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Items: 1 to 20 of 74

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.

3.

Prediction and extraction of microRNA2target interactions associated with leukemia.

Gong L, Yan Q, Yang R, Sun X.

Genet Mol Res. 2014 Mar 24;13(1):2120-9. doi: 10.4238/2014.March.24.19.

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
5.
6.

OrthoClust: an orthology-based network framework for clustering data across multiple species.

Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M.

Genome Biol. 2014 Aug 28;15(8):R100. doi: 10.1186/gb-2014-15-8-r100.

7.

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
8.

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
9.

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
10.

Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.

Nature. 2014 Aug 28;512(7515):445-8. doi: 10.1038/nature13424.

11.

RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation.

Wang G, Wang Y, Shen C, Huang YW, Huang K, Huang TH, Nephew KP, Li L, Liu Y.

PLoS One. 2010 Nov 2;5(11):e13798. doi: 10.1371/journal.pone.0013798.

12.

MicroRNA binding sites in C. elegans 3' UTRs.

Liu C, Rennie WA, Mallick B, Kanoria S, Long D, Wolenc A, Carmack CS, Ding Y.

RNA Biol. 2014;11(6):693-701. Epub 2014 Apr 25.

13.

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
14.

Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.

Pu S, Turinsky AL, Vlasblom J, On T, Xiong X, Emili A, Zhang Z, Greenblatt J, Parkinson J, Wodak SJ.

PLoS One. 2010 Nov 29;5(11):e14122. doi: 10.1371/journal.pone.0014122.

15.

RFECS: a random-forest based algorithm for enhancer identification from chromatin state.

Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B.

PLoS Comput Biol. 2013;9(3):e1002968. doi: 10.1371/journal.pcbi.1002968. Epub 2013 Mar 14.

16.

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.

17.

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
18.

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.

19.

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.

20.

ChromClust: A semi-supervised chromatin clustering toolkit for mining histone modifications interplay.

Noureen N, Touseef M, Fazal S, Qadir MA.

Genomics. 2015 Dec;106(6):355-9. doi: 10.1016/j.ygeno.2015.11.002. Epub 2015 Nov 6.

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