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ENCODE Project at NHGRI ENCODE-funded Publications

Contents

Updated 12 March 2014

ENCODE Consortium publications

ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13;13(8):418.

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

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

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

ENCODE publications (316)

2014

Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B et al. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res. 2014 Jan;42(Database issue):D865-72. PMID: 24217909

Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S et al. Ensembl 2014. Nucleic Acids Res. 2014 Jan;42(Database issue):D749-55. PMID: 24316576

Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S et al. The Vertebrate Genome Annotation browser 10 years on. Nucleic Acids Res. 2014 Jan;42(Database issue):D771-9. PMID: 24316575

Marinov GK, Wang YE, Chan D, Wold BJ. Evidence for site-specific occupancy of the mitochondrial genome by nuclear transcription factors. PLoS One. 2014;9(1):e84713. PMID: 24465428; PMC: PMC3896368

Marinov GK, Williams BA, McCue K, Schroth GP, Gertz J, Myers RM, Wold BJ. From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing. Genome Res. 2014 Mar;24(3):496-510. PMID: 24299736

Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN. The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation. BMC Genomics. 2014 Feb 1;15:92. PMID: 24484546; PMC: PMC3928079

Ozel AB, Moroi SE, Reed DM, Nika M, Schmidt CM, Akbari S, Scott K, Rozsa F, Pawar H, Musch DC et al. Genome-wide association study and meta-analysis of intraocular pressure. Hum Genet. 2014 Jan;133(1):41-57. PMID: 24002674

2013

Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R et al. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013 Oct 25;342(6157):1241006. PMID: 24159046

Au KF, Sebastiano V, Afshar PT, Durruthy JD, Lee L, Williams BA, van Bakel H, Schadt EE, Reijo-Pera RA, Underwood JG et al. Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):E4821-30. PMID: 24282307; PMC: PMC3864310

Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L et al. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science. 2013 Oct 11;342(6155):253-7. PMID: 24115442

Blattler A, Farnham PJ. Cross-talk between site-specific transcription factors and DNA methylation states. J Biol Chem. 2013 Nov 29;288(48):34287-94. PMID: 24151070; PMC: PMC3843044

Blobel GA, Hardison RC. A cluster to remember. Cell. 2013 Aug 15;154(4):718-20. PMID: 23953105; PMC: PMC3878159

Bolisetty MT, Graveley BR. Circuitous route to transcription regulation. Mol Cell. 2013 Sep 26;51(6):705-6. PMID: 24074951; PMC: PMC3839245

Braunschweig U, Gueroussov S, Plocik AM, Graveley BR, Blencowe BJ. Dynamic integration of splicing within gene regulatory pathways. Cell. 2013 Mar 14;152(6):1252-69. PMID: 23498935; PMC: PMC3642998

Chan CS, Jungreis I, Kellis M. Heterologous stop codon readthrough of metazoan readthrough candidates in yeast. PLoS One. 2013;8(3):e59450. PMID: 23544069; PMC: PMC3609751

Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keleş S. dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP- Seq data. PLoS Comput Biol. 2013;9(10):e1003246. PMID: 24146601; PMC: PMC3798280

Dickel DE, Visel A, Pennacchio LA. Functional anatomy of distant-acting mammalian enhancers. Philos Trans R Soc Lond B Biol Sci. 2013;368(1620):20120359. PMID: 23650633; PMC: PMC3682724

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013 Jan 1;29(1):15-21. PMID: 23104886; PMC: PMC3530905

Dong X, Weng Z. The correlation between histone modifications and gene expression. Epigenomics. 2013 Apr;5(2):113-6. PMID: 23566087

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, RGASP Consortium, Alioto T, Behr J, Bertone P, Bohnert R et al. Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods. 2013 Dec;10(12):1185-91. PMID: 24185836

Feizi S, Marbach D, Médard M, Kellis M. Network deconvolution as a general method to distinguish direct dependencies in networks. Nat Biotechnol. 2013 Aug;31(8):726-33. PMID: 23851448; PMC: PMC3773370

Fleming JD, Pavesi G, Benatti P, Imbriano C, Mantovani R, Struhl K. NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors. Genome Res. 2013 Aug;23(8):1195-209. PMID: 23595228; PMC: PMC3730095

Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S et al. Ensembl 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55. PMID: 23203987; PMC: PMC3531136

Foley JW, Sidow A. Transcription-factor occupancy at HOT regions quantitatively predicts RNA polymerase recruitment in five human cell lines. BMC Genomics. 2013 Oct 20;14:720. PMID: 24138567; PMC: PMC3826616

Gao X, Johnson KD, Chang YI, Boyer ME, Dewey CN, Zhang J, Bresnick EH. Gata2 cis-element is required for hematopoietic stem cell generation in the mammalian embryo. J Exp Med. 2013 Dec 16;210(13):2833-42. PMID: 24297994; PMC: PMC3865483

Gertz J, Savic D, Varley KE, Partridge EC, Safi A, Jain P, Cooper GM, Reddy TE, Crawford GE, Myers RM. Distinct properties of cell-type-specific and shared transcription factor binding sites. Mol Cell. 2013 Oct 10;52(1):25-36. PMID: 24076218; PMC: PMC3811135

Gibcus JH, Dekker J. The hierarchy of the 3D genome. Mol Cell. 2013 Mar 7;49(5):773-82. PMID: 23473598; PMC: PMC3741673

Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol. 2013 Jul 1;14(7):R70. PMID: 23815980

Hardee J, Ouyang Z, Zhang Y, Kundaje A, Lacroute P, Snyder M. STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma. G3 (Bethesda). 2013 Dec 9;3(12):2173-85. PMID: 24142927; PMC: PMC3852380

Hardison RC, Blobel GA. Genetics. GWAS to therapy by genome edits?. Science. 2013 Oct 11;342(6155):206-7. PMID: 24115432

He HH, Meyer CA, Hu SS, Chen MW, Zang C, Liu Y, Rao PK, Fei T, Xu H, Long H et al. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods. 2014 Jan;11(1):73-8. PMID: 24317252

Hickey G, Paten B, Earl D, Zerbino D, Haussler D. HAL: a hierarchical format for storing and analyzing multiple genome alignments. Bioinformatics. 2013 May 15;29(10):1341-2. PMID: 23505295; PMC: PMC3654707

Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 2013 Jan;41(2):827-41. PMID: 23221638; PMC: PMC3553955

Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet. 2013 Oct;45(10):1198-206. PMID: 23995138

Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol. 2013;9(1):e1002893. PMID: 23382666; PMC: PMC3561073

John S, Sabo PJ, Canfield TK, Lee K, Vong S, Weaver M, Wang H, Vierstra J, Reynolds AP, Thurman RE et al. Genome-scale mapping of DNase I hypersensitivity. Curr Protoc Mol Biol. 2013 Jul;Chapter 27:Unit 21.27. PMID: 23821440

Kheradpour P, Kellis M. Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res. 2014 Mar 1;42(5):2976-87. PMID: 24335146; PMC: PMC3950668

Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A et al. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science. 2013 Oct 4;342(6154):1235587. PMID: 24092746; PMC: PMC3947637

Kuhn RM, Haussler D, Kent WJ. The UCSC genome browser and associated tools. Brief Bioinform. 2013 Mar;14(2):144-61. PMID: 22908213; PMC: PMC3603215

Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA et al. Probing DNA shape and methylation state on a genomic scale with DNase I. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6376-81. PMID: 23576721; PMC: PMC3631675

Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, Hur JK, Aravin AA, Tóth KF. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev. 2013 Feb 15;27(4):390-9. PMID: 23392610; PMC: PMC3589556

Lee JH, Ang JK, Xiao X. Analysis and design of RNA sequencing experiments for identifying RNA editing and other single- nucleotide variants. RNA. 2013 Jun;19(6):725-32. PMID: 23598527; PMC: PMC3683905

Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S et al. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol. 2013 Dec;20(12):1434-42. PMID: 24213538; PMC: PMC3918504

Marinov GK, Kundaje A, Park PJ, Wold BJ. Large-Scale Quality Analysis of Published ChIP-seq Data. G3 (Bethesda). 2014 Feb 19;4(2):209-23. PMID: 24347632; PMC: PMC3931556

McVicker G, van de Geijn B, Degner JF, Cain CE, Banovich NE, Raj A, Lewellen N, Myrthil M, Gilad Y, Pritchard JK. Identification of genetic variants that affect histone modifications in human cells. Science. 2013 Nov 8;342(6159):747-9. PMID: 24136359; PMC: PMC3947669

Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE. Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol. 2013 Dec;31(12):1133-6. PMID: 24013198; PMC: PMC3858395

Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS et al. DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements. Nat Genet. 2013 Aug;45(8):852-9. PMID: 23793028

Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013 Jan;41(Database issue):D64-9. PMID: 23155063; PMC: PMC3531082

Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ. Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. Genome Res. 2013 Dec;23(12):2136-48. PMID: 24170599; PMC: PMC3847782

Mudge JM, Frankish A, Harrow J. Functional transcriptomics in the post-ENCODE era. Genome Res. 2013 Dec;23(12):1961-73. PMID: 24172201; PMC: PMC3847767

Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nat Rev Genet. 2013 Apr;14(4):288-95. PMID: 23503198

Perez-Pinera P, Kocak DD, Vockley CM, Adler AF, Kabadi AM, Polstein LR, Thakore PI, Glass KA, Ousterout DG, Leong KW et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods. 2013 Oct;10(10):973-6. PMID: 23892895; PMC: PMC3911785

Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, Gersbach CA. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat Methods. 2013 Mar;10(3):239-42. PMID: 23377379; PMC: PMC3719416

Plocik AM, Graveley BR. New insights from existing sequence data: generating breakthroughs without a pipette. Mol Cell. 2013 Feb 21;49(4):605-17. PMID: 23438857; PMC: PMC3590807

Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA et al. Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair. Nat Biotechnol. 2014 Jan;32(1):71-5. PMID: 24336318

Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN et al. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Cell Rep. 2013 May 30;3(5):1567-79. PMID: 23707066; PMC: PMC3774301

Risk BA, Edwards NJ, Giddings MC. A peptide-spectrum scoring system based on ion alignment, intensity, and pair probabilities. J Proteome Res. 2013 Sep 6;12(9):4240-7. PMID: 23875887

Risk BA, Spitzer WJ, Giddings MC. Peppy: proteogenomic search software. J Proteome Res. 2013 Jun 7;12(6):3019-25. PMID: 23614390

Rivera CM, Ren B. Mapping human epigenomes. Cell. 2013 Sep 26;155(1):39-55. PMID: 24074860; PMC: PMC3838898

Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML. APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res. 2013 Jan;41(Database issue):D110-7. PMID: 23161672; PMC: PMC3531113

Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG et al. ENCODE data in the UCSC Genome Browser: year 5 update. Nucleic Acids Res. 2013 Jan;41(Database issue):D56-63. PMID: 23193274; PMC: PMC3531152

Sanchez-Castro M, Gordon CT, Petit F, Nord AS, Callier P, Andrieux J, Guérin P, Pichon O, David A, Abadie V et al. Congenital heart defects in patients with deletions upstream of SOX9. Hum Mutat. 2013 Dec;34(12):1628-31. PMID: 24115316

Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR et al. In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acids Res. 2013 Oct;41(19):e181. PMID: 23945932; PMC: PMC3799455

Savic D, Gertz J, Jain P, Cooper GM, Myers RM. Mapping genome-wide transcription factor binding sites in frozen tissues. Epigenetics Chromatin. 2013 Sep 16;6(1):30. PMID: 24279905; PMC: PMC3848595

Schjerven H, McLaughlin J, Arenzana TL, Frietze S, Cheng D, Wadsworth SE, Lawson GW, Bensinger SJ, Farnham PJ, Witte ON et al. Selective regulation of lymphopoiesis and leukemogenesis by individual zinc fingers of Ikaros. Nat Immunol. 2013 Oct;14(10):1073-83. PMID: 24013668; PMC: PMC3800053

Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E. De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements. Genome Res. 2013 Oct;23(10):1601-14. PMID: 23811145; PMC: PMC3787258

Sheffield NC, Thurman RE, Song L, Safi A, Stamatoyannopoulos JA, Lenhard B, Crawford GE, Furey TS. Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res. 2013 May;23(5):777-88. PMID: 23482648; PMC: PMC3638134

Smallwood A, Ren B. Genome organization and long-range regulation of gene expression by enhancers. Curr Opin Cell Biol. 2013 Jun;25(3):387-94. PMID: 23465541

Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE et al. Assessment of transcript reconstruction methods for RNA-seq. Nat Methods. 2013 Dec;10(12):1177-84. PMID: 24185837; PMC: PMC3851240

Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM et al. Exonic transcription factor binding directs codon choice and affects protein evolution. Science. 2013 Dec 13;342(6164):1367-72. PMID: 24337295

Stergachis AB, Neph S, Reynolds A, Humbert R, Miller B, Paige SL, Vernot B, Cheng JB, Thurman RE, Sandstrom R et al. Developmental fate and cellular maturity encoded in human regulatory DNA landscapes. Cell. 2013 Aug 15;154(4):888-903. PMID: 23953118

Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M. Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda). 2013 Mar;3(3):387-97. PMID: 23450794; PMC: PMC3583448

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; PMC: PMC3826950

Tsumagari K, Baribault C, Terragni J, Varley KE, Gertz J, Pradhan S, Badoo M, Crain CM, Song L, Crawford GE et al. Early de novo DNA methylation and prolonged demethylation in the muscle lineage. Epigenetics. 2013 Mar;8(3):317-32. PMID: 23417056; PMC: PMC3669123

Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013 Mar;23(3):555-67. PMID: 23325432; PMC: PMC3589544

Vierstra J, Wang H, John S, Sandstrom R, Stamatoyannopoulos JA. Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH. Nat Methods. 2014 Jan;11(1):66-72. PMID: 24185839

Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D et al. Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. PMID: 23203885; PMC: PMC3531197

Wang S, Sun H, Ma J, Zang C, Wang C, Wang J, Tang Q, Meyer CA, Zhang Y, Liu XS. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc. 2013 Dec;8(12):2502-15. PMID: 24263090

Wang Y, Xiao X, Zhang J, Choudhury R, Robertson A, Li K, Ma M, Burge CB, Wang Z. A complex network of factors with overlapping affinities represses splicing through intronic elements. Nat Struct Mol Biol. 2013 Jan;20(1):36-45. PMID: 23241926; PMC: PMC3537874

Wang YE, Marinov GK, Wold BJ, Chan DC. Genome-wide analysis reveals coating of the mitochondrial genome by TFAM. PLoS One. 2013;8(8):e74513. PMID: 23991223; PMC: PMC3753274

Winter DR, Song L, Mukherjee S, Furey TS, Crawford GE. DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types. Genome Res. 2013 Jul;23(7):1118-29. PMID: 23657885; PMC: PMC3698505

Xie D, Boyle AP, Wu L, Zhai J, Kawli T, Snyder M. Dynamic trans-acting factor colocalization in human cells. Cell. 2013 Oct 24;155(3):713-24. PMID: 24243024

Yang F, Nickols NG, Li BC, Marinov GK, Said JW, Dervan PB. Antitumor activity of a pyrrole-imidazole polyamide. Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1863-8. PMID: 23319609; PMC: PMC3562772

Zhang Y, Schulz VP, Reed BD, Wang Z, Pan X, Mariani J, Euskirchen G, Snyder MP, Vaccarino FM, Ivanova N et al. Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration. Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12361-6. PMID: 23836664; PMC: PMC3725080

Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013 Dec 12;504(7479):306-10. PMID: 24213634

Zheng R, Rebolledo-Jaramillo B, Zong Y, Wang L, Russo P, Hancock W, Stanger BZ, Hardison RC, Blobel GA. Function of GATA Factors in the Adult Mouse Liver. PLoS One. 2013;8(12):e83723. PMID: 24367609; PMC: PMC3867416

Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013 Jan 31;152(3):642-54. PMID: 23333102; PMC: PMC3563935

2012

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65. PMID: 23128226; PMC: PMC3498066

Arvey A, Agius P, Noble WS, Leslie C. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res. 2012 Sep;22(9):1723-34. PMID: 22955984; PMC: PMC3431489

Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE Jr, Kundaje A, Gunawardena HP, Yu Y, Xie L et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Res. 2012 Sep;22(9):1646-57. PMID: 22955977; PMC: PMC3431482

Barber MF, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K et al. SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature. 2012 Jul 5;487(7405):114-8. PMID: 22722849; PMC: PMC3412143

Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012 Sep;22(9):1790-7. PMID: 22955989; PMC: PMC3431494

Charos AE, Reed BD, Raha D, Szekely AM, Weissman SM, Snyder M. A highly integrated and complex PPARGC1A transcription factor binding network in HepG2 cells. Genome Res. 2012 Sep;22(9):1668-79. PMID: 22955979; PMC: PMC3431484

Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell. 2012 Mar 16;148(6):1293-307. PMID: 22424236; PMC: PMC3341616

Chen R, Snyder M. Systems biology: personalized medicine for the future?. Curr Opin Pharmacol. 2012 Oct;12(5):623-8. PMID: 22858243

Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y et al. Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res. 2012 Sep;22(9):1658-67. PMID: 22955978; PMC: PMC3431483

Chou ST, Byrska-Bishop M, Tober JM, Yao Y, Vandorn D, Opalinska JB, Mills JA, Choi JK, Speck NA, Gadue P et al. Trisomy 21-associated defects in human primitive hematopoiesis revealed through induced pluripotent stem cells. Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17573-8. PMID: 23045704; PMC: PMC3491490

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012 Sep;22(9):1775-89. PMID: 22955988; PMC: PMC3431493

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012 Apr 11;485(7398):376-80. PMID: 22495300; PMC: PMC3356448

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F et al. Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8. PMID: 22955620; PMC: PMC3684276

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Kowalczyk MS, Higgs DR, Gingeras TR. Molecular biology: RNA discrimination. Nature. 2012 Feb 15;482(7385):310-1. PMID: 22337043

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Lee BK, Bhinge AA, Battenhouse A, McDaniell RM, Liu Z, Song L, Ni Y, Birney E, Lieb JD, Furey TS et al. Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells. Genome Res. 2012 Jan;22(1):9-24. PMID: 22090374; PMC: PMC3246210

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Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 2012 Sep 6;489(7414):83-90. PMID: 22955618; PMC: PMC3736582

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Onodera CS, Underwood JG, Katzman S, Jacobs F, Greenberg D, Salama SR, Haussler D. Gene isoform specificity through enhancer-associated antisense transcription. PLoS One. 2012;7(8):e43511. PMID: 22937057; PMC: PMC3427357

Paige SL, Thomas S, Stoick-Cooper CL, Wang H, Maves L, Sandstrom R, Pabon L, Reinecke H, Pratt G, Keller G et al. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell. 2012 Sep 28;151(1):221-32. PMID: 22981225; PMC: PMC3462257

Park E, Williams B, Wold BJ, Mortazavi A. RNA editing in the human ENCODE RNA-seq data. Genome Res. 2012 Sep;22(9):1626-33. PMID: 22955975; PMC: PMC3431480

Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M et al. The GENCODE pseudogene resource. Genome Biol. 2012 Sep 26;13(9):R51. PMID: 22951037; PMC: PMC3491395

Reddy TE, Gertz J, Crawford GE, Garabedian MJ, Myers RM. The hypersensitive glucocorticoid response specifically regulates period 1 and expression of circadian genes. Mol Cell Biol. 2012 Sep;32(18):3756-67. PMID: 22801371; PMC: PMC3430195

Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L et al. Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res. 2012 May;22(5):860-9. PMID: 22300769; PMC: PMC3337432

Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H et al. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 2012 Jan;40(Database issue):D912-7. PMID: 22075998; PMC: PMC3245183

Sandhu KS, Li G, Poh HM, Quek YL, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F et al. Large-scale functional organization of long-range chromatin interaction networks. Cell Rep. 2012 Nov 29;2(5):1207-19. PMID: 23103170

Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012 Sep 6;489(7414):109-13. PMID: 22955621; PMC: PMC3555147

Saxena A, Wagatsuma A, Noro Y, Kuji T, Asaka-Oba A, Watahiki A, Gurnot C, Fagiolini M, Hensch TK, Carninci P. Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain. Biotechniques. 2012 Jun;52(6):381-5. PMID: 22668417; PMC: PMC3696583

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Schulz MH, Zerbino DR, Vingron M, Birney E. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012 Apr 15;28(8):1086-92. PMID: 22368243; PMC: PMC3324515

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Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nat Protoc. 2012 Jan 19;7(2):256-67. PMID: 22262007; PMC: PMC3784247

Simpson NE, Gertz J, Imberg K, Myers RM, Garabedian MJ. Research resource: enhanced genome-wide occupancy of estrogen receptor α by the cochaperone p23 in breast cancer cells. Mol Endocrinol. 2012 Jan;26(1):194-202. PMID: 22074947; PMC: PMC3248325

Spivakov M, Akhtar J, Kheradpour P, Beal K, Girardot C, Koscielny G, Herrero J, Kellis M, Furlong EE, Birney E. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome Biol. 2012 Sep 28;13(9):R49. PMID: 22950968; PMC: PMC3491393

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Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13;13(8):418. PMID: 22889292; PMC: PMC3491367

Takahashi H, Kato S, Murata M, Carninci P. CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Methods Mol Biol. 2012;786:181-200. PMID: 21938627

Takahashi H, Lassmann T, Murata M, Carninci P. 5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc. 2012 Feb 23;7(3):542-61. PMID: 22362160

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B et al. The accessible chromatin landscape of the human genome. Nature. 2012 Sep 6;489(7414):75-82. PMID: 22955617; PMC: PMC3721348

Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 2012 Sep;22(9):1616-25. PMID: 22955974; PMC: PMC3431479

Vernot B, Stergachis AB, Maurano MT, Vierstra J, Neph S, Thurman RE, Stamatoyannopoulos JA, Akey JM. Personal and population genomics of human regulatory variation. Genome Res. 2012 Sep;22(9):1689-97. PMID: 22955981; PMC: PMC3431486

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Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012 Jan;40(Database issue):D930-4. PMID: 22064851; PMC: PMC3245002

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Blahnik KR, Dou L, Echipare L, Iyengar S, O'Geen H, Sanchez E, Zhao Y, Marra MA, Hirst M, Costello JF et al. Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes. PLoS One. 2011 Feb 15;6(2):e17121. PMID: 21347206; PMC: PMC3039671

Boyle AP, Song L, Lee BK, London D, Keefe D, Birney E, Iyer VR, Crawford GE, Furey TS. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 2011 Mar;21(3):456-64. PMID: 21106903; PMC: PMC3044859

Buske OJ, Hoffman MM, Ponts N, Le Roch KG, Noble WS. Exploratory analysis of genomic segmentations with Segtools. BMC Bioinformatics. 2011 Oct 26;12:415. PMID: 22029426; PMC: PMC3224787

Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ. Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome. J Biol Chem. 2011 Apr 8;286(14):11985-96. PMID: 21310950; PMC: PMC3069401

Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A et al. The reality of pervasive transcription. PLoS Biol. 2011 Jul;9(7):e1000625; discussion e1001102. PMID: 21765801; PMC: PMC3134446

Cline MS, Karchin R. Using bioinformatics to predict the functional impact of SNVs. Bioinformatics. 2011 Feb 15;27(4):441-8. PMID: 21159622; PMC: PMC3105482

Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S et al. The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet. 2011 Jul;19(7):827-31. PMID: 21364695; PMC: PMC3137498

Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR et al. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011 Oct 23;43(12):1179-85. PMID: 22019781; PMC: PMC3576853

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res. 2011 Dec;21(12):2224-41. PMID: 21926179; PMC: PMC3227110

Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M et al. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 5;473(7345):43-9. PMID: 21441907; PMC: PMC3088773

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. PMID: 20959295; PMC: PMC3242726

George AD, Tenenbaum SA. Web-based tools for studying RNA structure and function. Methods Mol Biol. 2011;703:67-86. PMID: 21125484

Gertz J, Varley KE, Reddy TE, Bowling KM, Pauli F, Parker SL, Kucera KS, Willard HF, Myers RM. Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation. PLoS Genet. 2011 Aug;7(8):e1002228. PMID: 21852959; PMC: PMC3154961

Giardine B, Borg J, Higgs DR, Peterson KR, Philipsen S, Maglott D, Singleton BK, Anstee DJ, Basak AN, Clark B et al. Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach. Nat Genet. 2011 Mar 20;43(4):295-301. PMID: 21423179; PMC: PMC3878152

Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet. 2011 Jun 19;43(7):630-8. PMID: 21685913; PMC: PMC3436933

Hubisz MJ, Lin MF, Kellis M, Siepel A. Error and error mitigation in low-coverage genome assemblies. PLoS One. 2011 Feb 14;6(2):e17034. PMID: 21340033; PMC: PMC3038916

Iyengar S, Farnham PJ. KAP1 protein: an enigmatic master regulator of the genome. J Biol Chem. 2011 Jul 29;286(30):26267-76. PMID: 21652716; PMC: PMC3143589

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Jain R, Devine T, George AD, Chittur SV, Baroni TE, Penalva LO, Tenenbaum SA. RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling. Methods Mol Biol. 2011;703:247-63. PMID: 21125495

Jiang L, Schlesinger F, Davis CA, Zhang Y, Li R, Salit M, Gingeras TR, Oliver B. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 2011 Sep;21(9):1543-51. PMID: 21816910; PMC: PMC3166838

Karczewski KJ, Tatonetti NP, Landt SG, Yang X, Slifer T, Altman RB, Snyder M. Cooperative transcription factor associations discovered using regulatory variation. Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):13353-8. PMID: 21828005; PMC: PMC3156166

Kellermayer R, Dowd SE, Harris RA, Balasa A, Schaible TD, Wolcott RD, Tatevian N, Szigeti R, Li Z, Versalovic J et al. Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice. FASEB J. 2011 May;25(5):1449-60. PMID: 21228220; PMC: PMC3079304

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature. 2011 Mar 24;471(7339):480-5. PMID: 21179089; PMC: PMC3109908

Kucera KS, Reddy TE, Pauli F, Gertz J, Logan JE, Myers RM, Willard HF. Allele-specific distribution of RNA polymerase II on female X chromosomes. Hum Mol Genet. 2011 Oct 15;20(20):3964-73. PMID: 21791549; PMC: PMC3177651

Lamonica JM, Deng W, Kadauke S, Campbell AE, Gamsjaeger R, Wang H, Cheng Y, Billin AN, Hardison RC, Mackay JP et al. Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes. Proc Natl Acad Sci U S A. 2011 May 31;108(22):E159-68. PMID: 21536911; PMC: PMC3107332

Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ. Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation. Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):19867-72. PMID: 22135461; PMC: PMC3250192

Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics. 2011 Jul 1;27(13):i275-82. PMID: 21685081; PMC: PMC3117341

