Affiliation: Memorial Sloan-Kettering Cancer Center
- Structure-templated predictions of novel protein interactions from sequence informationDoron 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...
- The microRNA.org resource: targets and expressionDoron 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...
- Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sitesDoron 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...
- Computational analysis of mouse piRNA sequence and biogenesisDoron 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....
- SeqHound: biological sequence and structure database as a platform for bioinformatics researchKaterina 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...
- The expanding role of miR-302-367 in pluripotency and reprogrammingInna Lipchina
Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
Cell Cycle 11:1517-23. 2012....
- Analysis of domain correlations in yeast protein complexesDoron 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...
- BIND: the Biomolecular Interaction Network DatabaseGary 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...
- Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP responseInna 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...
- Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAsAly 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...
- Genome-wide identification of miRNA targets by PAR-CLIPMarkus Hafner
Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
Methods 58:94-105. 2012....
- Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREBPriyamvada 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...
- Kangaroo--a pattern-matching program for biological sequencesDoron Betel
Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
BMC Bioinformatics 3:20. 2002....
- Widespread regulatory activity of vertebrate microRNA* speciesJr 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...
- Neurophysiological defects and neuronal gene deregulation in Drosophila mir-124 mutantsKailiang 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...
- Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomasPing 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...
- Mutation profiling of mismatch repair-deficient colorectal cncers using an in silico genome scan to identify coding microsatellitesJane 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...