Chen-Hsiang Yeang

Institute of Statistical Science

Academia Sinica

No. 128 Academia Rd, Sec. 2, Nankang, Taipei 115, Taiwan


I am currently an associate research fellow at the Institute of Statistical Science of Academia Sinica. My research interests focus on two areas in computational biology: 1)cancer genomics, 2)molecular evolution. In cancer genomics, we examined the combinatorial patterns of somatic mutations in cancer and related them to pathway and functional implications (FASEB J. 2008). We also developed a statistical model and inference algorithms to integrate multiple types of molecular aberration data (BMC Bioinformatics 2010) and applied them to large-scale cancer genomic data analysis (BMC Systems Biology 2011, Nucleic Acids Res. 2013). In addition to data analysis, we also proposed optimization algorithms for combinatorial treatments for a heterogeneous tumor population (PNAS 2012). In molecular evolution, we built a computational model that identifies coevolving nucleic or amino acids from aligned sequences of multiple species (Mol. Biol. Evol. 2007; PLoS Comp. Biol. 2007). We also proposed an algorithm that reconstructs the evolutionary history of biomolecular networks according to parsimony (Genome. Biol. & Evol. 2012). Furthermore, we developed a model to quantify the strength of purifying selection of sequence motifs and applied this method to exhaustively identify functional 10-mers from mammalian promoters (Nucleic Acids Res. 2013).


Selected Publications

Journal Articles

K.L. Tiong, C.H. Yeang Explaining cancer type specific mutations with transcriptomic and epigenomic features in normal tissues. Scientific Reports 8(1):11456, 2018. [pdf],[pubmed link].


M. Simak, C.H. Yeang, H.H. Lu. Exploring candidate biological functions by Boolean function networks for Saccharomyces cerevisiae. PLoS One 12(10):e0185475, 2017. [pdf],[pubmed link].


J.W. Kim et al. Decomposing oncogenic transcriptional signatures to generate maps of divergent cellular states. Cell Systems 5(2):105-118, 2017. [pdf],[pubmed link].


Y.F. Chen, H.C. Lin, K.N. Chuang, C.H. Lin, H.S. Yen, and C.H. Yeang. A quantitative model for the rate-limiting process of UGA alternative assignments to stop and selenocysteine codons. PLoS Computational Biology 13(2):e1005367, 2017. [pdf],[pubmed link].


C.H. Yeang, R.A. Beckman. Long range personalized cancer treatment strategies incorporating evolutionary dynamics. Biology Direct 11(1):56, 2016. [pdf],[pubmed link].


S.J. Chou, C. Wang, N. Sintupisut, Z.X. Niou, C.H. Lin, K.C. Li, C.H. Yeang. Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain. Scientific Reports 6:19274, 2016. [pdf],[pubmed link].


A. Woolston, N. Sintupisut, T.P. Lu, L.C. Lai, M.H. Tsai, E.Y. Chuang, C.H. Yeang. Putative effectors for prognosis in lung adenocarcinoma are ethnic and gender specific. Oncotarget 6(23):19483-19499, 2015. [pdf],[pubmed link].


C.H. Yeang, G.C. Ma, H.W. Hsu, Y.S. Lin, S.M. Chang, P.J. Cheng, C.A. Chen, Y.H. Ni, M. Chen. Genome-wide normalized score: a novel algorithm to detect fetal trisomy 21 during non-invasive prenatal testing. Ultrasound Obstetrics and Gynaecology 2(2):189-204, 2014. [pdf],[pubmed link].


I.Y. Lin, F.L. Chiu, C.H. Yeang, H.F. Chen, C.Y. Chuang, S.Y. Yang, P.S. Hou, N. Sintupisut, H.N. Ho, H.C. Kuo, K.I. Lin. Suppression of the SOX2 neural rffector gene by PRDM1 promotes human germ cell fate in embryonic stem cells. Stem Cell Reports 2(2):189-204, 2014. [pdf],[pubmed link].


N. Sintupisut, P.L. Liu, C.H. Yeang. An integrative characterization of recurrent molecular aberrations in glioblastoma genomes. Nucleic Acids Research 41(19):8803-8821, 2013. [pdf],[pubmed link].


N. Sintupisut, C.H. Yeang. Sequence mutations of genes pertaining to malignancy in cancer. Journal of Data Science 11:673-714, 2013. [pdf].


D.H. Chen, A. Chang, B.Y. Liao, C.H. Yeang. Functional characterization of motif sequences under purifying selection. Nucleic Acids Research 41(4):2105-2120, 2013. [pdf],[pubmed link].


S. Suen, H.S. Lu, C.H. Yeang. Evolution of domain architectures and catalytic functions of enzymes in metabolic systems. Genome Biology & Evolution 4(9):852-869, 2012. [pdf],[pubmed link].


R.A. Beckman, G.S. Schemmann, C.H. Yeang. Impact of genetic dynamics and single-cell heterogeneity on development of nonstandard personalized medicine strategies for cancer. Proceedings, National Academy of Science, U.S.A. 109(36):14586-14591, 2012. [pdf],[pubmed link].


