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Items: 1 to 20 of 110

1.
2.

Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site.

Tabach Y, Brosh R, Buganim Y, Reiner A, Zuk O, Yitzhaky A, Koudritsky M, Rotter V, Domany E.

PLoS One. 2007 Aug 29;2(8):e807.

3.

Construction of a genome-scale structural map at single-nucleotide resolution.

Greenbaum JA, Pang B, Tullius TD.

Genome Res. 2007 Jun;17(6):947-53.

4.

The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci.

Rozowsky JS, Newburger D, Sayward F, Wu J, Jordan G, Korbel JO, Nagalakshmi U, Yang J, Zheng D, Guigó R, Gingeras TR, Weissman S, Miller P, Snyder M, Gerstein MB.

Genome Res. 2007 Jun;17(6):732-45.

5.

The human genomic melting map.

Liu F, Tøstesen E, Sundet JK, Jenssen TK, Bock C, Jerstad GI, Thilly WG, Hovig E.

PLoS Comput Biol. 2007 May;3(5):e93. Epub 2007 Apr 11.

6.

Genome-wide transcription and the implications for genomic organization.

Kapranov P, Willingham AT, Gingeras TR.

Nat Rev Genet. 2007 Jun;8(6):413-23. Epub 2007 May 8. Review.

PMID:
17486121
7.

Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs.

Ponjavic J, Ponting CP, Lunter G.

Genome Res. 2007 May;17(5):556-65. Epub 2007 Mar 26.

8.

Characterization and identification of microRNA core promoters in four model species.

Zhou X, Ruan J, Wang G, Zhang W.

PLoS Comput Biol. 2007 Mar 9;3(3):e37. Epub 2007 Jan 9.

9.

Large-scale identification of novel transcripts in the human genome.

Peters BA, St Croix B, Sjöblom T, Cummins JM, Silliman N, Ptak J, Saha S, Kinzler KW, Hatzis C, Velculescu VE.

Genome Res. 2007 Mar;17(3):287-92. Epub 2007 Jan 31.

10.

Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters.

Baek D, Davis C, Ewing B, Gordon D, Green P.

Genome Res. 2007 Feb;17(2):145-55. Epub 2007 Jan 8.

11.

Dynamic usage of transcription start sites within core promoters.

Kawaji H, Frith MC, Katayama S, Sandelin A, Kai C, Kawai J, Carninci P, Hayashizaki Y.

Genome Biol. 2006;7(12):R118.

12.

Ensembl 2007.

Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7. Epub 2006 Dec 5.

13.

The UCSC genome browser database: update 2007.

Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ.

Nucleic Acids Res. 2007 Jan;35(Database issue):D668-73. Epub 2006 Nov 16.

14.

Core promoter elements recognized by transcription factor IIB.

Deng W, Roberts SG.

Biochem Soc Trans. 2006 Dec;34(Pt 6):1051-3.

PMID:
17073748
15.
16.

PromoterExplorer: an effective promoter identification method based on the AdaBoost algorithm.

Xie X, Wu S, Lam KM, Yan H.

Bioinformatics. 2006 Nov 15;22(22):2722-8. Epub 2006 Sep 25.

PMID:
17000749
17.

GENCODE: producing a reference annotation for ENCODE.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

Genome Biol. 2006;7 Suppl 1:S4.1-9. Epub 2006 Aug 7.

18.

Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

Bajic VB, Brent MR, Brown RH, Frankish A, Harrow J, Ohler U, Solovyev VV, Tan SL.

Genome Biol. 2006;7 Suppl 1:S3.1-13. Epub 2006 Aug 7. Review.

19.

Automatic annotation of eukaryotic genes, pseudogenes and promoters.

Solovyev V, Kosarev P, Seledsov I, Vorobyev D.

Genome Biol. 2006;7 Suppl 1:S10.1-12. Epub 2006 Aug 7.

20.

ARTS: accurate recognition of transcription starts in human.

Sonnenburg S, Zien A, Rätsch G.

Bioinformatics. 2006 Jul 15;22(14):e472-80.

PMID:
16873509

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