Debashish Ray

Debashish Ray

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Debashish Ray

Debashish Ray

Publications by authors named "Debashish Ray"

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27Publications

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RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection.

Methods 2017 08 24;126:18-28. Epub 2017 Jun 24.

Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada; Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto M5S 2E4, Canada; Department of Electrical and Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada. Electronic address:

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August 2017

Oncogenic Activation of the RNA Binding Protein NELFE and MYC Signaling in Hepatocellular Carcinoma.

Cancer Cell 2017 07;32(1):101-114.e8

Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA. Electronic address:

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July 2017

An RRM-ZnF RNA recognition module targets RBM10 to exonic sequences to promote exon exclusion.

Nucleic Acids Res 2017 Jun;45(11):6761-6774

Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.

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June 2017

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins.

Methods 2017 04 10;118-119:3-15. Epub 2016 Dec 10.

Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Electronic address:

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April 2017

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians.

Elife 2016 08 9;5. Epub 2016 Aug 9.

Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany.

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August 2016

The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation.

Cell Rep 2015 Nov 29;13(6):1206-1220. Epub 2015 Oct 29.

Laboratory for RNA Biology, Biochemistry Center Regensburg, University of Regensburg, 93053 Regensburg, Germany. Electronic address:

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November 2015

Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints.

PLoS One 2013 11;8(11):e80701. Epub 2013 Nov 11.

Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

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February 2015

A pair of RNA-binding proteins controls networks of splicing events contributing to specialization of neural cell types.

Mol Cell 2014 Jun 5;54(6):946-59. Epub 2014 Jun 5.

FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

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June 2014

Identifying mRNA sequence elements for target recognition by human Argonaute proteins.

Genome Res 2014 May 24;24(5):775-85. Epub 2014 Mar 24.

Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada;

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May 2014

Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes.

Proc Natl Acad Sci U S A 2014 Feb 3;111(7):2542-7. Epub 2014 Feb 3.

Department of Molecular Genetics, Department of Computer Science, Donnelly Centre, University of Toronto, Toronto, ON, Canada M5S 3E1.

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February 2014

Cross-regulation between an alternative splicing activator and a transcription repressor controls neurogenesis.

Mol Cell 2011 Sep;43(5):843-50

Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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September 2011

Analysis of Escherichia coli RNase E and RNase III activity in vivo using tiling microarrays.

Nucleic Acids Res 2011 Apr 11;39(8):3188-203. Epub 2010 Dec 11.

Department of Genetics, University of Georgia, Athens, GA 30605, USA.

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April 2011

RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins.

PLoS Comput Biol 2010 Jul 1;6:e1000832. Epub 2010 Jul 1.

Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

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July 2010

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins.

Nat Biotechnol 2009 Jul 28;27(7):667-70. Epub 2009 Jun 28.

Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada.

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July 2009

Distinct RNA elements confer specificity to flavivirus RNA cap methylation events.

J Virol 2007 May 14;81(9):4412-21. Epub 2007 Feb 14.

Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12201, USA.

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May 2007

Structure and function of flavivirus NS5 methyltransferase.

J Virol 2007 Apr 31;81(8):3891-903. Epub 2007 Jan 31.

Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA.

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April 2007

Recent advances in flavivirus antiviral drug discovery and vaccine development.

Recent Pat Antiinfect Drug Discov 2006 Jan;1(1):45-55

Wadsworth Center, New York State Department of Health, Albany, New York, USA.

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January 2006

Structural properties of a multifunctional T-shaped RNA domain that mediate efficient tomato bushy stunt virus RNA replication.

J Virol 2004 Oct;78(19):10490-500

Department of Biology, York University, 4700 Keele St., Toronto, Ontario, Canada M3J 1P3.

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October 2004

3'-Terminal RNA secondary structures are important for accumulation of tomato bushy stunt virus DI RNAs.

Virology 2003 Sep;313(2):567-80

Department of Biology, York University, Toronto, Ontario, Canada.

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September 2003

An internally located RNA hairpin enhances replication of Tomato bushy stunt virus RNAs.

J Virol 2003 Jan;77(1):245-57

Department of Biology, York University, Toronto, Ontario, Canada M3J 1P3.

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January 2003