Jim C. Huang Ph.D. Candidate Probabilistic and Statistical Inference Group Edward S. Rogers Sr. Department of Electrical and Computer Engineering University of Toronto

Contact Information

Office
Bahen Centre for Information Technology, BA4165
40 St. George St.
Toronto, ON
M5S 3G4, Canada

Phone
(+1) 416 946 8809

E-mail
jim(at)psi(dot)toronto(dot)edu

I'm a Ph.D. student in the Probabilistic and Statistical Inference group with Brendan Frey. I am also affiliated with the Communications, Machine Learning and Computational Biology groups at the University of Toronto. I am interested in novel machine learning algorithms and frameworks and their applications to large data sets such as those found in computational systems biology and information retrieval.

Cumulative distribution networks: A novel graphical modelling framework

Using expression profiling data to identify human microRNA targets

Integrating functional genomics data with genetics to help understand human disease

J.C. Huang and B.J. Frey (2008). Structured ranking learning using cumulative distribution networks.
To appear in Proceedings of the Twenty-Second Annual Conference on Neural Information Processing Systems (NIPS).

J.C. Huang and B.J. Frey (2008). Cumulative distribution networks and the derivative-sum-product algorithm.
Proceedings of the Twenty-Fourth Conference on Uncertainty in Artificial Intelligence (UAI), AUAI Press.
(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.
Proceedings of the Pacific Symposium for Biocomputing 2008 (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
Proceedings of the 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.
Proceedings of the 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.
Proceedings of the 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, 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 (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.

Venice, Italy	Rome, Italy	Cambridge, UK	London, UK	Stockholm, Sweden
Amsterdam, Netherlands	Barcelona, Spain	Madrid, Spain	Valencia, Spain	Vienna, Austria
Prague, Czech Republic	Berlin, Germany	Munich, Germany	Oah'u Island, Hawaii, USA	Kauai Island, Hawaii, USA
Big Island, Hawaii, USA	Los Angeles, California, USA	New York City, New York, USA	Helsinki, Finland	Riga, Latvia
Florence, Italy	Paris, France	Mt. Rainier, Washington, USA