP-Seq: influence on retinoid X receptor alpha. Nucleic Acids Res. 2012 Aug 1;40(15):7416-29.
ENCODE TF ChIP, Histone modification ChIP, DNase, Fig 4A, S4, S6, Table S2, described in results

Conley AB, Jordan IK. Epigenetic regulation of human cis-natural antisense transcripts. Nucleic Acids Res. 2012 Feb;40(4):1438-45.
ENCODE CAGE, RNA, Histone modification ChIP, TF ChIP, used thoughout

Costessi A, Mahrour N, Tijchon E, Stunnenberg R, Stoel MA, Jansen PW, Sela D, Martin-Brown S, Washburn MP, Florens L et al. The tumour antigen PRAME is a subunit of a Cul2 ubiquitin ligase and associates with active NFY promoters. EMBO J. 2011 Aug 5;30(18):3786-98.
ENCODE histone modification ChIP, TF ChIP, Figure 5

Dai Z, Dai X. Gene expression divergence is coupled to evolution of DNA structure in coding regions. PLoS Comput Biol. 2011 Nov;7(11):e1002275.
ENCODE Pilot hydroxyl radical cleavage (ORChiD), Fig 3A

De Rijck J, Bartholomeeusen K, Ceulemans H, Debyser Z, Gijsbers R. High-resolution profiling of the LEDGF/p75 chromatin interaction in the ENCODE region. Nucleic Acids Res. 2010 Oct;38(18):6135-47.
ENCODE histone modification ChIP, TF ChIP, RNA, figure 6, 7, Table S2

Desai SS, Achrekar SK, Pathak BR, Desai SK, Mangoli VS, Mangoli RV, Mahale SD. Follicle-stimulating hormone receptor polymorphism (G-29A) is associated with altered level of receptor expression in Granulosa cells. J Clin Endocrinol Metab. 2011 Sep;96(9):2805-12.
ENCODE Pilot hydroxyl radical cleavage (ORChiD), Fig 1A, methods

Dong X, Navratilova P, Fredman D, Drivenes Ø, Becker TS, Lenhard B. Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons. Nucleic Acids Res. 2010 Mar;38(4):1071-85.
ENCODE pilot analysis (neutrally evolving sites), Figure S4

Evans KJ. Most transcription factor binding sites are in a few mosaic classes of the human genome. BMC Genomics. 2010 May 6;11:286.
ENCODE TF CHIP used throughout, summary in table 3

Fairfax BP, Makino S, Radhakrishnan J, Plant K, Leslie S, Dilthey A, Ellis P, Langford C, Vannberg FO, Knight JC. Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat Genet. 2012 Mar 25;44(5):502-10.
ENCODE RNA, DNase, Histone modification ChIP, TF ChIP, Fig 4c, S12

Ferraiuolo MA, Rousseau M, Miyamoto C, Shenker S, Wang XQ, Nadler M, Blanchette M, Dostie J. The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res. 2010 Nov;38(21):7472-84.
ENCODE TF ChIP, Figure 5C, S6C, S7C, S8C

Fredman D, Dong X, Lenhard B. Making enhancers from spare parts of the genome. Genome Biol. 2011 Dec 29;12(12):138.
ENCODE histone modification ChIP, Figure 2

Friedli M, Barde I, Arcangeli M, Verp S, Quazzola A, Zakany J, Lin-Marq N, Robyr D, Attanasio C, Spitz F et al. A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PLoS One. 2010 Dec 29;5(12):e15741.
ENCODE DNase, histone modification ChIP, described in text

Gewurz BE, Mar JC, Padi M, Zhao B, Shinners NP, Takasaki K, Bedoya E, Zou JY, Cahir-McFarland E, Quackenbush J et al. Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. J Virol. 2011 Jul;85(13):6764-73.
ENCODE TF ChIP, described in methods

Gorkin DU, Lee D, Reed X, Fletez-Brant C, Bessling SL, Loftus SK, Beer MA, Pavan WJ, McCallion AS. Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes. Genome Res. 2012 Sep 27;.
ENCODE and mouse ENCODE, TF ChIP, histone modification ChIP, DNase, Fig 3B, 3C, 7E, 7F

Guilbaud G, Rappailles A, Baker A, Chen CL, Arneodo A, Goldar A, d'Aubenton-Carafa Y, Thermes C, Audit B, Hyrien O. Evidence for sequential and increasing activation of replication origins along replication timing gradients in the human genome. PLoS Comput Biol. 2011 Dec;7(12):e1002322.
ENCODE DNase, origin mapping, Fig 11, table 1

Guillou E, Ibarra A, Coulon V, Casado-Vela J, Rico D, Casal I, Schwob E, Losada A, Méndez J. Cohesin organizes chromatin loops at DNA replication factories. Genes Dev. 2010 Dec 15;24(24):2812-22.
ENCODE TF ChIP, replication origins, Fig S6, 4B

Györy I, Boller S, Nechanitzky R, Mandel E, Pott S, Liu E, Grosschedl R. Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferation, and survival of B cells. Genes Dev. 2012 Apr 1;26(7):668-82.
Mouse ENCODE DNase data is part of Figure 1, 5