Lin MF, Kheradpour P, Washietl S, Parker BJ, Pedersen JS, Kellis M. Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res. 2011 Nov;21(11):1916-28. PMID: 21994248; PMC: PMC3205576

Linnemann AK, O'Geen H, Keles S, Farnham PJ, Bresnick EH. Genetic framework for GATA factor function in vascular biology. Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13641-6. PMID: 21808000; PMC: PMC3158141

Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, Salama SR, Kingsley DM, Lindblad-Toh K, Haussler D. Three periods of regulatory innovation during vertebrate evolution. Science. 2011 Aug 19;333(6045):1019-24. PMID: 21852499; PMC: PMC3511857

Mercer TR, Neph S, Dinger ME, Crawford J, Smith MA, Shearwood AM, Haugen E, Bracken CP, Rackham O, Stamatoyannopoulos JA et al. The human mitochondrial transcriptome. Cell. 2011 Aug 19;146(4):645-58. PMID: 21854988; PMC: PMC3160626

Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T, Harrow J. The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol. 2011 Oct;28(10):2949-59. PMID: 21551269; PMC: PMC3176834

Ozdemir A, Fisher-Aylor KI, Pepke S, Samanta M, Dunipace L, McCue K, Zeng L, Ogawa N, Wold BJ, Stathopoulos A. High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation. Genome Res. 2011 Apr;21(4):566-77. PMID: 21383317; PMC: PMC3065704

Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D. Cactus: Algorithms for genome multiple sequence alignment. Genome Res. 2011 Sep;21(9):1512-28. PMID: 21665927; PMC: PMC3166836

Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, Anderson SM, NISC Comparative Sequencing Center, Mullikin JC, Gallagher PG et al. Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. Blood. 2011 Oct 27;118(17):e139-48. PMID: 21900194; PMC: PMC3208289

Ponting CP, Hardison RC. What fraction of the human genome is functional?. Genome Res. 2011 Nov;21(11):1769-76. PMID: 21875934; PMC: PMC3205562

Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23;147(7):1628-39. PMID: 22196736; PMC: PMC3312319

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM et al. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2011 Jan;39(Database issue):D871-5. PMID: 21037257; PMC: PMC3013645

Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD. ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biol. 2011 Jul 25;12(7):R67. PMID: 21787385; PMC: PMC3218829

Salimullah M, Sakai M, Plessy C, Carninci P. NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harb Protoc. 2011 Jan 1;2011(1):pdb.prot5559. PMID: 21205859

Saxena A, Carninci P. Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays. 2011 Nov;33(11):830-9. PMID: 21915889; PMC: PMC3258546

Saxena A, Carninci P. Whole transcriptome analysis: what are we still missing?. Wiley Interdiscip Rev Syst Biol Med. 2011 Sep-Oct;3(5):527-43. PMID: 21197667

Schaible TD, Harris RA, Dowd SE, Smith CW, Kellermayer R. Maternal methyl-donor supplementation induces prolonged murine offspring colitis susceptibility in association with mucosal epigenetic and microbiomic changes. Hum Mol Genet. 2011 May 1;20(9):1687-96. PMID: 21296867; PMC: PMC3115577

Singh Sandhu K, Li G, Sung WK, Ruan Y. Chromatin interaction networks and higher order architectures of eukaryotic genomes. J Cell Biochem. 2011 Sep;112(9):2218-21. PMID: 21520242

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D et al. Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 2011 Oct;21(10):1757-67. PMID: 21750106; PMC: PMC3202292

Spudich GM, Fernández-Suárez XM. Disease and phenotype data at Ensembl. Curr Protoc Hum Genet. 2011 Apr;Chapter 6:Unit 6.11. PMID: 21400687; PMC: PMC3099348

Stergachis AB, MacLean B, Lee K, Stamatoyannopoulos JA, MacCoss MJ. Rapid empirical discovery of optimal peptides for targeted proteomics. Nat Methods. 2011 Nov 6;8(12):1041-3. PMID: 22056677; PMC: PMC3227787

Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res. 2011 Nov;21(11):1833-40. PMID: 21957152; PMC: PMC3205568

Trojer P, Cao AR, Gao Z, Li Y, Zhang J, Xu X, Li G, Losson R, Erdjument-Bromage H, Tempst P et al. L3MBTL2 protein acts in concert with PcG protein-mediated monoubiquitination of H2A to establish a repressive chromatin structure. Mol Cell. 2011 May 20;42(4):438-50. PMID: 21596310; PMC: PMC3142354

Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells. Nature. 2011 May 22;474(7352):516-20. PMID: 21602827; PMC: PMC3212987

Wang H, Zou J, Zhao B, Johannsen E, Ashworth T, Wong H, Pear WS, Schug J, Blacklow SC, Arnett KL et al. Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14908-13. PMID: 21737748; PMC: PMC3169118

Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 2011 Oct;21(10):1659-71. PMID: 21795386; PMC: PMC3202283

Zhao B, Zou J, Wang H, Johannsen E, Peng CW, Quackenbush J, Mar JC, Morton CC, Freedman ML, Blacklow SC et al. Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14902-7. PMID: 21746931; PMC: PMC3169132

2010

1000 Genomes Project Consortium, Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73. PMID: 20981092; PMC: PMC3042601

Adli M, Zhu J, Bernstein BE. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat Methods. 2010 Aug;7(8):615-8. PMID: 20622861; PMC: PMC2924612

Aiden AP, Rivera MN, Rheinbay E, Ku M, Coffman EJ, Truong TT, Vargas SO, Lander ES, Haber DA, Bernstein BE. Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Cell Stem Cell. 2010 Jun 4;6(6):591-602. PMID: 20569696; PMC: PMC2897075

Birney E, Lieb JD, Furey TS, Crawford GE, Iyer VR. Allele-specific and heritable chromatin signatures in humans. Hum Mol Genet. 2010 Oct 15;19(R2):R204-9. PMID: 20846943; PMC: PMC2953746

Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludäscher B, Korf I et al. Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP- seq data. Nucleic Acids Res. 2010 Jan;38(3):e13. PMID: 19906703; PMC: PMC2817454

Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS. A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data. Bioinformatics. 2010 Jun 15;26(12):i334-42. PMID: 20529925; PMC: PMC2881360

Ernst J, Kellis M. Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol. 2010 Aug;28(8):817-25. PMID: 20657582; PMC: PMC2919626

Frietze S, Lan X, Jin VX, Farnham PJ. Genomic targets of the KRAB and SCAN domain-containing zinc finger protein 263. J Biol Chem. 2010 Jan 8;285(2):1393-403. PMID: 19887448; PMC: PMC2801265

Frietze S, O'Geen H, Blahnik KR, Jin VX, Farnham PJ. ZNF274 recruits the histone methyltransferase SETDB1 to the 3' ends of ZNF genes. PLoS One. 2010 Dec 8;5(12):e15082. PMID: 21170338; PMC: PMC2999557

Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, Secchi A, Bosco D et al. A map of open chromatin in human pancreatic islets. Nat Genet. 2010 Mar;42(3):255-9. PMID: 20118932; PMC: PMC2828505

Gheldof N, Smith EM, Tabuchi TM, Koch CM, Dunham I, Stamatoyannopoulos JA, Dekker J. Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene. Nucleic Acids Res. 2010 Jul;38(13):4325-36. PMID: 20360044; PMC: PMC2910055

Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010 Jan;7(1):47-9. PMID: 19946276; PMC: PMC2862482

Hansen RS, Thomas S, Sandstrom R, Canfield TK, Thurman RE, Weaver M, Dorschner MO, Gartler SM, Stamatoyannopoulos JA. Sequencing newly replicated DNA reveals widespread plasticity in human replication timing. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):139-44. PMID: 19966280; PMC: PMC2806781

Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet. 2010 Jul;11(7):476-86. PMID: 20531367; PMC: PMC3321268

Hoffman MM, Buske OJ, Noble WS. The Genomedata format for storing large-scale functional genomics data. Bioinformatics. 2010 Jun 1;26(11):1458-9. PMID: 20435580; PMC: PMC2872006

Hung JH, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C. Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biol. 2010;11(2):R23. PMID: 20187943; PMC: PMC2872883

Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE et al. Variation in transcription factor binding among humans. Science. 2010 Apr 9;328(5975):232-5. PMID: 20299548; PMC: PMC2938768

Kellermayer R, Balasa A, Zhang W, Lee S, Mirza S, Chakravarty A, Szigeti R, Laritsky E, Tatevian N, Smith CW et al. Epigenetic maturation in colonic mucosa continues beyond infancy in mice. Hum Mol Genet. 2010 Jun 1;19(11):2168-76. PMID: 20197410; PMC: PMC2865374

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. PMID: 20639541; PMC: PMC2922891

Kokocinski F, Harrow J, Hubbard T. AnnoTrack--a tracking system for genome annotation. BMC Genomics. 2010 Oct 5;11:538. PMID: 20923551; PMC: PMC3091687

Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010 Mar;20(3):320-31. PMID: 20133333; PMC: PMC2840979

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. PMID: 20181287; PMC: PMC2872882

Madupu R, Brinkac LM, Harrow J, Wilming LG, Böhme U, Lamesch P, Hannick LI. Meeting report: a workshop on Best Practices in Genome Annotation. Database (Oxford). 2010;2010:baq001. PMID: 20428316; PMC: PMC2860899

Mariotti M, Guigó R. Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes. Bioinformatics. 2010 Nov 1;26(21):2656-63. PMID: 20861026; PMC: PMC2958745

McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A et al. Heritable individual-specific and allele-specific chromatin signatures in humans. Science. 2010 Apr 9;328(5975):235-9. PMID: 20299549; PMC: PMC2929018

Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol. 2010 May;17(5):635-40. PMID: 20418883; PMC: PMC3350333

O'Geen H, Lin YH, Xu X, Echipare L, Komashko VM, He D, Frietze S, Tanabe O, Shi L, Sartor MA et al. Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes. BMC Genomics. 2010 Dec 2;11:689. PMID: 21126370; PMC: PMC3019231

Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q et al. Long noncoding RNAs with enhancer-like function in human cells. Cell. 2010 Oct 1;143(1):46-58. PMID: 20887892

Plessy C, Bertin N, Takahashi H, Simone R, Salimullah M, Lassmann T, Vitezic M, Severin J, Olivarius S, Lazarevic D et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods. 2010 Jul;7(7):528-34. PMID: 20543846; PMC: PMC2906222

Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ et al. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. PMID: 19906737; PMC: PMC2808870

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. PMID: 19920125; PMC: PMC2808953

Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T et al. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet. 2010 Jul 15;6(7):e1001023. PMID: 20657823; PMC: PMC2904778

Song L, Crawford GE. DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harb Protoc. 2010 Feb;2010(2):pdb.prot5384. PMID: 20150147; PMC: PMC3627383

Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, Erdos MR, Welch R, Parker SC, Boyle AP, Scott LJ et al. Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metab. 2010 Nov 3;12(5):443-55. PMID: 21035756; PMC: PMC3026436

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5. PMID: 20436464; PMC: PMC3146043

Tress ML, Valencia A. Predicted residue-residue contacts can help the scoring of 3D models. Proteins. 2010 Jun;78(8):1980-91. PMID: 20408174

Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods. 2010 Dec;7(12):995-1001. PMID: 21057495; PMC: PMC3247016

Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Curr Protoc Bioinformatics. 2010 Sep;Chapter 11:Unit 11.5. PMID: 20836074; PMC: PMC2952100

Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol. 2010;11(3):R26. PMID: 20210993; PMC: PMC2864566

2009

Affymetrix ENCODE Transcriptome Project, Cold Spring Harbor Laboratory ENCODE Transcriptome Project. Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature. 2009 Feb 19;457(7232):1028-32. PMID: 19169241; PMC: PMC2719882

Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G, Hancock RE, Harrow JL. Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome. BMC Genomics. 2009 Dec 15;10:606. PMID: 20003482; PMC: PMC2807441

Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M. Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes. Genome Biol. 2009;10(1):R2. PMID: 19123937; PMC: PMC2687790

Boles MK, Wilkinson BM, Wilming LG, Liu B, Probst FJ, Harrow J, Grafham D, Hentges KE, Woodward LP, Maxwell A et al. Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin. PLoS Genet. 2009 Dec;5(12):e1000759. PMID: 20011118; PMC: PMC2782131

Boyle AP, Furey TS. High-resolution mapping studies of chromatin and gene regulatory elements. Epigenomics. 2009 Dec 1;1(2):319-329. PMID: 20514362; PMC: PMC2877397

Brunner AL, Johnson DS, Kim SW, Valouev A, Reddy TE, Neff NF, Anton E, Medina C, Nguyen L, Chiao E et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009 Jun;19(6):1044-56. PMID: 19273619; PMC: PMC2694474

Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet. 2009 Sep;10(9):605-16. PMID: 19668247; PMC: PMC2846386

Faulkner GJ, Carninci P. Altruistic functions for selfish DNA. Cell Cycle. 2009 Sep 15;8(18):2895-900. PMID: 19736519

Forrest AR, Abdelhamid RF, Carninci P. Annotating non-coding transcription using functional genomics strategies. Brief Funct Genomic Proteomic. 2009 Nov;8(6):437-43. PMID: 19833699; PMC: PMC2762128

Fujiwara T, O'Geen H, Keles S, Blahnik K, Linnemann AK, Kang YA, Choi K, Farnham PJ, Bresnick EH. Discovering hematopoietic mechanisms through genome-wide analysis of GATA factor chromatin occupancy. Mol Cell. 2009 Nov 25;36(4):667-81. PMID: 19941826; PMC: PMC2784893

Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009 Nov 5;462(7269):58-64. PMID: 19890323; PMC: PMC2774924

