ENCODE-funded Publications

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

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.

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, 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.

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.

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.

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.

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.

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.

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.

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.

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.

Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E et al. Modeling gene expression using chromatin features in various cellular contexts. Genome Biol. 2012 Sep 5;13(9):R53.

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.

Frietze S, Wang R, Yao L, Tak YG, Ye Z, Gaddis M, Witt H, Farnham PJ, Jin VX. Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biol. 2012 Sep 5;13(9):R52.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 2012 Sep 6;489(7414):91-100.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S et al. GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep;22(9):1760-74.

Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T et al. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res. 2012 Sep;22(9):1698-710.

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Res. 2012 Sep;22(9):1735-47.

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.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep;22(9):1813-31.

Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012 Sep 7;337(6099):1190-5.

Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U. Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res. 2012 Sep;22(9):1711-22.

Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. Circuitry and dynamics of human transcription factor regulatory networks. Cell. 2012 Sep 14;150(6):1274-86.

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.

Ni Y, Weber Hall A, Battenhouse A, Iyer VR. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genet. 2012 Sep 5;13:46.

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.

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 5;13(9):R51.

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

Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012 Sep;22(9):1748-59.

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 5;13(9):R49.

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.

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.

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.

Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R et al. Widespread plasticity in CTCF occupancy linked to DNA methylation. Genome Res. 2012 Sep;22(9):1680-8.

Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep;22(9):1798-812.

Ward LD, Kellis M. Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science. 2012 Sep 28;337(6102):1675-8.

Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, Myers RM, Weng Z. Functional analysis of transcription factor binding sites in human promoters. Genome Biol. 2012 Sep 5;13(9):R50.

Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M et al. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biol. 2012 Sep 5;13(9):R48.

2012

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.

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.

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.

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.

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.

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.

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

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

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.

Ernst J, Kellis M. ChromHMM: automating chromatin-state discovery and characterization. Nat Methods. 2012 Feb 28;9(3):215-6.

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

Frankish A, Mudge JM, Thomas M, Harrow J. The importance of identifying alternative splicing in vertebrate genome annotation. Database (Oxford). 2012;2012:bas014.

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

Harte RA, Farrell CM, Loveland JE, Suner MM, Wilming L, Aken B, Barrell D, Frankish A, Wallin C, Searle S et al. Tracking and coordinating an international curation effort for the CCDS Project. Database (Oxford). 2012;2012:bas008.

Hoffman MM, Buske OJ, Wang J, Weng Z, Bilmes JA, Noble WS. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat Methods. 2012 Mar 18;9(5):473-6.

Iyer VR. Nucleosome positioning: bringing order to the eukaryotic genome. Trends Cell Biol. 2012 May;22(5):250-6.

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.

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.

Lan X, Farnham PJ, Jin VX. Uncovering Transcription Factor Modules Using One- and Three-dimensional Analyses. J Biol Chem. 2012 Sep 7;287(37):30914-21.

Lan X, Witt H, Katsumura K, Ye Z, Wang Q, Bresnick EH, Farnham PJ, Jin VX. Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin linkages. Nucleic Acids Res. 2012 Sep 1;40(16):7690-7704.

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.

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.

Maurano MT, Wang H, Kutyavin T, Stamatoyannopoulos JA. Widespread site-dependent buffering of human regulatory polymorphism. PLoS Genet. 2012;8(3):e1002599.

Natarajan A, Yardimci GG, Sheffield NC, Crawford GE, Ohler U. Predicting cell-type-specific gene expression from regions of open chromatin. Genome Res. 2012 Sep;22(9):1711-22.

Neph S, Stergachis AB, Reynolds A, Sandstrom R, Borenstein E, Stamatoyannopoulos JA. Circuitry and dynamics of human transcription factor regulatory networks. Cell. 2012 Sep 14;150(6):1274-86.

Ni Y, Weber Hall A, Battenhouse A, Iyer VR. Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data. BMC Genet. 2012 Sep 5;13:46.

Nielsen CB, Younesy H, O'Geen H, Xu X, Jackson AR, Milosavljevic A, Wang T, Costello JF, Hirst M, Farnham PJ et al. Spark: A navigational paradigm for genomic data exploration. Genome Res. 2012 Oct 3;.

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.

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 5;13(9):R51.

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.

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.

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

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.

Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012 Sep;22(9):1748-59.

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.

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.

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.

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

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

Ward LD, Kellis M. Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science. 2012 Sep 28;337(6102):1675-8.

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.

Wiggs JL, Yaspan BL, Hauser MA, Kang JH, Allingham RR, Olson LM, Abdrabou W, Fan BJ, Wang DY, Brodeur W et al. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. PLoS Genet. 2012;8(4):e1002654.

Yusuf D, Butland SL, Swanson MI, Bolotin E, Ticoll A, Cheung WA, Zhang XY, Dickman CT, Fulton DL, Lim JS et al. The transcription factor encyclopedia. Genome Biol. 2012;13(3):R24.

2011

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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

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.

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

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

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.

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.

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.

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.

