ENCODE-funded 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.

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

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J et al. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One. 2012;7(1):e28213. PMID: 22238572; PMC: PMC3251577

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Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Mol Cell Biol. 2012 Jan;32(1):226-39. PMID: 22025678; PMC: PMC3255705

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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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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

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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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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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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

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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

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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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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

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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

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

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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

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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

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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

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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, 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

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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

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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

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

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

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

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

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

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

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

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

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

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

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

Han T, Manoharan AP, Harkins TT, Bouffard P, Fitzpatrick C, Chu DS, Thierry-Mieg D, Thierry-Mieg J, Kim JK. 26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18674-9. PMID: 19846761; PMC: PMC2765456

Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res. 2010 Jul;38(12):e131. PMID: 20395217; PMC: PMC2896536

Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S et al. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet. 2009 Jun;5(6):e1000525. PMID: 19543372; PMC: PMC2689934

Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD et al. Recombinant antibodies to histone post-translational modifications. Nat Methods. 2013 Oct;10(10):992-5. PMID: 23955773; PMC: PMC3828030

Henikoff S, Henikoff JG, Sakai A, Loeb GB, Ahmad K. Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Res. 2009 Mar;19(3):460-9. PMID: 19088306; PMC: PMC2661814

Herr A, Longworth M, Ji JY, Korenjak M, Macalpine DM, Dyson NJ. Identification of E2F target genes that are rate limiting for dE2F1-dependent cell proliferation. Dev Dyn. 2012 Nov;241(11):1695-707. PMID: 22972499; PMC: PMC3760379

Hillier LW, Reinke V, Green P, Hirst M, Marra MA, Waterston RH. Massively parallel sequencing of the polyadenylated transcriptome of C. elegans. Genome Res. 2009 Apr;19(4):657-66. PMID: 19181841; PMC: PMC2665784

Ho JW, Bishop E, Karchenko PV, Nègre N, White KP, Park PJ. ChIP-chip versus ChIP-seq: lessons for experimental design and data analysis. BMC Genomics. 2011 Feb 28;12:134. PMID: 21356108; PMC: PMC3053263

Hoskins RA, Landolin JM, Brown JB, Sandler JE, Takahashi H, Lassmann T, Yu C, Booth BW, Zhang D, Wan KH et al. Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res. 2011 Feb;21(2):182-92. PMID: 21177961; PMC: PMC3032922

Ikegami K, Egelhofer TA, Strome S, Lieb JD. Caenorhabditis elegans chromosome arms are anchored to the nuclear membrane via discontinuous association with LEM-2. Genome Biol. 2010;11(12):R120. PMID: 21176223; PMC: PMC3046480

Ikegami K, Lieb JD. Integral nuclear pore proteins bind to Pol III-transcribed genes and are required for Pol III transcript processing in C. elegans. Mol Cell. 2013 Sep 26;51(6):840-9. PMID: 24011592; PMC: PMC3788088

Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec;26(12):1351-9. PMID: 19029915; PMC: PMC2597701

Kim JC, Nordman J, Xie F, Kashevsky H, Eng T, Li S, MacAlpine DM, Orr-Weaver TL. Integrative analysis of gene amplification in Drosophila follicle cells: parameters of origin activation and repression. Genes Dev. 2011 Jul 1;25(13):1384-98. PMID: 21724831; PMC: PMC3134082

Kiontke KC, Félix MA, Ailion M, Rockman MV, Braendle C, Pénigault JB, Fitch DH. A phylogeny and molecular barcodes for Caenorhabditis, with numerous new species from rotting fruits. BMC Evol Biol. 2011 Nov 21;11:339. PMID: 22103856; PMC: PMC3277298

Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet. 2009 Mar;41(3):376-81. PMID: 19182803; PMC: PMC2648722

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

Ladewig E, Okamura K, Flynt AS, Westholm JO, Lai EC. Discovery of hundreds of mirtrons in mouse and human small RNA data. Genome Res. 2012 Sep;22(9):1634-45. PMID: 22955976; PMC: PMC3431481