Ho ES, Gunderson SI. Long conserved fragments upstream of Mammalian polyadenylation sites. Genome Biol Evol. 2011;3:654-66.
ENCODE DNase, Fig 6

Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell. 2011 Oct 7;44(1):17-28.
ENCODE histone modification ChIP, figure 3

Horakova AH, Moseley SC, McLaughlin CR, Tremblay DC, Chadwick BP. The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome. Hum Mol Genet. 2012 Oct 15;21(20):4367-77.
ENCODE TF ChIP, Fig 3

Huda A, Bowen NJ, Conley AB, Jordan IK. Epigenetic regulation of transposable element derived human gene promoters. Gene. 2011 Apr 1;475(1):39-48.
ENCODE histone modification ChIP, figures 2, 3, etc

Jeffries CD, Perkins DO, Guan X. Gene processing control loops suggested by sequencing, splicing, and RNA folding. BMC Bioinformatics. 2010 Dec 20;11:602.
ENCODE Gencode, described in text

Jia H, Osak M, Bogu GK, Stanton LW, Johnson R, Lipovich L. Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA. 2010 Aug;16(8):1478-87.
ENCODE TF ChIP, histone modification ChIP, in supplemental data sets 7, 8

Jiang Y, Lucas I, Young DJ, Davis EM, Karrison T, Rest JS, Le Beau MM. Common fragile sites are characterized by histone hypoacetylation. Hum Mol Genet. 2009 Dec 1;18(23):4501-12.
ENCODE histone modification ChIP, figure S3A

Kehayova P, Monahan K, Chen W, Maniatis T. Regulatory elements required for the activation and repression of the protocadherin-alpha gene cluster. Proc Natl Acad Sci U S A. 2011 Oct 11;108(41):17195-200.
ENCODE TF ChIP, Figures 5, S3

Kosti I, Radivojac P, Mandel-Gutfreund Y. An integrated regulatory network reveals pervasive cross-regulation among transcription and splicing factors. PLoS Comput Biol. 2012 Jul;8(7):e1002603.
ENCODE TF ChIP, described in methods

Levenstien MA, Klein RJ. Predicting functionally important SNP classes based on negative selection. BMC Bioinformatics. 2011 Jan 19;12:26.
ENCODE histone modification ChIP, DNase, TF ChIP, data downloaded through Ensembl, used in Tables 2-4, etc.

Managadze D, Rogozin IB, Chernikova D, Shabalina SA, Koonin EV. Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol Evol. 2011;3:1390-404.
ENCODE mouse RNA, described in methods

Martin DI, Singer M, Dhahbi J, Mao G, Zhang L, Schroth GP, Pachter L, Boffelli D. Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Res. 2011 Dec;21(12):2049-57.
ENCODE Histone modification ChIP, FAIRE, table 1

Martin MM, Ryan M, Kim R, Zakas AL, Fu H, Lin CM, Reinhold WC, Davis SR, Bilke S, Liu H et al. Genome-wide depletion of replication initiation events in highly transcribed regions. Genome Res. 2011 Nov;21(11):1822-32.
ENCODE histone modification ChIP, TF ChIP, DNase, methyl-RRBS, Figure 5, Figure 6, Table 3, Figure S2

Mikula M, Gaj P, Dzwonek K, Rubel T, Karczmarski J, Paziewska A, Dzwonek A, Bragoszewski P, Dadlez M, Ostrowski J. Comprehensive analysis of the palindromic motif TCTCGCGAGA: a regulatory element of the HNRNPK promoter. DNA Res. 2010 Aug;17(4):245-60.
ENCODE DNase, Figure 7

Mokry M, Hatzis P, Schuijers J, Lansu N, Ruzius FP, Clevers H, Cuppen E. Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes. Nucleic Acids Res. 2012 Jan;40(1):148-58.
ENCODE RNA, TF ChIP, Supplementary Figure S4, supplementary material 2

Morikawa M, Koinuma D, Tsutsumi S, Vasilaki E, Kanki Y, Heldin CH, Aburatani H, Miyazono K. ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif. Nucleic Acids Res. 2011 Nov 1;39(20):8712-27.
ENCODE histone modification ChIP, Fig 3D, S3C, results, methods

Morrissy AS, Griffith M, Marra MA. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res. 2011 Aug;21(8):1203-12.
ENCODE TF ChIP, Fig 4b and text

Moseley SC, Rizkallah R, Tremblay DC, Anderson BR, Hurt MM, Chadwick BP. YY1 associates with the macrosatellite DXZ4 on the inactive X chromosome and binds with CTCF to a hypomethylated form in some male carcinomas. Nucleic Acids Res. 2012 Feb;40(4):1596-608.
ENCODE histone modification ChIP, TF ChIP, Fig 5a

Nakken S, Rødland EA, Hovig E. Impact of DNA physical properties on local sequence bias of human mutation. Hum Mutat. 2010 Dec;31(12):1316-25.
ENCODE Pilot hydroxyl radical cleavage (ORChiD), Table 1, methods

