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Results: 1 to 20 of 89

1.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.

Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M.

Genome Biol. 2011;12(2):R15. doi: 10.1186/gb-2011-12-2-r15. Epub 2011 Feb 16.

PMID:
21324173
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

PMID:
21177976
[PubMed - indexed for MEDLINE]
Free PMC Article
3.
4.

Incremental fuzzy mining of gene expression data for gene function prediction.

Ma PC, Chan KC.

IEEE Trans Biomed Eng. 2011 May;58(5):1246-52. doi: 10.1109/TBME.2010.2047724. Epub 2010 Apr 15.

PMID:
20403777
[PubMed - indexed for MEDLINE]
5.

Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification.

Ohler U, Yekta S, Lim LP, Bartel DP, Burge CB.

RNA. 2004 Sep;10(9):1309-22.

PMID:
15317971
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Chromatin structure characteristics of pre-miRNA genomic sequences.

Zhu S, Jiang Q, Wang G, Liu B, Teng M, Wang Y.

BMC Genomics. 2011 Jun 25;12:329. doi: 10.1186/1471-2164-12-329.

PMID:
21702984
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Biclustering of linear patterns in gene expression data.

Gao Q, Ho C, Jia Y, Li JJ, Huang H.

J Comput Biol. 2012 Jun;19(6):619-31. doi: 10.1089/cmb.2012.0032.

PMID:
22697238
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Genetics. Revealing the dark matter of the genome.

Blaxter M.

Science. 2010 Dec 24;330(6012):1758-9. doi: 10.1126/science.1200700. Epub 2010 Dec 22. No abstract available.

PMID:
21177977
[PubMed - indexed for MEDLINE]
9.

Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map.

Heikkinen L, Kolehmainen M, Wong G.

Bioinformatics. 2011 May 1;27(9):1247-54. doi: 10.1093/bioinformatics/btr144. Epub 2011 Mar 21.

PMID:
21422073
[PubMed - indexed for MEDLINE]
Free Article
10.

Functional genomic, computational and proteomic analysis of C. elegans microRNAs.

Lehrbach NJ, Miska EA.

Brief Funct Genomic Proteomic. 2008 May;7(3):228-35. doi: 10.1093/bfgp/eln024. Epub 2008 Jun 19. Review.

PMID:
18565984
[PubMed - indexed for MEDLINE]
Free Article
11.

Computational prediction of intronic microRNA targets using host gene expression reveals novel regulatory mechanisms.

Radfar MH, Wong W, Morris Q.

PLoS One. 2011;6(6):e19312. doi: 10.1371/journal.pone.0019312. Epub 2011 Jun 9.

PMID:
21694770
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets.

Friedman Y, Naamati G, Linial M.

Bioinformatics. 2010 Aug 1;26(15):1920-1. doi: 10.1093/bioinformatics/btq298. Epub 2010 Jun 6.

PMID:
20529892
[PubMed - indexed for MEDLINE]
Free Article
13.

A native chromatin purification system for epigenomic profiling in Caenorhabditis elegans.

Ooi SL, Henikoff JG, Henikoff S.

Nucleic Acids Res. 2010 Mar;38(4):e26. doi: 10.1093/nar/gkp1090. Epub 2009 Dec 4.

PMID:
19966274
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans.

Jovanovic M, Reiter L, Picotti P, Lange V, Bogan E, Hurschler BA, Blenkiron C, Lehrbach NJ, Ding XC, Weiss M, Schrimpf SP, Miska EA, Grosshans H, Aebersold R, Hengartner MO.

Nat Methods. 2010 Oct;7(10):837-42. doi: 10.1038/nmeth.1504. Epub 2010 Sep 12.

PMID:
20835247
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Analyzing miRNA co-expression networks to explore TF-miRNA regulation.

Bandyopadhyay S, Bhattacharyya M.

BMC Bioinformatics. 2009 May 28;10:163. doi: 10.1186/1471-2105-10-163.

PMID:
19476620
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

The microRNAs of Caenorhabditis elegans.

Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP.

Genes Dev. 2003 Apr 15;17(8):991-1008. Epub 2003 Apr 2.

PMID:
12672692
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Global prediction of tissue-specific gene expression and context-dependent gene networks in Caenorhabditis elegans.

Chikina MD, Huttenhower C, Murphy CT, Troyanskaya OG.

PLoS Comput Biol. 2009 Jun;5(6):e1000417. doi: 10.1371/journal.pcbi.1000417. Epub 2009 Jun 19.

PMID:
19543383
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Computational analysis of microRNA targets in Caenorhabditis elegans.

Watanabe Y, Yachie N, Numata K, Saito R, Kanai A, Tomita M.

Gene. 2006 Jan 3;365:2-10. Epub 2005 Dec 13.

PMID:
16356665
[PubMed - indexed for MEDLINE]
19.

Modelling the correlation between the activities of adjacent genes in Drosophila.

Thygesen HH, Zwinderman AH.

BMC Bioinformatics. 2005 Jan 19;6:10.

PMID:
15659243
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes.

Ruepp A, Kowarsch A, Schmidl D, Buggenthin F, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Theis FJ.

Genome Biol. 2010 Jan 20;11(1):R6. doi: 10.1186/gb-2010-11-1-r6.

PMID:
20089154
[PubMed - indexed for MEDLINE]
Free PMC Article

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