Lau NC, Robine N, Martin R, Chung WJ, Niki Y, Berezikov E, Lai EC. Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line. Genome Res. 2009 Oct;19(10):1776-85. PMID: 19541914; PMC: PMC2765285

Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G. Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high- throughput sequencing are not conserved across closely related yeast species. PLoS Genet. 2008 Dec;4(12):e1000299. PMID: 19096707; PMC: PMC2601015

Lei H, Fukushige T, Niu W, Sarov M, Reinke V, Krause M. A widespread distribution of genomic CeMyoD binding sites revealed and cross validated by ChIP-Chip and ChIP-Seq techniques. PLoS One. 2010 Dec 29;5(12):e15898. PMID: 21209968; PMC: PMC3012110

Liu N, Okamura K, Tyler DM, Phillips MD, Chung WJ, Lai EC. The evolution and functional diversification of animal microRNA genes. Cell Res. 2008 Oct;18(10):985-96. PMID: 18711447; PMC: PMC2712117

Liu T, Rechtsteiner A, Egelhofer TA, Vielle A, Latorre I, Cheung MS, Ercan S, Ikegami K, Jensen M, Kolasinska-Zwierz P et al. Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res. 2011 Feb;21(2):227-36. PMID: 21177964; PMC: PMC3032926

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

MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Res. 2010 Feb;20(2):201-11. PMID: 19996087; PMC: PMC2813476

Mangone M, Macmenamin P, Zegar C, Piano F, Gunsalus KC. UTRome.org: a platform for 3'UTR biology in C. elegans. Nucleic Acids Res. 2008 Jan;36(Database issue):D57-62. PMID: 17986455; PMC: PMC2238901

Mangone M, Manoharan AP, Thierry-Mieg D, Thierry-Mieg J, Han T, Mackowiak SD, Mis E, Zegar C, Gutwein MR, Khivansara V et al. The landscape of C. elegans 3'UTRs. Science. 2010 Jul 23;329(5990):432-5. PMID: 20522740; PMC: PMC3142571

Mansisidor AR, Cecere G, Hoersch S, Jensen MB, Kawli T, Kennedy LM, Chavez V, Tan MW, Lieb JD, Grishok A. A conserved PHD finger protein and endogenous RNAi modulate insulin signaling in Caenorhabditis elegans. PLoS Genet. 2011 Sep;7(9):e1002299. PMID: 21980302; PMC: PMC3183084

McKay SJ, Vergara IA, Stajich JE. Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics. 2010 Sep;Chapter 9:Unit 9.12. PMID: 20836076; PMC: PMC3162311

Miura P, Shenker S, Andreu-Agullo C, Westholm JO, Lai EC. Widespread and extensive lengthening of 3' UTRs in the mammalian brain. Genome Res. 2013 May;23(5):812-25. PMID: 23520388; PMC: PMC3638137

Mohammed J, Flynt AS, Siepel A, Lai EC. The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution. RNA. 2013 Sep;19(9):1295-308. PMID: 23882112; PMC: PMC3753935

Müller P, Park S, Shor E, Huebert DJ, Warren CL, Ansari AZ, Weinreich M, Eaton ML, MacAlpine DM, Fox CA. The conserved bromo-adjacent homology domain of yeast Orc1 functions in the selection of DNA replication origins within chromatin. Genes Dev. 2010 Jul 1;24(13):1418-33. PMID: 20595233; PMC: PMC2895200

Nègre N, Brown CD, Ma L, Bristow CA, Miller SW, Wagner U, Kheradpour P, Eaton ML, Loriaux P, Sealfon R et al. A cis-regulatory map of the Drosophila genome. Nature. 2011 Mar 24;471(7339):527-31. PMID: 21430782; PMC: PMC3179250

Ni X, Zhang YE, Nègre N, Chen S, Long M, White KP. Adaptive evolution and the birth of CTCF binding sites in the Drosophila genome. PLoS Biol. 2012;10(11):e1001420. PMID: 23139640; PMC: PMC3491045

