Comparing sequence and expression for predicting microRNA targets using GenMiR3 (pdf)
J.C. Huang, B.J. Frey and Q.D. Morris
Pacific Symposium for Biocomputing (PSB) 13: 52-63, January 2008.
Cumulative distribution networks and the conditional propagation algorithm
J.C. Huang and B.J. Frey
Proceedings of the Twenty-Fourth Conference on Uncertainty in Artificial Intelligence (UAI), July 2008.
Clustering by passing messages between data points (pdf) (Perspective by Marc Mezard)
Brendan J. Frey and Delbert Dueck
Science, Vol 315, No 5814, pp 972-976, February 2007.
Capturing Long-Range Correlations with Patch Models (pdf)
V. Cheung, N. Jojic, and D. Samaras
In Proc. IEEE Intern. Conf. Computer Vision and Pattern Recognition (CVPR), June 2007.
Bayesian inference of microRNA targets from sequence and expression data. (pdf)
J.C. Huang, Q.D. Morris and B.J. Frey
J. Comp. Bio. 14(5): 550-563., June 2007.
Functional coordination of alternative splicing in the mammalian central nervous system (pdf)
M. Fagnani*, Y. Barash*, J. Y. Ip, C. Misquitta, Q. Pan, A. Saltzman, O Shai, L. Lee, A. Rozenhek, N. Mohammad, S. Willaime-Morawek, T. Babak, W. Zhang, T. R. Hughes, D. Kooy, B. J. Frey and B. J. Blencowe
Genome Biology 2007, 8:R108, June 2007.
(*): joint first authors.
Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations (pdf)
J.C. Huang, A. Kannan and J. Winn
Bioinformatics 23:i212-221, July 2007.
Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & Sixth European Conference on Computational Biology (ECCB).
Non-metric affinity propagation for unsupervised image categorization (pdf)
Dueck, D. and Frey, B.J.
Proceedings of the IEEE International Conference on Computer Vision (ICCV), October 2007.
Using expression profiling data to identify human microRNA targets (pdf)
J.C. Huang*, T. Babak*, T.W. Corson, G. Chua, S. Khan, B.L. Gallie, T.R. Hughes, B.J. Blencowe, B.J. Frey and Q.D. Morris
Nature Methods, Vol. 4, No. 12, November 2007.
(*): joint first authors.
Inferring global levels of alternative splicing isoforms using a generative model of microarray data (pdf) (jrnl)
O. Shai, Q. D. Morris, B. J. Blencowe, and B. J. Frey
Bioinformatics 22(5):606-613, January 2006.
Quantitative microarray profiling provides evidence against widespread coupling of alternative splicing with nonsense-mediated mRNA decay to control gene expression (PubMed)
Q. Pan, A.L. Saltzman, Y.K. Kim, C. Misquitta, O. Shai, L.E. Maquat, B.J. Frey, and B.J. Blencowe
Genes and Development, 20(2):153-8, January 2006.
Mixture modeling by Affinity Propagation (pdf)
Frey, B.J. and Dueck, D.
Neural Information Processing Systems 18: 379-386, January 2006.
How Many New Genes Are There? (pdf) (jrnl) (PubMed)
Leo J. Lee, Timothy R. Hughes, and Brendan J. Frey
Science, Vol. 311, No. 5768, pp. 1709, March 2006.
Detecting microRNA targets by linking sequence, microRNA and gene expression data
J.C. Huang, Q.D. Morris and B.J. Frey
Lecture Notes in Computer Science, Springer-Verlag, 3909: 114-129, April 2006.
Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB).
Factorgrams: A tool for visualizing multi-way associations in biological data (pdf)
V. Cheung, I. Givoni, D. Dueck, B. J. Frey
University of Toronto Technical Report PSI-2006-44, May 2006.
Matrix Tile Analysis (pdf)
Inmar Givoni, Vincent Cheung, and Brendan J. Frey
Presented at the 22nd Conference on Uncertainty in Artificial Intelligence (UAI), Cambridge, MA., July 2006.
Exploring the Mode-of-Action of Bioactive Compounds by Chemical-Genetic Profiling in Yeast (PubMed)
A.B. Parsons(*), A. Lopez(*), I.E. Givoni(*), D.E. Williams, C.A. Gray, J. Porter, G. Chua, R. Sopko, R.L. Brost, C. Ho, J.Wang, T. Ketela, C. Brenner, J.A. Brill, G.E. Fernandez , T.C. Lorenz , G.S. Payne, S. Ishihara, Y. Ohya, B. Andrews, T.R. Hughes, B.J. Frey, T.R. Graham, R.J. Andersen, C. Boone
Cell, Vol. 126, Issue 3, pp. 611-625, August 2006.
[(*): joint first authors].
Video epitomes (pdf)
V. Cheung, B. J. Frey, and N. Jojic
In Proc. IEEE Conf. Computer Vision and Pattern Recognition (CVPR), June 2005.
(Best paper honourable mention award).
GenXHC: A probabilistic generative model for cross-hybridization compensation in high-density, genome-wide microarray data (pdf)
J.C. Huang, Q.D. Morris, T.R. Hughes and B.J. Frey
Bioinformatics 21 Suppl 1:i222-i231, June 2005.
Thirteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB).
Probabilistic Sparse Matrix Factorization with an application to discovering gene functions in mouse mRNA expression data (pdf)
Dueck, D., Morris, Q., and Frey, B.J.
International Conference on Intelligent Systems for Molecular Biology (ISMB), June 2005.
A computational high-throughput method for detecting microRNA targets (pdf)
J.C. Huang, Q.D. Morris and B.J. Frey
University of Toronto Technical Report PSI TR 2005-026, August 2005.
