This page lists 404 papers that use ENCODE data, published by authors not funded by ENCODE. The ENCODE project tracks these papers to assess impact of the resource and to provide examples of how the resource can be used. The ENCODE lists below are non-overlapping; each paper is only assigned to one list. This page also has a separate list of 144 papers that use modENCODE data, published by authors not funded by modENCODE. Please contact Mike Pazin at NHGRI to suggest publications to add to these lists.

• Human disease publications
• Basic biology publications
• Tools, methods, and database publications
• modENCODE community publications

Updated 7 March 2014

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

Ahrens M, Ammerpohl O, von Schönfels W, Kolarova J, Bens S, Itzel T, Teufel A, Herrmann A, Brosch M, Hinrichsen H et al. DNA methylation analysis in nonalcoholic fatty liver disease suggests distinct disease-specific and remodeling signatures after bariatric surgery. Cell Metab. 2013 Aug 6;18(2):296-302. PMID: 23931760
ENCODE DNase, TF ChIP, Table S2, Methods

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. PMID: 22499810; PMCID: PMC3711120
ENCODE TF ChIP, Histone modification ChIP; Fig 2a, S2, S6, S7

Akizu N, Shembesh NM, Ben-Omran T, Bastaki L, Al-Tawari A, Zaki MS, Koul R, Spencer E, Rosti RO, Scott E et al. Whole-exome sequencing identifies mutated c12orf57 in recessive corpus callosum hypoplasia. Am J Hum Genet. 2013 Mar 7;92(3):392-400. PMID: 23453666; PMCID: PMC3591854
ENCODE RNA, TF ChIP, Histone modification, Figure 3B

Akrami R, Jacobsen A, Hoell J, Schultz N, Sander C, Larsson E. Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. PLoS One. 2013;8(11):e80306. PMID: 24265805; PMC: PMC3827191
ENCODE GENCODE lncRNA, used throughout (eg. Figure 1, S1) RNA, Fig 4

Alcina A, Fedetz M, Fernández O, Saiz A, Izquierdo G, Lucas M, Leyva L, García-León JA, Abad-Grau Mdel M, Alloza I et al. Identification of a functional variant in the KIF5A-CYP27B1-METTL1-FAM119B locus associated with multiple sclerosis. J Med Genet. 2013 Jan;50(1):25-33. PMID: 23160276; PMCID: PMC3538279
ENCODE Histone modification ChIP, DNase, TF ChIP, RNA, ChIA-PET, Fig 2a, 3

Ammerpohl O, Bens S, Appari M, Werner R, Korn B, Drop SL, Verheijen F, van der Zwan Y, Bunch T, Hughes I et al. Androgen receptor function links human sexual dimorphism to DNA methylation. PLoS One. 2013;8(9):e73288. PMID: 24023855; PMC: PMC3762730
ENCODE DNase, TF ChIP, histone modification ChIP, Figure S2

Anttila V, Winsvold BS, Gormley P, Kurth T, Bettella F, McMahon G, Kallela M, Malik R, de Vries B, Terwindt G et al. Genome-wide meta-analysis identifies new susceptibility loci for migraine. Nat Genet. 2013 Aug;45(8):912-7. PMID: 23793025
ENCODE DNase, RegulomeDB, TF ChIP. Fig S9, Table S8

Aran D, Hellman A. DNA methylation of transcriptional enhancers and cancer predisposition. Cell. 2013 Jul 3;154(1):11-3. PMID: 23827668
ENCODE Histone modification ChIP, TF ChIP, Fig 1

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

Bryzgalov LO, Antontseva EV, Matveeva MY, Shilov AG, Kashina EV, Mordvinov VA, Merkulova TI. Detection of regulatory SNPs in human genome using ChIP-seq ENCODE data. PLoS One. 2013;8(10):e78833. PMID: 24205329; PMC: PMC3812152
ENCODE TF ChIP used throughout, DNase Figure 4

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

Caiafa P, Zampieri M. Why is DNA methylation of Igf2 CpG island shore affected during ageing?. Aging (Albany NY). 2012 Jul;4(7):448-9. PMID: 22879347; PMC: PMC3433930
ENCODE DNase, DNA replication timing

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

Campagna DR, de Bie CI, Schmitz-Abe K, Sweeney M, Sendamarai AK, Schmidt PJ, Heeney MM, Yntema HG, Kannengiesser C, Grandchamp B et al. X-linked sideroblastic anemia due to ALAS2 intron 1 enhancer element GATA-binding site mutations. Am J Hematol. 2014 Mar;89(3):315-9. PMID: 24166784
ENCODE Histone modification ChIP, text

Caruso N, Herberth B, Bartoli M, Puppo F, Dumonceaux J, Zimmermann A, Denadai S, Lebossé M, Roche S, Geng L et al. Deregulation of the protocadherin gene FAT1 alters muscle shapes: implications for the pathogenesis of facioscapulohumeral dystrophy. PLoS Genet. 2013 Jun;9(6):e1003550. PMID: 23785297; PMC: PMC3681729
ENCODE Histone modification ChIP, chromatin states, Figure 10, S16b

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)

Claussnitzer M, Dankel SN, Klocke B, Grallert H, Glunk V, Berulava T, Lee H, Oskolkov N, Fadista J, Ehlers K et al. Leveraging cross-species transcription factor binding site patterns: from diabetes risk Loci to disease mechanisms. Cell. 2014 Jan 16;156(1-2):343-58. PMID: 24439387
ENCODE DHS, TF ChIP, RegulomeDB, Fig 2D, 2E, S2C, S2D, Table S9, S10

Coolen MW, Statham AL, Qu W, Campbell MJ, Henders AK, Montgomery GW, Martin NG, Clark SJ. Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins. PLoS One. 2011;6(10):e25590. PMID: 21991322; PMCID: PMC3184992
ENCODE TF ChIP, Fig 8

Cowell IG, Austin CA. Mechanism of generation of therapy related leukemia in response to anti-topoisomerase II agents. Int J Environ Res Public Health. 2012 Jun;9(6):2075-91. PMID: 22829791; PMC: PMC3397365
ENCODE DNase, TF ChIP, Figure 4

Cowper-Sal lari R, Zhang X, Wright JB, Bailey SD, Cole MD, Eeckhoute J, Moore JH, Lupien M. Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nat Genet. 2012 Nov;44(11):1191-8. PMID: 23001124; PMCID: PMC3483423
ENCODE RNA, Figure S3

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

Edwards SL, Beesley J, French JD, Dunning AM. Beyond GWASs: illuminating the dark road from association to function. Am J Hum Genet. 2013 Nov 7;93(5):779-97. PMID: 24210251; PMC: PMC3824120
ENCODE histone modification ChIP, TF ChIP, DNase, chromatin states, ChIA-PET, 5C, FAIRE, RegulomeDB, Haploreg, RNA, Figure 1, 2, Table 2

Fachel AA, Tahira AC, Vilella-Arias SA, Maracaja-Coutinho V, Gimba ER, Vignal GM, Campos FS, Reis EM, Verjovski-Almeida S. Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations. Mol Cancer. 2013 Nov 15;12(1):140. PMID: 24238219; PMC: PMC3834536
ENCODE histone modification ChIP, TF ChIP, RNA-seq, chromatin states, Figure 3, 5

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. PMID: 22306654; PMCID: PMC3693399
ENCODE histone modification ChIP, described in results

Feldman GJ, Parvizi J, Levenstien M, Scott K, Erickson JA, Fortina P, Devoto M, Peters CL. Developmental dysplasia of the hip: Linkage mapping and whole exome sequencing identify a shared variant in CX3CR1 in all affected members of a large multi-generation family. J Bone Miner Res. 2013 May 29. PMID: 23716478
ENCODE TF ChIP, histone modification ChIP, text

French JD, Ghoussaini M, Edwards SL, Meyer KB, Michailidou K, Ahmed S, Khan S, Maranian MJ, O'Reilly M, Hillman KM et al. Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers. Am J Hum Genet. 2013 Apr 4;92(4):489-503. PMID: 23540573; PMCID: PMC3617380
ENCODE histone modification ChIP, TF ChIP, Fig, 1b

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. PMID: 22416122; PMCID: PMC3324016
ENCODE histone modification ChIP, Figure 2

Gerasimova A, Chavez L, Li B, Seumois G, Greenbaum J, Rao A, Vijayanand P, Peters B. Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PLoS One. 2013;8(1):e54359. PMID: 23382893; PMCID: PMC3559682
ENCODE TF ChIP, HaploReg

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

Gheldof N, Witwicki RM, Migliavacca E, Leleu M, Didelot G, Harewood L, Rougemont J, Reymond A. Structural variation-associated expression changes are paralleled by chromatin architecture modifications. PLoS One. 2013;8(11):e79973. PMID: 24265791; PMC: PMC3827143
ENCODE RNA, DNase, histone modification ChIP, TF ChIP, FAIRE, Figures 1, 2, S10

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

Gudmundsson J, Sulem P, Gudbjartsson DF, Masson G, Agnarsson BA, Benediktsdottir KR, Sigurdsson A, Magnusson OT, Gudjonsson SA, Magnusdottir DN et al. A study based on whole-genome sequencing yields a rare variant at 8q24 associated with prostate cancer. Nat Genet. 2012 Dec;44(12):1326-9. PMID: 23104005; PMCID: PMC3562711
ENCODE DNase, DNA methylation, histone modification ChIP, Figure S1

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

Handel AE, Sandve GK, Disanto G, Berlanga-Taylor AJ, Gallone G, Hanwell H, Drabløs F, Giovannoni G, Ebers GC, Ramagopalan SV. Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease. BMC Med. 2013 Jul 12;11:163. PMID: 23849224; PMCID: PMC3710212
ENCODE TF ChIP, RegulomeDB, DNase, histone modification ChIP, blacklist, text, S11, Table S2, S4, S5

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

Horn S, Figl A, Rachakonda PS, Fischer C, Sucker A, Gast A, Kadel S, Moll I, Nagore E, Hemminki K et al. TERT promoter mutations in familial and sporadic melanoma. Science. 2013 Feb 22;339(6122):959-61. PMID: 23348503
ENCODE TF ChIP, Table S2

Huang L, Jolly LA, Willis-Owen S, Gardner A, Kumar R, Douglas E, Shoubridge C, Wieczorek D, Tzschach A, Cohen M et al. A noncoding, regulatory mutation implicates HCFC1 in nonsyndromic intellectual disability. Am J Hum Genet. 2012 Oct 5;91(4):694-702. PMID: 23000143; PMCID: PMC3484651
ENCODE RNA, described in results

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

Justice CM, Yagnik G, Kim Y, Peter I, Jabs EW, Erazo M, Ye X, Ainehsazan E, Shi L, Cunningham ML et al. A genome-wide association study identifies susceptibility loci for nonsyndromic sagittal craniosynostosis near BMP2 and within BBS9. Nat Genet. 2012 Dec;44(12):1360-4. PMID: 23160099; PMCID: PMC3736322
ENCODE DNase, chromatin states, TF-ChIP, Figure S3

Kirino Y, Bertsias G, Ishigatsubo Y, Mizuki N, Tugal-Tutkun I, Seyahi E, Ozyazgan Y, Sacli FS, Erer B, Inoko H et al. Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B*51 and ERAP1. Nat Genet. 2013 Feb;45(2):202-7. PMID: 23291587
ENCODE DNase, histone modification ChIP; in text

Klengel T, Mehta D, Anacker C, Rex-Haffner M, Pruessner JC, Pariante CM, Pace TW, Mercer KB, Mayberg HS, Bradley B et al. Allele-specific FKBP5 DNA demethylation mediates gene-childhood trauma interactions. Nat Neurosci. 2013 Jan;16(1):33-41. PMID: 23201972
ENCODE TF ChIP, statistical methods

Ko YA, Mohtat D, Suzuki M, Park AS, Izquierdo MC, Han SY, Kang HM, Si H, Hostetter T, Pullman JM et al. Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development. Genome Biol. 2013;14(10):R108. PMID: 24098934
ENCODE chromatin states, TF ChIP, histone modification ChIP, DNase, Figures 3C, 7G

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

Le Tallec B, Millot GA, Blin ME, Brison O, Dutrillaux B, Debatisse M. Common fragile site profiling in epithelial and erythroid cells reveals that most recurrent cancer deletions lie in fragile sites hosting large genes. Cell Rep. 2013 Aug 15;4(3):420-8. PMID: 23911288
ENCODE RNA-seq, GENCODE, Figure 3E

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

Lessard CJ, Li H, Adrianto I, Ice JA, Rasmussen A, Grundahl KM, Kelly JA, Dozmorov MG, Miceli- Richard C, Bowman S et al. Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome. Nat Genet. 2013 Nov;45(11):1284-92. PMID: 24097067; PMC: PMC3867192
ENCODE TF ChIP, chromatin states, histone modification ChIP, DNase, ChIA-PET, methods, figure S10, S13, S16, S19, S22, S25

Li M, Luo XJ, Rietschel M, Lewis CM, Mattheisen M, Müller-Myhsok B, Jamain S, Leboyer M, Landén M, Thompson PM et al. Allelic differences between Europeans and Chinese for CREB1 SNPs and their implications in gene expression regulation, hippocampal structure and function, and bipolar disorder susceptibility. Mol Psychiatry. 2013 Apr 9. PMID: 23568192
ENCODE TF ChIP, DNase, FAIRE, histone modification ChIP, RegulomeDB, Table S3

Li MJ, Wang LY, Xia Z, Sham PC, Wang J. GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W150-8. PMID: 23723249; PMCID: PMC3692118
ENCODE ChIA-PET, 5C, histone modification ChIP, TF ChIP, DHS, chromatin states, ENCODE motifs, text, Fig 1

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. PMID: 22961000; PMCID: PMC3459817
ENCODE DNase, FAIRE, Table 1, S7, S9, Figure 2, S9

Liu JZ, Hov JR, Folseraas T, Ellinghaus E, Rushbrook SM, Doncheva NT, Andreassen OA, Weersma RK, Weismüller TJ, Eksteen B et al. Dense genotyping of immune-related disease regions identifies nine new risk loci for primary sclerosing cholangitis. Nat Genet. 2013 Apr 21. PMID: 23603763; PMCID: PMC3667736
ENCODE DNase, FAIRE, histone modifications, HaploReg, Table 1, S6