Niu W, Lu ZJ, Zhong M, Sarov M, Murray JI, Brdlik CM, Janette J, Chen C, Alves P, Preston E et al. Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans. Genome Res. 2011 Feb;21(2):245-54. PMID: 21177963; PMC: PMC3032928

Nordman J, Li S, Eng T, Macalpine D, Orr-Weaver TL. Developmental control of the DNA replication and transcription programs. Genome Res. 2011 Feb;21(2):175-81. PMID: 21177957; PMC: PMC3032921

Oh H, Slattery M, Ma L, Crofts A, White KP, Mann RS, Irvine KD. Genome-wide association of Yorkie with chromatin and chromatin-remodeling complexes. Cell Rep. 2013 Feb 21;3(2):309-18. PMID: 23395637; PMC: PMC3633442

Okamura K, Balla S, Martin R, Liu N, Lai EC. Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat Struct Mol Biol. 2008 Jun;15(6):581-90. PMID: 18500351; PMC: PMC2713754

Okamura K, Liu N, Lai EC. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes. Mol Cell. 2009 Nov 13;36(3):431-44. PMID: 19917251; PMC: PMC2785079

Okamura K, Robine N, Liu Y, Liu Q, Lai EC. R2D2 organizes small regulatory RNA pathways in Drosophila. Mol Cell Biol. 2011 Feb;31(4):884-96. PMID: 21135122; PMC: PMC3028645

Ooi SL, Henikoff JG, Henikoff S. A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans. Nucleic Acids Res. 2010 Mar;38(4):e26. PMID: 19966274; PMC: PMC2831312

Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009 Oct;10(10):669-80. PMID: 19736561; PMC: PMC3191340

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

Rechtsteiner A, Ercan S, Takasaki T, Phippen TM, Egelhofer TA, Wang W, Kimura H, Lieb JD, Strome S. The histone H3K36 methyltransferase MES-4 acts epigenetically to transmit the memory of germline gene expression to progeny. PLoS Genet. 2010 Sep 2;6(9):e1001091. PMID: 20824077; PMC: PMC2932692

Riddle NC, Jung YL, Gu T, Alekseyenko AA, Asker D, Gui H, Kharchenko PV, Minoda A, Plachetka A, Schwartz YB et al. Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genet. 2012 Sep;8(9):e1002954. PMID: 23028361; PMC: PMC3447959

Riddle NC, Minoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D et al. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res. 2011 Feb;21(2):147-63. PMID: 21177972; PMC: PMC3032919

Robine N, Lau NC, Balla S, Jin Z, Okamura K, Kuramochi-Miyagawa S, Blower MD, Lai EC. A broadly conserved pathway generates 3'UTR-directed primary piRNAs. Curr Biol. 2009 Dec 29;19(24):2066-76. PMID: 20022248; PMC: PMC2812478

Sarov M, Murray JI, Schanze K, Pozniakovski A, Niu W, Angermann K, Hasse S, Rupprecht M, Vinis E, Tinney M et al. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 2012 Aug 17;150(4):855-66. PMID: 22901814

Schwartz YB, Linder-Basso D, Kharchenko PV, Tolstorukov MY, Kim M, Li HB, Gorchakov AA, Minoda A, Shanower G, Alekseyenko AA et al. Nature and function of insulator protein binding sites in the Drosophila genome. Genome Res. 2012 Nov;22(11):2188-98. PMID: 22767387; PMC: PMC3483548

Sharanya D, Thillainathan B, Marri S, Bojanala N, Taylor J, Flibotte S, Moerman DG, Waterston RH, Gupta BP. Genetic control of vulval development in Caenorhabditis briggsae. G3 (Bethesda). 2012 Dec;2(12):1625-41. PMID: 23275885; PMC: PMC3516484

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ENCODE Consortium publications

ENCODE publications (316)