A comparison of algorithms for inference and learning in probabilistic graphical models (pdf)
Brendan J Frey and Nebojsa Jojis
IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol 27, No 9, pp 1-25, September 2005.
Probabilistic Sparse Matrix Factorization (pdf)
Dueck, D. and Frey, B.J.
University of Toronto Technical Report PSI-2004-23, May 2004.
Iterative Analysis of Microarray Data (pdf)
Dueck, D., Huang, J., Morris, Q.D. and Frey, B.J.
Allerton Conference on Communication, Control, and Computing, October 2004.
Iterated conditional modes for cross-hybridization compensation in DNA microarray data. (pdf)
J.C. Huang, Q.D. Morris, B.J. Frey
University of Toronto Technical Report PSI TR 2004-031, October 2004.
Probabilistic Inference of Alternative Splicing Events in Microarray Data (pdf) (ps)
O. Shai, B. J. Frey, Q. D. Morris, Q. Pan, C. Misquitta, and B. J. Blencowe
Advances in Neural Information Processing Systema (NIPS) 17, 2205, 1241-1248, December 2004.
The functional landscape of mouse gene expression (pdf) (jrnl) (PubMed)
Zhang W, Morris QD, Chang R, Shai O, Bakowski MA, Mitsakakis N, Mohammad N, Robinson MD, Zirngibl R, Somogyi E, Laurin N, Eftekharpour E, Sat E, Grigull J, Pan Q, Peng WT, Krogan N, Greenblatt J, Fehlings M, van der Kooy D, Aubin J, Bruneau BG, Rossant J, Blencowe BJ, Frey BJ, Hughes TR
Journal of Biology 2004, 3:21, December 2004.
Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform (PubMed)
Q. Pan*, O. Shai*, C. Misquitta, W. Zhang, A.L. Saltzman, N. Mohammad, T. Babak, H. Siu, T.R. Hughes, Q.D. Morris, B.J. Frey, and B.J. Blencowe
Molecular Cell, 16(6):929-41, 2004., December 2004.
Factor graphs and the sum-product algorithm (pdf) (Shorter 1997 Conference Paper)
Frank R Kschischang, Brendan J Frey and Hans-A Loeliger
IEEE Transactions on Information Theory, Vol 47, No 2, pp 498-519, February 2001.
Topographic transformation as a discrete latent variable (pdf)
Nebojsa Jojic and Brendan J Frey
Advances in Neural Information Processing Systems (NIPS), MIT Press, 7 pages, June 2000.
Presented at the 1999 conference.
Variational learning in nonlinear Gaussian belief networks (pdf)
Brendan J Frey and Geoffrey E Hinton
Neural Computation, Vol 11, No 1, pp 193-214, January 1999.
Estimating mixture models of images and inferring spatial transformations using the EM algorithm (pdf)
Brendan J Frey and Nebojsa Jojic
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Ft. Collins, CO, 7 pages, June 1999.
Irregular turbocodes (pdf)
Brendan J Frey and David J C MacKay
Proceedings of the Allerton Conference on Communication, Control and Computing, Montecello, IL, 8 pages, June 1999.
Presented at the 1998 conference.
Transformed component analysis: Joint estimation of spatial transformations and image components (pdf)
Brendan J Frey and Nebojsa Jojic
Proceedings of the IEEE International Conference on Computer Vision, Kerkya, Greece, IEEE Computer Society Press, Los Alamitos, CA, 7 pages, September 1999.
Graphical Models for Machine Learning and Digital Communication
Brendan J Frey
MIT Press, January 1998.
Iterative decoding of compound codes by probability propagation in graphical models (pdf)
Frank R Kschischang and Brendan J Frey
IEEE Journal on Selected Areas in Communications, Vol 16, pp 219-230, January 1998.
Early detection and trellis splicing: Reduced-complexity iterative decoding (pdf)
Brendan J Frey and Frank R Kschischang
IEEE Journal on Selected Areas in Communications, Vol 16, pp 153-160, February 1998.
A revolution: Belief propagation in graphs with cycles (pdf)
Brendan J Frey and David J C MacKay
Advances in Neural Information Processing Systems (NIPS), June 1998.
Presented at the 1997 conference.
Trellis-constrained codes (pdf)
Brendan J Frey and David J C MacKay
Proceedings of the Allerton Conference on Communication, Control and Computing, Montecello, IL, 10 pages, June 1998.
Presented at the 1997 conference.
Factor graphs and algorithms (pdf)
Brendan J Frey, Frank R Kschischang, Hans-A Loeliger, Niclas Wiberg
Proceedings of the Allerton Conference on Communication, Control and Computing, Montecello, IL, 8 pages, September 1998.
A simple algorithm that discovers efficient perceptual codes (pdf) (ps)
B. J. Frey, P. Dayan and G. E. Hinton
In M. Jenkin and L. R. Harris (editors), Computational and Psychophysical Mechanisms of Visual Coding. Cambridge University Press: New York, NY, January 1997.
Efficient stochastic source coding and an application to a Bayesian network source model (ps)
Brendan J Frey and Geoffrey E Hinton
The Computer Journal, Vol 40, pp 157-165, January 1997.
Continuous sigmoidal belief networks trained using slice sampling (pdf)
Brendan J Frey
Advances in Neural Information Processing Systems (NIPS), June 1997.
Presented at the 1996 conference.
Does the wake-sleep algorithm produce good density estimators? (pdf)
B. J. Frey, G. E. Hinton and P. Dayan
In Advances in Neural Information Processing Systems (NIPS) , January 1996.
The "Wake-Sleep" Algorithm for Unsupervised Neural Networks (pdf) (ps)
Geoffrey E. Hinton, Peter Dayan, Brendan J. Frey, and Radford M. Neal
Science, Vol 268, May 1995.