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

Maller JB, McVean G, Byrnes J, Vukcevic D, Palin K, Su Z, Howson JM, Auton A, Myers S et al. Bayesian refinement of association signals for 14 loci in 3 common diseases. Nat Genet. 2012 Dec;44(12):1294-301. PMID: 23104008
ENCODE TF CHIP, DNase, Histone modification ChIP, FAIRE, Table 3

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

Marzese DM, Scolyer RA, Huynh JL, Huang SK, Hirose H, Chong KK, Kiyohara E, Wang J, Kawas NP, Donovan NC et al. Epigenome-wide DNA methylation landscape of melanoma progression to brain metastasis reveals aberrations on homeobox D cluster associated with prognosis. Hum Mol Genet. 2014 Jan 1;23(1):226-38. PMID: 24014427; PMC: PMC3857956
ENCODE DNase, Figure 5E

Michaelson JJ, Shi Y, Gujral M, Zheng H, Malhotra D, Jin X, Jian M, Liu G, Greer D, Bhandari A et al. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell. 2012 Dec 21;151(7):1431-42. PMID: 23260136; PMCID: PMC3712641
ENCODE DNase, Histone modifications, RNA, Fig 3, S6, Table S6

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

Mogilyansky E, Rigoutsos I. The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell Death Differ. 2013 Dec;20(12):1603-14. PMID: 24212931; PMC: PMC3824591
ENCODE TF ChIP RNA network, Figure 4

Munroe PB, Barnes MR, Caulfield MJ. Advances in blood pressure genomics. Circ Res. 2013 May 10;112(10):1365-79. PMID: 23661711
ENCODE, Table 2, 3

Myouzen K, Kochi Y, Okada Y, Terao C, Suzuki A, Ikari K, Tsunoda T, Takahashi A, Kubo M, Taniguchi A et al. Functional variants in NFKBIE and RTKN2 involved in activation of the NF-κB pathway are associated with rheumatoid arthritis in Japanese. PLoS Genet. 2012 Sep;8(9):e1002949. PMID: 23028356; PMCID: PMC3441678
ENCODE Histone modification ChIP, TF ChIP, DNase, Figures S3, S4

Nurminen R, Lehtonen R, Auvinen A, Tammela TL, Wahlfors T, Schleutker J. Fine mapping of 11q13.5 identifies regions associated with prostate cancer and prostate cancer death. Eur J Cancer. 2013 Oct;49(15):3335-43. PMID: 23830236
ENCODE chromatin states, DNase, TF ChIP, HaploReg, Tables S3, S4

Parikshak NN, Luo R, Zhang A, Won H, Lowe JK, Chandran V, Horvath S, Geschwind DH. Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell. 2013 Nov 21;155(5):1008-21. PMID: 24267887; PMC: PMC3934107
ENCODE GENCODE, TF ChIP, Table S3, described in methods

Parris T, Nik AM, Kotecha S, Langston C, Helou K, Platt C, Carlsson P. Inversion upstream of FOXF1 in a case of lethal alveolar capillary dysplasia with misalignment of pulmonary veins. Am J Med Genet A. 2013 Apr;161(4):764-70. PMID: 23444129
ENCODE conservation, Histone modification, TF ChIP, DNase, Fig 3, Fig S2

Perez-Andreu V, Roberts KG, Harvey RC, Yang W, Cheng C, Pei D, Xu H, Gastier-Foster J, E S, Lim JY et al. Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse. Nat Genet. 2013 Dec;45(12):1494-8. PMID: 24141364
ENCODE histone modification ChIP, TF ChIP, chromatin states, figure S13

Praetorius C, Grill C, Stacey SN, Metcalf AM, Gorkin DU, Robinson KC, Van Otterloo E, Kim RS, Bergsteinsdottir K, Ogmundsdottir MH et al. A polymorphism in IRF4 affects human pigmentation through a tyrosinase-dependent MITF/TFAP2A pathway. Cell. 2013 Nov 21;155(5):1022-33. PMID: 24267888; PMC: PMC3873608
ENCODE DNase, RNA, Figure 2

Rajaram M, Zhang J, Wang T, Li J, Kuscu C, Qi H, Kato M, Grubor V, Weil RJ, Helland A et al. Two Distinct Categories of Focal Deletions in Cancer Genomes. PLoS One. 2013;8(6):e66264. PMID: 23805207; PMCID: PMC3689739
ENCODE DNase, Fig S9

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

Rhie SK, Coetzee SG, Noushmehr H, Yan C, Kim JM, Haiman CA, Coetzee GA. Comprehensive functional annotation of seventy-one breast cancer risk Loci. PLoS One. 2013;8(5):e63925. PMID: 23717510; PMCID: PMC3661550
ENCODE RNA, histone modification, DNase, Figure 2, 3, S2, S6, Table S9

Ripke S, O'Dushlaine C, Chambert K, Moran JL, Kähler AK, Akterin S, Bergen SE, Collins AL, Crowley JJ, Fromer M et al. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat Genet. 2013 Aug 25. PMID: 23974872
ENCODE DHS, Table S1, Fig S1

Robinson DR, Wu YM, Kalyana-Sundaram S, Cao X, Lonigro RJ, Sung YS, Chen CL, Zhang L, Wang R, Su F et al. Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing. Nat Genet. 2013 Feb;45(2):180-5. PMID: 23313952; PMCID: PMC3654808
ENCODE TF ChIP, Fig S9, S10

Rogler LE, Kosmyna B, Moskowitz D, Bebawee R, Rahimzadeh J, Kutchko K, Laederach A, Notarangelo LD, Giliani S, Bouhassira E et al. Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage- hair hypoplasia. Hum Mol Genet. 2014 Jan 15;23(2):368-82. PMID: 24009312; PMC: PMC3869355
ENCODE RNA, described in methods

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

Rushworth SA, Zaitseva L, Murray MY, Shah NM, Bowles KM, MacEwan DJ. The high Nrf2 expression in human acute myeloid leukemia is driven by NF-κB and underlies its chemo-resistance. Blood. 2012 Dec 20;120(26):5188-98. PMID: 23077289
ENCODE TF ChIP, Fig 4D

Sanfilippo PG, Hewitt AW. Translating the ENCyclopedia Of DNA Elements Project findings to the clinic: ENCODE's implications for eye disease. Clin Experiment Ophthalmol. 2014 Jan-Feb;42(1):78-83. PMID: 24433357
ENCODE RNA, DNase, TF CHIP, histone modification ChIP, Figure 3

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

Savage SA, Mirabello L, Wang Z, Gastier-Foster JM, Gorlick R, Khanna C, Flanagan AM, Tirabosco R, Andrulis IL, Wunder JS et al. Genome-wide association study identifies two susceptibility loci for osteosarcoma. Nat Genet. 2013 Jul;45(7):799-803. PMID: 23727862
ENCODE histone modification ChIP, DNase, TF ChIP, RegulomeDB, Table S3

Schaefer AS, Bochenek G, Manke T, Nothnagel M, Graetz C, Thien A, Jockel-Schneider Y, Harks I, Staufenbiel I, Wijmenga C et al. Validation of reported genetic risk factors for periodontitis in a large-scale replication study. J Clin Periodontol. 2013 Jun;40(6):563-72. PMID: 23587006
ENCODE histone modification ChIP, TF ChIP, Fig 1, text

Schoofs T, Rohde C, Hebestreit K, Klein HU, Göllner S, Schulze I, Lerdrup M, Dietrich N, Agrawal-Singh S, Witten A et al. DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding. Blood. 2013 Jan 3;121(1):178-87. PMID: 23152544
ENCODE TF ChIP, Fig 4

Shukla R, Upton KR, Muñoz-Lopez M, Gerhardt DJ, Fisher ME, Nguyen T, Brennan PM, Baillie JK, Collino A, Ghisletti S et al. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell. 2013 Mar 28;153(1):101-11. PMID: 23540693
ENCODE enhancer predictions, used in Fig 3C, text

Siltanen S, Fischer D, Rantapero T, Laitinen V, Mpindi JP, Kallioniemi O, Wahlfors T, Schleutker J. ARLTS1 and prostate cancer risk--analysis of expression and regulation. PLoS One. 2013;8(8):e72040. PMID: 23940804; PMC: PMC3734304
ENCODE HaploReg, RegulomeDB, TF ChIP, histone modification ChIP, chromatin states

Singh PK, Campbell MJ. The Interactions of microRNA and Epigenetic Modifications in Prostate Cancer. Cancers (Basel). 2013 Aug 9;5(3):998-1019. PMID: 24202331; PMC: PMC3795376
ENCODE RNA, GENCODE, DNase, DNA methylation, Figure 3

Skuse DH, Lori A, Cubells JF, Lee I, Conneely KN, Puura K, Lehtimäki T, Binder EB, Young LJ. Common polymorphism in the oxytocin receptor gene (OXTR) is associated with human social recognition skills. Proc Natl Acad Sci U S A. 2014 Feb 4;111(5):1987-92. PMID: 24367110; PMC: PMC3918840
ENCODE DNase, TF ChIP, Figure S2

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

Szafranski P, Dharmadhikari AV, Brosens E, Gurha P, Kolodziejska KE, Zhishuo O, Dittwald P, Majewski T, Mohan KN, Chen B et al. Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder. Genome Res. 2013 Jan;23(1):23-33. PMID: 23034409; PMCID: PMC3530681
ENCODE TF ChIP, histone modification ChIP, Fig 2a, S8

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

Treppendahl MB, Qiu X, Søgaard A, Yang X, Nandrup-Bus C, Hother C, Andersen MK, Kjeldsen L, Möllgård L, Hellström-Lindberg E et al. Allelic methylation levels of the noncoding VTRNA2-1 located on chromosome 5q31.1 predict outcome in AML. Blood. 2012 Jan 5;119(1):206-16. PMID: 22058117; PMCID: PMC3251229
ENCODE TF ChIP, discussion

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

Trynka G, Sandor C, Han B, Xu H, Stranger BE, Liu XS, Raychaudhuri S. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet. 2013 Feb;45(2):124-30. PMID: 23263488
Table S1, Fig 2; S2, S3, S7

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

Yıldırım Y, Kerem M, Köroğlu C, Tolun A. A homozygous 237-kb deletion at 1p31 identified as the locus for midline cleft of the upper and lower lip in a consanguineous family. Eur J Hum Genet. 2013 Jul 17;. PMID: 23860042
ENCODE histone modification ChIP, TF ChIP, DNase, RNA, DNA methylation, FAIRE, chromatin states, Fig S2

Yoskovitz G, Garcia-Giralt N, Rodriguez-Sanz M, Urreizti R, Guerri R, Ariño-Ballester S, Prieto-Alhambra D, Mellibovsky L, Grinberg D, Nogues X et al. Analyses of RANK and RANKL in the post-GWAS context; functional evidence of vitamin D stimulation through a RANKL distal region. J Bone Miner Res. 2013 Jun 6. PMID: 23744843
ENCODE histone modification ChIP, DNase, TF ChIP, Fig 3b

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. PMID: 22665440; PMCID: PMC3409257
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

Akdemir KC, Jain AK, Allton K, Aronow B, Xu X, Cooney AJ, Li W, Barton MC. Genome-wide profiling reveals stimulus-specific functions of p53 during differentiation and DNA damage of human embryonic stem cells. Nucleic Acids Res. 2014 Jan;42(1):205-23. PMID: 24078252; PMC: PMC3874181
ENCODE histone modification ChIP

Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML et al. Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. Cell Stem Cell. 2013 Jun 6;12(6):699-712. PMID: 23665121; PMCID: PMC3725985
ENCODE mouse TF ChIP, histone modification ChIP, DNase, Fig 3, Table S3

Arbiza L, Gronau I, Aksoy BA, Hubisz MJ, Gulko B, Keinan A, Siepel A. Genome-wide inference of natural selection on human transcription factor binding sites. Nat Genet. 2013 Jul;45(7):723-9. PMID: 23749186
ENCODE TF ChIP, text

Ayub Q, Yngvadottir B, Chen Y, Xue Y, Hu M, Vernes SC, Fisher SE, Tyler-Smith C. FOXP2 Targets Show Evidence of Positive Selection in European Populations. Am J Hum Genet. 2013 May 2;92(5):696-706. PMID: 23602712; PMCID: PMC3644635
ENCODE TF ChIP, DNase, Fig 2, 4

Bacolla A, Temiz NA, Yi M, Ivanic J, Cer RZ, Donohue DE, Ball EV, Mudunuri US, Wang G, Jain A et al. Guanine holes are prominent targets for mutation in cancer and inherited disease. PLoS Genet. 2013;9(9):e1003816. PMID: 24086153; PMC: PMC3784513
ENCODE mappability, described in text

Bailey TL, Machanick P. Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res. 2012 Sep 1;40(17):e128. PMID: 22610855; PMCID: PMC3458523
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

Barbeau DJ, La KT, Kim DS, Kerpedjieva SS, Shurin GV, Tamama K. Early growth response-2 signaling mediates immunomodulatory effects of human multipotential stromal cells. Stem Cells Dev. 2014 Jan 15;23(2):155-66. PMID: 24007274; PMC: PMC3887418
ENCODE histone modification ChIP, methods

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. PMID: 22150271; PMCID: PMC3713072
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

Bersten DC, Wright JA, McCarthy PJ, Whitelaw ML. Regulation of the neuronal transcription factor NPAS4 by REST and microRNAs. Biochim Biophys Acta. 2014 Jan;1839(1):13-24. PMID: 24291638
ENCODE TF ChIP, Figure 4

Bhattacharya A, Chen CY, Ho S, Mitchell JA. Upstream distal regulatory elements contact the Lmo2 promoter in mouse erythroid cells. PLoS One. 2012;7(12):e52880. PMID: 23285212; PMCID: PMC3528669
mouse ENCODE TF ChIP, Histone modification ChIP, DNase, Figure 1, 4, S4

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

Bischof JM, Gillen AE, Song L, Gosalia N, London D, Furey TS, Crawford GE, Harris A. A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function. Biol Reprod. 2013 Oct;89(4):104. PMID: 24006278
ENCODE DNase, TF ChIP, Histone modification ChIP, Figures 4, 5, 6, Table 1