Nelms BL, Labosky PA. A predicted hairpin cluster correlates with barriers to PCR, sequencing and possibly BAC recombineering. Sci Rep. 2011;1:106.
ENCODE histone modification ChIP, DNase, Figure 2

Nozaki T, Yachie N, Ogawa R, Saito R, Tomita M. Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA. Gene. 2011 May 1;476(1-2):10-4.
ENCODE Pilot hydroxyl radical cleavage (ORChiD), Fig 2, 3B, methods

Oh YM, Kim JK, Choi S, Yoo JY. Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices. Nucleic Acids Res. 2012 Mar;40(5):e38.
ENCODE TF ChIP data used throughout, described in Table S2D

Ott CJ, Bischof JM, Unti KM, Gillen AE, Leir SH, Harris A. Nucleosome occupancy reveals regulatory elements of the CFTR promoter. Nucleic Acids Res. 2012 Jan;40(2):625-37.
ENCODE DNase, 28 mammals conservation, Fig 3C, 6B, 6C, 6D, S3

Prendergast JG, Tong P, Hay DC, Farrington SM, Semple CA. A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci. Epigenetics Chromatin. 2012 May 19;5(1):6.
ENCODE RNA, histone modification ChIP, TF ChIP, used throughout, listed in additional file 6 (also Roadmap Epigenomics RNA, DNAme, histone modification CHIP)

Previti C, Harari O, Zwir I, del Val C. Profile analysis and prediction of tissue-specific CpG island methylation classes. BMC Bioinformatics. 2009 Apr 21;10:116.
ENCODE Pilot hydroxyl radical cleavage (ORChiD), Table 4, methods

Raab JR, Chiu J, Zhu J, Katzman S, Kurukuti S, Wade PA, Haussler D, Kamakaka RT. Human tRNA genes function as chromatin insulators. EMBO J. 2011 Nov 15;31(2):330-50.
ENCODE data used in Figure 2A; used in findings presented in text before Figure 1, during Figure 3, and maybe part of Figure 8A

Rackham O, Shearwood AM, Mercer TR, Davies SM, Mattick JS, Filipovska A. Long noncoding RNAs are generated from the mitochondrial genome and regulated by nuclear-encoded proteins. RNA. 2011 Dec;17(12):2085-93.
ENCODE RNA analyzed, described in methods

Radwan A, Younis A, Luykx P, Khuri S. Prediction and analysis of nucleosome exclusion regions in the human genome. BMC Genomics. 2008 Apr 22;9:186.
ENCODE Pilot DNase, hydroxyl radical cleavage (ORChiD), Fig 7, 8, methods

Raj B, O'Hanlon D, Vessey JP, Pan Q, Ray D, Buckley NJ, Miller FD, Blencowe BJ. Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis. Mol Cell. 2011 Sep 2;43(5):843-50.
ENCODE TF ChIP, Figure 3C

Ren L, Shi M, Wang Y, Yang Z, Wang X, Zhao Z. CTCF and cohesin cooperatively mediate the cell-type specific interchromatin interaction between Bcl11b and Arhgap6 loci. Mol Cell Biochem. 2012 Jan;360(1-2):243-51.
ENCODE TF ChIP, Fig 1B

Restivo G, Nguyen BC, Dziunycz P, Ristorcelli E, Ryan RJ, Özuysal ÖY, Di Piazza M, Radtke F, Dixon MJ, Hofbauer GF et al. IRF6 is a mediator of Notch pro-differentiation and tumour suppressive function in keratinocytes. EMBO J. 2011 Nov 16;30(22):4571-85.
ENCODE histone modification ChIP, TF ChIP, DNase, Figure 4a

Rose D, Stadler PF. Molecular evolution of the non-coding eosinophil granule ontogeny transcript. Front Genet. 2011;2:69.
ENCODE DNase, histone modification ChIP, RNA, Figure 5, A3, results

Ruppert SM, Chehtane M, Zhang G, Hu H, Li X, Khaled AR. JunD/AP-1-mediated gene expression promotes lymphocyte growth dependent on interleukin-7 signal transduction. PLoS One. 2012;7(2):e32262.
ENCODE TF ChIP, methods, Figure S2, Data S1

Schmidt D, Schwalie PC, Wilson MD, Ballester B, Gonçalves A, Kutter C, Brown GD, Marshall A, Flicek P, Odom DT. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell. 2012 Jan 20;148(1-2):335-48.
ENCODE TF ChIP, related to Fig 1, S1

Schödel J, Oikonomopoulos S, Ragoussis J, Pugh CW, Ratcliffe PJ, Mole DR. High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq. Blood. 2011 Jun 9;117(23):e207-17.
ENCODE DNase, Fig 5, S10

Shu W, Chen H, Bo X, Wang S. Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains. Nucleic Acids Res. 2011 Sep 1;39(17):7428-43.
ENCODE DNase, Histone modification ChIP, TF ChIP, GENCODE genes, used throughout