Fullwood MJ, Ruan Y. ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem. 2009 May 1;107(1):30-9. PMID: 19247990; PMC: PMC2748757

Fullwood MJ, Wei CL, Liu ET, Ruan Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. PMID: 19339662; PMC: PMC3807531

George AD, Tenenbaum SA. Informatic resources for identifying and annotating structural RNA motifs. Mol Biotechnol. 2009 Feb;41(2):180-93. PMID: 18979204; PMC: PMC2770092

Gingeras T. Missing lincs in the transcriptome. Nat Biotechnol. 2009 Apr;27(4):346-7. PMID: 19352372

Gingeras TR. Implications of chimaeric non-co-linear transcripts. Nature. 2009 Sep 10;461(7261):206-11. PMID: 19741701

Giresi PG, Lieb JD. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). Methods. 2009 Jul;48(3):233-9. PMID: 19303047; PMC: PMC2710428

Guo X, Zhang Z, Gerstein MB, Zheng D. Small RNAs originated from pseudogenes: cis- or trans-acting?. PLoS Comput Biol. 2009 Jul;5(7):e1000449. PMID: 19649160; PMC: PMC2708354

Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R. Identifying protein-coding genes in genomic sequences. Genome Biol. 2009;10(1):201. PMID: 19226436; PMC: PMC2687780

Heintzman ND, Ren B. Finding distal regulatory elements in the human genome. Curr Opin Genet Dev. 2009 Dec;19(6):541-9. PMID: 19854636; PMC: PMC3321269

Hesselberth JR, Chen X, Zhang Z, Sabo PJ, Sandstrom R, Reynolds AP, Thurman RE, Neph S, Kuehn MS, Noble WS et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nat Methods. 2009 Apr;6(4):283-9. PMID: 19305407; PMC: PMC2668528

Hua S, Kittler R, White KP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell. 2009 Jun 26;137(7):1259-71. PMID: 19563758; PMC: PMC3374131

Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD et al. Planning the human variome project: the Spain report. Hum Mutat. 2009 Apr;30(4):496-510. PMID: 19306394

Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M et al. The UCSC Genome Browser Database: update 2009. Nucleic Acids Res. 2009 Jan;37(Database issue):D755-61. PMID: 18996895; PMC: PMC2686463

Lajoie BR, van Berkum NL, Sanyal A, Dekker J. My5C: web tools for chromosome conformation capture studies. Nat Methods. 2009 Oct;6(10):690-1. PMID: 19789528; PMC: PMC2859197

Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB. Pseudofam: the pseudogene families database. Nucleic Acids Res. 2009 Jan;37(Database issue):D738-43. PMID: 18957444; PMC: PMC2686518

Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 9;326(5950):289-93. PMID: 19815776; PMC: PMC2858594

Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB. Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics. 2009 Oct 16;10:480. PMID: 19835609; PMC: PMC2770531

Lu DV, Brown RH, Arumugam M, Brent MR. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner. Bioinformatics. 2009 Jul 1;25(13):1587-93. PMID: 19414532; PMC: PMC2732315

Makrythanasis P, Kapranov P, Bartoloni L, Reymond A, Deutsch S, Guigó R, Denoeud F, Drenkow J, Rossier C, Ariani F et al. Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Hum Mutat. 2009 Sep;30(9):E866-79. PMID: 19562714; PMC: PMC3708316

Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009 Nov;6(11 Suppl):S22-32. PMID: 19844228

Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ et al. The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res. 2009 Jul;19(7):1316-23. PMID: 19498102; PMC: PMC2704439

Reddy TE, Pauli F, Sprouse RO, Neff NF, Newberry KM, Garabedian MJ, Myers RM. Genomic determination of the glucocorticoid response reveals unexpected mechanisms of gene regulation. Genome Res. 2009 Dec;19(12):2163-71. PMID: 19801529; PMC: PMC2792167

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol. 2009 Jan;27(1):66-75. PMID: 19122651; PMC: PMC2924752

Sekimata M, Pérez-Melgosa M, Miller SA, Weinmann AS, Sabo PJ, Sandstrom R, Dorschner MO, Stamatoyannopoulos JA, Wilson CB. CCCTC-binding factor and the transcription factor T-bet orchestrate T helper 1 cell-specific structure and function at the interferon-gamma locus. Immunity. 2009 Oct 16;31(4):551-64. PMID: 19818655; PMC: PMC2810421

Stamatoyannopoulos JA, Adzhubei I, Thurman RE, Kryukov GV, Mirkin SM, Sunyaev SR. Human mutation rate associated with DNA replication timing. Nat Genet. 2009 Apr;41(4):393-5. PMID: 19287383; PMC: PMC2914101

2008

Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics. 2008 Nov 1;24(21):2537-8. PMID: 18784119; PMC: PMC2732284

Cotterman R, Jin VX, Krig SR, Lemen JM, Wey A, Farnham PJ, Knoepfler PS. N-Myc regulates a widespread euchromatic program in the human genome partially independent of its role as a classical transcription factor. Cancer Res. 2008 Dec 1;68(23):9654-62. PMID: 19047142; PMC: PMC2637654

Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R et al. An endogenous small interfering RNA pathway in Drosophila. Nature. 2008 Jun 5;453(7196):798-802. PMID: 18463631; PMC: PMC2895258

Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR et al. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods. 2008 Jul;5(7):629-35. PMID: 18500348; PMC: PMC2713501

Fu Y, Sinha M, Peterson CL, Weng Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 2008 Jul 25;4(7):e1000138. PMID: 18654629; PMC: PMC2453330

Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JG, Halls K, Harrow JL et al. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics. 2008 Jan;60(1):1-18. PMID: 18193213; PMC: PMC2206249

Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F et al. The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 2008 Jan;36(Database issue):D773-9. PMID: 18086701; PMC: PMC2238835

Mendenhall EM, Bernstein BE. Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev. 2008 Apr;18(2):109-15. PMID: 18339538; PMC: PMC2486450

Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. PMID: 18516045

Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG, Harrow JL. Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice. Genome Biol. 2008;9(5):R91. PMID: 18507838; PMC: PMC2441477

Stoecklin G, Tenenbaum SA, Mayo T, Chittur SV, George AD, Baroni TE, Blackshear PJ, Anderson P. Genome-wide analysis identifies interleukin-10 mRNA as target of tristetraprolin. J Biol Chem. 2008 Apr 25;283(17):11689-99. PMID: 18256032; PMC: PMC2431067

Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J et al. Determination and validation of principal gene products. Bioinformatics. 2008 Jan 1;24(1):11-7. PMID: 18006548; PMC: PMC2734078

Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods. 2008 Sep;5(9):829-34. PMID: 19160518; PMC: PMC2917543

Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL. The vertebrate genome annotation (Vega) database. Nucleic Acids Res. 2008 Jan;36(Database issue):D753-60. PMID: 18003653; PMC: PMC2238886

Zhang ZD, Cayting P, Weinstock G, Gerstein M. Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories. Mol Biol Evol. 2008 Jan;25(1):131-43. PMID: 18065488

2007

Day N, Hemmaplardh A, Thurman RE, Stamatoyannopoulos JA, Noble WS. Unsupervised segmentation of continuous genomic data. Bioinformatics. 2007 Jun 1;23(11):1424-6. PMID: 17384021

ENCODE Technology Development publications (133)

ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40. PMID: 15499007

Adli M, Zhu J, Bernstein BE. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat Methods. 2010 Aug;7(8):615-8. PMID: 20622861; PMC: PMC2924612

Arvey A, Agius P, Noble WS, Leslie C. Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome Res. 2012 Sep;22(9):1723-34. PMID: 22955984; PMC: PMC3431489

Arvey A, Tempera I, Tsai K, Chen HS, Tikhmyanova N, Klichinsky M, Leslie C, Lieberman PM. An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions. Cell Host Microbe. 2012 Aug 16;12(2):233-45. PMID: 22901543; PMC: PMC3424516

Baroni TE, Chittur SV, George AD, Tenenbaum SA. Advances in RIP-chip analysis : RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol. 2008;419:93-108. PMID: 18369977

Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR. Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Res. 2007 Jun;17(6):910-6. PMID: 17568006; PMC: PMC1891349

Bieda M, Xu X, Singer MA, Green R, Farnham PJ. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res. 2006 May;16(5):595-605. PMID: 16606705; PMC: PMC1457046

Birnbaum RY, Everman DB, Murphy KK, Gurrieri F, Schwartz CE, Ahituv N. Functional characterization of tissue-specific enhancers in the DLX5/6 locus. Hum Mol Genet. 2012 Nov 15;21(22):4930-8. PMID: 22914741; PMC: PMC3529576

Booker BM, Murphy KK, Ahituv N. Functional analysis of limb enhancers in the developing fin. Dev Genes Evol. 2013 Nov;223(6):395-9. PMID: 24068387; PMC: PMC3869458

Burden HE, Weng Z. Identification of conserved structural features at sequentially degenerate locations in transcription factor binding sites. Genome Inform. 2005;16(1):49-58. PMID: 16362906

Castillo HA, Cravo RM, Azambuja AP, Simões-Costa MS, Sura-Trueba S, Gonzalez J, Slonimsky E, Almeida K, Abreu JG, de Almeida MA et al. Insights into the organization of dorsal spinal cord pathways from an evolutionarily conserved raldh2 intronic enhancer. Development. 2010 Feb;137(3):507-18. PMID: 20081195

Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008 Jun 13;133(6):1106-17. PMID: 18555785

Chiu KP, Ariyaratne P, Xu H, Tan A, Ng P, Liu ET, Ruan Y, Wei CL, Sung WK. Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. BMC Cancer. 2007 Jun 26;7:109. PMID: 17594473; PMC: PMC1929113

Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WK, Ruan Y. PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data. BMC Bioinformatics. 2006 Aug 25;7:390. PMID: 16934139; PMC: PMC1564156

Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 2011 Nov 18;44(4):667-78. PMID: 21963238; PMC: PMC3249421

Dekker J. The three 'C' s of chromosome conformation capture: controls, controls, controls. Nat Methods. 2006 Jan;3(1):17-21. PMID: 16369547

Dekker J. GC- and AT-rich chromatin domains differ in conformation and histone modification status and are differentially modulated by Rpd3p. Genome Biol. 2007;8(6):R116. PMID: 17577398; PMC: PMC2394764

Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res. 2007 Jun;17(6):928-39. PMID: 17568008; PMC: PMC1891351

Di Marco S, Mazroui R, Dallaire P, Chittur S, Tenenbaum SA, Radzioch D, Marette A, Gallouzi IE. NF-kappa B-mediated MyoD decay during muscle wasting requires nitric oxide synthase mRNA stabilization, HuR protein, and nitric oxide release. Mol Cell Biol. 2005 Aug;25(15):6533-45. PMID: 16024790; PMC: PMC1190341

Dostie J, Dekker J. Mapping networks of physical interactions between genomic elements using 5C technology. Nat Protoc. 2007;2(4):988-1002. PMID: 17446898

Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, Rubio ED, Krumm A, Lamb J, Nusbaum C et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 Oct;16(10):1299-309. PMID: 16954542; PMC: PMC1581439

Doyle F, Zaleski C, George AD, Stenson EK, Ricciardi A, Tenenbaum SA. Bioinformatic tools for studying post-transcriptional gene regulation : The UAlbany TUTR collection and other informatic resources. Methods Mol Biol. 2008;419:39-52. PMID: 18369974

Einstein F, Thompson RF, Bhagat TD, Fazzari MJ, Verma A, Barzilai N, Greally JM. Cytosine methylation dysregulation in neonates following intrauterine growth restriction. PLoS One. 2010 Jan 26;5(1):e8887. PMID: 20126273; PMC: PMC2811176

Elnitski L, Jin VX, Farnham PJ, Jones SJ. Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res. 2006 Dec;16(12):1455-64. PMID: 17053094

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. PMID: 17571346; PMC: PMC2212820

Flynn RA, Chang HY. Active chromatin and noncoding RNAs: an intimate relationship. Curr Opin Genet Dev. 2012 Apr;22(2):172-8. PMID: 22154525; PMC: PMC3319162

Frith MC, Fu Y, Yu L, Chen JF, Hansen U, Weng Z. Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res. 2004;32(4):1372-81. PMID: 14988425; PMC: PMC390287

Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y. Chromatin interaction analysis using paired-end tag sequencing. Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. PMID: 20069536

Fullwood MJ, Liu MH, Pan YF, Liu J, Xu H, Mohamed YB, Orlov YL, Velkov S, Ho A, Mei PH et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature. 2009 Nov 5;462(7269):58-64. PMID: 19890323; PMC: PMC2774924

Fullwood MJ, Ruan Y. ChIP-based methods for the identification of long-range chromatin interactions. J Cell Biochem. 2009 May 1;107(1):30-9. PMID: 19247990; PMC: PMC2748757

Fullwood MJ, Tan JJ, Ng PW, Chiu KP, Liu J, Wei CL, Ruan Y. The use of multiple displacement amplification to amplify complex DNA libraries. Nucleic Acids Res. 2008 Mar;36(5):e32. PMID: 18285362; PMC: PMC2275127

Fullwood MJ, Wei CL, Liu ET, Ruan Y. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. PMID: 19339662; PMC: PMC3807531

Garcia-Bassets I, Kwon YS, Telese F, Prefontaine GG, Hutt KR, Cheng CS, Ju BG, Ohgi KA, Wang J, Escoubet-Lozach L et al. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell. 2007 Feb 9;128(3):505-18. PMID: 17289570; PMC: PMC1994663

