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Results: 20

1.

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.

Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D.

Genome Biol. 2013;14(9):R95.

PMID:
24020486
[PubMed - in process]
Free PMC Article
2.

Genome-wide identification of miRNA targets by PAR-CLIP.

Hafner M, Lianoglou S, Tuschl T, Betel D.

Methods. 2012 Oct;58(2):94-105. doi: 10.1016/j.ymeth.2012.08.006. Epub 2012 Aug 19.

PMID:
22926237
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

The expanding role of miR-302-367 in pluripotency and reprogramming.

Lipchina I, Studer L, Betel D.

Cell Cycle. 2012 Apr 15;11(8):1517-23. doi: 10.4161/cc.19846. Epub 2012 Apr 15.

PMID:
22436490
[PubMed - indexed for MEDLINE]
4.

Neurophysiological defects and neuronal gene deregulation in Drosophila mir-124 mutants.

Sun K, Westholm JO, Tsurudome K, Hagen JW, Lu Y, Kohwi M, Betel D, Gao FB, Haghighi AP, Doe CQ, Lai EC.

PLoS Genet. 2012 Feb;8(2):e1002515. doi: 10.1371/journal.pgen.1002515. Epub 2012 Feb 9.

PMID:
22347817
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response.

Lipchina I, Elkabetz Y, Hafner M, Sheridan R, Mihailovic A, Tuschl T, Sander C, Studer L, Betel D.

Genes Dev. 2011 Oct 15;25(20):2173-86. doi: 10.1101/gad.17221311.

PMID:
22012620
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Widespread regulatory activity of vertebrate microRNA* species.

Yang JS, Phillips MD, Betel D, Mu P, Ventura A, Siepel AC, Chen KC, Lai EC.

RNA. 2011 Feb;17(2):312-26. doi: 10.1261/rna.2537911. Epub 2010 Dec 22.

PMID:
21177881
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites.

Betel D, Koppal A, Agius P, Sander C, Leslie C.

Genome Biol. 2010;11(8):R90. doi: 10.1186/gb-2010-11-8-r90. Epub 2010 Aug 27.

PMID:
20799968
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas.

Mu P, Han YC, Betel D, Yao E, Squatrito M, Ogrodowski P, de Stanchina E, D'Andrea A, Sander C, Ventura A.

Genes Dev. 2009 Dec 15;23(24):2806-11. doi: 10.1101/gad.1872909.

PMID:
20008931
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB.

Rajasethupathy P, Fiumara F, Sheridan R, Betel D, Puthanveettil SV, Russo JJ, Sander C, Tuschl T, Kandel E.

Neuron. 2009 Sep 24;63(6):803-17. doi: 10.1016/j.neuron.2009.05.029.

PMID:
19778509
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs.

Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS.

Nat Biotechnol. 2009 Jun;27(6):549-55. doi: 10.1038/nbt.1543. Erratum in: Nat Biotechnol. 2009 Jul;27(7):671.

PMID:
19465925
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

The microRNA.org resource: targets and expression.

Betel D, Wilson M, Gabow A, Marks DS, Sander C.

Nucleic Acids Res. 2008 Jan;36(Database issue):D149-53. Epub 2007 Dec 23.

PMID:
18158296
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Computational analysis of mouse piRNA sequence and biogenesis.

Betel D, Sheridan R, Marks DS, Sander C.

PLoS Comput Biol. 2007 Nov;3(11):e222. Epub 2007 Sep 28.

PMID:
17997596
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Structure-templated predictions of novel protein interactions from sequence information.

Betel D, Breitkreuz KE, Isserlin R, Dewar-Darch D, Tyers M, Hogue CW.

PLoS Comput Biol. 2007 Sep;3(9):1783-9.

PMID:
17892321
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

The Biomolecular Interaction Network Database and related tools 2005 update.

Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D'Abreo C, Donaldson I, Dorairajoo D, Dumontier MJ, Dumontier MR, Earles V, Farrall R, Feldman H, Garderman E, Gong Y, Gonzaga R, Grytsan V, Gryz E, Gu V, Haldorsen E, Halupa A, Haw R, Hrvojic A, Hurrell L, Isserlin R, Jack F, Juma F, Khan A, Kon T, Konopinsky S, Le V, Lee E, Ling S, Magidin M, Moniakis J, Montojo J, Moore S, Muskat B, Ng I, Paraiso JP, Parker B, Pintilie G, Pirone R, Salama JJ, Sgro S, Shan T, Shu Y, Siew J, Skinner D, Snyder K, Stasiuk R, Strumpf D, Tuekam B, Tao S, Wang Z, White M, Willis R, Wolting C, Wong S, Wrong A, Xin C, Yao R, Yates B, Zhang S, Zheng K, Pawson T, Ouellette BF, Hogue CW.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24.

PMID:
15608229
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Analysis of domain correlations in yeast protein complexes.

Betel D, Isserlin R, Hogue CW.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i55-62.

PMID:
15262781
[PubMed - indexed for MEDLINE]
Free Article
16.

BIND: the Biomolecular Interaction Network Database.

Bader GD, Betel D, Hogue CW.

Nucleic Acids Res. 2003 Jan 1;31(1):248-50.

PMID:
12519993
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

SeqHound: biological sequence and structure database as a platform for bioinformatics research.

Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW.

BMC Bioinformatics. 2002 Oct 25;3:32. Epub 2002 Oct 25.

PMID:
12401134
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Kangaroo--a pattern-matching program for biological sequences.

Betel D, Hogue CW.

BMC Bioinformatics. 2002 Jul 31;3:20.

PMID:
12150718
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Mutation profiling of mismatch repair-deficient colorectal cncers using an in silico genome scan to identify coding microsatellites.

Park J, Betel D, Gryfe R, Michalickova K, Di Nicola N, Gallinger S, Hogue CW, Redston M.

Cancer Res. 2002 Mar 1;62(5):1284-8.

PMID:
11888892
[PubMed - indexed for MEDLINE]
Free Article

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