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Items: 1 to 20 of 74

1.

Human Transcriptome and Chromatin Modifications: An ENCODE Perspective.

Shen L, Choi I, Nestler EJ, Won KJ.

Genomics Inform. 2013 Jun;11(2):60-7. doi: 10.5808/GI.2013.11.2.60. Epub 2013 Jun 30.

PMID:
23843771
2.

ENCODE: A Sourcebook of Epigenomes and Chromatin Language.

Yavartanoo M, Choi JK.

Genomics Inform. 2013 Mar;11(1):2-6. doi: 10.5808/GI.2013.11.1.2. Epub 2013 Mar 31.

PMID:
23613676
3.

Epigenetics, chromatin and genome organization: recent advances from the ENCODE project.

Siggens L, Ekwall K.

J Intern Med. 2014 Sep;276(3):201-14. doi: 10.1111/joim.12231. Epub 2014 Mar 27. Review.

PMID:
24605849
4.

A comprehensive view of nuclear receptor cancer cistromes.

Tang Q, Chen Y, Meyer C, Geistlinger T, Lupien M, Wang Q, Liu T, Zhang Y, Brown M, Liu XS.

Cancer Res. 2011 Nov 15;71(22):6940-7. doi: 10.1158/0008-5472.CAN-11-2091. Epub 2011 Sep 22.

PMID:
21940749
5.

[The ENCODE project and functional genomics studies].

Ding N, Qu H, Fang X.

Yi Chuan. 2014 Mar;36(3):237-47. Review. Chinese.

PMID:
24846964
6.

A brief review on the Human Encyclopedia of DNA Elements (ENCODE) project.

Qu H, Fang X.

Genomics Proteomics Bioinformatics. 2013 Jun;11(3):135-41. doi: 10.1016/j.gpb.2013.05.001. Epub 2013 May 28. Review.

PMID:
23722115
7.

Integrative annotation of chromatin elements from ENCODE data.

Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS.

Nucleic Acids Res. 2013 Jan;41(2):827-41. doi: 10.1093/nar/gks1284. Epub 2012 Dec 5.

PMID:
23221638
8.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A.

Genome Res. 2012 Sep;22(9):1698-710. doi: 10.1101/gr.134478.111.

PMID:
22955982
9.

The ENCODE project: implications for psychiatric genetics.

Kavanagh DH, Dwyer S, O'Donovan MC, Owen MJ.

Mol Psychiatry. 2013 May;18(5):540-2. doi: 10.1038/mp.2013.13. Epub 2013 Mar 12. Review.

PMID:
23478746
10.

A decade of human genome project conclusion: Scientific diffusion about our genome knowledge.

Moraes F, Góes A.

Biochem Mol Biol Educ. 2016 May 6;44(3):215-23. doi: 10.1002/bmb.20952. Epub 2016 Mar 7. Review.

PMID:
26952518
11.

Proteogenomics Dashboard for the Human Proteome Project.

Tabas-Madrid D, Alves-Cruzeiro J, Segura V, Guruceaga E, Vialas V, Prieto G, García C, Corrales FJ, Albar JP, Pascual-Montano A.

J Proteome Res. 2015 Sep 4;14(9):3738-49. doi: 10.1021/acs.jproteome.5b00466. Epub 2015 Jul 16.

PMID:
26144527
12.

Histone modifications in zebrafish development.

Cunliffe VT.

Methods Cell Biol. 2016;135:361-85. doi: 10.1016/bs.mcb.2016.05.005. Epub 2016 Jun 20.

PMID:
27443936
13.

Finding the active genes in deep RNA-seq gene expression studies.

Hart T, Komori HK, LaMere S, Podshivalova K, Salomon DR.

BMC Genomics. 2013 Nov 11;14:778. doi: 10.1186/1471-2164-14-778.

PMID:
24215113
14.

Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.

Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D, Birney E, Hung JH, Weng Z.

Nucleic Acids Res. 2013 Jan;41(Database issue):D171-6. doi: 10.1093/nar/gks1221. Epub 2012 Nov 29.

PMID:
23203885
15.

Combinatorial chromatin modification patterns in the human genome revealed by subspace clustering.

Ucar D, Hu Q, Tan K.

Nucleic Acids Res. 2011 May;39(10):4063-75. doi: 10.1093/nar/gkr016. Epub 2011 Jan 25.

PMID:
21266477
16.

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R.

Genome Res. 2012 Sep;22(9):1775-89. doi: 10.1101/gr.132159.111.

PMID:
22955988
17.

Using the ENCODE Resource for Functional Annotation of Genetic Variants.

Pazin MJ.

Cold Spring Harb Protoc. 2015 Mar 11;2015(6):522-36. doi: 10.1101/pdb.top084988. Review.

PMID:
25762420
18.

ENCODE data at the ENCODE portal.

Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee BT, Rowe LD, Dreszer TR, Roe G, Podduturi NR, Tanaka F, Hong EL, Cherry JM.

Nucleic Acids Res. 2016 Jan 4;44(D1):D726-32. doi: 10.1093/nar/gkv1160. Epub 2015 Nov 2.

PMID:
26527727
19.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium..

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

PMID:
25409824
20.

AceView: a comprehensive cDNA-supported gene and transcripts annotation.

Thierry-Mieg D, Thierry-Mieg J.

Genome Biol. 2006;7 Suppl 1:S12.1-14. Epub 2006 Aug 7.

PMID:
16925834

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