George AD, Tenenbaum SA. MicroRNA modulation of RNA-binding protein regulatory elements. RNA Biol. 2006 Apr;3(2):57-9. PMID: 17114943

Gheldof N, Tabuchi TM, Dekker J. The active FMR1 promoter is associated with a large domain of altered chromatin conformation with embedded local histone modifications. Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12463-8. PMID: 16891414; PMC: PMC1567902

Giresi PG, Gupta M, Lieb JD. Regulation of nucleosome stability as a mediator of chromatin function. Curr Opin Genet Dev. 2006 Apr;16(2):171-6. PMID: 16503136

Giresi PG, Kim J, McDaniell RM, Iyer VR, Lieb JD. FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin. Genome Res. 2007 Jun;17(6):877-85. PMID: 17179217; PMC: PMC1891346

Glass JL, Fazzari MJ, Ferguson-Smith AC, Greally JM. CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains. Mamm Genome. 2009 Sep-Oct;20(9-10):633-43. PMID: 19921333

Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010 Jan;7(1):47-9. PMID: 19946276; PMC: PMC2862482

Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I. Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers. Genome Res. 2010 May;20(5):565-77. PMID: 20363979; PMC: PMC2860159

Greenbaum JA, Pang B, Tullius TD. Construction of a genome-scale structural map at single-nucleotide resolution. Genome Res. 2007 Jun;17(6):947-53. PMID: 17568010; PMC: PMC1891353

Greenbaum JA, Parker SC, Tullius TD. Detection of DNA structural motifs in functional genomic elements. Genome Res. 2007 Jun;17(6):940-6. PMID: 17568009; PMC: PMC1891352

Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods. 2010 Feb;7(2):133-6. PMID: 20062050; PMC: PMC2860480

Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010 Apr 15;464(7291):1071-6. PMID: 20393566; PMC: PMC3049919

Hagège H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, de Laat W, Forné T. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc. 2007;2(7):1722-33. PMID: 17641637

Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat Genet. 2011 Jun 19;43(7):630-8. PMID: 21685913; PMC: PMC3436933

Haverty PM, Hsiao LL, Gullans SR, Hansen U, Weng Z. Limited agreement among three global gene expression methods highlights the requirement for non- global validation. Bioinformatics. 2004 Dec 12;20(18):3431-41. PMID: 15256402

Haverty PM, Weng Z. CisML: an XML-based format for sequence motif detection software. Bioinformatics. 2004 Jul 22;20(11):1815-7. PMID: 15001475

Hua S, Kittler R, White KP. Genomic antagonism between retinoic acid and estrogen signaling in breast cancer. Cell. 2009 Jun 26;137(7):1259-71. PMID: 19563758; PMC: PMC3374131

Jeddeloh JA, Greally JM, Rando OJ. Reduced-representation methylation mapping. Genome Biol. 2008;9(8):231. PMID: 18771577; PMC: PMC2575507

Jin VX, O'Geen H, Iyengar S, Green R, Farnham PJ. Identification of an OCT4 and SRY regulatory module using integrated computational and experimental genomics approaches. Genome Res. 2007 Jun;17(6):807-17. PMID: 17567999; PMC: PMC1891340

Jin VX, Rabinovich A, Squazzo SL, Green R, Farnham PJ. A computational genomics approach to identify cis-regulatory modules from chromatin immunoprecipitation microarray data--a case study using E2F1. Genome Res. 2006 Dec;16(12):1585-95. PMID: 17053090; PMC: PMC1665642

Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E. Genome-wide measurement of RNA secondary structure in yeast. Nature. 2010 Sep 2;467(7311):103-7. PMID: 20811459; PMC: PMC3847670

Kim MJ, Oksenberg N, Hoffmann TJ, Vaisse C, Ahituv N. Functional characterization of SIM1-associated enhancers. Hum Mol Genet. 2014 Apr 1;23(7):1700-8. PMID: 24203700; PMC: PMC3943516

Kleckner N, Zickler D, Jones GH, Dekker J, Padmore R, Henle J, Hutchinson J. A mechanical basis for chromosome function. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12592-7. PMID: 15299144; PMC: PMC515102

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P et al. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res. 2007 Jun;17(6):691-707. PMID: 17567990; PMC: PMC1891331

Krig SR, Jin VX, Bieda MC, O'Geen H, Yaswen P, Green R, Farnham PJ. Identification of genes directly regulated by the oncogene ZNF217 using chromatin immunoprecipitation (ChIP)-chip assays. J Biol Chem. 2007 Mar 30;282(13):9703-12. PMID: 17259635; PMC: PMC2269729

Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA. Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci U S A. 2012 Nov 20;109(47):19498-503. PMID: 23129659; PMC: PMC3511131

Kwon YS, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M et al. Sensitive ChIP-DSL technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):4852-7. PMID: 17360330; PMC: PMC1821125

Lanzuolo C, Roure V, Dekker J, Bantignies F, Orlando V. Polycomb response elements mediate the formation of chromosome higher-order structures in the bithorax complex. Nat Cell Biol. 2007 Oct;9(10):1167-74. PMID: 17828248

Larson JL, Huttenhower C, Quackenbush J, Yuan GC. A tiered hidden Markov model characterizes multi-scale chromatin states. Genomics. 2013 Jul;102(1):1-7. PMID: 23570996; PMC: PMC3676702

Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010 Mar;20(3):320-31. PMID: 20133333; PMC: PMC2840979

Leyfer D, Bond A, Tworog E, Perron D, Maska S, Brito A, Kamens J, Weng Z, Voss J. cis-Element clustering correlates with dose-dependent pro- and antisignaling effects of IL18. Genes Immun. 2004 Aug;5(5):354-62. PMID: 15190265

Leyfer D, Weng Z. Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii197-203. PMID: 16204103

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol. 2010;11(2):R22. PMID: 20181287; PMC: PMC2872882

Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012 Jan 20;148(1-2):84-98. PMID: 22265404; PMC: PMC3339270

Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A et al. An optimized algorithm for detecting and annotating regional differential methylation. BMC Bioinformatics. 2013;14 Suppl 5:S10. PMID: 23735126; PMC: PMC3622633

Lim CA, Yao F, Wong JJ, George J, Xu H, Chiu KP, Sung WK, Lipovich L, Vega VB, Chen J et al. Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol Cell. 2007 Aug 17;27(4):622-35. PMID: 17707233

Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z. Transcription factor binding and modified histones in human bidirectional promoters. Genome Res. 2007 Jun;17(6):818-27. PMID: 17568000; PMC: PMC1891341

Lin JM, Weng Z. Systematic detection of statistically overrepresented DNA motif association rules. Genome Inform. 2006;17(1):124-33. PMID: 17503362

Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008 May 2;133(3):523-36. PMID: 18423832; PMC: PMC2723732

Mazroui R, Di Marco S, Clair E, von Roretz C, Tenenbaum SA, Keene JD, Saleh M, Gallouzi IE. Caspase-mediated cleavage of HuR in the cytoplasm contributes to pp32/PHAP-I regulation of apoptosis. J Cell Biol. 2008 Jan 14;180(1):113-27. PMID: 18180367; PMC: PMC2213623

Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 7;454(7205):766-70. PMID: 18600261; PMC: PMC2896277

Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I. Genome-wide discovery of human heart enhancers. Genome Res. 2010 Mar;20(3):381-92. PMID: 20075146; PMC: PMC2840982

Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK et al. Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes. Nucleic Acids Res. 2006 Jul 13;34(12):e84. PMID: 16840528; PMC: PMC1524903

Nobrega MA. Journal club. A human geneticist explores the ways that genes are regulated. Nature. 2010 Jul 1;466(7302):11. PMID: 20595974

O'Geen H, Nicolet CM, Blahnik K, Green R, Farnham PJ. Comparison of sample preparation methods for ChIP-chip assays. Biotechniques. 2006 Nov;41(5):577-80. PMID: 17140114; PMC: PMC2268903

O'Geen H, Squazzo SL, Iyengar S, Blahnik K, Rinn JL, Chang HY, Green R, Farnham PJ. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet. 2007 Jun;3(6):e89. PMID: 17542650; PMC: PMC1885280

Oda M, Glass JL, Thompson RF, Mo Y, Olivier EN, Figueroa ME, Selzer RR, Richmond TA, Zhang X, Dannenberg L et al. High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 2009 Jul;37(12):3829-39. PMID: 19386619; PMC: PMC2709560

Oksenberg N, Stevison L, Wall JD, Ahituv N. Function and regulation of AUTS2, a gene implicated in autism and human evolution. PLoS Genet. 2013;9(1):e1003221. PMID: 23349641; PMC: PMC3547868

Ouyang Z, Zheng GX, Chang HY. Noncoding RNA landmarks of pluripotency and reprogramming. Cell Stem Cell. 2010 Dec 3;7(6):649-50. PMID: 21112559; PMC: PMC3027494

Paulsen MT, Veloso A, Prasad J, Bedi K, Ljungman EA, Tsan YC, Chang CW, Tarrier B, Washburn JG, Lyons R et al. Coordinated regulation of synthesis and stability of RNA during the acute TNF-induced proinflammatory response. Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2240-5. PMID: 23345452; PMC: PMC3568384

Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Res. 2007 Aug;17(8):1170-7. PMID: 17620451; PMC: PMC1933512

Poser I, Sarov M, Hutchins JR, Hériché JK, Toyoda Y, Pozniakovsky A, Weigl D, Nitzsche A, Hegemann B, Bird AW et al. BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals. Nat Methods. 2008 May;5(5):409-15. PMID: 18391959; PMC: PMC2871289

Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ. E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res. 2008 Nov;18(11):1763-77. PMID: 18836037; PMC: PMC2577861

Ricarte-Filho JC, Li S, Garcia-Rendueles ME, Montero-Conde C, Voza F, Knauf JA, Heguy A, Viale A, Bogdanova T, Thomas GA et al. Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers. J Clin Invest. 2013 Nov 1;123(11):4935-44. PMID: 24135138; PMC: PMC3809792

Rosario K, Nilsson C, Lim YW, Ruan Y, Breitbart M. Metagenomic analysis of viruses in reclaimed water. Environ Microbiol. 2009 Nov;11(11):2806-20. PMID: 19555373

Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P et al. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res. 2007 Jun;17(6):828-38. PMID: 17568001; PMC: PMC1891342

Sakabe NJ, Nobrega MA. Genome-wide maps of transcription regulatory elements. Wiley Interdiscip Rev Syst Biol Med. 2010 Jul-Aug;2(4):422-37. PMID: 20836039

Samstein RM, Arvey A, Josefowicz SZ, Peng X, Reynolds A, Sandstrom R, Neph S, Sabo P, Kim JM, Liao W et al. Foxp3 exploits a pre-existent enhancer landscape for regulatory T cell lineage specification. Cell. 2012 Sep 28;151(1):153-66. PMID: 23021222; PMC: PMC3493256

Savic D, Distler MG, Sokoloff G, Shanahan NA, Dulawa SC, Palmer AA, Nobrega MA. Modulation ofTcf7l2 expression alters behavior in mice. PLoS One. 2011;6(10):e26897. PMID: 22046400; PMC: PMC3203170

Savic D, Ye H, Aneas I, Park SY, Bell GI, Nobrega MA. Alterations in TCF7L2 expression define its role as a key regulator of glucose metabolism. Genome Res. 2011 Sep;21(9):1417-25. PMID: 21673050; PMC: PMC3166827

Schneider I, Aneas I, Gehrke AR, Dahn RD, Nobrega MA, Shubin NH. Appendage expression driven by the Hoxd Global Control Region is an ancient gnathostome feature. Proc Natl Acad Sci U S A. 2011 Aug 2;108(31):12782-6. PMID: 21765002; PMC: PMC3150877

Schnetz MP, Handoko L, Akhtar-Zaidi B, Bartels CF, Pereira CF, Fisher AG, Adams DJ, Flicek P, Crawford GE, Laframboise T et al. CHD7 targets active gene enhancer elements to modulate ES cell-specific gene expression. PLoS Genet. 2010 Jul 15;6(7):e1001023. PMID: 20657823; PMC: PMC2904778

Shalem O, Dahan O, Levo M, Martinez MR, Furman I, Segal E, Pilpel Y. Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation. Mol Syst Biol. 2008;4:223. PMID: 18854817; PMC: PMC2583085

Shen T, Aneas I, Sakabe N, Dirschinger RJ, Wang G, Smemo S, Westlund JM, Cheng H, Dalton N, Gu Y et al. Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. J Clin Invest. 2011 Dec;121(12):4640-54. PMID: 22080862; PMC: PMC3223071

Simon JM, Giresi PG, Davis IJ, Lieb JD. A detailed protocol for formaldehyde-assisted isolation of regulatory elements (FAIRE). Curr Protoc Mol Biol. 2013;Chapter 21:Unit21.26. PMID: 23547014

Singh Sandhu K, Li G, Sung WK, Ruan Y. Chromatin interaction networks and higher order architectures of eukaryotic genomes. J Cell Biochem. 2011 Sep;112(9):2218-21. PMID: 21520242

Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol. 2013 Jul 18;14(7):R72. PMID: 23867016

Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N. Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat Genet. 2013 Sep;45(9):1021-8. PMID: 23892608; PMC: PMC3775494

Squazzo SL, O'Geen H, Komashko VM, Krig SR, Jin VX, Jang SW, Margueron R, Reinberg D, Green R, Farnham PJ. Suz12 binds to silenced regions of the genome in a cell-type-specific manner. Genome Res. 2006 Jul;16(7):890-900. PMID: 16751344; PMC: PMC1484456