Smith AM, Calero-Nieto FJ, Schütte J, Kinston S, Timms RT, Wilson NK, Hannah RL, Landry JR, Göttgens B. Integration of Elf-4 into stem/progenitor and erythroid regulatory networks through locus-wide chromatin studies coupled with in vivo functional validation. Mol Cell Biol. 2012 Feb;32(4):763-73.
ENCODE histone modification ChIP, DNase, TF ChIP, mouse and human, referred to in text as Figure S3, S4; S5 at http://hscl.cimr.cam.ac.uk/genomic_supplementary.html which links to the data at http://hscl.cimr.cam.ac.uk/Supplementary_Data/Supplementary_data_Smith.pdf

Somel M, Liu X, Tang L, Yan Z, Hu H, Guo S, Jiang X, Zhang X, Xu G, Xie G et al. MicroRNA-driven developmental remodeling in the brain distinguishes humans from other primates. PLoS Biol. 2011 Dec;9(12):e1001214.
ENCODE histone modication ChIP, DNase, Fig S9

Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011 Dec 14;480(7378):490-5.
ENCODE mouse and human DNase, Fig 2, S2, S6

Stoltzfus A. Evidence for a predominant role of oxidative damage in germline mutation in mammals. Mutat Res. 2008 Sep 26;644(1-2):71-3.
ENCODE hydroxyl radical cleavage (ORChiD), Fig 1, 2

Taft RJ, Hawkins PG, Mattick JS, Morris KV. The relationship between transcription initiation RNAs and CCCTC-binding factor (CTCF) localization. Epigenetics Chromatin. 2011 Aug 3;4:13.
ENCODE TF ChIP, Figure 2

Tanaka Y, Nakamura A, Morioka MS, Inoue S, Tamamori-Adachi M, Yamada K, Taketani K, Kawauchi J, Tanaka-Okamoto M, Miyoshi J et al. Systems analysis of ATF3 in stress response and cancer reveals opposing effects on pro-apoptotic genes in p53 pathway. PLoS One. 2011;6(10):e26848.
ENCODE TF ChIP, used in discussion

Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics. 2007 Sep;Chapter 10:Unit 10.5.
ENCODE TF ChIP, used in basic protocol 2, 3

Teng L, Firpi HA, Tan K. Enhancers in embryonic stem cells are enriched for transposable elements and genetic variations associated with cancers. Nucleic Acids Res. 2011 Sep 1;39(17):7371-9.
ENCODE histone modification ChIP, TF ChIP, DNase, data analyzed

Terrenoire E, McRonald F, Halsall JA, Page P, Illingworth RS, Taylor AM, Davison V, O'Neill LP, Turner BM. Immunostaining of modified histones defines high-level features of the human metaphase epigenome. Genome Biol. 2010;11(11):R110.
ENCODE histone modification ChIP, Figure 5

Tiana M, Villar D, Pérez-Guijarro E, Gómez-Maldonado L, Moltó E, Fernández-Miñán A, Gómez-Skarmeta JL, Montoliu L, del Peso L. A role for insulator elements in the regulation of gene expression response to hypoxia. Nucleic Acids Res. 2012 Mar;40(5):1916-27.
ENCODE TF ChIP, Fig S1, S4

Tsai KN, Wang D. Identification of activated cryptic 5' splice sites using structure profiles and odds measure. Nucleic Acids Res. 2012 May;40(10):e73.
ENCODE Pilot hydroxyl radical cleavage (ORChiD), results, methods

Wang YM, Zhou P, Wang LY, Li ZH, Zhang YN, Zhang YX. Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells. PLoS One. 2012;7(8):e42414.
ENCODE DNase, TF ChIP, Fig S2, Tables S7, S8

Woodfine K, Huddleston JE, Murrell A. Quantitative analysis of DNA methylation at all human imprinted regions reveals preservation of epigenetic stability in adult somatic tissue. Epigenetics Chromatin. 2011 Jan 31;4(1):1.
ENCODE TF ChIP, Table 1, Figure S3

You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang G, Jones PA. OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes. Proc Natl Acad Sci U S A. 2011 Aug 30;108(35):14497-502.
ENCODE TF ChIP, Methyl-Seq, Fig 4C

Zemojtel T, Kielbasa SM, Arndt PF, Behrens S, Bourque G, Vingron M. CpG deamination creates transcription factor-binding sites with high efficiency. Genome Biol Evol. 2011;3:1304-11.
ENCODE TF ChIP, described in text, used in Table S2, and Supplementary material

Abeel T, Saeys Y, Bonnet E, Rouzé P, Van de Peer Y. Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res. 2008 Feb;18(2):310-23.
ENCODE Pilot DNase, GENCODE genes, described in results

Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E. Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data. Bioinformatics. 2011 Dec 15;27(24):3333-40.
ENCODE TF ChIP, histone modification ChIP, RNA, Fig 1, Table 1, S6

Althammer S, Pagès A, Eyras E. Predictive models of gene regulation from high-throughput epigenomics data. Comp Funct Genomics. 2012;2012:284786.
ENCODE RNA, DNase, Histone modification ChIP, TF ChIP, Methyl-RRBS, GENCODE, used throughout, Table 2

Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012 Oct;22(10):2008-17.
ENCODE RNA, Fig S5, S6

Bedo J, Kowalczyk A. Genome annotation test with validation on transcription start site and ChIP-Seq for Pol-II binding data. Bioinformatics. 2011 Jun 15;27(12):1610-7.
ENCODE TF CHIP, Table 1, used throughout

