Brendan J Frey

Summary

Affiliation: University of Toronto
Country: Canada

Publications

  1. ncbi request reprint A comparison of algorithms for inference and learning in probabilistic graphical models
    Brendan J Frey
    Electrical and Computer Engineering Department, University of Toronto, 10 King s College Road, Toronto, ON M5S 3G4, Canada
    IEEE Trans Pattern Anal Mach Intell 27:1392-416. 2005
  2. ncbi request reprint Clustering by passing messages between data points
    Brendan J Frey
    Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
    Science 315:972-6. 2007
  3. pmc Functional coordination of alternative splicing in the mammalian central nervous system
    Matthew Fagnani
    Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1
    Genome Biol 8:R108. 2007
  4. ncbi request reprint Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
    Brendan J Frey
    Electrical and Computer Engineering, University of Toronto, 10 King s College Rd, Toronto, Ontario M5S 3G4, Canada
    Nat Genet 37:991-6. 2005
  5. ncbi request reprint GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data
    Brendan J Frey
    Department of Electrical and Computer Engineering, University of Toronto, Ontario, Canada
    J Comput Biol 13:200-14. 2006
  6. pmc The functional landscape of mouse gene expression
    Wen Zhang
    Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
    J Biol 3:21. 2004
  7. ncbi request reprint Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Mol Cell 16:929-41. 2004
  8. ncbi request reprint Alternative splicing of conserved exons is frequently species-specific in human and mouse
    Qun Pan
    CH Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
    Trends Genet 21:73-7. 2005
  9. ncbi request reprint Using expression profiling data to identify human microRNA targets
    Jim C Huang
    Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
    Nat Methods 4:1045-9. 2007
  10. ncbi request reprint Inferring global levels of alternative splicing isoforms using a generative model of microarray data
    Ofer Shai
    Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada M5S 3G8
    Bioinformatics 22:606-13. 2006

