I am currently a postdoctoral researcher at Professor David Haussler's group at UCSC.  My research interests focus on building computational models of the mechanisms and evolution of biological systems from multiple data sources.  Specifically, my past and current works involve in reconstructing gene regulatory networks from physical interaction and gene expression data, inferring the coupling between gene regulation and metabolic reactions from gene expression and metabolic flux data, and identifying and characterizing the dependent evolution of components in a molecular apparatus.

Selected Publications

Journal Articles

C.H. Yeang, M. Vingron.  A joint model of regulatory and metabolic networks.  BMC Bioinformatics 7:332 2006.   [pdf], [pubmed link].

C.H. Yeang, T. Jaakkola. Modeling the combinatorial functions of multiple transcription factors. Journal of Computational Biology (JCB), 13(2): 463-480, 2006. [pdf], [pubmed link].

C.H. Yeang, C. Mak, C. Workman, S. McCuine, T. Jaakkola, T. Ideker.  Validation and refinement of gene-regulatory pathways on a network of physical interactions.  Genome Biology 6:R62.1-R62.10, 2005.   [pdf], [pubmed link].

C.H. Yeang, T. Ideker, T Jaakkola.  Physical network models.  Journal of Computational Biology (JCB), 11(2-3): 243-262, 2004.  [pdf], [pubmed link].

S. Ramaswamy et al. Multiclass cancer diagnosis using tumor gene expression signatures.  Proceedings of National Academy of Science U.S.A. (PNAS) 98:15149-15154, 2001.  [pdf], [pubmed link].

Peer-reviewed Conference Papers 

L. Perez-Breva, L.E. Ortiz, C.H. Yeang, T. Jaakkola.  Game theoretic algorithms for protein-DNA binding.  Proceedings, the 12^th Annual Conference on Neural Information Processing (NIPS), Vancouver, Canada, 2006. To appear. 

J. Darot, C.H. Yeang, D. Haussler.  Detecting the dependent evolution of biosequences.  Proceedings, the 10^th Annual International Conference of the Research in Computational Molecular Biology (RECOMB), Venice, Italy, 2006.  [pdf].

C.H. Yeang and T. Jaakkola.  Modeling the combinatorial functions of multiple transcription factors.  Proceedings, the 9^th Annual International Conference of the Research in Computational Molecular Biology (RECOMB), Boston, Massachusetts, U.S.A., 2005.  [pdf].

C.H. Yeang and M. Szummer. Continuous Markov random walks.  Proceedings, the 18^th conference of uncertainty in artificial intelligence (UAI), Acapulco, Mexico, 2003.  [pdf].

C.H. Yeang and T. Jaakkola, Physical network models and multi-source data integration.  Proceedings, the 7^th conference on research in computational biology (RECOMB), Berlin, Germany, 2003.  [pdf].

C.H. Yeang and T. Jaakkola.  Time-series analysis of gene expression and location data.  Proceedings, the 3^rd IEEE conference on bioinformatics and bioengineering (BIBE), Bethesda, Maryland, U.S.A., 2003.  [pdf].

C.H. Yeang.  An information geometric perspective on active learning.  Proceedings, the 13^th European conference on machine learning (ECML), Helsinki, Finland, 2002.  [pdf].

C.H. Yeang et al. Molecular classification of multiple tumor types.  Proceedings, the 9^th conference on intelligent systems for molecular biology (ISMB), Copenhagen, Denmark, 2001.  [pdf], [pubmed link].

Thesis

Inferring regulatory networks from multiple sources of genomic data.  Sc. D. Thesis.  Supervisor: Tommi Jaakkola.  Massachusetts Institute of Technology, 2004.  [pdf].

Curriculum Vitae

Past and Current Collaborators

David Haussler, Center for Molecular Science and Engineering, UC Santa Cruz.

Josh Stuart, Department of Biomolecular Engineering, UC Santa Cruz.

Harry Noller, Center for Molecular Biology of RNA, UC Santa Cruz.

Tommi Jaakkola, Electrical Engineering and Computer Science Department, MIT.

Trey Ideker, Department of Bioengineering, UC San Diego.

Martin Vingron, Max-Planck Institute for Molecular Genetics.

Student Collaborators

Charlie Vaske, Department of Biomolecular Engineering, UC Santa Cruz.

Pinal Kanabar, Department of Biomolecular Engineering, UC Santa Cruz.

Jeremy Darot, European Bioinformatics Institute.