Berlanga-Taylor AJ, Disanto G, Ebers GC, Ramagopalan SV. Vitamin D-gene interactions in multiple sclerosis. J Neurol Sci. 2011 Dec 15;311(1-2):32-6.
ENCODE histone modifcation ChIP in text, comparison of ENCODE His-ChIP-seq and VDR described

Bhattacharyya S, Tian J, Bouhassira EE, Locker J. Systematic targeted integration to study Albumin gene control elements. PLoS One. 2011;6(8):e23234.
ENCODE TF ChIP, figure 8 legend

Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E. De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res. 2010 Jun;38(11):e126.
ENCODE TF ChIP, Figure 2, 3

Cai X, Hou L, Su N, Hu H, Deng M, Li X. Systematic identification of conserved motif modules in the human genome. BMC Genomics. 2010 Oct 14;11:567.
ENCODE TF ChIP, methods, used throughout, additional file 1

Carstensen L, Sandelin A, Winther O, Hansen NR. Multivariate Hawkes process models of the occurrence of regulatory elements. BMC Bioinformatics. 2010 Sep 9;11:456.
ENCODE TF ChIP, Histone modification ChIP, Figures 5, 6, 7, 8, 9

Chang HW, Cheng YH, Chuang LY, Yang CH. SNP-RFLPing 2: an updated and integrated PCR-RFLP tool for SNP genotyping. BMC Bioinformatics. 2010 Apr 8;11:173.
Java application for annotating SNPs, includes ENCODE annotations

Chen Y, Jørgensen M, Kolde R, Zhao X, Parker B, Valen E, Wen J, Sandelin A. Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data. BMC Genomics. 2011 Nov 3;12:544.
ENCODE histone modification ChIP, TF ChIP, RNA, used throughout; scheme in figure 1

Coetzee SG, Rhie SK, Berman BP, Coetzee GA, Noushmehr H. FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs. Nucleic Acids Res. 2012 Oct 1;40(18):e139.
ENCODE TF ChIP, DNase, FAIRE, Histone modification ChIP, Fig 3, 4, S1, S2, Supplement

Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A et al. Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics. 2012 Jan 15;28(2):167-75.
ENCODE mappability, results and Fig S8

Dozmorov MG, Cara LR, Giles CB, Wren JD. GenomeRunner: automating genome exploration. Bioinformatics. 2012 Feb 1;28(3):419-20.
ENCODE data used in analyses, Picture on their website, supplement

Enroth S, Andersson CR, Andersson R, Wadelius C, Gustafsson MG, Komorowski J. A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements. Algorithms Mol Biol. 2012 Jan 16;7(1):2.
ENCODE TF ChIP; Table 1, Figure 2

Firpi HA, Ucar D, Tan K. Discover regulatory DNA elements using chromatin signatures and artificial neural network. Bioinformatics. 2010 Jul 1;26(13):1579-86.
ENCODE histone modification ChIP, Table 2

Halder K, Halder R, Chowdhury S. Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals. Mol Biosyst. 2009 Dec;5(12):1703-12.
ENCODE DNase, FAIRE

Håndstad T, Rye MB, Drabløs F, Sætrom P. A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites. PLoS One. 2011 Apr 14;6(4):e18430.
ENCODE TF-ChIP

Huda A, Tyagi E, Mariño-Ramírez L, Bowen NJ, Jjingo D, Jordan IK. Prediction of transposable element derived enhancers using chromatin modification profiles. PLoS One. 2011;6(11):e27513.
ENCODE histone modification ChIP, DNase, RNA, analyzed throughout

Lee D, Karchin R, Beer MA. Discriminative prediction of mammalian enhancers from DNA sequence. Genome Res. 2011 Dec;21(12):2167-80.
mouse ENCODE DNase, Figure 5, Table 2

Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA et al. Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell. 2008 Jul 25;31(2):294-301.
ENCODE histone modification ChIP, discussion

Martin P, Barton A, Eyre S. ASSIMILATOR: a new tool to inform selection of associated genetic variants for functional studies. Bioinformatics. 2011 Jan 1;27(1):144-6.
ENCODE Histone modification ChIP, TF ChIP, RNA, DNase, GENCODE Figure 1A

McLeay RC, Leat CJ, Bailey TL. Tissue-specific prediction of directly regulated genes. Bioinformatics. 2011 Sep 1;27(17):2354-60.
ENCODE TF ChIP, Histone modification ChIP, Table 1, Table 2

Mittal VK, McDonald JF. R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. Nucleic Acids Res. 2012 May;40(9):e67.
ENCODE RNA, used in Table 5, Fig 6, 7

Mortlock DP, Pregizer S. Identifying functional annotation for noncoding genomic sequences. Curr Protoc Hum Genet. 2012 Jan;Chapter 1:Unit1.10.
ENCODE RNA, histone modification ChIP, DNase, TF ChIP, Figure 1, 2

Nix DA, Di Sera TL, Dalley BK, Milash BA, Cundick RM, Quinn KS, Courdy SJ. Next generation tools for genomic data generation, distribution, and visualization. BMC Bioinformatics. 2010 Sep 9;11:455.
ENCODE Histone modification ChIP, Fig 11