Stoecklin G, Tenenbaum SA, Mayo T, Chittur SV, George AD, Baroni TE, Blackshear PJ, Anderson P. Genome-wide analysis identifies interleukin-10 mRNA as target of tristetraprolin. J Biol Chem. 2008 Apr 25;283(17):11689-99. PMID: 18256032; PMC: PMC2431067

Suzuki M, Greally JM. DNA methylation profiling using HpaII tiny fragment enrichment by ligation-mediated PCR (HELP). Methods. 2010 Nov;52(3):218-22. PMID: 20434563; PMC: PMC2954265

Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM. Optimized design and data analysis of tag-based cytosine methylation assays. Genome Biol. 2010;11(4):R36. PMID: 20359321; PMC: PMC2884539

Suzuki M, Oda M, Ramos MP, Pascual M, Lau K, Stasiek E, Agyiri F, Thompson RF, Glass JL, Jing Q et al. Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome. Genome Res. 2011 Nov;21(11):1833-40. PMID: 21957152; PMC: PMC3205568

Taher L, McGaughey DM, Maragh S, Aneas I, Bessling SL, Miller W, Nobrega MA, McCallion AS, Ovcharenko I. Genome-wide identification of conserved regulatory function in diverged sequences. Genome Res. 2011 Jul;21(7):1139-49. PMID: 21628450; PMC: PMC3129256

Thompson RF, Atzmon G, Gheorghe C, Liang HQ, Lowes C, Greally JM, Barzilai N. Tissue-specific dysregulation of DNA methylation in aging. Aging Cell. 2010 Aug;9(4):506-18. PMID: 20497131; PMC: PMC2935175

Thompson RF, Fazzari MJ, Niu H, Barzilai N, Simmons RA, Greally JM. Experimental intrauterine growth restriction induces alterations in DNA methylation and gene expression in pancreatic islets of rats. J Biol Chem. 2010 May 14;285(20):15111-8. PMID: 20194508; PMC: PMC2865297

Thompson RF, Suzuki M, Lau KW, Greally JM. A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Bioinformatics. 2009 Sep 1;25(17):2164-70. PMID: 19561019; PMC: PMC2800352

Tompa M, Li N, Bailey TL, Church GM, De Moor B, Eskin E, Favorov AV, Frith MC, Fu Y, Kent WJ et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat Biotechnol. 2005 Jan;23(1):137-44. PMID: 15637633

Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M et al. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res. 2007 Jun;17(6):720-31. PMID: 17567992; PMC: PMC1891333

Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science. 2010 Aug 6;329(5992):689-93. PMID: 20616235; PMC: PMC2967777

Vakoc CR, Letting DL, Gheldof N, Sawado T, Bender MA, Groudine M, Weiss MJ, Dekker J, Blobel GA. Proximity among distant regulatory elements at the beta-globin locus requires GATA-1 and FOG-1. Mol Cell. 2005 Feb 4;17(3):453-62. PMID: 15694345

Veloso A, Biewen B, Paulsen MT, Berg N, Carmo de Andrade Lima L, Prasad J, Bedi K, Magnuson B, Wilson TE, Ljungman M. Genome-wide transcriptional effects of the anti-cancer agent camptothecin. PLoS One. 2013;8(10):e78190. PMID: 24194914; PMC: PMC3806802

Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY. Understanding the transcriptome through RNA structure. Nat Rev Genet. 2011 Aug 18;12(9):641-55. PMID: 21850044; PMC: PMC3858389

Wang KC, Chang HY. Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011 Sep 16;43(6):904-14. PMID: 21925379; PMC: PMC3199020

Wasserman NF, Aneas I, Nobrega MA. An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer. Genome Res. 2010 Sep;20(9):1191-7. PMID: 20627891; PMC: PMC2928497

White MA, Myers CA, Corbo JC, Cohen BA. Massively parallel in vivo enhancer assay reveals that highly local features determine the cis- regulatory function of ChIP-seq peaks. Proc Natl Acad Sci U S A. 2013 Jul 16;110(29):11952-7. PMID: 23818646; PMC: PMC3718143

Xi H, Shulha HP, Lin JM, Vales TR, Fu Y, Bodine DM, McKay RD, Chenoweth JG, Tesar PJ, Furey TS et al. Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. PLoS Genet. 2007 Aug;3(8):e136. PMID: 17708682; PMC: PMC1950163

Xi H, Yu Y, Fu Y, Foley J, Halees A, Weng Z. Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1. Genome Res. 2007 Jun;17(6):798-806. PMID: 17567998; PMC: PMC1891339

Xu X, Bieda M, Jin VX, Rabinovich A, Oberley MJ, Green R, Farnham PJ. A comprehensive ChIP-chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members. Genome Res. 2007 Nov;17(11):1550-61. PMID: 17908821; PMC: PMC2045138

Yazaki J, Gregory BD, Ecker JR. Mapping the genome landscape using tiling array technology. Curr Opin Plant Biol. 2007 Oct;10(5):534-42. PMID: 17703988; PMC: PMC2665186

Yu L, Haverty PM, Mariani J, Wang Y, Shen HY, Schwarzschild MA, Weng Z, Chen JF. Genetic and pharmacological inactivation of adenosine A2A receptor reveals an Egr-2-mediated transcriptional regulatory network in the mouse striatum. Physiol Genomics. 2005 Sep 21;23(1):89-102. PMID: 16046619

Zeller KI, Zhao X, Lee CW, Chiu KP, Yao F, Yustein JT, Ooi HS, Orlov YL, Shahab A, Yong HC et al. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci U S A. 2006 Nov 21;103(47):17834-9. PMID: 17093053; PMC: PMC1635161

Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 2007 May;5(5):e129. PMID: 17439305; PMC: PMC1852588

Zhang X, Germann S, Blus BJ, Khorasanizadeh S, Gaudin V, Jacobsen SE. The Arabidopsis LHP1 protein colocalizes with histone H3 Lys27 trimethylation. Nat Struct Mol Biol. 2007 Sep;14(9):869-71. PMID: 17676062

Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE. Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4536-41. PMID: 17360559; PMC: PMC1810338

Zhang X, Jacobsen SE. Genetic analyses of DNA methyltransferases in Arabidopsis thaliana. Cold Spring Harb Symp Quant Biol. 2006;71:439-47. PMID: 17381326

Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell. 2006 Sep 22;126(6):1189-201. PMID: 16949657

Zhang Y, Wong CH, Birnbaum RY, Li G, Favaro R, Ngan CY, Lim J, Tai E, Poh HM, Wong E et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature. 2013 Dec 12;504(7479):306-10. PMID: 24213634

Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res. 2007 Jun;17(6):787-97. PMID: 17567997; PMC: PMC1891338

Zhao J, Shi H, Ahituv N. Classification of topological domains based on gene expression and regulation. Genome. 2013 Jul;56(7):415-23. PMID: 24099394; PMC: PMC3873163

Zhao XD, Han X, Chew JL, Liu J, Chiu KP, Choo A, Orlov YL, Sung WK, Shahab A, Kuznetsov VA et al. Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell. 2007 Sep 13;1(3):286-98. PMID: 18371363

ENCODE pilot project publications (81)

Arumugam M, Wei C, Brown RH, Brent MR. Pairagon+N-SCAN_EST: a model-based gene annotation pipeline. Genome Biol. 2006;7 Suppl 1:S5.1-10. PMID: 16925839; PMC: PMC1810554

Attanasio C, Reymond A, Humbert R, Lyle R, Kuehn MS, Neph S, Sabo PJ, Goldy J, Weaver M, Haydock A et al. Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biol. 2008;9(12):R168. PMID: 19055709; PMC: PMC2646272

Bishop EP, Rohs R, Parker SC, West SM, Liu P, Mann RS, Honig B, Tullius TD. A map of minor groove shape and electrostatic potential from hydroxyl radical cleavage patterns of DNA. ACS Chem Biol. 2011 Dec 16;6(12):1314-20. PMID: 21967305; PMC: PMC3241897

Brent MR. Genome annotation past, present, and future: how to define an ORF at each locus. Genome Res. 2005 Dec;15(12):1777-86. PMID: 16339376

Brent MR, Guigó R. Recent advances in gene structure prediction. Curr Opin Struct Biol. 2004 Jun;14(3):264-72. PMID: 15193305

Chatterji S, Pachter L. Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor. Genomics. 2007 Jul;90(1):44-8. PMID: 17499477; PMC: PMC2034525

Chatterji S, Pachter L. Reference based annotation with GeneMapper. Genome Biol. 2006;7(4):R29. PMID: 16600017; PMC: PMC1557983

Collins PJ, Kobayashi Y, Nguyen L, Trinklein ND, Myers RM. The ets-related transcription factor GABP directs bidirectional transcription. PLoS Genet. 2007 Nov;3(11):e208. PMID: 18020712; PMC: PMC2077898

Cooper SJ, Trinklein ND, Anton ED, Nguyen L, Myers RM. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res. 2006 Jan;16(1):1-10. PMID: 16344566; PMC: PMC1356123

Cooper SJ, Trinklein ND, Nguyen L, Myers RM. Serum response factor binding sites differ in three human cell types. Genome Res. 2007 Feb;17(2):136-44. PMID: 17200232; PMC: PMC1781345

Day N, Hemmaplardh A, Thurman RE, Stamatoyannopoulos JA, Noble WS. Unsupervised segmentation of continuous genomic data. Bioinformatics. 2007 Jun 1;23(11):1424-6. PMID: 17384021

De Gobbi M, Anguita E, Hughes J, Sloane-Stanley JA, Sharpe JA, Koch CM, Dunham I, Gibbons RJ, Wood WG, Higgs DR. Tissue-specific histone modification and transcription factor binding in alpha globin gene expression. Blood. 2007 Dec 15;110(13):4503-10. PMID: 17715390

Dennis JH, Fan HY, Reynolds SM, Yuan G, Meldrim JC, Richter DJ, Peterson DG, Rando OJ, Noble WS, Kingston RE. Independent and complementary methods for large-scale structural analysis of mammalian chromatin. Genome Res. 2007 Jun;17(6):928-39. PMID: 17568008; PMC: PMC1891351

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J et al. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res. 2007 Jun;17(6):746-59. PMID: 17567994; PMC: PMC1891335

Dewey CN, Huggins PM, Woods K, Sturmfels B, Pachter L. Parametric alignment of Drosophila genomes. PLoS Comput Biol. 2006 Jun 23;2(6):e73. PMID: 16789815; PMC: PMC1480539

Dewey CN, Pachter L. Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Hum Mol Genet. 2006 Apr 15;15 Spec No 1:R51-6. PMID: 16651369

Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR et al. Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods. 2008 Jul;5(7):629-35. PMID: 18500348; PMC: PMC2713501

Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res. 2005 Feb;15(2):330-40. PMID: 15687296; PMC: PMC546535

Do CB, Woods DA, Batzoglou S. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics. 2006 Jul 15;22(14):e90-8. PMID: 16873527

Dorschner MO, Hawrylycz M, Humbert R, Wallace JC, Shafer A, Kawamoto J, Mack J, Hall R, Goldy J, Sabo PJ et al. High-throughput localization of functional elements by quantitative chromatin profiling. Nat Methods. 2004 Dec;1(3):219-25. PMID: 15782197

Du J, Rozowsky JS, Korbel JO, Zhang ZD, Royce TE, Schultz MH, Snyder M, Gerstein M. A supervised hidden markov model framework for efficiently segmenting tiling array data in transcriptional and chIP-chip experiments: systematically incorporating validated biological knowledge. Bioinformatics. 2006 Dec 15;22(24):3016-24. PMID: 17038339

Elnitski LL, Shah P, Moreland RT, Umayam L, Wolfsberg TG, Baxevanis AD. The ENCODEdb portal: simplified access to ENCODE Consortium data. Genome Res. 2007 Jun;17(6):954-9. PMID: 17568011; PMC: PMC1891354

Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M et al. Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. Genome Res. 2007 Jun;17(6):886-97. PMID: 17119069; PMC: PMC1891347

ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004 Oct 22;306(5696):636-40. PMID: 15499007

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816. PMID: 17571346; PMC: PMC2212820

Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies. Genome Res. 2007 Jun;17(6):898-909. PMID: 17568005; PMC: PMC1891348

Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C et al. Gene finding in the chicken genome. BMC Bioinformatics. 2005 May 30;6:131. PMID: 15924626; PMC: PMC1174864

Flannick J, Batzoglou S. Using multiple alignments to improve seeded local alignment algorithms. Nucleic Acids Res. 2005;33(14):4563-77. PMID: 16100379; PMC: PMC1185574

Flannick J, Novak A, Srinivasan BS, McAdams HH, Batzoglou S. Graemlin: general and robust alignment of multiple large interaction networks. Genome Res. 2006 Sep;16(9):1169-81. PMID: 16899655; PMC: PMC1557769

Fratkin E, Naughton BT, Brutlag DL, Batzoglou S. MotifCut: regulatory motifs finding with maximum density subgraphs. Bioinformatics. 2006 Jul 15;22(14):e150-7. PMID: 16873465

Georlette D, Ahn S, MacAlpine DM, Cheung E, Lewis PW, Beall EL, Bell SP, Speed T, Manak JR, Botchan MR. Genomic profiling and expression studies reveal both positive and negative activities for the Drosophila Myb MuvB/dREAM complex in proliferating cells. Genes Dev. 2007 Nov 15;21(22):2880-96. PMID: 17978103; PMC: PMC2049191

Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M. What is a gene, post-ENCODE? History and updated definition. Genome Res. 2007 Jun;17(6):669-81. PMID: 17567988