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

Bogdanović O, van Heeringen SJ, Veenstra GJ. The epigenome in early vertebrate development. Genesis. 2012 Mar;50(3):192-206. PMID: 22139962; PMC: PMC3294079
ENCODE Histone modification ChIP, Figure 1

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

Bolouri H, Ruzzo WL. Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions. J Comput Biol. 2012 Sep;19(9):989-97. PMID: 22897152
ENCODE TF ChIP, histone modification ChIP, DNase, platform characterization

Burdach J, Funnell AP, Mak KS, Artuz CM, Wienert B, Lim WF, Tan LY, Pearson RC, Crossley M. Regions outside the DNA-binding domain are critical for proper in vivo specificity of an archetypal zinc finger transcription factor. Nucleic Acids Res. 2014 Jan;42(1):276-89. PMID: 24106088; PMC: PMC3874204
ENCODE DNase, TF ChIP, Figures 3, 5, S7

Burzynski GM, Reed X, Taher L, Stine ZE, Matsui T, Ovcharenko I, McCallion AS. Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control. Genome Res. 2012 Nov;22(11):2278-89. PMID: 22759862; PMCID: PMC3483557
ENCODE histone modification, described in methods section

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

Campbell MR, Karaca M, Adamski KN, Chorley BN, Wang X, Bell DA. Novel hematopoietic target genes in the NRF2-mediated transcriptional pathway. Oxid Med Cell Longev. 2013;2013:120305. PMID: 23766848; PMCID: PMC3677633
ENCODE TF ChIP, chromatin states, Fig 2

Chen DH, Chang AY, Liao BY, Yeang CH. Functional characterization of motif sequences under purifying selection. Nucleic Acids Res. 2013 Feb 1;41(4):2105-20. PMID: 23303791; PMCID: PMC3575792
ENCODE TF ChIP, data sources

Chen G, Chen J, Shi C, Shi L, Tong W, Shi T. Dissecting the Characteristics and Dynamics of Human Protein Complexes at Transcriptome Cascade Using RNA-Seq Data. PLoS One. 2013;8(6):e66521. PMID: 23824284; PMC: PMC3688907
ENCODE GENCODE

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 L. Characterization and comparison of human nuclear and cytosolic editomes. Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):E2741-7. PMID: 23818636; PMC: PMC3718162
ENCODE RNA-seq, Figure 1

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

Chen YC, Cheng JH, Tsai ZT, Tsai HK, Chuang TJ. The impact of trans-regulation on the evolutionary rates of metazoan proteins. Nucleic Acids Res. 2013 Jul 1;41(13):6371-80. PMID: 23658220; PMCID: PMC3711421
ENCODE TF ChIP, ENCODE mouse TF ChIP, modENCODE fly TF CHIP, text, Table 1, 2

Cheng C, Ung M, Grant GD, Whitfield ML. Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PLoS Comput Biol. 2013;9(7):e1003132. PMID: 23874175; PMC: PMC3708869
ENCODE TF ChIP, GENCODE, used throughout, Figure 4

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

Cocozza S, Akhtar MM, Miele G, Monticelli A. CpG islands undermethylation in human genomic regions under selective pressure. PLoS One. 2011;6(8):e23156. PMID: 21829712; PMCID: PMC3149076
ENCODE DNA methylation, Fig 1, 2, S1, Table S1, S2, etc

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

Corradin O, Saiakhova A, Akhtar-Zaidi B, Myeroff L, Willis J, Cowper-Sal lari R, Lupien M, Markowitz S, Scacheri PC. Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res. 2014 Jan;24(1):1-13. PMID: 24196873; PMC: PMC3875850
ENCODE DNase, histone modification ChIP, RNA, TF ChIP,ChIA-PET, 5C, Figure 1, PreSTIGE tool

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

Demare LE, Leng J, Cotney J, Reilly SK, Yin J, Sarro R, Noonan JP. The genomic landscape of cohesin-associated chromatin interactions. Genome Res. 2013 Aug;23(8):1224-34. PMID: 23704192; PMCID: PMC3730097
ENCODE mouse histone modification ChIP, Fig S3

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

Dumon S, Walton DS, Volpe G, Wilson N, Dassé E, Del Pozzo W, Landry JR, Turner B, O'Neill LP, Göttgens B et al. Itga2b regulation at the onset of definitive hematopoiesis and commitment to differentiation. PLoS One. 2012;7(8):e43300. PMID: 22952660; PMCID: PMC3429474
ENCODE RNA, histone modification ChIP, TF ChIP, DNase, mouse, Fig 3, S2

Engreitz JM, Agarwala V, Mirny LA. Three-dimensional genome architecture influences partner selection for chromosomal translocations in human disease. PLoS One. 2012;7(9):e44196. PMID: 23028501; PMCID: PMC3460994
ENCODE Histone modification ChIP, TF ChIP, DNase, Fig 4 B, C, S2

Eun B, Sampley ML, Van Winkle MT, Good AL, Kachman MM, Pfeifer K. The Igf2/H19 muscle enhancer is an active transcriptional complex. Nucleic Acids Res. 2013 Sep;41(17):8126-34. PMID: 23842673; PMC: PMC3783178
ENCODE TF ChIP, text

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

Fang W, Wei Y, Kang Y, Landweber LF. Detection of a common chimeric transcript between human chromosomes 7 and 16. Biol Direct. 2012 Dec 29;7:49. PMID: 23273016; PMCID: PMC3538553
ENCODE RNA, described in text

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

Fraser HB. Cell-cycle regulated transcription associates with DNA replication timing in yeast and human. Genome Biol. 2013;14(10):R111. PMID: 24098959
ENCODE RNA-seq, figure 4

Fredman D, Dong X, Lenhard B. Making enhancers from spare parts of the genome. Genome Biol. 2011 Dec 29;12(12):138. PMID: 22206586; PMCID: PMC3334608
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

Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK. Controls of nucleosome positioning in the human genome. PLoS Genet. 2012;8(11):e1003036. PMID: 23166509; PMCID: PMC3499251
ENCODE chromatin states, TF ChIP, figure 4, 5, S11, S12, S15

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

Giannopoulou EG, Elemento O. Inferring chromatin-bound protein complexes from genome-wide binding assays. Genome Res. 2013 Aug;23(8):1295-306. PMID: 23554462; PMCID: PMC3730103
ENCODE TF ChIP, histone modification ChIP, used throughout, described in Table S1

Gokcumen O, Zhu Q, Mulder LC, Iskow RC, Austermann C, Scharer CD, Raj T, Boss JM, Sunyaev S, Price A et al. Balancing selection on a regulatory region exhibiting ancient variation that predates human- neandertal divergence. PLoS Genet. 2013 Apr;9(4):e1003404. PMID: 23593015; PMCID: PMC3623772
ENCODE TF ChIP, Fig 5

Gokhman D, Livyatan I, Sailaja BS, Melcer S, Meshorer E. Multilayered chromatin analysis reveals E2f, Smad and Zfx as transcriptional regulators of histones. Nat Struct Mol Biol. 2013 Jan;20(1):119-26. PMID: 23222641
ENCODE TF ChIP, described in Table S1

Gorbatenko A, Olesen CW, Mørup N, Thiel G, Kallunki T, Valen E, Pedersen SF. ErbB2 upregulates the Na+,HCO3(-)-cotransporter NBCn1/SLC4A7 in human breast cancer cells via Akt, ERK, Src, and Kruppel-like factor 4. FASEB J. 2014 Jan;28(1):350-63. PMID: 24088818
ENCODE histone modification ChIP, TF ChIP, DNase, Figure 4

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 Nov;22(11):2290-301. PMID: 23019145; PMCID: PMC3483558
ENCODE and mouse ENCODE, TF ChIP, histone modification ChIP, DNase, Fig 3B, 3C, 7E, 7F

Grant GD, Brooks L 3rd, Zhang X, Mahoney JM, Martyanov V, Wood TA, Sherlock G, Cheng C, Whitfield ML. Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors. Mol Biol Cell. 2013 Dec;24(23):3634-50. PMID: 24109597; PMC: PMC3842991
ENCODE TF ChIP, Figure 6, 8, Table 2

Groth AC, Liu M, Wang H, Lovelett E, Emery DW. Identification and characterization of enhancer-blocking insulators to reduce retroviral vector genotoxicity. PLoS One. 2013;8(10):e76528. PMID: 24098520; PMC: PMC3789682
ENCODE DNase, TF ChIP, Table 1, figure 5A, methods

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

Guo Y, Mahony S, Gifford DK. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. PLoS Comput Biol. 2012;8(8):e1002638. PMID: 22912568; PMCID: PMC3415389
ENCODE TF ChIP; Fig 1, 2, 6, 7, 8

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. PMID: 22431510; PMCID: PMC3323878
Mouse ENCODE DNase data is part of Figure 1, 5

Habibi E, Brinkman AB, Arand J, Kroeze LI, Kerstens HH, Matarese F, Lepikhov K, Gut M, Brun-Heath I, Hubner NC et al. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell. 2013 Sep 5;13(3):360-9. PMID: 23850244
ENCODE DNase, described in Experimental Procedures

Håndstad T, Rye M, Močnik R, Drabløs F, Sætrom P. Cell-type specificity of ChIP-predicted transcription factor binding sites. BMC Genomics. 2012 Aug 3;13:372. PMID: 22863112; PMCID: PMC3574057
ENCODE TF ChIP, RNA, DNase, histone modification ChIP, Fig 1-8

Hangauer MJ, Vaughn IW, McManus MT. Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet. 2013 Jun;9(6):e1003569. PMID: 23818866; PMCID: PMC3688513
ENCODE RNA, GENCODE, Fig S6, Dataset S9, Table S1, S2

Heger P, Marin B, Bartkuhn M, Schierenberg E, Wiehe T. The chromatin insulator CTCF and the emergence of metazoan diversity. Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17507-12. PMID: 23045651; PMCID: PMC3491479
ENCODE TF ChIP, modENCODE fly TF ChIP, Figures 3, S7, S8, Table S2

Hernando H, Shannon-Lowe C, Islam AB, Al-Shahrour F, Rodríguez-Ubreva J, Rodríguez-Cortez VC, Javierre BM, Mangas C, Fernández AF, Parra M et al. The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion. Genome Biol. 2013 Jan 15;14(1):R3. PMID: 23320978; PMCID: PMC3663113
ENCODE TF-CHIP, Fig 3D

Higareda-Almaraz JC, Valtierra-Gutiérrez IA, Hernandez-Ortiz M, Contreras S, Hernandez E, Encarnacion S. Analysis and prediction of pathways in HeLa cells by integrating biological levels of organization with systems-biology approaches. PLoS One. 2013;8(6):e65433. PMID: 23785426; PMCID: PMC3680226
ENCODE RNA, GENCODE, text, Fig 3

Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, Hoke HA, Young RA. Super-enhancers in the control of cell identity and disease. Cell. 2013 Nov 7;155(4):934-47. PMID: 24119843; PMC: PMC3841062
ENCODE Histone modification ChIP, TF ChIP, Figure 1, 2, Table S6

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. PMID: 21924933; PMCID: PMC3412369; PMCID: PMC3157836
ENCODE histone modification ChIP, figure 3

Hoque M, Ji Z, Zheng D, Luo W, Li W, You B, Park JY, Yehia G, Tian B. Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing. Nat Methods. 2013 Feb;10(2):133-9. PMID: 23241633; PMCID: PMC3560312
ENCODE RNA, described in text

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. PMID: 22791747; PMCID: PMC3459461
ENCODE TF ChIP, Fig 3

Hu HY, Guo S, Xi J, Yan Z, Fu N, Zhang X, Menzel C, Liang H, Yang H, Zhao M et al. MicroRNA expression and regulation in human, chimpanzee, and macaque brains. PLoS Genet. 2011 Oct;7(10):e1002327. PMID: 22022286; PMCID: PMC3192836
ENCODE histone modification ChIP, DNase, Fig 7

Huang HT, Kathrein KL, Barton A, Gitlin Z, Huang YH, Ward TP, Hofmann O, Dibiase A, Song A, Tyekucheva S et al. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Nat Cell Biol. 2013 Dec;15(12):1516-25. PMID: 24240475
ENCODE TF ChIP, methods, Figure S4

Huang SS, Clarke DC, Gosline SJ, Labadorf A, Chouinard CR, Gordon W, Lauffenburger DA, Fraenkel E. Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. PLoS Comput Biol. 2013 Feb;9(2):e1002887. PMID: 23408876; PMCID: PMC3567149
ENCODE TF ChIP, Table S5

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

Hwang YC, Zheng Q, Gregory BD, Wang LS. High-throughput identification of long-range regulatory elements and their target promoters in the human genome. Nucleic Acids Res. 2013 May 1;41(9):4835-46. PMID: 23525463; PMCID: PMC3643598
ENCODE DNase, Histone modification ChIP, 5C, Fig 4, 5

Jacques PÉ, Jeyakani J, Bourque G. The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet. 2013 May;9(5):e1003504. PMID: 23675311; PMCID: PMC3649963
ENCODE DNase, TF ChIP, RNA, chromatin states, Fig 1-4, S1, S5, S6, S12, S13, S15, S16, Table 1

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

Johnson ME, Deliard S, Zhu F, Xia Q, Wells AD, Hankenson KD, Grant SF. A ChIP-seq-Defined Genome-Wide Map of MEF2C Binding Reveals Inflammatory Pathways Associated with Its Role in Bone Density Determination. Calcif Tissue Int. 2013 Dec 15;. PMID: 24337390
ENCODE TF ChIP used throughout, Figures 1-2

Julienne H, Zoufir A, Audit B, Arneodo A. Human genome replication proceeds through four chromatin states. PLoS Comput Biol. 2013;9(10):e1003233. PMID: 24130466; PMC: PMC3794905
ENCODE histone modification ChIP, TF ChIP, RNA; Figure 4 and 5, described in materials and methods

Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, Yandell M, Feschotte C. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet. 2013 Apr;9(4):e1003470. PMID: 23637635; PMCID: PMC3636048
ENCODE DNase, RNA, GENCODE ncRNA, text, table 1, S7, Figure 1, 2, 6, S1-S4

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. PMID: 21949399; PMCID: PMC3193253
ENCODE TF ChIP, Figures 5, S3

Khrameeva EE, Mironov AA, Fedonin GG, Khaitovich P, Gelfand MS. Spatial proximity and similarity of the epigenetic state of genome domains. PLoS One. 2012;7(4):e33947. PMID: 22496774; PMC: PMC3319547
ENCODE DNA methylation, DNase, histone modification ChIP, described in Methods

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

Lam EY, Beraldi D, Tannahill D, Balasubramanian S. G-quadruplex structures are stable and detectable in human genomic DNA. Nat Commun. 2013;4:1796. PMID: 23653208; PMC: PMC3736099
ENCODE quality metrics, mappability, Table S1, Figure S6

Landan G, Cohen NM, Mukamel Z, Bar A, Molchadsky A, Brosh R, Horn-Saban S, Zalcenstein DA, Goldfinger N, Zundelevich A et al. Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet. 2012 Nov;44(11):1207-14. PMID: 23064413
ENCODE DNA methylation analzyed (see table S1)

Landry JJ, Pyl PT, Rausch T, Zichner T, Tekkedil MM, Stütz AM, Jauch A, Aiyar RS, Pau G, Delhomme N et al. The Genomic and Transcriptomic Landscape of a HeLa Cell Line. G3 (Bethesda). 2013 Mar 26. PMID: 23550136; PMCID: PMC3737162
ENCODE RNA

Lasalle JM, Powell WT, Yasui DH. Epigenetic layers and players underlying neurodevelopment. Trends Neurosci. 2013 Aug;36(8):460-70. PMID: 23731492; PMCID: PMC3735843
ENCODE chromatin states, Fig 2

Lee CY, Chen L. Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines. Bioinformatics. 2013 Jul 15;29(14):1713-7. PMID: 23740743; PMCID: PMC3702257
ENCODE RNA, histone modification ChIP, DNase, MNase, text, Fig 1-3,

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.

Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X et al. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. Nature. 2013 Jun 27;498(7455):516-20. PMID: 23728302; PMCID: PMC3718886
ENCODE histone modification ChIP, Fig S3d, S8a

Li Y, Huang W, Niu L, Umbach DM, Covo S, Li L. Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes. BMC Genomics. 2013 Aug 14;14:553. PMID: 23945083; PMC: PMC3765723
ENCODE TF ChIP, histone modification ChIP, DNase, FAIRE, ChIA-PET, used throughout, Table 1

Lu X, Göke J, Sachs F, Jacques PÉ, Liang H, Feng B, Bourque G, Bubulya PA, Ng HH. SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells. Nat Cell Biol. 2013 Oct;15(10):1141-52. PMID: 24013217
ENCODE histone modification ChIP, Figure 5c

Lu Y, Zhou Y, Tian W. Combining Hi-C data with phylogenetic correlation to predict the target genes of distal regulatory elements in human genome. Nucleic Acids Res. 2013 Dec;41(22):10391-402. PMID: 24003029; PMC: PMC3905853
ENCODE DNase, TF ChIP, histone modification ChIP, ChIA-PET, used throughout, Figure 1, S1

Lubliner S, Keren L, Segal E. Sequence features of yeast and human core promoters that are predictive of maximal promoter activity. Nucleic Acids Res. 2013 Jun;41(11):5569-81. PMID: 23599004; PMCID: PMC3675475
ENCODE RNA, described in Supplementary methods

Lukic S, Nicolas JC, Levine AJ. The diversity of zinc-finger genes on human chromosome 19 provides an evolutionary mechanism for defense against inherited endogenous retroviruses. Cell Death Differ. 2014 Mar;21(3):381-7. PMID: 24162661; PMC: PMC3921586
ENCODE DNase, TF ChIP, Table 1

Luo H, Sun S, Li P, Bu D, Cao H, Zhao Y. Comprehensive characterization of 10,571 mouse large intergenic noncoding RNAs from whole transcriptome sequencing. PLoS One. 2013;8(8):e70835. PMID: 23951020; PMC: PMC3741367
ENCODE mouse histone modification ChIP, figure 4

Lützner N, De-Castro Arce J, Rösl F. Gene expression of the tumour suppressor LKB1 is mediated by Sp1, NF-Y and FOXO transcription factors. PLoS One. 2012;7(3):e32590. PMID: 22412893; PMC: PMC3295762
ENCODE DNase, Figure 1A

Luu PL, Schöler HR, Araúzo-Bravo MJ. Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs. Genome Res. 2013 Dec;23(12):2013-29. PMID: 24149073; PMC: PMC3847772
ENCODE histone modification ChIP, TF ChIP, RNA, Figure 5, S6

Lv J, Cui W, Liu H, He H, Xiu Y, Guo J, Liu H, Liu Q, Zeng T, Chen Y et al. Identification and characterization of long non-coding RNAs related to mouse embryonic brain development from available transcriptomic data. PLoS One. 2013;8(8):e71152. PMID: 23967161; PMC: PMC3743905
ENCODE mouse RNA-seq, histone modification ChIP, GENCODE

Malin J, Aniba MR, Hannenhalli S. Enhancer networks revealed by correlated DNAse hypersensitivity states of enhancers. Nucleic Acids Res. 2013 Aug 1;41(14):6828-38. PMID: 23700312; PMCID: PMC3737527
ENCODE DNase, TF ChIP, chromatin states, Fig 2, 4, S1, Table S1-S3

Mallinjoud P, Villemin JP, Mortada H, Polay Espinoza M, Desmet FO, Samaan S, Chautard E, Tranchevent LC, Auboeuf D. Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin. Genome Res. 2014 Mar;24(3):511-21. PMID: 24307554
ENCODE RNA exon arrays used throughout, ,Figure 1, Table S1, S2

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

Marinello J, Chillemi G, Bueno S, Manzo SG, Capranico G. Antisense transcripts enhanced by camptothecin at divergent CpG-island promoters associated with bursts of topoisomerase I-DNA cleavage complex and R-loop formation. Nucleic Acids Res. 2013 Dec;41(22):10110-23. PMID: 23999093; PMC: PMC3905886
ENCODE histone modification ChIP, TF ChIP, DNase, Figure 3, S8, Table 1

Marques AC, Hughes J, Graham B, Kowalczyk MS, Higgs DR, Ponting CP. Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol. 2013 Nov 29;14(11):R131. PMID: 24289259
ENCODE RNA, File S12

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. PMID: 21813623; PMCID: PMC3205567
ENCODE histone modification ChIP, TF ChIP, DNase, methyl-RRBS, Figure 5, Figure 6, Table 3, Figure S2

McClellan MJ, Wood CD, Ojeniyi O, Cooper TJ, Kanhere A, Arvey A, Webb HM, Palermo RD, Harth-Hertle ML, Kempkes B et al. Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming. PLoS Pathog. 2013 Sep;9(9):e1003636. PMID: 24068937; PMC: PMC3771879
ENCODE histone modification ChIP, TF ChIP, Figure 2, 3, 5, 7, 9, S3-S7

McCord RP, Zhou VW, Yuh T, Bulyk ML. Distant cis-regulatory elements in human skeletal muscle differentiation. Genomics. 2011 Dec;98(6):401-11. PMID: 21907276; PMCID: PMC3229301
ENCODE histone modification ChIP, TF ChIP, Fig 1, 3, S3-S5, DNase

Megraw M, Mukherjee S, Ohler U. Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome Biol. 2013 Aug 23;14(8):R85. PMID: 23972209
ENCODE TF ChIP RNA network, modENCODE Fly TF ChIP RNA network, Figure 7

Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Léveillé N, Kalluri R et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell. 2013 Feb 7;49(3):524-35. PMID: 23273978
ENCODE histone modification ChIP, TF ChIP, Figure 1, 3, S1

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

Mitchell JA, Clay I, Umlauf D, Chen CY, Moir CA, Eskiw CH, Schoenfelder S, Chakalova L, Nagano T, Fraser P. Nuclear RNA sequencing of the mouse erythroid cell transcriptome. PLoS One. 2012;7(11):e49274. PMID: 23209567; PMCID: PMC3510205
ENCODE mouse RNA, TF ChIP, Table S6, S7

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. PMID: 21914722; PMCID: PMC3245935
ENCODE RNA, TF ChIP, Supplementary Figure S4, supplementary material 2

Moleirinho A, Seixas S, Lopes AM, Bento C, Prata MJ, Amorim A. Evolutionary constraints in the β-globin cluster: the signature of purifying selection at the δ-globin (HBD) locus and its role in developmental gene regulation. Genome Biol Evol. 2013 Jan;5(3):559-71. PMID: 23431002; PMCID: PMC3622298
ENCODE DNase, FAIRE, TF ChIP, 5C. Fig S4

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

Mousavi K, Zare H, Dell'orso S, Grontved L, Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell. 2013 Sep 12;51(5):606-17. PMID: 23993744; PMC: PMC3786356
ENCODE DNase, Figure 3A

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

Nepal C, Hadzhiev Y, Previti C, Haberle V, Li N, Takahashi H, Suzuki AM, Sheng Y, Abdelhamid RF, Anand S et al. Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res. 2013 Nov;23(11):1938-50. PMID: 24002785; PMC: PMC3814893
ENCODE RNA CAGE, Figure 3

Nielsen MM, Tehler D, Vang S, Sudzina F, Hedegaard J, Nordentoft I, Orntoft TF, Lund AH, Pedersen JS. Identification of expressed and conserved human noncoding RNAs. RNA. 2014 Feb;20(2):236-51. PMID: 24344320; PMC: PMC3895275
ENCODE RNA, DNase, GENCODE

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

Oger F, Dubois-Chevalier J, Gheeraert C, Avner S, Durand E, Froguel P, Salbert G, Staels B, Lefebvre P, Eeckhoute J. Peroxisome Proliferator-activated Receptor γ Regulates Genes Involved in Insulin/Insulin-like Growth Factor Signaling and Lipid Metabolism during Adipogenesis through Functionally Distinct Enhancer Classes. J Biol Chem. 2014 Jan 10;289(2):708-22. PMID: 24288131; PMC: PMC3887199
ENCODE mouse TF ChIP, Table 2

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

Onyshchenko MI, Gaynutdinov TI, Englund EA, Appella DH, Neumann RD, Panyutin IG. Quadruplex formation is necessary for stable PNA invasion into duplex DNA of BCL2 promoter region. Nucleic Acids Res. 2011 Sep 1;39(16):7114-23. PMID: 21593130; PMCID: PMC3167611
ENCODE DNase, TF ChIP, Fig 1

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

Paliwal A, Temkin AM, Kerkel K, Yale A, Yotova I, Drost N, Lax S, Nhan-Chang CL, Powell C, Borczuk A et al. Comparative anatomy of chromosomal domains with imprinted and non-imprinted allele-specific DNA methylation. PLoS Genet. 2013 Aug;9(8):e1003622. PMID: 24009515; PMC: PMC3757050
ENCODE TF ChIP, histone modification ChIP, RNA, Figure 3, 4, 5, 6a, 7, S3, S6

Pandiyan K, You JS, Yang X, Dai C, Zhou XJ, Baylin SB, Jones PA, Liang G. Functional DNA demethylation is accompanied by chromatin accessibility. Nucleic Acids Res. 2013 Apr;41(7):3973-85. PMID: 23408854; PMCID: PMC3627572
ENCODE DNase, FAIRE, histone modification, Fig 1, S1

Pappalardo-Carter DL, Balaraman S, Sathyan P, Carter ES, Chen WJ, Miranda RC. Suppression and epigenetic regulation of MiR-9 contributes to ethanol teratology: evidence from zebrafish and murine fetal neural stem cell models. Alcohol Clin Exp Res. 2013 Oct;37(10):1657-67. PMID: 23800254; PMC: PMC3785568
ENCODE TF ChIP, methods

Paul DS, Albers CA, Rendon A, Voss K, Stephens J, HaemGen Consortium, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH et al. Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci. Genome Res. 2013 Jul;23(7):1130-41. PMID: 23570689; PMCID: PMC3698506
ENCODE FAIRE, TF ChIP, RegulomeDB, DNase, Fig 1, 2, Table 1

Pham TH, Minderjahn J, Schmidl C, Hoffmeister H, Schmidhofer S, Chen W, Längst G, Benner C, Rehli M. Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1. Nucleic Acids Res. 2013 Jul 1;41(13):6391-6402. PMID: 23658224; PMCID: PMC3711439
ENCODE TF ChIP, DNase, GENCODE, Fig S1-3, S9, S10

Phillips-Cremins JE, Corces VG. Chromatin insulators: linking genome organization to cellular function. Mol Cell. 2013 May 23;50(4):461-74. PMID: 23706817; PMCID: PMC3670141
ENCODE mouse histone modification ChIP, Fig 3

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

Prokop JW, Rauscher FJ, Peng H, Liu Y, Araujo FC, Watanabe I, Reis FM, Milsted A. MAS promoter regulation: a role for Sry and tyrosine nitration of the KRAB domain of ZNF274 as a feedback mechanism. Clin Sci (Lond). 2014 May 1;126(10):727-38. PMID: 24128372
ENCODE TF ChIP, Figure 1, Table 2

Qiao Y, Giannopoulou EG, Chan CH, Park SH, Gong S, Chen J, Hu X, Elemento O, Ivashkiv LB. Synergistic activation of inflammatory cytokine genes by interferon-γ-induced chromatin remodeling and toll-like receptor signaling. Immunity. 2013 Sep 19;39(3):454-69. PMID: 24012417; PMC: PMC3857147
ENCODE DNase, Figure 3C, 5C, 5D

Quenneville S, Turelli P, Bojkowska K, Raclot C, Offner S, Kapopoulou A, Trono D. The KRAB-ZFP/KAP1 system contributes to the early embryonic establishment of site-specific DNA methylation patterns maintained during development. Cell Rep. 2012 Oct 25;2(4):766-73. PMID: 23041315; PMCID: PMC3677399
ENCODE DNA methylation RRBS, CpG islands (human and mouse)

Quon G, Lippert C, Heckerman D, Listgarten J. Patterns of methylation heritability in a genome-wide analysis of four brain regions. Nucleic Acids Res. 2013 Feb 1;41(4):2095-104. PMID: 23303775; PMCID: PMC3575819
ENCODE FAIRE, described in text