Pickrell JK, Gaffney DJ, Gilad Y, Pritchard JK. False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions. Bioinformatics. 2011 Aug 1;27(15):2144-6.
ENCODE TF ChIP, Figure 1

Pinello L, Lo Bosco G, Hanlon B, Yuan GC. A motif-independent metric for DNA sequence specificity. BMC Bioinformatics. 2011 Oct 21;12:408.
ENCODE TF ChIP, histone modification ChIP, Fig 2, 3, Table 3, 4, 5

Pique-Regi R, Degner JF, Pai AA, Gaffney DJ, Gilad Y, Pritchard JK. Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 2011 Mar;21(3):447-55.
ENCODE DNase, histone modification ChIP, TF ChIP, Fig 1, 2, 3, 6 etc

Rolfe PA, Gifford DK. ReadDB provides efficient storage for mapped short reads. BMC Bioinformatics. 2011 Jul 7;12:278.
ENCODE DNase, CTCF ChIP, described in text and used throughout

Rye M, Sætrom P, Håndstad T, Drabløs F. Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements. BMC Biol. 2011 Nov 24;9:80.
ENCODE TF ChIP, DNase, FAIRE, histone modification ChIP, RNA, used throughout; summarized in Table S7

Sadri J, Diallo AB, Blanchette M. Predicting site-specific human selective pressure using evolutionary signatures. Bioinformatics. 2011 Jul 1;27(13):i266-74.
ENCODE DNase, histone modification ChIP, figure 4

Singer M, Boffelli D, Dhahbi J, Schönhuth A, Schroth GP, Martin DI, Pachter L. MetMap enables genome-scale Methyltyping for determining methylation states in populations. PLoS Comput Biol. 2010 Aug 19;6(8):e1000888.
ENCODE FAIRE data, Table 3

Smith AJ, Howard P, Shah S, Eriksson P, Stender S, Giambartolomei C, Folkersen L, Tybjærg-Hansen A, Kumari M, Palmen J et al. Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays. PLoS Genet. 2012 Aug;8(8):e1002908.
ENCODE TF ChIP, DNase, Histone modification ChIP, FAIRE, Figure 4

Su J, Teichmann SA, Down TA. Assessing computational methods of cis-regulatory module prediction. PLoS Comput Biol. 2010 Dec 2;6(12):e1001020.
ENCODE DNase, ENCODE regions, figures 9,10

Sulonen AM, Ellonen P, Almusa H, Lepistö M, Eldfors S, Hannula S, Miettinen T, Tyynismaa H, Salo P, Heckman C et al. Comparison of solution-based exome capture methods for next generation sequencing. Genome Biol. 2011 Sep 28;12(9):R94.
ENCODE mappability, described in text

Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Using galaxy to perform large-scale interactive data analyses. Curr Protoc Bioinformatics. 2007 Sep;Chapter 10:Unit 10.5.
ENCODE TF ChIP, used in basic protocol 2, 3

Valen E, Sandelin A, Winther O, Krogh A. Discovery of regulatory elements is improved by a discriminatory approach. PLoS Comput Biol. 2009 Nov;5(11):e1000562.
ENCODE TF ChIP, table S7

Veiga DF, Deus HF, Akdemir C, Vasconcelos AT, Almeida JS. DASMiner: discovering and integrating data from DAS sources. BMC Syst Biol. 2009 Nov 17;3:109.
ENCODE histone modification ChIP, figure 4

Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010 Sep;38(16):e164.
ENCODE DNase, Histone modification ChIP, TF ChIP, GENCODE genes, ChIP-Seq peaks, RNA-Seq peaks, or many other annotations on genomic intervals, reported on web site

Whitington T, Frith MC, Johnson J, Bailey TL. Inferring transcription factor complexes from ChIP-seq data. Nucleic Acids Res. 2011 Aug;39(15):e98.
ENCODE TF ChIP, Table 1, 2, 3, S1, S3, S4

Yaffe E, Tanay A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet. 2011 Oct 16;43(11):1059-65.
ENCODE DNase, histone modification ChIP, TF ChIP, Figure 3

Zambelli F, Prazzoli GM, Pesole G, Pavesi G. Cscan: finding common regulators of a set of genes by using a collection of genome-wide ChIP-seq datasets. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W510-5.
ENCODE TF ChIP, histone modification ChIP, chromatin states

Zhang Y, Lv J, Liu H, Zhu J, Su J, Wu Q, Qi Y, Wang F, Li X. HHMD: the human histone modification database. Nucleic Acids Res. 2010 Jan;38(Database issue):D149-54.
ENCODE histone modification ChIP, Table 2 and database

Zhang Z, Zhang MQ. Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. BMC Bioinformatics. 2011 May 14;12:155.
ENCODE RNA, histone modification ChIP, methyl-seq, figure 3, table 3

Ahn SJ, Vogel H, Heckel DG. Comparative analysis of the UDP-glycosyltransferase multigene family in insects. Insect Biochem Mol Biol. 2012 Feb;42(2):133-47.
modENCODE fly RNA-seq data were used