Ghosh S, Hirsch HA, Sekinger EA, Kapranov P, Struhl K, Gingeras TR. Differential analysis for high density tiling microarray data. BMC Bioinformatics. 2007 Sep 24;8:359. PMID: 17892592; PMC: PMC2231405

Ghosh S, Hirsch HA, Sekinger E, Struhl K, Gingeras TR. Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments. BMC Bioinformatics. 2006 Oct 5;7:434. PMID: 17022824; PMC: PMC1615882

Gibbons FD, Proft M, Struhl K, Roth FP. Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome Biol. 2005;6(11):R96. PMID: 16277751; PMC: PMC1297652

Gingeras TR. Origin of phenotypes: genes and transcripts. Genome Res. 2007 Jun;17(6):682-90. PMID: 17567989

Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A. 2005 May 3;102(18):6419-24. PMID: 15845769; PMC: PMC1088349

Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007 Jun 8;316(5830):1497-502. PMID: 17540862

Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 2008 Mar;18(3):393-403. PMID: 18258921; PMC: PMC2259103

Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science. 2007 Jun 8;316(5830):1484-8. PMID: 17510325

Karnani N, Taylor C, Malhotra A, Dutta A. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res. 2007 Jun;17(6):865-76. PMID: 17568004; PMC: PMC1891345

Keibler E, Arumugam M, Brent MR. The Treeterbi and Parallel Treeterbi algorithms: efficient, optimal decoding for ordinary, generalized and pair HMMs. Bioinformatics. 2007 Mar 1;23(5):545-54. PMID: 17237054

Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD, Zhang MQ, Lobanenkov VV, Ren B. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell. 2007 Mar 23;128(6):1231-45. PMID: 17382889; PMC: PMC2572726

Kim TH, Barrera LO, Qu C, Van Calcar S, Trinklein ND, Cooper SJ, Luna RM, Glass CK, Rosenfeld MG, Myers RM et al. Direct isolation and identification of promoters in the human genome. Genome Res. 2005 Jun;15(6):830-9. PMID: 15899964; PMC: PMC1142473

Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, Richmond TA, Wu Y, Green RD, Ren B. A high-resolution map of active promoters in the human genome. Nature. 2005 Aug 11;436(7052):876-80. PMID: 15988478; PMC: PMC1895599

Kim TH, Ren B. Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet. 2006;7:81-102. PMID: 16722805

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P et al. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res. 2007 Jun;17(6):691-707. PMID: 17567990; PMC: PMC1891331

Kwong C, Adryan B, Bell I, Meadows L, Russell S, Manak JR, White R. Stability and dynamics of polycomb target sites in Drosophila development. PLoS Genet. 2008 Sep 5;4(9):e1000178. PMID: 18773083; PMC: PMC2525605

Levasseur DN, Wang J, Dorschner MO, Stamatoyannopoulos JA, Orkin SH. Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. Genes Dev. 2008 Mar 1;22(5):575-80. PMID: 18283123; PMC: PMC2259027

Lin JM, Collins PJ, Trinklein ND, Fu Y, Xi H, Myers RM, Weng Z. Transcription factor binding and modified histones in human bidirectional promoters. Genome Res. 2007 Jun;17(6):818-27. PMID: 17568000; PMC: PMC1891341

Liu Y, Liu XS, Wei L, Altman RB, Batzoglou S. Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res. 2004 Mar;14(3):451-8. PMID: 14993210; PMC: PMC353232

Manak JR, Dike S, Sementchenko V, Kapranov P, Biemar F, Long J, Cheng J, Bell I, Ghosh S, Piccolboni A et al. Biological function of unannotated transcription during the early development of Drosophila melanogaster. Nat Genet. 2006 Oct;38(10):1151-8. PMID: 16951679

Margulies EH, Cooper GM, Asimenos G, Thomas DJ, Dewey CN, Siepel A, Birney E, Keefe D, Schwartz AS, Hou M et al. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 2007 Jun;17(6):760-74. PMID: 17567995; PMC: PMC1891336

Maynard ND, Chen J, Stuart RK, Fan JB, Ren B. Genome-wide mapping of allele-specific protein-DNA interactions in human cells. Nat Methods. 2008 Apr;5(4):307-9. PMID: 18345007

Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B. Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire. Genome Res. 2006 Oct;16(10):1208-21. PMID: 16963704; PMC: PMC1581430

Naughton BT, Fratkin E, Batzoglou S, Brutlag DL. A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites. Nucleic Acids Res. 2006;34(20):5730-9. PMID: 17041233; PMC: PMC1635261

Parker SC, Hansen L, Abaan HO, Tullius TD, Margulies EH. Local DNA topography correlates with functional noncoding regions of the human genome. Science. 2009 Apr 17;324(5925):389-92. PMID: 19286520; PMC: PMC2749491

Parker SC, Harlap A, Tullius TD. A computational method to search for DNA structural motifs in functional genomic elements. Methods Mol Biol. 2011;759:367-79. PMID: 21863498

Parker SC, Margulies EH, Tullius TD. The relationship between fine scale DNA structure, GC content, and functional elements in 1% of the human genome. Genome Inform. 2008;20:199-211. PMID: 19425134

Parker SC, Tullius TD. DNA shape, genetic codes, and evolution. Curr Opin Struct Biol. 2011 Jun;21(3):342-7. PMID: 21439813; PMC: PMC3112471

Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Res. 2007 Aug;17(8):1170-7. PMID: 17620451; PMC: PMC1933512

Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C. Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders. Genome Res. 2008 Mar;18(3):380-92. PMID: 18230803; PMC: PMC2259102

Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF et al. Butyrate mediates decrease of histone acetylation centered on transcription start sites and down- regulation of associated genes. Genome Res. 2007 Jun;17(6):708-19. PMID: 17567991; PMC: PMC1891332

Rada-Iglesias A, Wallerman O, Koch C, Ameur A, Enroth S, Clelland G, Wester K, Wilcox S, Dovey OM, Ellis PD et al. Binding sites for metabolic disease related transcription factors inferred at base pair resolution by chromatin immunoprecipitation and genomic microarrays. Hum Mol Genet. 2005 Nov 15;14(22):3435-47. PMID: 16221759

Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R et al. The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res. 2007 Jun;17(6):732-45. PMID: 17567993; PMC: PMC1891334

Srinivasan BS, Shah NH, Flannick JA, Abeliuk E, Novak AF, Batzoglou S. Current progress in network research: toward reference networks for key model organisms. Brief Bioinform. 2007 Sep;8(5):318-32. PMID: 17728341

Teer JK, Dutta A. Regulation of S phase. Results Probl Cell Differ. 2006;42:31-63. PMID: 16903207

Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J et al. The ENCODE Project at UC Santa Cruz. Nucleic Acids Res. 2007 Jan;35(Database issue):D663-7. PMID: 17166863; PMC: PMC1781110

Thurman RE, Day N, Noble WS, Stamatoyannopoulos JA. Identification of higher-order functional domains in the human ENCODE regions. Genome Res. 2007 Jun;17(6):917-27. PMID: 17568007; PMC: PMC1891350

Trinklein ND, Karaöz U, Wu J, Halees A, Force Aldred S, Collins PJ, Zheng D, Zhang ZD, Gerstein MB, Snyder M et al. Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome. Genome Res. 2007 Jun;17(6):720-31. PMID: 17567992; PMC: PMC1891333

Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A et al. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007 Jun;17(6):852-64. PMID: 17568003; PMC: PMC1891344

Willingham AT, Dike S, Cheng J, Manak JR, Bell I, Cheung E, Drenkow J, Dumais E, Duttagupta R, Ganesh M et al. Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes. Cold Spring Harb Symp Quant Biol. 2006;71:101-10. PMID: 17480199

Yang A, Zhu Z, Kapranov P, McKeon F, Church GM, Gingeras TR, Struhl K. Relationships between p63 binding, DNA sequence, transcription activity, and biological function in human cells. Mol Cell. 2006 Nov 17;24(4):593-602. PMID: 17188034

Zhang Z, Carriero N, Zheng D, Karro J, Harrison PM, Gerstein M. PseudoPipe: an automated pseudogene identification pipeline. Bioinformatics. 2006 Jun 15;22(12):1437-9. PMID: 16574694

Zhang ZD, Paccanaro A, Fu Y, Weissman S, Weng Z, Chang J, Snyder M, Gerstein MB. Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions. Genome Res. 2007 Jun;17(6):787-97. PMID: 17567997; PMC: PMC1891338

Zhang ZD, Rozowsky J, Lam HY, Du J, Snyder M, Gerstein M. Tilescope: online analysis pipeline for high-density tiling microarray data. Genome Biol. 2007;8(5):R81. PMID: 17501994; PMC: PMC1929149

Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M et al. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res. 2007 Jun;17(6):839-51. PMID: 17568002; PMC: PMC1891343

Zheng D, Gerstein MB. A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biol. 2006;7 Suppl 1:S13.1-10. PMID: 16925835; PMC: PMC1810550

Zheng D, Gerstein MB. The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?. Trends Genet. 2007 May;23(5):219-24. PMID: 17382428

Mouse ENCODE (26)

ENCODE Project Consortium. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046. PMID: 21526222; PMC: PMC3079585

Attanasio C, Nord AS, Zhu Y, Blow MJ, Li Z, Liberton DK, Morrison H, Plajzer-Frick I, Holt A, Hosseini R et al. Fine tuning of craniofacial morphology by distant-acting enhancers. Science. 2013 Oct 25;342(6157):1241006. PMID: 24159046

ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMC: PMC3439153

Blobel GA, Hardison RC. A cluster to remember. Cell. 2013 Aug 15;154(4):718-20. PMID: 23953105; PMC: PMC3878159

Chou ST, Byrska-Bishop M, Tober JM, Yao Y, Vandorn D, Opalinska JB, Mills JA, Choi JK, Speck NA, Gadue P et al. Trisomy 21-associated defects in human primitive hematopoiesis revealed through induced pluripotent stem cells. Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17573-8. PMID: 23045704; PMC: PMC3491490

Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012 Apr 11;485(7398):376-80. PMID: 22495300; PMC: PMC3356448

Giardine B, Borg J, Higgs DR, Peterson KR, Philipsen S, Maglott D, Singleton BK, Anstee DJ, Basak AN, Clark B et al. Systematic documentation and analysis of human genetic variation in hemoglobinopathies using the microattribution approach. Nat Genet. 2011 Mar 20;43(4):295-301. PMID: 21423179; PMC: PMC3878152

Hardison RC. Evolution of hemoglobin and its genes. Cold Spring Harb Perspect Med. 2012 Dec 1;2(12):a011627. PMID: 23209182; PMC: PMC3543078

Hardison RC. Genome-wide epigenetic data facilitate understanding of disease susceptibility association studies. J Biol Chem. 2012 Sep 7;287(37):30932-40. PMID: 22952232; PMC: PMC3438926

Hardison RC, Taylor J. Genomic approaches towards finding cis-regulatory modules in animals. Nat Rev Genet. 2012 Jun 18;13(7):469-83. PMID: 22705667; PMC: PMC3541939

Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat Rev Genet. 2010 Jul;11(7):476-86. PMID: 20531367; PMC: PMC3321268

Heintzman ND, Ren B. Finding distal regulatory elements in the human genome. Curr Opin Genet Dev. 2009 Dec;19(6):541-9. PMID: 19854636; PMC: PMC3321269

Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 2013 Jan;41(2):827-41. PMID: 23221638; PMC: PMC3553955

Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet. 2013 Oct;45(10):1198-206. PMID: 23995138

Hu M, Deng K, Qin Z, Dixon J, Selvaraj S, Fang J, Ren B, Liu JS. Bayesian inference of spatial organizations of chromosomes. PLoS Comput Biol. 2013;9(1):e1002893. PMID: 23382666; PMC: PMC3561073

Kadauke S, Udugama MI, Pawlicki JM, Achtman JC, Jain DP, Cheng Y, Hardison RC, Blobel GA. Tissue-specific mitotic bookmarking by hematopoietic transcription factor GATA1. Cell. 2012 Aug 17;150(4):725-37. PMID: 22901805; PMC: PMC3425057

Kaput J, Cotton RG, Hardman L, Watson M, Al Aqeel AI, Al-Aama JY, Al-Mulla F, Alonso S, Aretz S, Auerbach AD et al. Planning the human variome project: the Spain report. Hum Mutat. 2009 Apr;30(4):496-510. PMID: 19306394

Lamonica JM, Deng W, Kadauke S, Campbell AE, Gamsjaeger R, Wang H, Cheng Y, Billin AN, Hardison RC, Mackay JP et al. Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes. Proc Natl Acad Sci U S A. 2011 May 31;108(22):E159-68. PMID: 21536911; PMC: PMC3107332

Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature. 2012 Sep 6;489(7414):83-90. PMID: 22955618; PMC: PMC3736582

Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, Anderson SM, NISC Comparative Sequencing Center, Mullikin JC, Gallagher PG et al. Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. Blood. 2011 Oct 27;118(17):e139-48. PMID: 21900194; PMC: PMC3208289

Ponting CP, Hardison RC. What fraction of the human genome is functional?. Genome Res. 2011 Nov;21(11):1769-76. PMID: 21875934; PMC: PMC3205562

Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV et al. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012 Aug 2;488(7409):116-20. PMID: 22763441

Smallwood A, Ren B. Genome organization and long-range regulation of gene expression by enhancers. Curr Opin Cell Biol. 2013 Jun;25(3):387-94. PMID: 23465541

Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R et al. An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol. 2012 Aug 13;13(8):418. PMID: 22889292; PMC: PMC3491367

Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D et al. Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 2011 Oct;21(10):1659-71. PMID: 21795386; PMC: PMC3202283

Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL, Ren B. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell. 2012 Feb 17;148(4):816-31. PMID: 22341451; PMC: PMC3343639

modENCODE publications (145)

Consortium publications

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24;330(6012):1775-87. PMID: 21177976; PMC: PMC3142569

modENCODE Consortium, Roy S, Ernst J, Kharchenko PV, Kheradpour P, Negre N, Eaton ML, Landolin JM, Bristow CA, Ma L et al. Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science. 2010 Dec 24;330(6012):1787-97. PMID: 21177974; PMC: PMC3192495

All publications

Aagaard JE, Vacquier VD, MacCoss MJ, Swanson WJ. ZP domain proteins in the abalone egg coat include a paralog of VERL under positive selection that binds lysin and 18-kDa sperm proteins. Mol Biol Evol. 2010 Jan;27(1):193-203. PMID: 19767347; PMC: PMC2877556

Acharya P, Negre N, Johnston J, Wei Y, White KP, Henry RW, Arnosti DN. Evidence for autoregulation and cell signaling pathway regulation from genome-wide binding of the Drosophila retinoblastoma protein. G3 (Bethesda). 2012 Nov;2(11):1459-72. PMID: 23173097; PMC: PMC3484676

Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E et al. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet. 2012;8(4):e1002646. PMID: 22570616; PMC: PMC3343056

Allen MA, Hillier LW, Waterston RH, Blumenthal T. A global analysis of C. elegans trans-splicing. Genome Res. 2011 Feb;21(2):255-64. PMID: 21177958; PMC: PMC3032929

Atanesyan L, Günther V, Celniker SE, Georgiev O, Schaffner W. Characterization of MtnE, the fifth metallothionein member in Drosophila. J Biol Inorg Chem. 2011 Oct;16(7):1047-56. PMID: 21870250

Axtell MJ, Westholm JO, Lai EC. Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biol. 2011;12(4):221. PMID: 21554756; PMC: PMC3218855

Bansal MS, Alm EJ, Kellis M. Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics. 2012 Jun 15;28(12):i283-91. PMID: 22689773; PMC: PMC3371857

Bansal MS, Alm EJ, Kellis M. Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss. J Comput Biol. 2013 Oct;20(10):738-54. PMID: 24033262; PMC: PMC3791060

Bejarano F, Bortolamiol-Becet D, Dai Q, Sun K, Saj A, Chou YT, Raleigh DR, Kim K, Ni JQ, Duan H et al. A genome-wide transgenic resource for conditional expression of Drosophila microRNAs. Development. 2012 Aug;139(15):2821-31. PMID: 22745315; PMC: PMC3392707

Bereman MS, Canterbury JD, Egertson JD, Horner J, Remes PM, Schwartz J, Zabrouskov V, MacCoss MJ. Evaluation of front-end higher energy collision-induced dissociation on a benchtop dual-pressure linear ion trap mass spectrometer for shotgun proteomics. Anal Chem. 2012 Feb 7;84(3):1533-9. PMID: 22192247; PMC: PMC3277647

Bereman MS, Egertson JD, MacCoss MJ. Comparison between procedures using SDS for shotgun proteomic analyses of complex samples. Proteomics. 2011 Jul;11(14):2931-5. PMID: 21656683; PMC: PMC3517139

Berezikov E, Liu N, Flynt AS, Hodges E, Rooks M, Hannon GJ, Lai EC. Evolutionary flux of canonical microRNAs and mirtrons in Drosophila. Nat Genet. 2010 Jan;42(1):6-9; author reply 9-10. PMID: 20037610

Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol- Becet D, Martin R et al. Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence. Genome Res. 2011 Feb;21(2):203-15. PMID: 21177969; PMC: PMC3032924

Berkseth M, Ikegami K, Arur S, Lieb JD, Zarkower D. TRA-1 ChIP-seq reveals regulators of sexual differentiation and multilevel feedback in nematode sex determination. Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16033-8. PMID: 24046365; PMC: PMC3791753

Blanchette M, Green RE, MacArthur S, Brooks AN, Brenner SE, Eisen MB, Rio DC. Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell. 2009 Feb 27;33(4):438-49. PMID: 19250905; PMC: PMC2674966

Booker M, Samsonova AA, Kwon Y, Flockhart I, Mohr SE, Perrimon N. False negative rates in Drosophila cell-based RNAi screens: a case study. BMC Genomics. 2011 Jan 20;12:50. PMID: 21251254; PMC: PMC3036618

Brent MR. Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet. 2008 Jan;9(1):62-73. PMID: 18087260

Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. RNA. 2011 Oct;17(10):1884-94. PMID: 21865603; PMC: PMC3185920

Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res. 2011 Feb;21(2):193-202. PMID: 20921232; PMC: PMC3032923

Bryson TD, Weber CM, Henikoff S. Baculovirus-encoded protein expression for epigenomic profiling in Drosophila cells. Fly (Austin). 2010 Jul-Sep;4(3):258-65. PMID: 20495356

Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics. 2010 Feb 18;11:94. PMID: 20167110; PMC: PMC2838869

Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM et al. Unlocking the secrets of the genome. Nature. 2009 Jun 18;459(7249):927-30. PMID: 19536255; PMC: PMC2843545

Chen RA, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J. The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Genome Res. 2013 Aug;23(8):1339-47. PMID: 23550086; PMC: PMC3730107

Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J et al. Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods. 2012 Jun;9(6):609-14. PMID: 22522655; PMC: PMC3477507

Cherbas L, Willingham A, Zhang D, Yang L, Zou Y, Eads BD, Carlson JW, Landolin JM, Kapranov P, Dumais J et al. The transcriptional diversity of 25 Drosophila cell lines. Genome Res. 2011 Feb;21(2):301-14. PMID: 21177962; PMC: PMC3032933

Cheung MS, Down TA, Latorre I, Ahringer J. Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res. 2011 Aug;39(15):e103. PMID: 21646344; PMC: PMC3159482

Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC. Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res. 2011 Feb;21(2):286-300. PMID: 21177960; PMC: PMC3032932

Chung WJ, Okamura K, Martin R, Lai EC. Endogenous RNA interference provides a somatic defense against Drosophila transposons. Curr Biol. 2008 Jun 3;18(11):795-802. PMID: 18501606; PMC: PMC2812477

Contrino S, Smith RN, Butano D, Carr A, Hu F, Lyne R, Rutherford K, Kalderimis A, Sullivan J, Carbon S et al. modMine: flexible access to modENCODE data. Nucleic Acids Res. 2012 Jan;40(Database issue):D1082-8. PMID: 22080565; PMC: PMC3245176

Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R et al. An endogenous small interfering RNA pathway in Drosophila. Nature. 2008 Jun 5;453(7196):798-802. PMID: 18463631; PMC: PMC2895258

Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR et al. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 2011 Oct 23;43(12):1179-85. PMID: 22019781; PMC: PMC3576853

Ding Q, MacAlpine DM. Preferential re-replication of Drosophila heterochromatin in the absence of geminin. PLoS Genet. 2010 Sep 9;6(9):e1001112. PMID: 20838463; PMC: PMC2936543

Ding Q, MacAlpine DM. Defining the replication program through the chromatin landscape. Crit Rev Biochem Mol Biol. 2011 Apr;46(2):165-79. PMID: 21417598; PMC: PMC3074350

Dreszer TR, Karolchik D, Zweig AS, Hinrichs AS, Raney BJ, Kuhn RM, Meyer LR, Wong M, Sloan CA, Rosenbloom KR et al. The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Res. 2012 Jan;40(Database issue):D918-23. PMID: 22086951; PMC: PMC3245018

Eaton ML, Galani K, Kang S, Bell SP, MacAlpine DM. Conserved nucleosome positioning defines replication origins. Genes Dev. 2010 Apr 15;24(8):748-53. PMID: 20351051; PMC: PMC2854390

Eaton ML, Prinz JA, MacAlpine HK, Tretyakov G, Kharchenko PV, MacAlpine DM. Chromatin signatures of the Drosophila replication program. Genome Res. 2011 Feb;21(2):164-74. PMID: 21177973; PMC: PMC3032920

Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA, Cheung MS, Day DS, Gadel S, Gorchakov AA et al. An assessment of histone-modification antibody quality. Nat Struct Mol Biol. 2011 Jan;18(1):91-3. PMID: 21131980; PMC: PMC3017233

Engelmann I, Griffon A, Tichit L, Montañana-Sanchis F, Wang G, Reinke V, Waterston RH, Hillier LW, Ewbank JJ. A comprehensive analysis of gene expression changes provoked by bacterial and fungal infection in C. elegans. PLoS One. 2011;6(5):e19055. PMID: 21602919; PMC: PMC3094335

Ercan S, Dick LL, Lieb JD. The C. elegans dosage compensation complex propagates dynamically and independently of X chromosome sequence. Curr Biol. 2009 Nov 17;19(21):1777-87. PMID: 19853451; PMC: PMC2783177

Ercan S, Giresi PG, Whittle CM, Zhang X, Green RD, Lieb JD. X chromosome repression by localization of the C. elegans dosage compensation machinery to sites of transcription initiation. Nat Genet. 2007 Mar;39(3):403-8. PMID: 17293863; PMC: PMC2753834

Feizi S, Marbach D, Médard M, Kellis M. Network deconvolution as a general method to distinguish direct dependencies in networks. Nat Biotechnol. 2013 Aug;31(8):726-33. PMID: 23851448; PMC: PMC3773370

Feng J, Liu T, Zhang Y. Using MACS to identify peaks from ChIP-Seq data. Curr Protoc Bioinformatics. 2011 Jun;Chapter 2:Unit 2.14. PMID: 21633945; PMC: PMC3120977

Fernandez AG, Bargmann BO, Mis EK, Edgley ML, Birnbaum KD, Piano F. High-throughput fluorescence-based isolation of live C. elegans larvae. Nat Protoc. 2012 Jul 19;7(8):1502-10. PMID: 22814389

Fernandez AG, Mis EK, Bargmann BO, Birnbaum KD, Piano F. Automated sorting of live C. elegans using laFACS. Nat Methods. 2010 Jun;7(6):417-8. PMID: 20436474; PMC: PMC2896029

Findlay GD, MacCoss MJ, Swanson WJ. Proteomic discovery of previously unannotated, rapidly evolving seminal fluid genes in Drosophila. Genome Res. 2009 May;19(5):886-96. PMID: 19411605; PMC: PMC2675977

Flynt A, Liu N, Martin R, Lai EC. Dicing of viral replication intermediates during silencing of latent Drosophila viruses. Proc Natl Acad Sci U S A. 2009 Mar 31;106(13):5270-5. PMID: 19251644; PMC: PMC2663985

Flynt AS, Greimann JC, Chung WJ, Lima CD, Lai EC. MicroRNA biogenesis via splicing and exosome-mediated trimming in Drosophila. Mol Cell. 2010 Jun 25;38(6):900-7. PMID: 20620959; PMC: PMC2904328

Fox RM, Watson JD, Von Stetina SE, McDermott J, Brodigan TM, Fukushige T, Krause M, Miller DM 3rd. The embryonic muscle transcriptome of Caenorhabditis elegans. Genome Biol. 2007;8(9):R188. PMID: 17848203; PMC: PMC2375026

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. PMID: 20959295; PMC: PMC3242726

Gan HH, Gunsalus KC. Tertiary structure-based analysis of microRNA-target interactions. RNA. 2013 Apr;19(4):539-51. PMID: 23417009; PMC: PMC3677264

Gassmann R, Rechtsteiner A, Yuen KW, Muroyama A, Egelhofer T, Gaydos L, Barron F, Maddox P, Essex A, Monen J et al. An inverse relationship to germline transcription defines centromeric chromatin in C. elegans. Nature. 2012 Apr 8;484(7395):534-7. PMID: 22495302; PMC: PMC3538161

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science. 2010 Dec 24;330(6012):1775-87. PMID: 21177976; PMC: PMC3142569

Gingeras TR. Implications of chimaeric non-co-linear transcripts. Nature. 2009 Sep 10;461(7261):206-11. PMID: 19741701

Graveley BR. The haplo-spliceo-transcriptome: common variations in alternative splicing in the human population. Trends Genet. 2008 Jan;24(1):5-7. PMID: 18054116; PMC: PMC2372159

Graveley BR, Brooks AN, Carlson JW, Duff MO, Landolin JM, Yang L, Artieri CG, van Baren MJ, Boley N, Booth BW et al. The developmental transcriptome of Drosophila melanogaster. Nature. 2011 Mar 24;471(7339):473-9. PMID: 21179090; PMC: PMC3075879

Gunsalus KC. A Caenorhabditis elegans genetic-interaction map wiggles into view. J Biol. 2008;7(3):8. PMID: 18341704; PMC: PMC2323036

Gunsalus KC, Rhrissorrakrai K. Networks in Caenorhabditis elegans. Curr Opin Genet Dev. 2011 Dec;21(6):787-98. PMID: 22054717

Hagen JW, Lai EC. microRNA control of cell-cell signaling during development and disease. Cell Cycle. 2008 Aug;7(15):2327-32. PMID: 18677099; PMC: PMC2697031

Hallem EA, Spencer WC, McWhirter RD, Zeller G, Henz SR, Rätsch G, Miller DM 3rd, Horvitz HR, Sternberg PW, Ringstad N. Receptor-type guanylate cyclase is required for carbon dioxide sensation by Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2011 Jan 4;108(1):254-9. PMID: 21173231; PMC: PMC3017194

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