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. PMID: 22085927; PMCID: PMC3261562
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

Raddatz G, Hagemann S, Aran D, Söhle J, Kulkarni PP, Kaderali L, Hellman A, Winnefeld M, Lyko F. Aging is associated with highly defined epigenetic changes in the human epidermis. Epigenetics Chromatin. 2013 Oct 31;6(1):36. PMID: 24279375; PMC: PMC3819645
ENCODE histone modification ChIP, TF ChIP, chromatin states, Figure 4, S3, S4

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

Rebollo R, Miceli-Royer K, Zhang Y, Farivar S, Gagnier L, Mager DL. Epigenetic interplay between mouse endogenous retroviruses and host genes. Genome Biol. 2012 Oct 3;13(10):R89. PMID: 23034137; PMCID: PMC3491417
ENCODE mouse Histone modification ChIP, TF ChIP, Fig S2, S4

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

Ritter DI, Dong Z, Guo S, Chuang JH. Transcriptional enhancers in protein-coding exons of vertebrate developmental genes. PLoS One. 2012;7(5):e35202. PMID: 22567096; PMCID: PMC3342275
ENCODE TF ChIP

Rose D, Stadler PF. Molecular evolution of the non-coding eosinophil granule ontogeny transcript. Front Genet. 2011;2:69. PMID: 22303364; PMCID: PMC3268622
ENCODE DNase, histone modification ChIP, RNA, Figure 5, A3, results

Rosin JM, Abassah-Oppong S, Cobb J. Comparative transgenic analysis of enhancers from the human SHOX and mouse Shox2 genomic regions. Hum Mol Genet. 2013 Aug 1;22(15):3063-76. PMID: 23575226
ENCODE DNase, Histone modification ChIP, Fig 2b, 6a

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

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. PMID: 22115494; PMCID: PMC3239327
ENCODE TF ChIP, histone modification ChIP, DNase, FAIRE, RNA, used throughout: basic biology

Ryynänen J, Carlberg C. Primary 1,25-dihydroxyvitamin D3 response of the interleukin 8 gene cluster in human monocyte- and macrophage-like cells. PLoS One. 2013;8(10):e78170. PMID: 24250750; PMC: PMC3824026
ENCODE TF ChIP, ChIA-PET, figure 1, described in text

Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. Cell-type specific features of circular RNA expression. PLoS Genet. 2013;9(9):e1003777. PMID: 24039610; PMC: PMC3764148
ENCODE RNA, used throughout, described in text and Table 1

Santoni FA, Guerra J, Luban J. HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology. 2012 Dec 20;9:111. PMID: 23253934; PMCID: PMC3558390
ENCODE RNA

Satoh J, Kawana N, Yamamoto Y. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. Gene Regul Syst Bio. 2013;7:139-52. PMID: 24250222; PMC: PMC3825669
ENCODE TF-ChIP, used throughout

Satoh J, Tabunoki H. A Comprehensive Profile of ChIP-Seq-Based STAT1 Target Genes Suggests the Complexity of STAT1-Mediated Gene Regulatory Mechanisms. Gene Regul Syst Bio. 2013;7:41-56. PMID: 23645984; PMCID: PMC3623615
ENCODE TF ChIP, text, Fig 1, 2

Savic D, Park SY, Bailey KA, Bell GI, Nobrega MA. In vitro scan for enhancers at the TCF7L2 locus. Diabetologia. 2013 Jan;56(1):121-5. PMID: 23011354; PMCID: PMC3525810
ENCODE histone modification ChIP, Fig 1a

Scharer CD, Barwick BG, Youngblood BA, Ahmed R, Boss JM. Global DNA methylation remodeling accompanies CD8 T cell effector function. J Immunol. 2013 Sep 15;191(6):3419-29. PMID: 23956425; PMC: PMC3800465
ENCODE histone modification ChIP, Figure 4, Table 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

Shakes LA, Du H, Wolf HM, Hatcher C, Norford DC, Precht P, Sen R, Chatterjee PK. Using BAC transgenesis in zebrafish to identify regulatory sequences of the amyloid precursor protein gene in humans. BMC Genomics. 2012 Sep 4;13:451. PMID: 22947103; PMCID: PMC3546842
ENCODE histone modification ChIP, described in text

Shen L, Choi I, Nestler EJ, Won KJ. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective. Genomics Inform. 2013 Jun;11(2):60-7. PMID: 23843771; PMC: PMC3704928
ENCODE data and quality metrics reviewed

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

Smirnov NA, Didych DA, Akopov SB, Nikolaev LG, Sverdlov ED. Assay of insulator enhancer-blocking activity with the use of transient transfection. Biochemistry (Mosc). 2013 Aug;78(8):895-903. PMID: 24228877
ENCODE TF ChIP, histone modification ChIP, DNase, Tables 1,2

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. PMID: 22158964; PMCID: PMC3272979
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

Sompallae R, Hofmann O, Maher CA, Gedye C, Behren A, Vitezic M, Daub CO, Devalle S, Caballero OL, Carninci P et al. A comprehensive promoter landscape identifies a novel promoter for CD133 in restricted tissues, cancers, and stem cells. Front Genet. 2013;4:209. PMID: 24194746; PMC: PMC3810939
ENCODE TF ChIP, DNA methylation, RNA, chromatin states, described in text, Figure 2

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. PMID: 22170606
ENCODE mouse and human DNase, Fig 2, S2, S6

Stelzer Y, Ronen D, Bock C, Boyle P, Meissner A, Benvenisty N. Identification of novel imprinted differentially methylated regions by global analysis of human- parthenogenetic-induced pluripotent stem cells. Stem Cell Reports. 2013;1(1):79-89. PMID: 24052944; PMC: PMC3757747
ENCODE TF ChIP, Figure 1, 2

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

Sun J, Lin Y, Wu J. Long non-coding RNA expression profiling of mouse testis during postnatal development. PLoS One. 2013;8(10):e75750. PMID: 24130740; PMC: PMC3794988
ENCODE mouse histone modification ChIP, GENCODE, described in text

Sun L, Luo H, Bu D, Zhao G, Yu K, Zhang C, Liu Y, Chen R, Zhao Y. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013 Sep;41(17):e166. PMID: 23892401; PMC: PMC3783192
ENCODE GENCODE, Tables S1-S3

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

Teif VB, Vainshtein Y, Caudron-Herger M, Mallm JP, Marth C, Höfer T, Rippe K. Genome-wide nucleosome positioning during embryonic stem cell development. Nat Struct Mol Biol. 2012 Nov;19(11):1185-92. PMID: 23085715
mouse ENCODE TF ChIP, Fig 1b, Fig 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

Tsukiji N, Amano T, Shiroishi T. A novel regulatory element for Shh expression in the lung and gut of mouse embryos. Mech Dev. 2014 Feb;131:127-36. PMID: 24157522
ENCODE mouse DNase, histone modification ChIP, Figure 2

Ulitsky I, Bartel DP. lincRNAs: genomics, evolution, and mechanisms. Cell. 2013 Jul 3;154(1):26-46. PMID: 23827673; PMC: PMC3924787
ENCODE histone modification ChIP, RNA-seq, CAGE, GENCODE, Figure 1A

Venters BJ, Pugh BF. Genomic organization of human transcription initiation complexes. Nature. 2013 Oct 3;502(7469):53-8. PMID: 24048476
ENCODE TF ChIP, RNA-seq, blacklist, Extended Figures 1A, 5

Vihervaara A, Sergelius C, Vasara J, Blom MA, Elsing AN, Roos-Mattjus P, Sistonen L. Transcriptional response to stress in the dynamic chromatin environment of cycling and mitotic cells. Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3388-97. PMID: 23959860; PMC: PMC3767495
ENCODE TF ChIP, DNase, Figure 1, 3, 4, 6b, S3, Table S1

Wang D, Rendon A, Wernisch L. Transcription factor and chromatin features predict genes associated with eQTLs. Nucleic Acids Res. 2013 Feb 1;41(3):1450-63. PMID: 23275551; PMCID: PMC3561974
ENCODE TF ChIP, chromatin states, FAIRE, described in methods, used throughout

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

Wang Z, Cao R, Taylor K, Briley A, Caldwell C, Cheng J. The properties of genome conformation and spatial gene interaction and regulation networks of normal and malignant human cell types. PLoS One. 2013;8(3):e58793. PMID: 23536826; PMCID: PMC3594155
ENCODE histone modification ChIP, DNase, TF ChIP, Fig S39

Wang Z, Willard HF. Evidence for sequence biases associated with patterns of histone methylation. BMC Genomics. 2012 Aug 2;13:367. PMID: 22857523; PMCID: PMC3532361
ENCODE histone modification ChIP, Fig 5, Table S6

Wei W, Gyenesei A, Semple CA, Haley CS. Properties of local interactions and their potential value in complementing genome-wide association studies. PLoS One. 2013;8(8):e71203. PMID: 23940718; PMC: PMC3733963
ENCODE RNA, TF ChIP, histone modification ChIP, DNase, DNA methylation, RegulomeDB, Figure 4B

Weikard R, Hadlich F, Kuehn C. Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing. BMC Genomics. 2013 Nov 14;14:789. PMID: 24225384; PMC: PMC3833843
ENCODE GENCODE

Wen B, Wu H, Loh YH, Briem E, Daley GQ, Feinberg AP. Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions. BMC Genomics. 2012 Oct 26;13:566. PMID: 23102236; PMCID: PMC3507770
ENCODE TF ChIP, Histone modification ChIP, DNase, MNase, Table S3

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

Yang J, Mitra A, Dojer N, Fu S, Rowicka M, Brasier AR. A probabilistic approach to learn chromatin architecture and accurate inference of the NF-κB/RelA regulatory network using ChIP-Seq. Nucleic Acids Res. 2013 Aug 1;41(15):7240-7259. PMID: 23771139; PMCID: PMC3753626
ENCODE TF ChIP, DNase, GENCODE, text, Table 3

Yavartanoo M, Choi JK. ENCODE: A Sourcebook of Epigenomes and Chromatin Language. Genomics Inform. 2013 Mar;11(1):2-6. PMID: 23613676; PMC: PMC3630381
ENCODE DHS, TF ChIP, histone modification ChIP, chromatin states

You JS, De Carvalho DD, Dai C, Liu M, Pandiyan K, Zhou XJ, Liang G, Jones PA. SNF5 is an essential executor of epigenetic regulation during differentiation. PLoS Genet. 2013 Apr;9(4):e1003459. PMID: 23637628; PMC: PMC3636213
ENCODE TF ChIP data, DNA methylation, DNase, Fig 1, S5

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

Young JM, Whiddon JL, Yao Z, Kasinathan B, Snider L, Geng LN, Balog J, Tawil R, van der Maarel SM, Tapscott SJ. DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PLoS Genet. 2013 Nov;9(11):e1003947. PMID: 24278031; PMC: PMC3836709
ENCODE TF ChIP, described in text

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

Zhou Y, Lu Y, Tian W. Epigenetic features are significantly associated with alternative splicing. BMC Genomics. 2012 Mar 29;13:123. PMID: 22455468; PMC: PMC3362759
ENCODE,histone modification ChIP, TF ChIP, described in text, additional file 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

Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE. methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol. 2012 Oct 3;13(10):R87. PMID: 23034086; PMCID: PMC3491415
ENCODE chromatin states, Fig 6D

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. PMID: 21994224; PMCID: PMC3232367
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. PMID: 22722343; PMCID: PMC3460195
ENCODE RNA, Fig S5, S6

Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 2013 Mar 1;339(6123):1074-7. PMID: 23328393
modENCODE Fly Histone modification, TF, RNA, Human DNase, Histone modification, RNA, TF, Fig 3, S19, S30, S31

Bao Y, Vinciotti V, Wit E, 't Hoen PA. Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data. BMC Bioinformatics. 2013 May 30;14:169. PMID: 23721376; PMCID: PMC3717085
ENCODE histone modification ChIP, DNase, TF ChIP, Chromatin states, ENCODE mappability, Fig 3

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

Benner C, Konovalov S, Mackintosh C, Hutt KR, Stunnenberg R, Garcia-Bassets I. Decoding a signature-based model of transcription cofactor recruitment dictated by cardinal cis- regulatory elements in proximal promoter regions. PLoS Genet. 2013 Nov;9(11):e1003906. PMID: 24244184; PMC: PMC3820735
ENCODE TF ChIP, histone modification ChIP, DNase, Figures 5, S1

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

Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013 Dec;10(12):1213-8. PMID: 24097267
ENCODE TF ChIP, DNase, Histone modification ChIP, FAIRE, RNA, Chromatin states, Figures 1,3,4

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 C, Zhang S, Zhang XS. Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis. Nucleic Acids Res. 2013 Nov 1;41(20):9230-42. PMID: 23945931; PMC: PMC3814353
ENCODE TF ChIP, Histone modification ChIP, DNase, used throughout

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. PMID: 22684628; PMCID: PMC3467035
ENCODE TF ChIP, DNase, FAIRE, Histone modification ChIP, Fig 3, 4, S1, S2, Supplement

Davis MP, van Dongen S, Abreu-Goodger C, Bartonicek N, Enright AJ. Kraken: a set of tools for quality control and analysis of high-throughput sequence data. Methods. 2013 Sep 1;63(1):41-9. PMID: 23816787
ENCODE RNA-seq, Figure 4

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

Eksi R, Li HD, Menon R, Wen Y, Omenn GS, Kretzler M, Guan Y. Systematically differentiating functions for alternatively spliced isoforms through integrating RNA- seq data. PLoS Comput Biol. 2013 Nov;9(11):e1003314. PMID: 24244129; PMC: PMC3820534
ENCODE RNA-seq, Figure 1, Dataset S1

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. PMID: 22248020; PMCID: PMC3371767
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

Gilfillan GD, Hughes T, Sheng Y, Hjorthaug HS, Straub T, Gervin K, Harris JR, Undlien DE, Lyle R. Limitations and possibilities of low cell number ChIP-seq. BMC Genomics. 2012 Nov 21;13:645. PMID: 23171294; PMCID: PMC3533509
ENCODE histone modification ChIP, Table 2