Bushey AM, Ramos E, Corces VG. Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev. 2009 Jun 1;23(11):1338-50.
modENCODE Fly S2 ChIP, CP190 and dCTCF

Cardoso-Moreira M, Emerson JJ, Clark AG, Long M. Drosophila duplication hotspots are associated with late-replicating regions of the genome. PLoS Genet. 2011 Nov;7(11):e1002340.
modENCODE Fly Replication timing maps, Kc, S2, Bg3, were used

Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, Lo Sardo F, Saxena A, Miyoshi K, Siomi H et al. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature. 2011 Nov 6;480(7377):391-5.
modENCODE Fly CAGE data used to determine antisense transcription frequent at heat shock loci

Cline TW, Dorsett M, Sun S, Harrison MM, Dines J, Sefton L, Megna L. Evolution of the Drosophila feminizing switch gene Sex-lethal. Genetics. 2010 Dec;186(4):1321-36.
modENCODE Fly RNA-seq splice junction data used

Cryderman DE, Vitalini MW, Wallrath LL. Heterochromatin protein 1a is required for an open chromatin structure. Transcription. 2011 Mar;2(2):95-99.
modENCODE fly chromatin states, histone modifications, expression

DeMaso CR, Kovacevic I, Uzun A, Cram EJ. Structural and functional evaluation of C. elegans filamins FLN-1 and FLN-2. PLoS One. 2011;6(7):e22428.
modENCODE worm data used, SL1 binding, RNA-seq data used for expression and exon/isoform determination

Feller C, Prestel M, Hartmann H, Straub T, Söding J, Becker PB. The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset. Nucleic Acids Res. 2012 Feb;40(4):1509-22.
modENCODE Fly data used; Figure 1, Figure 2, Figure 5; Pol II ChIP, chromatin factors and histone modifications, and "all available modENCODE chromatin ChIP-chip data sets were screened"

Fischer SE, Montgomery TA, Zhang C, Fahlgren N, Breen PC, Hwang A, Sullivan CM, Carrington JC, Ruvkun G. The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications. PLoS Genet. 2011 Nov;7(11):e1002369.
modENCODE Worm data; intron/exon structures of genes from RNA-seq

Gangishetti U, Veerkamp J, Bezdan D, Schwarz H, Lohmann I, Moussian B. The transcription factor Grainy head and the steroid hormone ecdysone cooperate during differentiation of the skin of Drosophila melanogaster. Insect Mol Biol. 2012 Jun;21(3):283-95.
modENCODE fly data on bFtzF1 binding, used in Fig 7

Gilchrist DA, Adelman K. Coupling polymerase pausing and chromatin landscapes for precise regulation of transcription. Biochim Biophys Acta. 2012 Jul;1819(7):700-6.
modENCODE fly histone modifications, chromatin states, Pol II binding used in Figure 3B

Greer EL, Maures TJ, Ucar D, Hauswirth AG, Mancini E, Lim JP, Benayoun BA, Shi Y, Brunet A. Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans. Nature. 2011 Oct 19;479(7373):365-71.
modENCODE Worm H3K4me3 data used

Ihuegbu NE, Stormo GD, Buhler J. Fast, sensitive discovery of conserved genome-wide motifs. J Comput Biol. 2012 Feb;19(2):139-47.
modENCODE worm TF HOT regions; data used for Table 3

Katzemich A, Long JY, Jani K, Lee BR, Schöck F. Muscle type-specific expression of Zasp52 isoforms in Drosophila. Gene Expr Patterns. 2011 Dec;11(8):484-90.
modENCODE fly data mentioned in discussion, used to confirm exons

Kellner WA, Ramos E, Van Bortle K, Takenaka N, Corces VG. Genome-wide phosphoacetylation of histone H3 at Drosophila enhancers and promoters. Genome Res. 2012 Jun;22(6):1081-8.
modENCODE data: Fig 1A, Pol II ChIP-chip, Fig S4, ChIP-chip, RNA used in Figure 6 analysis; refer to antibodies as validated in modENCODE

Kvon EZ, Stampfel G, Yáñez-Cuna JO, Dickson BJ, Stark A. HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature. Genes Dev. 2012 May 1;26(9):908-13.
modENCODE fly HOT regions were analyzed in this work; modENCODE RNA-seq used; modENCODE tracks in Fig 2B

Majumdar A, Cesario WC, White-Grindley E, Jiang H, Ren F, Khan MR, Li L, Choi EM, Kannan K, Guo F et al. Critical role of amyloid-like oligomers of Drosophila Orb2 in the persistence of memory. Cell. 2012 Feb 3;148(3):515-29.
modENCODE Fly data used to determine Orb2 encodes 6 isoforms (S1B)

McQuilton P, St Pierre SE, Thurmond J, FlyBase Consortium. FlyBase 101--the basics of navigating FlyBase. Nucleic Acids Res. 2012 Jan;40(Database issue):D706-14.
modENCODE fly genome-wide data available