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

Iyengar S, Ivanov AV, Jin VX, Rauscher FJ 3rd, Farnham PJ. Functional analysis of KAP1 genomic recruitment. Mol Cell Biol. 2011 May;31(9):1833-47.

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

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

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.

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.

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.

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

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.

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

2010

1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.

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.

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

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

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

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

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

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

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

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

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.

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.

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.

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

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

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.

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.

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

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

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

Li G, 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.

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.

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

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

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

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.

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.

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

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

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.

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

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

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.

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

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

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

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.

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.

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.

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.

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.

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

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.

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

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

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

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

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

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

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

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

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

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.

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

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

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.

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.

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

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

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

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

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.

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

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

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

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.

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.

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

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

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.

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

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

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.

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

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

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.

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

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.

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

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

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

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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.

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

Fullwood MJ, 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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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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.

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.

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.

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.

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.

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.

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.

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

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.

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

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

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

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.

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.

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.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

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

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

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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

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.

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.

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

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).

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.

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.

Sher N, Bell GW, Li S, Nordman J, Eng T, Eaton ML, Macalpine DM, Orr-Weaver TL. Developmental control of gene copy number by repression of replication initiation and fork progression. Genome Res. 2012 Jan;22(1):64-75.

Smibert P, Lai EC. A view from Drosophila: multiple biological functions for individual microRNAs. Semin Cell Dev Biol. 2010 Sep;21(7):745-53.

Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB et al. Global patterns of tissue-specific alternative polyadenylation in Drosophila. Cell Rep. 2012 Mar 29;1(3):277-89.

Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. Model-based analysis of two-color arrays (MA2C). Genome Biol. 2007;8(8):R178.

Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J et al. A spatial and temporal map of C. elegans gene expression. Genome Res. 2011 Feb;21(2):325-41.

Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD. Co-orientation of replication and transcription preserves genome integrity. PLoS Genet. 2010 Jan 15;6(1):e1000810.

Stoeckius M, Maaskola J, Colombo T, Rahn HP, Friedländer MR, Li N, Chen W, Piano F, Rajewsky N. Large-scale sorting of C. elegans embryos reveals the dynamics of small RNA expression. Nat Methods. 2009 Oct;6(10):745-51.

Tian F, Shah PK, Liu X, Negre N, Chen J, Karpenko O, White KP, Grossman RL. Flynet: a genomic resource for Drosophila melanogaster transcriptional regulatory networks. Bioinformatics. 2009 Nov 15;25(22):3001-4.

Tolstorukov MY, Kharchenko PV, Park PJ. Analysis of primary structure of chromatin with next-generation sequencing. Epigenomics. 2010 Apr;2(2):187-197.

Tolstorukov MY, Volfovsky N, Stephens RM, Park PJ. Impact of chromatin structure on sequence variability in the human genome. Nat Struct Mol Biol. 2011 Apr;18(4):510-5.

Venken KJ, Carlson JW, Schulze KL, Pan H, He Y, Spokony R, Wan KH, Koriabine M, de Jong PJ, White KP et al. Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nat Methods. 2009 Jun;6(6):431-4.

Von Stetina SE, Watson JD, Fox RM, Olszewski KL, Spencer WC, Roy PJ, Miller DM 3rd. Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. Genome Biol. 2007;8(7):R135.

Wang Y, Wu W, Negre NN, White KP, Li C, Shah PK. Determinants of antigenicity and specificity in immune response for protein sequences. BMC Bioinformatics. 2011 Jun 21;12:251.

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

Watson JD, Wang S, Von Stetina SE, Spencer WC, Levy S, Dexheimer PJ, Kurn N, Heath JD, Miller DM 3rd. Complementary RNA amplification methods enhance microarray identification of transcripts expressed in the C. elegans nervous system. BMC Genomics. 2008 Feb 19;9:84.

Westholm JO, Ladewig E, Okamura K, Robine N, Lai EC. Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs. RNA. 2012 Feb;18(2):177-92.

Whittle CM, McClinic KN, Ercan S, Zhang X, Green RD, Kelly WG, Lieb JD. The genomic distribution and function of histone variant HTZ-1 during C. elegans embryogenesis. PLoS Genet. 2008 Sep 12;4(9):e1000187.

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.

Zhang Y, Malone JH, Powell SK, Periwal V, Spana E, Macalpine DM, Oliver B. Expression in aneuploid Drosophila S2 cells. PLoS Biol. 2010 Feb 23;8(2):e1000320.

Zhong M, Niu W, Lu ZJ, Sarov M, Murray JI, Janette J, Raha D, Sheaffer KL, Lam HY, Preston E et al. Genome-wide identification of binding sites defines distinct functions for Caenorhabditis elegans PHA-4/FOXA in development and environmental response. PLoS Genet. 2010 Feb 19;6(2):e1000848.

Contents

ENCODE Consortium publications

Recent publications of special interest

ENCODE publications (200)

2012

2011

2010

2009

2008

2007

ENCODE Technology Development publications (108)

ENCODE pilot project publications (80)

Mouse ENCODE (7)

modENCODE publications (108)

Consortium publications

All publications