Gu F, Doderer MS, Huang YW, Roa JC, Goodfellow PJ, Kizer EL, Huang TH, Chen Y. CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers. PLoS One. 2013;8(4):e60980. PMID: 23630576; PMCID: PMC3632540
ENCODE histone modification ChIP, Fig 1

Guo L, Du Y, Chang S, Zhang K, Wang J. rSNPBase: a database for curated regulatory SNPs. Nucleic Acids Res. 2014 Jan;42(Database issue):D1033-9. PMID: 24285297
ENCODE DNase, FAIRE, ChIA-PET, 5C, DNA methylation, histone modification ChIP, RBP, TF ChIP, used throughout, listed in Table S1, Figure 1

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

Hu P, Shen Z, Tu H, Zhang L, Shi T. Integrating multiple resources to identify specific transcriptional cooperativity with a Bayesian approach. Bioinformatics. 2013 Nov 8;. PMID: 24192543
ENCODE TF matrices, TF networks

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. PMID: 22087331; PMCID: PMC3210180
ENCODE histone modification ChIP, DNase, RNA, analyzed throughout

Jankowski A, Szczurek E, Jauch R, Tiuryn J, Prabhakar S. Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Genome Res. 2013 Aug;23(8):1307-18. PMID: 23554463; PMC: PMC3730104
ENCODE DNase used throughout

Karnik R, Meissner A. Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. Cell Stem Cell. 2013 Jul 3;13(1):14-21. PMID: 23827707; PMCID: PMC3750740
ENCODE DNA methylation, Fig S1-4

Kumar V, Muratani M, Rayan NA, Kraus P, Lufkin T, Ng HH, Prabhakar S. Uniform, optimal signal processing of mapped deep-sequencing data. Nat Biotechnol. 2013 Jul;31(7):615-22. PMID: 23770639
ENCODE TF ChIP, RNA, DNase, FAIRE, Fig 1-4

Kutmon M, Kelder T, Mandaviya P, Evelo CT, Coort SL. CyTargetLinker: A Cytoscape App to Integrate Regulatory Interactions in Network Analysis. PLoS One. 2013;8(12):e82160. PMID: 24340000; PMC: PMC3855388
ENCODE TF ChIP, Figure 1,3,4

Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z. Probabilistic error correction for RNA sequencing. Nucleic Acids Res. 2013 May 1;41(10):e109. PMID: 23558750; PMCID: PMC3664804
ENCODE RNA, text, Table 3, Table S5

Lee C, Huang CH. Searching for transcription factor binding sites in vector spaces. BMC Bioinformatics. 2012 Aug 27;13:215. PMID: 23244338; PMCID: PMC3543194
ENCODE TF ChIP, Table 3

Lee C, Huang CH. LASAGNA: a novel algorithm for transcription factor binding site alignment. BMC Bioinformatics. 2013 Mar 24;14:108. PMID: 23522376; PMC: PMC3747862
ENCODE mouse Histone modification ChIP, TF ChIP, used throughout, additional file 3

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

LeGault LH, Dewey CN. Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. Bioinformatics. 2013 Sep 15;29(18):2300-10. PMID: 23846746; PMC: PMC3753571
ENCODE RNA, modENCODE Fly RNA, Table 1, S1

Li Y, Xie X. A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues. BMC Bioinformatics. 2013;14 Suppl 5:S11. PMID: 23735186; PMCID: PMC3622628
ENCODE RNA, text, Fig 4

Li Y, Zhao DY, Greenblatt JF, Zhang Z. RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments. Nucleic Acids Res. 2013 Apr;41(8):e94. PMID: 23455476; PMCID: PMC3632129
ENCODE RBP, Fig 5, 6, Table S1

Ma X, Zhang X. NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data. BMC Bioinformatics. 2013 Jul 10;14:220. PMID: 23837734; PMCID: PMC3717102
ENCODE RNA, text, Table 1

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

Mathelier A, Wasserman WW. The next generation of transcription factor binding site prediction. PLoS Comput Biol. 2013;9(9):e1003214. PMID: 24039567; PMC: PMC3764009
ENCODE TF ChIP, mouse TF ChIP, mappability, used throughout, described in text

Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014 Jan;42(Database issue):D142-7. PMID: 24194598
ENCODE TF ChIP, mouse TF ChIP, fly TF ChIP, worm TF ChIP

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

McLeay RC, Lesluyes T, Cuellar Partida G, Bailey TL. Genome-wide in silico prediction of gene expression. Bioinformatics. 2012 Nov 1;28(21):2789-96. PMID: 22954627; PMCID: PMC3476338
ENCODE RNA, TF-ChIP, Histone modification ChIP, DNase, Figures S1, S2, S3, S15, S16, S17, S18, S19, S20

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. PMID: 22241655
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

Paila U, Chapman BA, Kirchner R, Quinlan AR. GEMINI: integrative exploration of genetic variation and genome annotations. PLoS Comput Biol. 2013;9(7):e1003153. PMID: 23874191; PMC: PMC3715403
ENCODE TF ChIP, DNase, chromatin states, Figure 1

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

Piper J, Elze MC, Cauchy P, Cockerill PN, Bonifer C, Ott S. Wellington: a novel method for the accurate identification of digital genomic footprints from DNase- seq data. Nucleic Acids Res. 2013 Nov;41(21):e201. PMID: 24071585; PMC: PMC3834841
ENCODE DNase, TF ChIP, Figure 2-5, S4-6, Table S1

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

Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D. Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol. 2013 Sep 10;14(9):R95. PMID: 24020486
ENCODE RNA used throughout, Figure 4, 5

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

Roy S, Lagree S, Hou Z, Thomson JA, Stewart R, Gasch AP. Integrated module and gene-specific regulatory inference implicates upstream signaling networks. PLoS Comput Biol. 2013;9(10):e1003252. PMID: 24146602; PMC: PMC3798279
ENCODE DNase, TF ChIP and networks, Figure 7

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

Schmitt T, Ogris C, Sonnhammer EL. FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res. 2014 Jan;42(Database issue):D380-8. PMID: 24185702
ENCODE mouse TF ChIP, human TF ChIP, modENCODE fly TF ChIP, worm, TF ChIP, table 1, described in text

Shao Z, Zhang Y, Yuan GC, Orkin SH, Waxman DJ. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biol. 2012 Mar 16;13(3):R16. PMID: 22424423; PMC: PMC3439967
ENCODE histone modification ChIP, TF ChIP, RNA, used throughout, Table S1, described in materials and methods

Shen L, Shao NY, Liu X, Maze I, Feng J, Nestler EJ. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One. 2013;8(6):e65598. PMID: 23762400; PMCID: PMC3677880
ENCODE Histone modification ChIP, Figs 1-6, Table 1, Text S1

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

Slieker RC, Bos SD, Goeman JJ, Bovée JV, Talens RP, van der Breggen R, Suchiman HE, Lameijer EW, Putter H, van den Akker EB et al. Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. Epigenetics Chromatin. 2013 Aug 6;6(1):26. PMID: 23919675; PMC: PMC3750594
ENCODE DNase, TF ChIP, Figure S9, S10, Additional file 17, 18

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. PMID: 22916038; PMCID: PMC3420950
ENCODE TF ChIP, DNase, Histone modification ChIP, FAIRE, Figure 4

Spicuglia S, Maqbool MA, Puthier D, Andrau JC. An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function. Methods. 2013 Sep 1;63(1):3-17. PMID: 23597756
GENCODE, Table 1

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

Sun H, Guns T, Fierro AC, Thorrez L, Nijssen S, Marchal K. Unveiling combinatorial regulation through the combination of ChIP information and in silico cis- regulatory module detection. Nucleic Acids Res. 2012 Jul;40(12):e90. PMID: 22422841; PMC: PMC3384348
ENCODE TF ChIP, 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

Teng L, Tan K. Finding combinatorial histone code by semi-supervised biclustering. BMC Genomics. 2012 Jul 3;13:301. PMID: 22759587; PMCID: PMC3443427
ENCODE histone modification ChIP, TF ChIP, Fig 3, 4, Table S3, S6

Türei D, Papp D, Fazekas D, Földvári-Nagy L, Módos D, Lenti K, Csermely P, Korcsmáros T. NRF2-ome: an integrated web resource to discover protein interaction and regulatory networks of NRF2. Oxid Med Cell Longev. 2013;2013:737591. PMID: 23710289; PMC: PMC3654349
ENCODE TF ChIP network, RNA

Tzeng DT, Tseng YT, Ung M, Liao IE, Liu CC, Cheng C. DPRP: a database of phenotype-specific regulatory programs derived from transcription factor binding data. Nucleic Acids Res. 2014 Jan;42(Database issue):D178-83. PMID: 24302579
ENCODE TF ChIP

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

Wrzodek C, Büchel F, Hinselmann G, Eichner J, Mittag F, Zell A. Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands. PLoS One. 2012;7(4):e35327. PMID: 22558141; PMC: PMC3340366
ENCODE, DNA methylation, described in materials and methods

Xiao ZD, Diao LT, Yang JH, Xu H, Huang MB, Deng YJ, Zhou H, Qu LH. Deciphering the transcriptional regulation of microRNA genes in humans with ACTLocater. Nucleic Acids Res. 2013 Jan 7;41(1):e5. PMID: 22941648; PMC: PMC3592406
ENCODE DNase, FAIRE, histone modification ChIP, TF ChIP; described in text, Table S2

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

Yang JH, Li JH, Jiang S, Zhou H, Qu LH. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. PMID: 23161675; PMCID: PMC3531181
ENCODE TF ChIP, modENCODE worm TF CHIP, modENCODE fly TF ChIP, used throughout, listed in Table S1

Zambelli F, Pesole G, Pavesi G. PscanChIP: Finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W535-43. PMID: 23748563; PMCID: PMC3692095
ENCODE TF ChIP, Fig 1, 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. PMID: 22669907; PMCID: PMC3394253
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

Zhou X, Lowdon RF, Li D, Lawson HA, Madden PA, Costello JF, Wang T. Exploring long-range genome interactions using the WashU Epigenome Browser. Nat Methods. 2013 May;10(5):375-6. PMID: 23629413
ENCODE ChIA-PET, Fig 1

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

Antão JM, Mason JM, Déjardin J, Kingston RE. Protein landscape at Drosophila melanogaster telomere-associated sequence repeats. Mol Cell Biol. 2012 Jun;32(12):2170-82. PMID: 22493064; PMCID: PMC3372267
modENCODE Fly RNA

Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science. 2013 Mar 1;339(6123):1074-7. PMID: 23328393
modENCODE Fly Histone modification

Assis R, Zhou Q, Bachtrog D. Sex-biased transcriptome evolution in Drosophila. Genome Biol Evol. 2012;4(11):1189-200. PMID: 23097318; PMCID: PMC3514954
modENCODE fly RNA data

Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A. Identification of transcription factor binding sites from ChIP-seq data at high resolution. Bioinformatics. 2013 Nov 1;29(21):2705-13. PMID: 23980024; PMC: PMC3799470
modENCODE worm TF ChIP; methods development

Belyaeva ES, Goncharov FP, Demakova OV, Kolesnikova TD, Boldyreva LV, Semeshin VF, Zhimulev IF. Late replication domains in polytene and non-polytene cells of Drosophila melanogaster. PLoS One. 2012;7(1):e30035. PMID: 22253867; PMC: PMC3254639
modENCODE Fly histone modification ChIP, chromatin states, protein localization, DNA replication; basic biology

Bergwitz C, Rasmussen MD, DeRobertis C, Wee MJ, Sinha S, Chen HH, Huang J, Perrimon N. Roles of major facilitator superfamily transporters in phosphate response in Drosophila. PLoS One. 2012;7(2):e31730. PMID: 22359624; PMC: PMC3280997
modENCODE Fly RNA, Table S3, S4; basic biology

Billi AC, Freeberg MA, Day AM, Chun SY, Khivansara V, Kim JK. A conserved upstream motif orchestrates autonomous, germline-enriched expression of Caenorhabditis elegans piRNAs. PLoS Genet. 2013 Mar;9(3):e1003392. PMID: 23516384; PMCID: PMC3597512
modENCODE worm TF ChIP

Bowman SK, Simon MD, Deaton AM, Tolstorukov M, Borowsky ML, Kingston RE. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. BMC Genomics. 2013 Jul 9;14:466. PMID: 23837789; PMC: PMC3711846
modENCODE Fly Histone modification ChIP, Figure 3; methods development

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

Cecere G, Hoersch S, Jensen MB, Dixit S, Grishok A. The ZFP-1(AF10)/DOT-1 complex opposes H2B ubiquitination to reduce Pol II transcription. Mol Cell. 2013 Jun 27;50(6):894-907. PMID: 23806335; PMC: PMC3784254
modENCODE worm TF ChIP, Figure 4, S6; basic biology

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

Chandrasekaran S, Ament SA, Eddy JA, Rodriguez-Zas SL, Schatz BR, Price ND, Robinson GE. Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states. Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):18020-5. PMID: 21960440; PMCID: PMC3207651
modENCODE fly TF ChIP

Chen YC, Cheng JH, Tsai ZT, Tsai HK, Chuang TJ. The impact of trans-regulation on the evolutionary rates of metazoan proteins. Nucleic Acids Res. 2013 Jul;41(13):6371-80. PMID: 23658220; PMCID: PMC3711421
ENCODE TF ChIP, ENCODE mouse TF ChIP, modENCODE fly TF CHIP, text, Table 1, 2

Chiu JC, Jiang X, Zhao L, Hamm CA, Cridland JM, Saelao P, Hamby KA, Lee EK, Kwok RS, Zhang G et al. Genome of Drosophila suzukii, the spotted wing drosophila. G3 (Bethesda). 2013 Dec 9;3(12):2257-71. PMID: 24142924; PMC: PMC3852387
modENCODE fly RNA, Methods and Materials; basic biology

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

Cooper MT, Kennison JA. Molecular genetic analyses of polytene chromosome region 72A-D in Drosophila melanogaster reveal a gene desert in 72D. PLoS One. 2011;6(8):e23509. PMID: 21853143; PMCID: PMC3154481
modENCODE fly RNA, text

