Brendan J Frey

Brendan J Frey

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Brendan J Frey

Publications by authors named "Brendan J Frey"

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Deep learning in biomedicine.

Nat Biotechnol 2018 10 6;36(9):829-838. Epub 2018 Sep 6.

Deep Genomics Inc., MaRS Discovery District, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nbt.4233DOI Listing
October 2018

Inference of the human polyadenylation code.

Bioinformatics 2018 09;34(17):2889-2898

Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1093/bioinformatics/bty211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129302PMC
September 2018

Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder.

Nat Neurosci 2017 Apr 6;20(4):602-611. Epub 2017 Mar 6.

The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.

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http://dx.doi.org/10.1038/nn.4524DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501701PMC
April 2017

Automated analysis of high-content microscopy data with deep learning.

Mol Syst Biol 2017 04 18;13(4):924. Epub 2017 Apr 18.

Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408780PMC
http://dx.doi.org/10.15252/msb.20177551DOI Listing
April 2017

Computer vision for high content screening.

Crit Rev Biochem Mol Biol 2016 24;51(2):102-9. Epub 2016 Jan 24.

a The Donnelly Centre, University of Toronto , Toronto , ON , Canada and.

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http://dx.doi.org/10.3109/10409238.2015.1135868DOI Listing
November 2016

Classifying and segmenting microscopy images with deep multiple instance learning.

Bioinformatics 2016 06;32(12):i52-i59

Department of Electrical and Computer Engineering, University of Toronto, Toronto, M5S 2E4, Canada The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btw252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908336PMC
June 2016

Whole-Genome Sequencing Suggests Schizophrenia Risk Mechanisms in Humans with 22q11.2 Deletion Syndrome.

G3 (Bethesda) 2015 Sep 16;5(11):2453-61. Epub 2015 Sep 16.

Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada Department of Psychiatry University of Toronto, Ontario, M5T 1R8 Canada, University of Toronto, Toronto, Ontario, Canada Department of Psychiatry, and Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, M5S 2S1 Canada The Dalglish Family Hearts and Minds Clinic for 22q11.2 Deletion Syndrome, Toronto General Hospital, University Health Network, Toronto, Ontario, M5G 2C4 Canada

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http://dx.doi.org/10.1534/g3.115.021345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632064PMC
September 2015

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning.

Nat Biotechnol 2015 Aug 27;33(8):831-8. Epub 2015 Jul 27.

1] Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada. [2] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [3] Canadian Institute for Advanced Research, Programs on Genetic Networks and Neural Computation, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nbt.3300DOI Listing
August 2015

C2H2 zinc finger proteins greatly expand the human regulatory lexicon.

Nat Biotechnol 2015 May 18;33(5):555-62. Epub 2015 Feb 18.

1] Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. [3] Canadian Institutes for Advanced Research, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nbt.3128DOI Listing
May 2015

RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Science 2015 Jan 18;347(6218):1254806. Epub 2014 Dec 18.

Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada. Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada. Program on Genetic Networks and Program on Neural Computation & Adaptive Perception, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada. Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada. McLaughlin Centre, University of Toronto, Toronto, Ontario M5G 0A4, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. eScience Group, Microsoft Research, Redmond, WA 98052, USA.

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http://dx.doi.org/10.1126/science.1254806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4362528PMC
January 2015

Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder.

Nat Genet 2014 Jul 25;46(7):742-7. Epub 2014 May 25.

1] The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada. [2] McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada. [3] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/ng.2980DOI Listing
July 2014

Deep learning of the tissue-regulated splicing code.

Bioinformatics 2014 Jun;30(12):i121-9

Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada and Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, CanadaDepartment of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada and Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, CanadaDepartment of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada and Canadian Institute for Advanced Research, Toronto, Ontario M5G 1Z8, Canada.

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http://www.psi.toronto.edu/publications/2014/DeepSplicingCod
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btu277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4058935PMC
June 2014

Network cleanup.

Nat Biotechnol 2013 Aug;31(8):714-5

Department of Electrical Engineering and the Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1038/nbt.2657DOI Listing
August 2013

Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry.

Bioinformatics 2013 Apr 17;29(7):821-9. Epub 2013 Feb 17.

Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt056DOI Listing
April 2013

A generalizable pre-clinical research approach for orphan disease therapy.

Orphanet J Rare Dis 2012 Jun 15;7:39. Epub 2012 Jun 15.

Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.

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http://dx.doi.org/10.1186/1750-1172-7-39DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458970PMC
June 2012

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data.

BMC Bioinformatics 2012 Apr 19;13 Suppl 6:S11. Epub 2012 Apr 19.

Department of Electrical and Computer Engineering, University of Toronto, ON, Canada.

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http://dx.doi.org/10.1186/1471-2105-13-S6-S11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3330053PMC
April 2012

Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context.

Bioinformatics 2011 Sep 29;27(18):2554-62. Epub 2011 Jul 29.

Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btr444DOI Listing
September 2011

Computational refinement of post-translational modifications predicted from tandem mass spectrometry.

Bioinformatics 2011 Mar 22;27(6):797-806. Epub 2011 Jan 22.

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

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http://dx.doi.org/10.1093/bioinformatics/btr017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3051323PMC
March 2011

Deciphering the splicing code.