Collaborators

Detail Information

Publications32

  1. ncbi request reprint A comparison of algorithms for inference and learning in probabilistic graphical models
    Brendan J Frey
    Electrical and Computer Engineering Department, University of Toronto, 10 King s College Road, Toronto, ON M5S 3G4, Canada
    IEEE Trans Pattern Anal Mach Intell 27:1392-416. 2005
    ..We describe how each technique can be applied in a vision model of multiple, occluding objects and contrast the behaviors and performances of the techniques using a unifying cost function, free energy...
  2. ncbi request reprint Clustering by passing messages between data points
    Brendan J Frey
    Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
    Science 315:972-6. 2007
    ..Affinity propagation found clusters with much lower error than other methods, and it did so in less than one-hundredth the amount of time...
  3. pmc Functional coordination of alternative splicing in the mammalian central nervous system
    Matthew Fagnani
    Banting and Best Department of Medical Research, Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario, Canada, M5S 3E1
    Genome Biol 8:R108. 2007
    ..However, the extent to which AS coordinates functions in a cell and tissue type specific manner is not known. Moreover, the sequence code that underlies cell and tissue type specific regulation of AS is poorly understood...
  4. ncbi request reprint Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs
    Brendan J Frey
    Electrical and Computer Engineering, University of Toronto, 10 King s College Rd, Toronto, Ontario M5S 3G4, Canada
    Nat Genet 37:991-6. 2005
    ..GenRate also detected tens of thousands of potential new exons and reconciled discrepancies in current cDNA databases by 'stitching' new transcribed regions into previously annotated genes...
  5. ncbi request reprint GenRate: a generative model that reveals novel transcripts in genome-tiling microarray data
    Brendan J Frey
    Department of Electrical and Computer Engineering, University of Toronto, Ontario, Canada
    J Comput Biol 13:200-14. 2006
    ..As new problems arise, additional hidden variables can be incorporated into the model in a principled fashion, so we believe that GenRate will prove to be a useful tool in the new era of genome-wide tiling microarray analysis...
  6. pmc The functional landscape of mouse gene expression
    Wen Zhang
    Banting and Best Department of Medical Research, University of Toronto, 1 King s College Circle, Toronto, ON M5S 1A8, Canada
    J Biol 3:21. 2004
    ....
  7. ncbi request reprint Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada
    Mol Cell 16:929-41. 2004
    ..These results demonstrate the utility of our quantitative microarray platform and data for revealing important global regulatory features of AS...
  8. ncbi request reprint Alternative splicing of conserved exons is frequently species-specific in human and mouse
    Qun Pan
    CH Best Institute, University of Toronto, 112 College Street, Toronto, Ontario, Canada M5G 1L6
    Trends Genet 21:73-7. 2005
    ..The results thus provide evidence that species-specific AS of conserved exons constitutes an additional potential source of complexity and species-specific differences between mammals...
  9. ncbi request reprint Using expression profiling data to identify human microRNA targets
    Jim C Huang
    Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto, Ontario M5S 3G4, Canada
    Nat Methods 4:1045-9. 2007
    ..Compared to sequence-based predictions, our high-scoring GenMiR++ predictions had much more consistent Gene Ontology annotations and were more accurate predictors of which mRNA levels respond to changes in let-7b levels...
  10. ncbi request reprint Inferring global levels of alternative splicing isoforms using a generative model of microarray data
    Ofer Shai
    Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada M5S 3G8
    Bioinformatics 22:606-13. 2006
    ..GenASAP has been successfully applied to the global discovery and analysis of AS in mammalian cells and tissues...
  11. ncbi request reprint GenXHC: a probabilistic generative model for cross-hybridization compensation in high-density genome-wide microarray data
    Jim C Huang
    Probabilistic and Statistical Inference Group, Department of Electrical and Computer Engineering, University of Toronto Toronto, ON, Canada M5S 3G4
    Bioinformatics 21:i222-31. 2005
    ....
  12. ncbi request reprint Multi-way clustering of microarray data using probabilistic sparse matrix factorization
    Delbert Dueck
    Department of Electrical and Computer Engineering, University of Toronto Toronto, Ontario, Canada M5S 3G4
    Bioinformatics 21:i144-51. 2005
    ..PSMF allows for varying levels of sensor noise in the data, uncertainty in the hidden prototypes used to explain the data and uncertainty as to the prototypes selected to explain each data vector...
  13. pmc Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, Ontario, M5G 1L6, Canada
    Genes Dev 20:153-8. 2006
    ..Our results suggest that most PTC-introducing AS events are not under positive selection pressure and therefore may not contribute important functional roles...
  14. doi request reprint Bayesian prediction of tissue-regulated splicing using RNA sequence and cellular context
    Hui Yuan Xiong
    Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada
    Bioinformatics 27:2554-62. 2011
    ..An important goal in understanding this phenomenon is to infer a 'splicing code' that predicts how splicing is regulated in different cell types by features derived from RNA, DNA and epigenetic modifiers...
  15. doi request reprint The evolutionary landscape of alternative splicing in vertebrate species
    Nuno L Barbosa-Morais
    Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Science 338:1587-93. 2012
    ..These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species...
  16. pmc Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
    Boyko Kakaradov
    Department of Electrical and Computer Engineering, University of Toronto, ON, Canada
    BMC Bioinformatics 13:S11. 2012