Cornman RS, Lopez D, Evans JD. Transcriptional response of honey bee larvae infected with the bacterial pathogen Paenibacillus larvae. PLoS One. 2013;8(6):e65424. PMID: 23762370; PMC: PMC3675105
modENCODE fly RNA, expression networks; basic biology

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

Darbo E, Herrmann C, Lecuit T, Thieffry D, van Helden J. Transcriptional and epigenetic signatures of zygotic genome activation during early drosophila embryogenesis. BMC Genomics. 2013 Apr 5;14(1):226. PMID: 23560912; PMCID: PMC3706223
modENCODE fly TF ChIP, histone modification ChIP, and DNase

Demakov SA, Vatolina TY, Babenko VN, Semeshin VF, Belyaeva ES, Zhimulev IF. Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster. BMC Genomics. 2011 Nov 18;12:566. PMID: 22093916; PMCID: PMC3240664
modENCODE fly TF ChIP, histone modification ChIP

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

Díaz-Castillo C, Xia XQ, Ranz JM. Evaluation of the role of functional constraints on the integrity of an ultraconserved region in the genus Drosophila. PLoS Genet. 2012 Feb;8(2):e1002475. PMID: 22319453; PMC: PMC3271063
modENCODE fly RNA expression; basic biology

Fay A, Misulovin Z, Li J, Schaaf CA, Gause M, Gilmour DS, Dorsett D. Cohesin selectively binds and regulates genes with paused RNA polymerase. Curr Biol. 2011 Oct 11;21(19):1624-34. PMID: 21962715; PMCID: PMC3193539
modENCODE fly TF ChIP, histone modification ChIP

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"

Figueiredo ML, Philip P, Stenberg P, Larsson J. HP1a recruitment to promoters is independent of H3K9 methylation in Drosophila melanogaster. PLoS Genet. 2012;8(11):e1003061. PMID: 23166515; PMC: PMC3499360
modENCODE fly, RNA, TF ChIP, histone modification ChIP, DNase, Figure 4, S3; basic biology

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

Follmer NE, Wani AH, Francis NJ. A polycomb group protein is retained at specific sites on chromatin in mitosis. PLoS Genet. 2012;8(12):e1003135. PMID: 23284300; PMC: PMC3527277
modENCODE fly TF ChIP, Table 2, 3, figure 7; basic biology

Friedman AA, Tucker G, Singh R, Yan D, Vinayagam A, Hu Y, Binari R, Hong P, Sun X, Porto M et al. Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signaling. Sci Signal. 2011 Oct 25;4(196):rs10. PMID: 22028469; PMCID: PMC3439136
modENCODE fly RNA

Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJ. Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Res. 2014 Jan;42(1):153-62. PMID: 24068555; PMC: PMC3874175
modENCODE worm TF ChIP, Figure 2; basic biology

Ganesan S, Karr JE, Featherstone DE. Drosophila glutamate receptor mRNA expression and mRNP particles. RNA Biol. 2011 Sep-Oct;8(5):771-81. PMID: 21743295; PMCID: PMC3256355
modENCODE fly RNA

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. PMID: 22458773
modENCODE fly data on bFtzF1 binding, used in Fig 7

Gao Q, Ho C, Jia Y, Li JJ, Huang H. Biclustering of linear patterns in gene expression data. J Comput Biol. 2012 Jun;19(6):619-31. PMID: 22697238; PMC: PMC3375643
modENCODE fly and worm RNA; methods development

Gatchalian J, Fütterer A, Rothbart SB, Tong Q, Rincon-Arano H, Sánchez de Diego A, Groudine M, Strahl BD, Martínez-A C, van Wely KH et al. Dido3 PHD modulates cell differentiation and division. Cell Rep. 2013 Jul 11;4(1):148-58. PMID: 23831028
modENCODE fly Histone modification ChIP, FIgure 2; basic biology

Ghezzi A, Krishnan HR, Lew L, Prado FJ 3rd, Ong DS, Atkinson NS. Alcohol-induced histone acetylation reveals a gene network involved in alcohol tolerance. PLoS Genet. 2013 Dec;9(12):e1003986. PMID: 24348266; PMC: PMC3861128
modENCODE Fly histone modification ChIP, RNA, Figure 2; basic biology

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

Gisselbrecht SS, Barrera LA, Porsch M, Aboukhalil A, Estep PW 3rd, Vedenko A, Palagi A, Kim Y, Zhu X, Busser BW et al. Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos. Nat Methods. 2013 Aug;10(8):774-80. PMID: 23852450; PMC: PMC3733245
modENCODE fly Histone modification ChIP, DNase, Figure 4; basic biology

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

Grentzinger T, Armenise C, Pelisson A, Brun C, Mugat B, Chambeyron S. A user-friendly chromatographic method to purify small regulatory RNAs. Methods. 2013 May 28;. PMID: 23727218
modENCODE Fly RNA

Guertin MJ, Lis JT. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet. 2010 Sep 9;6(9). PMID: 20844575; PMCID: PMC2936546
modENCODE fly TF ChIP, histone modification ChIP

Guillén Y, Ruiz A. Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution. BMC Genomics. 2012 Feb 1;13:53. PMID: 22296923; PMC: PMC3355041
modENCODE Fly RNA

Haenni S, Ji Z, Hoque M, Rust N, Sharpe H, Eberhard R, Browne C, Hengartner MO, Mellor J, Tian B et al. Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq. Nucleic Acids Res. 2012 Jul;40(13):6304-18. PMID: 22467213; PMC: PMC3401467
modENCODE worm RNA, described in materials and methods

Hansen ME, Kulathinal RJ. Sex-biased networks and nodes of sexually antagonistic conflict in Drosophila. Int J Evol Biol. 2013;2013:545392. PMID: 23431497; PMCID: PMC3566611
modENCODE fly RNA, TF ChIP

Harvey R, Schuster E, Jennings BH. Pleiohomeotic interacts with the core transcription elongation factor Spt5 to regulate gene expression in Drosophila. PLoS One. 2013;8(7):e70184. PMID: 23894613; PMC: PMC3718797
modENCODE Fly TF ChIP

Heger P, Marin B, Bartkuhn M, Schierenberg E, Wiehe T. The chromatin insulator CTCF and the emergence of metazoan diversity. Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17507-12. PMID: 23045651; PMCID: PMC3491479
modENCODE fly TF ChIP

Helfer S, Schott J, Stoecklin G, Förstemann K. AU-rich element-mediated mRNA decay can occur independently of the miRNA machinery in mouse embryonic fibroblasts and Drosophila S2-cells. PLoS One. 2012;7(1):e28907. PMID: 22253700; PMC: PMC3258239
modENCODE Fly RNA

Herrmann C, Van de Sande B, Potier D, Aerts S. i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis- regulatory modules. Nucleic Acids Res. 2012 Aug;40(15):e114. PMID: 22718975; PMCID: PMC3424583
modENCODE Fly TF ChIP

Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B. Neural-specific elongation of 3' UTRs during Drosophila development. Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15864-9. PMID: 21896737; PMCID: PMC3179109
modENCODE fly RNA

Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN. Deep sequencing the circadian and diurnal transcriptome of Drosophila brain. Genome Res. 2012 Jul;22(7):1266-81. PMID: 22472103; PMC: PMC3396368
modENCODE Fly RNA

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

Ji JY, Miles WO, Korenjak M, Zheng Y, Dyson NJ. In vivo regulation of E2F1 by Polycomb group genes in Drosophila. G3 (Bethesda). 2012 Dec;2(12):1651-60. PMID: 23275887; PMC: PMC3516486
modENCODE Fly histone modification ChIP; Figures S1-4

Jin H, Stojnic R, Adryan B, Ozdemir A, Stathopoulos A, Frasch M. Genome-wide screens for in vivo Tinman binding sites identify cardiac enhancers with diverse functional architectures. PLoS Genet. 2013 Jan;9(1):e1003195. PMID: 23326246; PMCID: PMC3542182
modENCODE fly TF ChIP

Johnson AN, Mokalled MH, Haden TN, Olson EN. JAK/Stat signaling regulates heart precursor diversification in Drosophila. Development. 2011 Nov;138(21):4627-38. PMID: 21965617; PMCID: PMC3190381
modENCODE fly TF ChIP

Jung I, Kim SK, Kim M, Han YM, Kim YS, Kim D, Lee D. H2B monoubiquitylation is a 5'-enriched active transcription mark and correlates with exon-intron structure in human cells. Genome Res. 2012 Jun;22(6):1026-35. PMID: 22421545; PMC: PMC3371706
modENCODE Fly histone modification ChIP, RNA

Kagoshima H, Cassata G, Tong YG, Pujol N, Niklaus G, Bürglin TR. The LIM homeobox gene ceh-14 is required for phasmid function and neurite outgrowth. Dev Biol. 2013 Aug 15;380(2):314-23. PMID: 23608457
modENCODE Worm; TF ChIP, RNA, figure 1, Table S1

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

Kaur T, Rockman MV. Crossover heterogeneity in the absence of hotspots in Caenorhabditis elegans. Genetics. 2014 Jan;196(1):137-48. PMID: 24172135; PMC: PMC3872180
modENCODE worm TF ChIP, table 1, figure 3, materials and methods

Kazemian M, Pham H, Wolfe SA, Brodsky MH, Sinha S. Widespread evidence of cooperative DNA binding by transcription factors in Drosophila development. Nucleic Acids Res. 2013 Sep;41(17):8237-52. PMID: 23847101; PMC: PMC3783179
modENCODE Fly; TF ChIP, DNase, Table S1, materials and methods

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. PMID: 22508764; PMCID: PMC3371715
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

Kenigsberg E, Tanay A. Drosophila functional elements are embedded in structurally constrained sequences. PLoS Genet. 2013 May;9(5):e1003512. PMID: 23750124; PMCID: PMC3671938
modENCODE fly TF ChIP

Kranz AL, Jiao CY, Winterkorn LH, Albritton SE, Kramer M, Ercan S. Genome-wide analysis of condensin binding in Caenorhabditis elegans. Genome Biol. 2013;14(10):R112. PMID: 24125077
modENCODE worm histone modification ChIP, TF ChIP; Figure 3, 4, S1, S3, Table S1

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

Langlais KK, Brown JL, Kassis JA. Polycomb group proteins bind an engrailed PRE in both the "ON" and "OFF" transcriptional states of engrailed. PLoS One. 2012;7(11):e48765. PMID: 23139817; PMC: PMC3490902
modENCODE fly RNA Figure 1, described in text

LeGault LH, Dewey CN. Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs. Bioinformatics. 2013 Sep 15;29(18):2300-10. PMID: 23846746; PMC: PMC3753571
ENCODE RNA, modENCODE Fly RNA, Table 1, S1; Methods development

Li G, Zhou L. Genome-wide identification of chromatin transitional regions reveals diverse mechanisms defining the boundary of facultative heterochromatin. PLoS One. 2013;8(6):e67156. PMID: 23840609; PMC: PMC3696093
modENCODE Fly TF CHIP, Fig 3

Li J, Waterhouse RM, Zdobnov EM. A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits. BMC Evol Biol. 2011 Nov 18;11:337. PMID: 22098672; PMC: PMC3240667
modENCODE fly RNA, Additional file 4

Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP. Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila. Nucleic Acids Res. 2013 Mar 1;41(5):2963-80. PMID: 23358822; PMCID: PMC3597698
modENCODE fly TF ChIP, histone modification ChIP, RNA

Lin CH, Paulson A, Abmayr SM, Workman JL. HP1a targets the Drosophila KDM4A demethylase to a subset of heterochromatic genes to regulate H3K36me3 levels. PLoS One. 2012;7(6):e39758. PMID: 22761891; PMC: PMC3384587
modENCODE fly histone modification ChIP, TF ChIP, Figure 2, 3, S1

MacDonald WA, Menon D, Bartlett NJ, Sperry GE, Rasheva V, Meller V, Lloyd VK. The Drosophila homolog of the mammalian imprint regulator, CTCF, maintains the maternal genomic imprint in Drosophila melanogaster. BMC Biol. 2010 Jul 30;8:105. PMID: 2067333; PMCID: PMC2922095
modENCODE fly TF ChIP

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)

Massouras A, Waszak SM, Albarca-Aguilera M, Hens K, Holcombe W, Ayroles JF, Dermitzakis ET, Stone EA, Jensen JD, Mackay TF et al. Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genet. 2012;8(11):e1003055. PMID: 23189034; PMC: PMC3499359
modENCODE fly histone modification ChIP, Figure S6, Table S12

Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen CY, Chou A, Ienasescu H et al. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2014 Jan;42(Database issue):D142-7. PMID: 24194598
ENCODE TF ChIP, mouse TF ChIP, fly TF ChIP, worm TF ChIP; methods development

Matilainen O, Arpalahti L, Rantanen V, Hautaniemi S, Holmberg CI. Insulin/IGF-1 signaling regulates proteasome activity through the deubiquitinating enzyme UBH-4. Cell Rep. 2013 Jun 27;3(6):1980-95. PMID: 23770237
modENCODE worm TF ChIP, Figure S4D

Matzat LH, Dale RK, Moshkovich N, Lei EP. Tissue-specific regulation of chromatin insulator function. PLoS Genet. 2012;8(11):e1003069. PMID: 23209434; PMC: PMC3510032
modENCODE fly TF ChIP, histone modification ChIP, Figure 6, S4; basic biology

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 RNA, TF ChIP, histone modification ChIP, DNA replication origins, Figure 1, 3, Table 2

Megraw M, Mukherjee S, Ohler U. Sustained-input switches for transcription factors and microRNAs are central building blocks of eukaryotic gene circuits. Genome Biol. 2013 Aug 23;14(8):R85. PMID: 23972209
ENCODE TF ChIP RNA network, modENCODE Fly TF ChIP RNA network, Figure 7; basic biology

Mikoláš P, Kollárová J, Sebková K, Saudek V, Yilma P, Kostrouchová M, Krause MW, Kostrouch Z, Kostrouchová M. GEI-8, a homologue of vertebrate nuclear receptor corepressor NCoR/SMRT, regulates gonad development and neuronal functions in Caenorhabditis elegans. PLoS One. 2013;8(3):e58462. PMID: 23484030; PMCID: PMC3590189
modENCODE worm RNA

