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Items: 19

1.

The impact of next-generation sequencing technology on genetics.

Mardis ER.

Trends Genet. 2008 Mar;24(3):133-41. doi: 10.1016/j.tig.2007.12.007. Epub 2008 Feb 11. Review.

PMID:
18262675
2.

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.

Rada-Iglesias A, Ameur A, Kapranov P, Enroth S, Komorowski J, Gingeras TR, Wadelius C.

Genome Res. 2008 Mar;18(3):380-92. doi: 10.1101/gr.6880908. Epub 2008 Jan 29.

3.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

4.

RNA maps reveal new RNA classes and a possible function for pervasive transcription.

Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.

Science. 2007 Jun 8;316(5830):1484-8. Epub 2007 May 17.

5.

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
6.

Activating gene expression in mammalian cells with promoter-targeted duplex RNAs.

Janowski BA, Younger ST, Hardy DB, Ram R, Huffman KE, Corey DR.

Nat Chem Biol. 2007 Mar;3(3):166-73. Epub 2007 Jan 28.

PMID:
17259978
7.

snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

Yang JH, Zhang XC, Huang ZP, Zhou H, Huang MB, Zhang S, Chen YQ, Qu LH.

Nucleic Acids Res. 2006;34(18):5112-23. Epub 2006 Sep 20.

8.

Genome-wide analysis of mammalian promoter architecture and evolution.

Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engström PG, Frith MC, Forrest AR, Alkema WB, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y.

Nat Genet. 2006 Jun;38(6):626-35. Epub 2006 Apr 28. Erratum in: Nat Genet. 2007 Sep;39(9):1174.

PMID:
16645617
9.

CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis.

Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J, Carninci P, Hayashizaki Y.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D632-6.

11.

A strategy for probing the function of noncoding RNAs finds a repressor of NFAT.

Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, Hogenesch JB, Schultz PG.

Science. 2005 Sep 2;309(5740):1570-3.

12.

Short double-stranded RNA induces transcriptional gene silencing in human cancer cells in the absence of DNA methylation.

Ting AH, Schuebel KE, Herman JG, Baylin SB.

Nat Genet. 2005 Aug;37(8):906-10. Epub 2005 Jul 17.

13.

Small interfering RNA-induced transcriptional gene silencing in human cells.

Morris KV, Chan SW, Jacobsen SE, Looney DJ.

Science. 2004 Aug 27;305(5688):1289-92. Epub 2004 Aug 5.

14.

RNA regulation: a new genetics?

Mattick JS.

Nat Rev Genet. 2004 Apr;5(4):316-23. Review. No abstract available.

PMID:
15131654
15.

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage.

Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, Fukuda S, Sasaki D, Podhajska A, Harbers M, Kawai J, Carninci P, Hayashizaki Y.

Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15776-81. Epub 2003 Dec 8.

16.
17.

RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse.

Hüttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H, Bachellerie JP, Brosius J.

EMBO J. 2001 Jun 1;20(11):2943-53.

18.

Exon recognition in vertebrate splicing.

Berget SM.

J Biol Chem. 1995 Feb 10;270(6):2411-4. Review. No abstract available.

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