• 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 Biology , 2013 Sep 10;14(9):R95, Highly Accessed
    [Publication] [PubMed] [arXiv] [source code & data]

  • Genome-wide identification of miRNA targets by PAR-CLIP
    Hafner M, Lianoglou S, Tuschl T, Betel D.
    METHODS , 2012 Aug.19.
    [Publication] [PubMed] [data]

  • 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
    [Publication] [PubMed]

  • 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
    [Publication] [PubMed]

  • 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; 25:2173-2186
    [Publication] [PubMed] [data]

  • 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
    [Publication] [PubMed]

  • Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    Betel D, Koppal A, Agius P, Sander C, Leslie CS
    Genome Biology, 2010;11(8):R90, Highly Accessed
    [Publication] [PubMed]

  • Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B cell lymphomas
    Mu P, Han Y-C, Betel D, Yao E, Squatrito M, Ogrodowski P, Stanchina Ed, D’Andrea A, Sander C, Ventura A,
    Genes & Dev., 2009 Dec. 15,23:2806-11
    [Publication] [PubMed] [data]

  • 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.
    [Publication] [PubMed]

  • Transfection of small RNAs globally perturbs regulation by endogenous microRNAs
    Khan AA, Betel D, Miller ML, Sander C, Leslie CS, Marks DS,
    Nature Biotechnology. 2009 Jun;27(6):549-55
    [Publication] [PubMed]

  • 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.
    [Publication] PubMed

  • Computational analysis of mouse piRNA sequence and biogenesis
    Betel D, Sheridan R, Marks DS, Sander C.,
    PLoS Comput Biol. 2007 Nov; 3(11):e222.
    [Publication] [PubMed]

  • 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 21;3(9):1783-9.
    [Publication] [PubMed]

  • The Biomolecular Interaction Network Database and related tools 2005 update
    Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, ... , Pawson T, Ouellette BF, Hogue CW.,
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D418-24.
    [Publication] [PubMed]

  • Analysis of domain correlations in Yeast protein complexes
    Betel D, Isserlin R, Hogue CWV
    Bioinformatics 2004 Aug 4;20 Suppl1:i55-i62. (Proceedings of the 12th Int. Conference On Intelligent Systems for Molecular Biology (ISMB) and 3rd European Conference on Computational Biology, 2004.)
    [Publication] [PubMed]

  • BIND - The Biomolecular Interaction Database
    Bader GD, Betel D, Hogue CWV,
    Nucleic Acids Res. 2003 Jan 1;31(1): 248-250.
    [Publication] [PubMed]

  • 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 CWV
    BMC Bioinformatics 2002 Oct 25;3(1):32.
    [Publication] [PubMed]

  • Kangaroo - A pattern-matching program for biological sequences
    Betel D, Hogue CWV
    BMC Bioinformatics 2002 Jul 31;3(1):20.
    [Publication] [PubMed]

  • Mutation profiling of mismatch repair-deficient colorectal cancers using an in silico genome scan to identify coding microsatellites
    Park J*, Betel D*, Gryfe R, Michalickova K, Di Nicola N, Gallinger S, Hogue CWV, Redston M
    Cancer Res. 2002 Mar 1;62(5):1284-8.
    [Publication] [PubMed]

  • Cloning and expression of a novel UDP-GlcNAc:alpha-D-mannoside beta1,2-N-acetylglucosaminyltransferase homologous to UDP-GlcNAc:alpha-3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I
    Zhang W, Betel D, Schachter H,
    Biochem J. 2002 Jan 1;361(Pt 1):153-62.
    [Publication] [PubMed]

    • Book Chapter

  • Systems Biology of microRNAs
    Betel D, Khanin R
    Handbook of Statistical Systems Biology, Eds. Stumpf M., Balding DJ., Girolami M., John Wiley & Sons, Dec. 2011, ISBN: 978-0-470-71086-9
    Wiley Online Library