Miller DL, Budde MW, Roth MB. HIF-1 and SKN-1 coordinate the transcriptional response to hydrogen sulfide in Caenorhabditis elegans. PLoS One. 2011;6(9):e25476. PMID: 21980473; PMCID: PMC3183046
modENCODE worm TF ChIP

Montgomery TA, Rim YS, Zhang C, Dowen RH, Phillips CM, Fischer SE, Ruvkun G. PIWI associated siRNAs and piRNAs specifically require the Caenorhabditis elegans HEN1 ortholog henn-1. PLoS Genet. 2012;8(4):e1002616. PMID: 22536158; PMC: PMC3334881
modENCODE worm RNA, Figure 4A

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

Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK, Lei EP. RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes Dev. 2011 Aug 15;25(16):1686-701. PMID: 21852534; PMCID: PMC3165934
modENCODE fly TF CHIP

Napoletano F, Occhi S, Calamita P, Volpi V, Blanc E, Charroux B, Royet J, Fanto M. Polyglutamine Atrophin provokes neurodegeneration in Drosophila by repressing fat. EMBO J. 2011 Mar 2;30(5):945-58. PMID: 21278706; PMCID: PMC3049215
modENCODE fly TF ChIP

Nien CY, Liang HL, Butcher S, Sun Y, Fu S, Gocha T, Kirov N, Manak JR, Rushlow C. Temporal coordination of gene networks by Zelda in the early Drosophila embryo. PLoS Genet. 2011 Oct;7(10):e1002339. PMID: 22028675; PMCID: PMC3197689
modENCODE fly TF ChIP

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

O'Brien RV, Davis RW, Khosla C, Hillenmeyer ME. Computational identification and analysis of orphan assembly-line polyketide synthases. J Antibiot (Tokyo). 2014 Jan;67(1):89-97. PMID: 24301183
modENCODE worm RNA

Ogata N, Yokoyama T, Iwabuchi K. Transcriptome responses of insect fat body cells to tissue culture environment. PLoS One. 2012;7(4):e34940. PMID: 22493724; PMC: PMC3321044
modENCODE fly RNA, Figure 4 and 5

Oortveld MA, Keerthikumar S, Oti M, Nijhof B, Fernandes AC, Kochinke K, Castells-Nobau A, van Engelen E, Ellenkamp T, Eshuis L et al. Human intellectual disability genes form conserved functional modules in Drosophila. PLoS Genet. 2013 Oct;9(10):e1003911. PMID: 24204314; PMC: PMC3814316
modENCODE fly RNA, Figure 6, S4

Paro S, Li X, O'Connell MA, Keegan LP. Regulation and functions of ADAR in drosophila. Curr Top Microbiol Immunol. 2012;353:221-36. PMID: 21761288
modENCODE fly RNA

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

Pennington KL, Marr SK, Chirn GW, Marr MT 2nd. Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription. Proc Natl Acad Sci U S A. 2013 May 7;110(19):7678-83. PMID: 23610421; PMCID: PMC3651496
modENCODE fly TF ChIP

Peters NC, Thayer NH, Kerr SA, Tompa M, Berg CA. Following the 'tracks': Tramtrack69 regulates epithelial tube expansion in the Drosophila ovary through Paxillin, Dynamin, and the homeobox protein Mirror. Dev Biol. 2013 Jun 15;378(2):154-69. PMID: 23545328
modENCODE fly TF ChIP

Philip P, Pettersson F, Stenberg P. Sequence signatures involved in targeting the Male-Specific Lethal complex to X-chromosomal genes in Drosophila melanogaster. BMC Genomics. 2012 Mar 19;13:97. PMID: 22424303; PMC: PMC3355045
modENCODE fly TF ChIP

Poelchau MF, Reynolds JA, Elsik CG, Denlinger DL, Armbruster PA. Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus. Proc Biol Sci. 2013 May 22;280(1759):20130143. PMID: 23516243; PMCID: PMC3619507
modENCODE fly RNA

Pruteanu-Malinici I, Mace DL, Ohler U. Automatic annotation of spatial expression patterns via sparse Bayesian factor models. PLoS Comput Biol. 2011 Jul;7(7):e1002098. PMID: 21814502; PMCID: PMC3140966
modENCODE fly TF CHIP, network

Rach EA, Winter DR, Benjamin AM, Corcoran DL, Ni T, Zhu J, Ohler U. Transcription initiation patterns indicate divergent strategies for gene regulation at the chromatin level. PLoS Genet. 2011 Jan 13;7(1):e1001274. PMID: 21249180; PMCID: PMC3020932
modENCODE fly TF ChIP, histone modification ChIP

Riedel CG, Dowen RH, Lourenco GF, Kirienko NV, Heimbucher T, West JA, Bowman SK, Kingston RE, Dillin A, Asara JM et al. DAF-16 employs the chromatin remodeller SWI/SNF to promote stress resistance and longevity. Nat Cell Biol. 2013 May;15(5):491-501. PMID: 23604319; PMCID: PMC3748955
modENCODE worm TF ChIP

Rodriguez J, Menet JS, Rosbash M. Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila. Mol Cell. 2012 Jul 13;47(1):27-37. PMID: 22658416; PMCID: PMC3409466
modENCODE fly editing data used, fig 3A, text

Rogers RL, Bedford T, Lyons AM, Hartl DL. Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10943-8. PMID: 20534482; PMCID: PMC2890713
modENCODE fly RNA

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

Ruths T, Nakhleh L. ncDNA and drift drive binding site accumulation. BMC Evol Biol. 2012 Aug 30;12:159. PMID: 22935101; PMC: PMC3556125
modENCODE fly TF ChIP, worm TF ChIP

Saito TL, Hashimoto S, Gu SG, Morton JJ, Stadler M, Blumenthal T, Fire A, Morishita S. The transcription start site landscape of C. elegans. Genome Res. 2013 Aug;23(8):1348-61. PMID: 23636945; PMCID: PMC3730108
modENCODE worm TF ChIP

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

Satija R, Bradley RK. The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo. Genome Res. 2012 Apr;22(4):656-65. PMID: 22247430; PMC: PMC3317148
modENCODE fly; DNase, DNA replication

Schauer T, Schwalie PC, Handley A, Margulies CE, Flicek P, Ladurner AG. CAST-ChIP maps cell-type-specific chromatin states in the Drosophila central nervous system. Cell Rep. 2013 Oct 17;5(1):271-82. PMID: 24095734
modENCODE fly histone modification ChIP, TF ChIP, Figure 7, S6, S7

Schmitt T, Ogris C, Sonnhammer EL. FunCoup 3.0: database of genome-wide functional coupling networks. Nucleic Acids Res. 2014 Jan;42(Database issue):D380-8. PMID: 24185702
ENCODE mouse TF ChIP, human TF ChIP, modENCODE fly TF ChIP, worm, TF ChIP, table 1, described in text; methods development

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

Sher N, Von Stetina JR, Bell GW, Matsuura S, Ravid K, Orr-Weaver TL. Fundamental differences in endoreplication in mammals and Drosophila revealed by analysis of endocycling and endomitotic cells. Proc Natl Acad Sci U S A. 2013 Jun 4;110(23):9368-73. PMID: 23613587; PMC: PMC3677442
modENCODE fly RNA, figure S5

Shibata Y, Sawa H, Nishiwaki K. HTZ-1/H2A.z and MYS-1/MYST HAT act redundantly to maintain cell fates in somatic gonadal cells through repression of ceh-22 in C. elegans. Development. 2014 Jan;141(1):209-18. PMID: 24346701
modENCODE worm, histone modification ChIP, Figure 5

Singari S, Javeed N, Tardi NJ, Marada S, Carlson JC, Kirk S, Thorn JM, Edwards KA. Inducible protein traps with dominant phenotypes for functional analysis of the Drosophila genome. Genetics. 2014 Jan;196(1):91-105. PMID: 24172131; PMC: PMC3872200
modENCODE Fly RNA, described in text

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

Suh J, Hutter H. A survey of putative secreted and transmembrane proteins encoded in the C. elegans genome. BMC Genomics. 2012 Jul 23;13:333. PMID: 22823938; PMC: PMC3534327
modENCODE worm RNA

Swaminathan A, Barnes VL, Fox S, Gammouh S, Pile LA. Identification of genetic suppressors of the Sin3A knockdown wing phenotype. PLoS One. 2012;7(11):e49563. PMID: 23166712; PMC: PMC3499482
modENCODE fly RNA

Tamburino AM, Ryder SP, Walhout AJ. A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels. G3 (Bethesda). 2013 Feb;3(2):297-304. PMID: 23390605; PMCID: PMC3564989
modENCODE worm TF ChIP, 3'UTR

Thiel K, Heier C, Haberl V, Thul PJ, Oberer M, Lass A, Jäckle H, Beller M. The evolutionarily conserved protein CG9186 is associated with lipid droplets, required for their positioning and for fat storage. J Cell Sci. 2013 May 15;126(Pt 10):2198-212. PMID: 23525007; PMC: PMC3880856
modENCODE, fly RNA

Van Nostrand EL, Sánchez-Blanco A, Wu B, Nguyen A, Kim SK. Roles of the developmental regulator unc-62/Homothorax in limiting longevity in Caenorhabditis elegans. PLoS Genet. 2013 Feb;9(2):e1003325. PMID: 23468654; PMCID: PMC3585033
modENCODE worm TF ChIP

van Oosten-Hawle P, Porter RS, Morimoto RI. Regulation of organismal proteostasis by transcellular chaperone signaling. Cell. 2013 Jun 6;153(6):1366-78. PMID: 23746847
modENCODE worm TF ChIP, decribed in text

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

Venables JP, Tazi J, Juge F. Regulated functional alternative splicing in Drosophila. Nucleic Acids Res. 2012 Jan;40(1):1-10. PMID: 21908400; PMCID: PMC3245913
modENCODE fly RNA

Villar-Garea A, Forne I, Vetter I, Kremmer E, Thomae A, Imhof A. Developmental regulation of N-terminal H2B methylation in Drosophila melanogaster. Nucleic Acids Res. 2012 Feb;40(4):1536-49. PMID: 22053083; PMCID: PMC3287205
modENCODE fly RNA

Vorobyeva NE, Mazina MU, Golovnin AK, Kopytova DV, Gurskiy DY, Nabirochkina EN, Georgieva SG, Georgiev PG, Krasnov AN. Insulator protein Su(Hw) recruits SAGA and Brahma complexes and constitutes part of Origin Recognition Complex-binding sites in the Drosophila genome. Nucleic Acids Res. 2013 Apr 22. PMID: 23609538; PMCID: PMC3287205
modENCODE fly TF ChIP

Vorobyeva NE, Nikolenko JV, Nabirochkina EN, Krasnov AN, Shidlovskii YV, Georgieva SG. SAYP and Brahma are important for 'repressive' and 'transient' Pol II pausing. Nucleic Acids Res. 2012 Aug;40(15):7319-31. PMID: 22638575; PMCID: PMC3424582
modENCODE fly TF ChIP

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

Wedeles CJ, Wu MZ, Claycomb JM. A multitasking Argonaute: exploring the many facets of C. elegans CSR-1. Chromosome Res. 2013 Dec;21(6-7):573-86. PMID: 24178449
modENCODE worm histone modification ChIP, Table 1

Wells MB, Snyder MJ, Custer LM, Csankovszki G. Caenorhabditis elegans dosage compensation regulates histone H4 chromatin state on X chromosomes. Mol Cell Biol. 2012 May;32(9):1710-9. PMID: 22393255; PMCID: PMC3347233
modENCODE worm histone modification ChIP, TF ChIP

Wilczynski B, Liu YH, Yeo ZX, Furlong EE. Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state. PLoS Comput Biol. 2012;8(12):e1002798. PMID: 23236268; PMC: PMC3516547
modENCODE fly histone modification ChIP, TF ChIP

Will S, Yu M, Berger B. Structure-based whole-genome realignment reveals many novel noncoding RNAs. Genome Res. 2013 Apr 8. PMID: 23296921; PMCID: PMC3668356
modENCODE fly RNA

Woo S, Cha SW, Merrihew G, He Y, Castellana N, Guest C, MacCoss M, Bafna V. Proteogenomic database construction driven from large scale RNA-seq data. J Proteome Res. 2014 Jan 3;13(1):21-8. PMID: 23802565
modENCODE worm RNA

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

Xu X, Kim SK. The GATA transcription factor egl-27 delays aging by promoting stress resistance in Caenorhabditis elegans. PLoS Genet. 2012;8(12):e1003108. PMID: 23271974; PMC: PMC3521710
modENCODE worm TF ChIP

Yan B, Memar N, Gallinger J, Conradt B. Coordination of cell proliferation and cell fate determination by CES-1 snail. PLoS Genet. 2013 Oct;9(10):e1003884. PMID: 24204299; PMC: PMC3814331
modENCODE worm TF ChIP, Figure 5

Yang J, Ramos E, Corces VG. The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species. Genome Res. 2012 Nov;22(11):2199-207. PMID: 22895281; PMCID: PMC3483549
modENCODE fly RNA, TF ChIP, Histone modification ChIP

Yang JH, Li JH, Jiang S, Zhou H, Qu LH. ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res. 2013 Jan;41(Database issue):D177-87. PMID: 23161675; PMCID: PMC3531181
modENCODE worm TF CHIP, modENCODE fly TF ChIP

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

Zelle KM, Lu B, Pyfrom SC, Ben-Shahar Y. The genetic architecture of degenerin/epithelial sodium channels in Drosophila. G3 (Bethesda). 2013 Mar;3(3):441-50. PMID: 23449991; PMCID: PMC3583452
modENCODE fly RNA

Zhang YW, Arnosti DN. Conserved catalytic and C-terminal regulatory domains of the C-terminal binding protein corepressor fine-tune the transcriptional response in development. Mol Cell Biol. 2011 Jan;31(2):375-84. PMID: 21078873; PMCID: PMC3019976
modENCODE fly TF ChIP

Zhao G, Ihuegbu N, Lee M, Schriefer L, Wang T, Stormo GD. Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans. G3 (Bethesda). 2012 Apr;2(4):469-81. PMID: 22540038; PMCID: PMC3337475
modENCODE worm TF ChIP