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Items: 1 to 20 of 26


Identification of low abundance microbiome in clinical samples using whole genome sequencing.

Zhang C, Cleveland K, Schnoll-Sussman F, McClure B, Bigg M, Thakkar P, Schultz N, Shah MA, Betel D.

Genome Biol. 2015 Nov 27;16:265. doi: 10.1186/s13059-015-0821-z.


Erratum to: 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. 2015 Nov 23;16:261. doi: 10.1186/s13059-015-0813-z. No abstract available.


Response to Zhou and Robinson.

Betel D, Socci ND, Khanin R, Mason CE, Rapaport F.

Genome Biol. 2015 Oct 8;16:223. doi: 10.1186/s13059-015-0782-2. No abstract available.


Multiplexing of ChIP-Seq Samples in an Optimized Experimental Condition Has Minimal Impact on Peak Detection.

Kacmarczyk TJ, Bourque C, Zhang X, Jiang Y, Houvras Y, Alonso A, Betel D.

PLoS One. 2015 Jun 11;10(6):e0129350. doi: 10.1371/journal.pone.0129350. eCollection 2015.


An allelic series of miR-17 ∼ 92-mutant mice uncovers functional specialization and cooperation among members of a microRNA polycistron.

Han YC, Vidigal JA, Mu P, Yao E, Singh I, González AJ, Concepcion CP, Bonetti C, Ogrodowski P, Carver B, Selleri L, Betel D, Leslie C, Ventura A.

Nat Genet. 2015 Jul;47(7):766-75. doi: 10.1038/ng.3321. Epub 2015 Jun 1.


Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution.

Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, Ishii J, Betel D, Alonso A, Mason CE, Figueroa ME, Melnick AM.

J Vis Exp. 2015 Feb 24;(96):e52246. doi: 10.3791/52246.


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. Erratum in: Genome Biol. 2015;16:261.


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.


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.


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.


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.


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.


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.


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.


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.


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.


The 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.


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.


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.


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.

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