J.C. Huang and B.J. Frey (2009). Structured ranking learning using cumulative distribution networks.
Advances in Neural Information Processing Systems (NIPS) 21. Supplemental File

J.C. Huang and B.J. Frey (2008). Cumulative distribution networks and the derivative-sum-product algorithm.
Twenty-Fourth Conference on Uncertainty in Artificial Intelligence (UAI), AUAI Press: 290-297.
(Oral Presentation. Acceptance rate: 12.5%. Best Student Paper Runner-Up)

J.C. Huang, B.J. Frey and Q.D. Morris (2008). Comparing sequence and expression for predicting microRNA targets using GenMiR3.
Pacific Symposium for Biocomputing (PSB) 13: 52-63.

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 (2007).
Using expression profiling data to identify human microRNA targets.
Nature Methods 4: 1045-1049. (*Joint first authors)

J.C. Huang, A. Kannan and J. Winn (2007). Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations.
Bioinformatics 23:i212-221
Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) &
Sixth European Conference on Computational Biology (ECCB) (Oral presentation. Acceptance rate: 16%)

J.C. Huang, Q.D. Morris and B.J. Frey (2007). Bayesian inference of microRNA targets from sequence and expression data.
Journal of Computational Biology 14: 550-563.

J.C. Huang, Q.D. Morris and B.J. Frey (2006). Detecting microRNA targets by linking sequence, microRNA and gene expression data.
Lecture Notes in Computer Science, Springer-Verlag 3909:114-129.
Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB). (Oral presentation. Acceptance rate: 18%)

J.C. Huang, Q.D. Morris, T.R. Hughes and B.J. Frey (2005). GenXHC: A probabilistic generative model for cross-hybridization compensation in high-density, genome-wide microarray data.
Bioinformatics 21:i222-i231.
Thirteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB). (Oral presentation. Acceptance rate: 13%)

D. Dueck*, J.C. Huang*, Q.D. Morris and B.J. Frey (2004). Iterative analysis of microarray data.
Proceedings of the Forty-Second Annual Allerton Conference on Communication, Control and Computing. (*Joint first authors)

J.C. Huang and B.J. Frey (2009). Cumulative distribution networks: Graphical models for cumulative distribution functions.
The Learning Workshop (LEARNING 2009).

N. Jojic, T. Hertz and J.C. Huang (2009). HLA viral targeting.
UCSD Information Theory and Applications Workshop (ITA).

J.C. Huang, Q.D. Morris and B.J. Frey (2006). Computational discovery of microRNA regulatory networks in retinoblastoma from sequence and expression data.
Sixth Cold Spring Harbor Laboratory/Wellcome Trust (CSHL/WT) Conference on Genome Informatics.

Non-peer-reviewed publications

J.C. Huang, Q.D. Morris and B.J. Frey (2005). A computational high-throughput method for detecting microRNA targets.
University of Toronto Technical Report PSI TR 2005-026, August 15, 2005.

J.C. Huang, Q.D. Morris, B.J. Frey (2004). Iterated conditional modes for cross-hybridization compensation in DNA microarray data.
University of Toronto Technical Report PSI TR 2004-031, October 6, 2004.

J.C. Huang and B.J. Frey (2009). Cumulative distribution networks: Graphical models for cumulative distribution functions.
The Learning Workshop (LEARNING 2009),
Clearwater, FL, USA, April 13-16, 2009.

N. Jojic, T. Hertz and J.C. Huang (2009). HLA viral targeting.
UCSD Information Theory and Applications Workshop (ITA),
La Jolla, CA, USA, February 9-13, 2009.

J.C. Huang and B.J. Frey (2008). Structured ranking learning using cumulative distribution networks.
Twenty-Second Annual Conference on Neural Information Processing Systems (NIPS),
Vancouver, BC, Canada, December 8-13, 2008.

J.C. Huang and B.J. Frey (2008). Cumulative distribution networks and the derivative-sum-product algorithm.
Twenty-Fourth Conference on Uncertainty in Artificial Intelligence (UAI),
Helsinki, Finland, July 9-12, 2008.

J.C. Huang, B.J. Frey and Q.D. Morris (2008). Comparing sequence and expression for predicting microRNA targets using GenMiR3.
Pacific Symposium for Biocomputing (PSB),
Big Island, HI, USA, January 4-8, 2008.

J.C. Huang, A. Kannan and J. Winn (2007). Bayesian association of haplotypes and non-genetic factors to regulatory and phenotypic variation in human populations.
Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & Sixth European Conference on Computational Biology (ECCB),
Vienna, Austria, July 21-25, 2007.

J.C. Huang, Q.D. Morris and B.J. Frey (2006). Computational discovery of microRNA regulatory networks in retinoblastoma from sequence and expression data.
Sixth Cold Spring Harbor Laboratory/Wellcome Trust (CSHL/WT) Conference on Genome Informatics,
Hinxton, Cambridge, UK, September 13-17, 2006.

J.C. Huang, Q.D. Morris and B.J. Frey (2006). Detecting microRNA targets by linking sequence, microRNA and gene expression data.
Tenth Annual International Conference on Research in Computational Molecular Biology (RECOMB),
Venice, Italy, April 2-5, 2006.

J.C. Huang, Q.D. Morris, T.R. Hughes and B.J. Frey (2005). GenXHC: A probabilistic generative model for cross-hybridization compensation in high-density, genome-wide microarray data.
Thirteenth Annual International Conference on Intelligent Systems for Molecular Biology (ISMB),
Detroit, MI, USA, June 25-29, 2005.

J.C. Huang, Q.D. Morris, T.R. Hughes and B.J. Frey (2004). Detection and compensation of cross-hybridization in DNA microarray data.
Third Annual Information Processing Workshop,
Toronto, ON, Canada, August 8, 2004.