Morton JJ, Blumenthal T. Identification of transcription start sites of trans-spliced genes: uncovering unusual operon arrangements. RNA. 2011 Feb;17(2):327-37.
modENCODE Worm Htz and Pol II ChIP, 3. end formation sites, and RNA-seq used

Nowak SJ, Aihara H, Gonzalez K, Nibu Y, Baylies MK. Akirin links twist-regulated transcription with the Brahma chromatin remodeling complex during embryogenesis. PLoS Genet. 2012;8(3):e1002547.
modENCODE fly histone modification data

Noyes A, Stefaniuk C, Cheng Y, Kennison JA, Kassis JA. Modulation of the activity of a polycomb-group response element in Drosophila by a mutation in the transcriptional activator woc. G3 (Bethesda). 2011 Nov;1(6):471-8.
modENCODE fly HP1c ChIP data were used

Paro S, Li X, O'Connell MA, Keegan LP. Regulation and functions of ADAR in drosophila. Curr Top Microbiol Immunol. 2012;353:221-36.
modENCODE fly data to supplement published data on Adar gene transcription, and splicing

Pearson JC, Watson JD, Crews ST. Drosophila melanogaster Zelda and Single-minded collaborate to regulate an evolutionarily dynamic CNS midline cell enhancer. Dev Biol. 2012 Jun 15;366(2):420-32.
modENCODE fly RNA-Seq data, timecourse, analyzed to determine transcription start, stop, splice sites, and expression pattern

Peng HW, Slattery M, Mann RS. Transcription factor choice in the Hippo signaling pathway: homothorax and yorkie regulation of the microRNA bantam in the progenitor domain of the Drosophila eye imaginal disc. Genes Dev. 2009 Oct 1;23(19):2307-19.
modENCODE Fly data used to find TSS for bantam; Figure 6C

Rodriguez J, Menet JS, Rosbash M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol Cell. 2012 Jul 13;47(1):27-37.
modENCODE fly editing data used, fig 3A, text

Rogers RL, Hartl DL. Chimeric genes as a source of rapid evolution in Drosophila melanogaster. Mol Biol Evol. 2012 Feb;29(2):517-29.
modENCODE Fly RNA-seq data used

Rotstein B, Molnar D, Adryan B, Llimargas M. Tramtrack is genetically upstream of genes controlling tracheal tube size in Drosophila. PLoS One. 2011;6(12):e28985.
modENCODE Fly data used, ChIP for Tramtrack, Figure 4, Figure S4

Sakoparnig T, Kockmann T, Paro R, Beisel C, Beerenwinkel N. Binding profiles of chromatin-modifying proteins are predictive for transcriptional activity and promoter-proximal pausing. J Comput Biol. 2012 Feb;19(2):126-38.
modENCODE Fly S2 TF, chromatin organizers, insulator protein data used, also RNA-seq

Schrider DR, Stevens K, Cardeño CM, Langley CH, Hahn MW. Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster. Genome Res. 2011 Dec;21(12):2087-95.
modENCODE Fly data, cDNA, EST, and RNA-seq data, used for intron/exon structure of some genes

Spradling AC, Bellen HJ, Hoskins RA. Drosophila P elements preferentially transpose to replication origins. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15948-53.
modENCODE fly ORC data used to identify replication origins

Vatolina TY, Boldyreva LV, Demakova OV, Demakov SA, Kokoza EB, Semeshin VF, Babenko VN, Goncharov FP, Belyaeva ES, Zhimulev IF. Identical functional organization of nonpolytene and polytene chromosomes in Drosophila melanogaster. PLoS One. 2011;6(10):e25960.
modENCODE Fly ChIP data used in Figure 2, 6, chromatin states also used

Vujatovic O, Zaragoza K, Vaquero A, Reina O, Bernués J, Azorín F. Drosophila melanogaster linker histone dH1 is required for transposon silencing and to preserve genome integrity. Nucleic Acids Res. 2012 Jul;40(12):5402-14.
modENCODE Fly H1 ChIP data, S2 and BG3 cells

Wallace HA, Plata MP, Kang HJ, Ross M, Labrador M. Chromatin insulators specifically associate with different levels of higher-order chromatin organization in Drosophila. Chromosoma. 2010 Apr;119(2):177-94.
modENCODE FLY data were used; ChIP-chip Su(Hw), CP190, BEAF-32, CTCF

Xiao T, Wang Y, Luo H, Liu L, Wei G, Chen X, Sun Y, Chen X, Skogerbø G, Chen R. A differential sequencing-based analysis of the C. elegans noncoding transcriptome. RNA. 2012 Apr;18(4):626-39.
modENCODE Worm data used; RNA-seq, H3K4me3, 22 TFs

Yook K, Harris TW, Bieri T, Cabunoc A, Chan J, Chen WJ, Davis P, de la Cruz N, Duong A, Fang R et al. WormBase 2012: more genomes, more data, new website. Nucleic Acids Res. 2012 Jan;40(Database issue):D735-41.
modENCODE worm genome-wide data available

Young RS, Marques AC, Tibbit C, Haerty W, Bassett AR, Liu JL, Ponting CP. Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome. Genome Biol Evol. 2012;4(4):427-42.
modENCODE fly whole transcriptome (RNA-seq) data