    ..This comparison demonstrates the challenges in estimating the percent inclusion of alternatively spliced junctions and illuminates the tradeoffs between different approaches...
  17. doi request reprint Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    Qun Pan
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
    Nat Genet 40:1413-5. 2008
    ..From a comparison with quantitative alternative splicing microarray profiling data, we also show that mRNA-Seq data provide reliable measurements for exon inclusion levels...
  18. pmc Computational refinement of post-translational modifications predicted from tandem mass spectrometry
    Clement Chung
    Department of Computer Science, University of Toronto, Toronto, Canada
    Bioinformatics 27:797-806. 2011
    ..However, these approaches are subject to noise in mass measurements and in the predicted modification site (amino acid position) within peptides, which can result in false PTM assignments...
  19. pmc Model-based detection of alternative splicing signals
    Yoseph Barash
    Banting and Best Department of Medical Research, University of Toronto, ON, Canada
    Bioinformatics 26:i325-33. 2010
    ..It is necessary to accurately identify such splicing changes to elucidate the underlying regulatory programs or link the splicing changes to specific diseases...
  20. doi request reprint Deciphering the splicing code
    Yoseph Barash
    Biomedical Engineering, Department of Electrical and Computer Engineering, University of Toronto, 10 King s College Road, Toronto M5S 3G4, Canada
    Nature 465:53-9. 2010
    ..The code facilitates the discovery and detailed characterization of regulated alternative splicing events on a genome-wide scale...
  21. pmc A systematic analysis of intronic sequences downstream of 5' splice sites reveals a widespread role for U-rich motifs and TIA1/TIAL1 proteins in alternative splicing regulation
    Isabel Aznarez
    Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
    Genome Res 18:1247-58. 2008
    ..Based on our results, we estimate that approximately 15% of alternative cassette exons are regulated by TIA1/TIAL1 via U-rich intronic elements...
  22. pmc Identifying transcription factor functions and targets by phenotypic activation
    Gordon Chua
    Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON, Canada M5S 1A8
    Proc Natl Acad Sci U S A 103:12045-50. 2006
    ..The general strategy outlined here presents a straightforward approach to discovery of TF activities and mapping targets that could be adapted to any organism with transgenic technology...
  23. ncbi request reprint Exploring the mode-of-action of bioactive compounds by chemical-genetic profiling in yeast
    Ainslie B Parsons
    Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario M5G 1L6, Canada
    Cell 126:611-25. 2006
    ..This compendium should serve as a valuable key for interpreting cellular effects of novel compounds with similar activities...
  24. doi request reprint A binary variable model for affinity propagation
    Inmar E Givoni
    Probabilistic and Statistical Inference Group, Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
    Neural Comput 21:1589-600. 2009
    ..For those wishing to investigate or extend the graphical model of the AP algorithm, we suggest using this new formulation since it allows a simpler and more intuitive model manipulation...
  25. doi request reprint MBNL proteins repress ES-cell-specific alternative splicing and reprogramming
    Hong Han
    Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Nature 498:241-5. 2013
    ....
  26. ncbi request reprint Bayesian inference of MicroRNA targets from sequence and expression data
    Jim C Huang
    Probabilistic and Statistical Inference Group, University of Toronto, Toronto, Canada
    J Comput Biol 14:550-63. 2007
    ..Our high-confidence targets represent a significant increase in the number of miRNA targets and represent a starting point for a global understanding of gene regulation...
  27. pmc Transcriptional profiling of endocrine cerebro-osteodysplasia using microarray and next-generation sequencing
    Piya Lahiry
    Robarts Research Institute, London, Ontario, Canada
    PLoS ONE 6:e25400. 2011
    ..To date, most mRNA profiling of tissues has been accomplished using microarrays, but next-generation sequencing can offer a richer and more comprehensive picture...
  28. doi request reprint A compendium of RNA-binding motifs for decoding gene regulation
    Debashish Ray
    Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
    Nature 499:172-7. 2013
    ..These data provide an unprecedented overview of RNA-binding proteins and their targets, and constitute an invaluable resource for determining post-transcriptional regulatory mechanisms in eukaryotes. ..
  29. doi request reprint Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry
    Clement Chung
    Department of Computer Science, University of Toronto, Toronto, M5S 2E4, Canada
    Bioinformatics 29:821-9. 2013
    ..The use of this new modeling approach enables iPTMClust to provide a confidence score per modification site that allows fine-tuning and interpreting resulting PTM predictions...
  30. ncbi request reprint A panoramic view of yeast noncoding RNA processing
    Wen Tao Peng
    Banting and Best Department of Medical Research, University of Toronto, 112 College Street, M5G 1L6, Toronto, Ontario, Canada
    Cell 113:919-33. 2003
    ..These data present a global view of yeast noncoding RNA processing and confirm that many currently uncharacterized yeast proteins are involved in biogenesis of noncoding RNA...
  31. ncbi request reprint How many new genes are there?
    Leo J Lee
    Science 311:1709-11; author reply 1709-11. 2006
  32. ncbi request reprint Unwrapping of MR phase images using a Markov random field model
    Lei Ying
    Department of Electrical Engineering and Computer Science, University of Wisconsin, Milwaukee, WI 53201, USA
    IEEE Trans Med Imaging 25:128-36. 2006
    ..g., the popular least-squares method) in handling noisy phase images with rapid phase variations...