Nature 2010 May;465(7294):53-9

Biomedical Engineering, Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto M5S 3G4, Canada.

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http://dx.doi.org/10.1038/nature09000DOI Listing
May 2010

A binary variable model for affinity propagation.

Neural Comput 2009 Jun;21(6):1589-600

Probabilistic and Statistical Inference Group, Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada.

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http://dx.doi.org/10.1162/neco.2009.05-08-785DOI Listing
June 2009

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing.

Nat Genet 2008 Dec 2;40(12):1413-5. Epub 2008 Nov 2.

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

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http://dx.doi.org/10.1038/ng.259DOI Listing
December 2008

Functional coordination of alternative splicing in the mammalian central nervous system.

Genome Biol 2007 ;8(6):R108

Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1.

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http://dx.doi.org/10.1186/gb-2007-8-6-r108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2394768PMC
February 2008

Using expression profiling data to identify human microRNA targets.

Nat Methods 2007 Dec 18;4(12):1045-9. Epub 2007 Nov 18.

Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada.

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http://dx.doi.org/10.1038/nmeth1130DOI Listing
December 2007

Bayesian inference of MicroRNA targets from sequence and expression data.

J Comput Biol 2007 Jun;14(5):550-63

Probabilistic and Statistical Inference Group, University of Toronto, Toronto, Canada.

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http://dx.doi.org/10.1089/cmb.2007.R002DOI Listing
June 2007

Clustering by passing messages between data points.

Science 2007 Feb 11;315(5814):972-6. Epub 2007 Jan 11.

Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada.

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http://dx.doi.org/10.1126/science.1136800DOI Listing
February 2007

Identifying transcription factor functions and targets by phenotypic activation.

Proc Natl Acad Sci U S A 2006 Aug 31;103(32):12045-50. Epub 2006 Jul 31.

Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 1A8.

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http://dx.doi.org/10.1073/pnas.0605140103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1567694PMC
August 2006

Inferring global levels of alternative splicing isoforms using a generative model of microarray data.

Bioinformatics 2006 Mar 10;22(5):606-13. Epub 2006 Jan 10.

Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada M5S 3G8.

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http://dx.doi.org/10.1093/bioinformatics/btk028DOI Listing
March 2006

How many new genes are there?

Science 2006 Mar;311(5768):1709-11; author reply 1709-11

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http://dx.doi.org/10.1126/science.311.5768.1709bDOI Listing
March 2006

GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data.

J Comput Biol 2006 Mar;13(2):200-14

Department of Electrical and Computer Engineering, University of Toronto, Ontario, Canada.

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http://dx.doi.org/10.1089/cmb.2006.13.200DOI Listing
March 2006

Unwrapping of MR phase images using a Markov random field model.

IEEE Trans Med Imaging 2006 Jan;25(1):128-36

Department of Electrical Engineering and Computer Science, University of Wisconsin, Milwaukee, WI 53201, USA.

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http://dx.doi.org/10.1109/TMI.2005.861021DOI Listing
January 2006

Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs.

Nat Genet 2005 Sep 28;37(9):991-6. Epub 2005 Aug 28.

Electrical and Computer Engineering, University of Toronto, 10 King's College Rd., Toronto, Ontario M5S 3G4, Canada.

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http://dx.doi.org/10.1038/ng1630DOI Listing
September 2005

A comparison of algorithms for inference and learning in probabilistic graphical models.

IEEE Trans Pattern Anal Mach Intell 2005 Sep;27(9):1392-416

Electrical and Computer Engineering Department, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada.

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http://www.psi.toronto.edu/~frey/ece1510/ReviewPaper.pdf
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http://www.psi.toronto.edu/~psi/pubs2/2005/freyJojicTutorial
Web Search
http://www.isit2004.org/tutorial_files/FreyTutorial.pdf
Web Search
http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumbe
Publisher Site
http://dx.doi.org/10.1109/TPAMI.2005.169DOI Listing
September 2005

Multi-way clustering of microarray data using probabilistic sparse matrix factorization.

Bioinformatics 2005 Jun;21 Suppl 1:i144-51

Department of Electrical and Computer Engineering, University of Toronto Toronto, Ontario, Canada M5S 3G4.

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http://www.psi.utoronto.ca/pubs/2005/Dueck,Morris,Frey%20--%
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/bti1041DOI Listing
June 2005

GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data.

Bioinformatics 2005 Jun;21 Suppl 1:i222-31

Probabilistic and Statistical Inference Group, Department of Electrical and Computer Engineering, University of Toronto Toronto, ON, Canada M5S 3G4.

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http://dx.doi.org/10.1093/bioinformatics/bti1045DOI Listing
June 2005

Genrate: a generative model that finds and scores new genes and exons in genomic microarray data.

Pac Symp Biocomput 2005 :495-506

Dept of Electrical and Computer Engineering, University of Toronto, Toronto, ON, M5S 3G4, Canada.

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April 2005

Alternative splicing of conserved exons is frequently species-specific in human and mouse.

Trends Genet 2005 Feb;21(2):73-7

CH Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6.

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http://dx.doi.org/10.1016/j.tig.2004.12.004DOI Listing
February 2005

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform.

Mol Cell 2004 Dec;16(6):929-41

Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada.

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http://dx.doi.org/10.1016/j.molcel.2004.12.004DOI Listing
December 2004