Doron Betel

Summary

Affiliation: Memorial Sloan-Kettering Cancer Center
Country: USA

Publications

  1. pmc Structure-templated predictions of novel protein interactions from sequence information
    Doron Betel
    Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
    PLoS Comput Biol 3:1783-9. 2007
  2. pmc The microRNA.org resource: targets and expression
    Doron Betel
    Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, NY, USA
    Nucleic Acids Res 36:D149-53. 2008
  3. pmc Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    Doron Betel
    Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, 10065, NY, USA
    Genome Biol 11:R90. 2010
  4. pmc Computational analysis of mouse piRNA sequence and biogenesis
    Doron Betel
    Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS Comput Biol 3:e222. 2007
  5. pmc SeqHound: biological sequence and structure database as a platform for bioinformatics research
    Katerina Michalickova
    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    BMC Bioinformatics 3:32. 2002
  6. doi request reprint The expanding role of miR-302-367 in pluripotency and reprogramming
    Inna Lipchina
    Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Cell Cycle 11:1517-23. 2012
  7. ncbi request reprint Analysis of domain correlations in yeast protein complexes
    Doron Betel
    Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Toronto, Canada
    Bioinformatics 20:i55-62. 2004
  8. pmc BIND: the Biomolecular Interaction Network Database
    Gary D Bader
    Department of Biochemistry, Samuel Lunenfeld Research Institute, University of Toronto, Toronto M5G 1X5, Canada
    Nucleic Acids Res 31:248-50. 2003
  9. pmc Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response
    Inna Lipchina
    Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York 10065, USA
    Genes Dev 25:2173-86. 2011
  10. pmc Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
    Aly A Khan
    Department of Computer Science, Columbia University, New York, New York, USA
    Nat Biotechnol 27:549-55. 2009

Collaborators

Detail Information

Publications17

  1. pmc Structure-templated predictions of novel protein interactions from sequence information
    Doron Betel
    Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Toronto, Ontario, Canada
    PLoS Comput Biol 3:1783-9. 2007
    ..These results demonstrate that new protein interactions can be predicted exclusively from sequence information...
  2. pmc The microRNA.org resource: targets and expression
    Doron Betel
    Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, NY, USA
    Nucleic Acids Res 36:D149-53. 2008
    ..The web resource provides users with functional information about the growing number of microRNAs and their interaction with target genes in many species and facilitates novel discoveries in microRNA gene regulation...
  3. pmc Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
    Doron Betel
    Computational Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, 10065, NY, USA
    Genome Biol 11:R90. 2010
    ..Importantly, the method identifies a significant number of experimentally determined non-canonical and non-conserved sites...
  4. pmc Computational analysis of mouse piRNA sequence and biogenesis
    Doron Betel
    Computational and Systems Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS Comput Biol 3:e222. 2007
    ....
  5. pmc SeqHound: biological sequence and structure database as a platform for bioinformatics research
    Katerina Michalickova
    Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
    BMC Bioinformatics 3:32. 2002
    ..SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment...
  6. doi request reprint The expanding role of miR-302-367 in pluripotency and reprogramming
    Inna Lipchina
    Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Cell Cycle 11:1517-23. 2012
    ....
  7. ncbi request reprint Analysis of domain correlations in yeast protein complexes
    Doron Betel
    Samuel Lunenfeld Research Institute, Mt Sinai Hospital, Toronto, Canada
    Bioinformatics 20:i55-62. 2004
    ..In this work, we analyzed high-throughput protein complexes using the domain composition of their protein constituents. Domains that mediate similar or related functions may consistently co-occur in protein complexes...
  8. pmc BIND: the Biomolecular Interaction Network Database
    Gary D Bader
    Department of Biochemistry, Samuel Lunenfeld Research Institute, University of Toronto, Toronto M5G 1X5, Canada
    Nucleic Acids Res 31:248-50. 2003
    ..Continued input from users has helped further mature the BIND data specification, which now includes the ability to store detailed information about genetic interactions. The BIND data specification is available as ASN.1 and XML DTD...
  9. pmc Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response
    Inna Lipchina
    Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York 10065, USA
    Genes Dev 25:2173-86. 2011
    ..This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area...
  10. pmc Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs
    Aly A Khan
    Department of Computer Science, Columbia University, New York, New York, USA
    Nat Biotechnol 27:549-55. 2009
    ..The competition and saturation effects have practical implications for miRNA target prediction, the design of siRNA and short hairpin RNA (shRNA) genomic screens and siRNA therapeutics...
  11. pmc Genome-wide identification of miRNA targets by PAR-CLIP
    Markus Hafner
    Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
    Methods 58:94-105. 2012
    ....
  12. pmc Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB
    Priyamvada Rajasethupathy
    Department of Neuroscience, Columbia University, New York, NY 10032, USA
    Neuron 63:803-17. 2009
    ..We therefore present direct evidence that a modulatory neurotransmitter important for learning can regulate the levels of small RNAs and present a role for miR-124 in long-term plasticity of synapses in the mature nervous system...
  13. pmc Kangaroo--a pattern-matching program for biological sequences
    Doron Betel
    Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
    BMC Bioinformatics 3:20. 2002
    ....
  14. pmc Widespread regulatory activity of vertebrate microRNA* species
    Jr Shiuan Yang
    Department of Developmental Biology, Sloan Kettering Institute, New York, New York 10065, USA
    RNA 17:312-26. 2011
    ..Overall, our data demonstrate that miRNA* species have demonstrable impact on vertebrate regulatory networks and should be taken into account in studies of miRNA functions and their contribution to disease states...
  15. pmc Neurophysiological defects and neuronal gene deregulation in Drosophila mir-124 mutants
    Kailiang Sun
    Department of Developmental Biology, Sloan Kettering Institute, New York, New York, USA
    PLoS Genet 8:e1002515. 2012
    ..Altogether, these studies demonstrate complex consequences of miR-124 loss on neural gene expression and neurophysiology...
  16. pmc Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas
    Ping Mu
    Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Genes Dev 23:2806-11. 2009
    ..Finally, by combining computational target prediction, gene expression profiling, and an in vitro screening strategy, we identify a subset of miR-19 targets that mediate its prosurvival activity...
  17. ncbi request reprint Mutation profiling of mismatch repair-deficient colorectal cncers using an in silico genome scan to identify coding microsatellites
    Jane Park
    Centre for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, and Department of Laboratory Medicine University of Toronto, Toronto, Ontario, Canada M5G 1X5
    Cancer Res 62:1284-8. 2002
    ..This algorithm allows comprehensive mutation profiling of MMR-deficient cancers, an important step in understanding the pathogenesis of these neoplasms...