C.H. Yeang et al. Genome-wide gene expression analysis implicates the immune response and lymphangiogenesis in the pathogenesis of fetal chylothorax. PLoS One 7(4):e34901, 2012. [pdf],[pubmed link].


S.D. Li, T. Tagami, Y.F. Ho, and C.H. Yeang. Deciphering causal and statistical relations of molecular aberrations and gene expressions in NCI-60 cell lines. BMC Systems Biology 5:186, 2011. [pdf],[pubmed link].

C.H. Yeang. An integrated analysis of molecular aberrations in NCI-60 cell lines. BMC Bioinformatics 11:495, 2010. [pdf],[pubmed link].

C.J. Vaske, C. House, T. Luu, B. Frank, C.H. Yeang, N. Lee, and J.M. Stuart. A factor graph nested effects model to identify networks from genetic perturbations. PLoS Computational Biology 9(5):e1000274, 2009. [pdf],[pubmed link].

C.H. Yeang, F. McCormick, A. Levine. Combinatorial patterns of somatic gene mutations in cancer. The FASEB Journal 22:2605-2622, 2008. [pdf], [pubmed link].

C.H. Yeang. Identifying coevolving partners from paralogous gene families. Evolutionary Bioinformatics 4:91-107, 2008. [pdf].

C.H. Yeang, D. Haussler. Detecting coevolution in and among protein domains. PLoS Computational Biology 3(11):e211, 2007. [pdf], [pubmed link].

C.H. Yeang, J.F.J. Darot, H.F. Noller, D. Haussler. Detecting the coevolution of biosequences – an example of RNA interaction prediction. Molecular Biology and Evolution 24(9):2119-2131, 2007. [pdf], [errata], [pubmed link].

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 interactionsGenome Biology 6:R62.1-R62.10, 2005.   [pdf], [pubmed link].

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

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

Peer-reviewed Conference Papers 

C.H. Yeang, L.C. Huang, W.C. Liu. Recurrent structural motifs reflect characteristics of distinct networks. Proceedings, The 2012 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), Istanbul, Turkey, 2012. [pdf].

C.H. Yeang. A probabilistic graphical model of quantum systems. Proceedings, the 9th International Conference on Machine Learning and Applications (ICMLA), Washington DC, USA, 2010. [pdf].

C.H. Yeang. Quantifying the strength of natural selection of a motif sequence. Proceedings, the 10th Workshop on Algorithms in Bioinformatics (WABI), Liverpool, U.K., 2010. [pdf].

C.H. Yeang. Exact loopy belief propagation on Euler graphs. Proceedings, the 2010 World Congress in Computer Science, Computer Engineering and Applied Computing (WORLDCOMP), Las Vegas, U.S.A., 2010. [pdf].

C.H. Yeang. Analysis of the bipartite networks of domain compositions and metabolic reactions. Proceedings, the Second International Conference on Biomedical Engineering and Informatics (BMEI), Tianjin, China, 2009. [pdf].

C.H. Yeang, N.A. Baas Evolution of domain compositions in the metabolic networks of human and Escherichia coli. Proceedings, the 2009 World Congress in Computer Science, Computer Engineering and Applied Computing (WORLDCOMP), Las Vegas, U.S.A., 2009. [pdf].

P.N. Kanabar, C.J. Vaske, C.H. Yeang, F.H. Yildiz, and J.M. Stuart. Inferring disease-related pathways using a probabilistic epistasis model. Proceedings, the 15th Pacific Symposium of Biocomputing (PSB), Hawaii, U.S.A., 2009. [pdf].

L. Perez-Breva, L.E. Ortiz, C.H. Yeang, T. Jaakkola.  Game theoretic algorithms for protein-DNA bindingProceedings, the 12th Annual Conference on Neural Information Processing (NIPS), Vancouver, Canada, 2006. [pdf].

J. Darot, C.H. Yeang, D. Haussler.  Detecting the dependent evolution of biosequencesProceedings, the 10th 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 factorsProceedings, the 9th 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 walksProceedings, the 18th conference of uncertainty in artificial intelligence (UAI), Acapulco, Mexico, 2003.  [pdf].

C.H. Yeang and T. Jaakkola. Physical network models and multi-source data integrationProceedings, the 7th 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 dataProceedings, the 3rd IEEE conference on bioinformatics and bioengineering (BIBE), Bethesda, Maryland, U.S.A., 2003.  [pdf].

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

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

Book Chapters

C.H. Yeang. Integration of metabolic reactions and gene regulation. In Plants Systems Biology. Series of Methods in Molecular Biology, Vol 553. Belostotsky D.A. (Ed.), 2009.


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


Downloadable Software and Source Codes

Inferring Association Modules from Integrated Cancer Genomic Data (Nucleic Acids Res. 2013; BMC Systems Biology. 2011).

Coevolutionary Continuous-Time Markove Process Model (PLoS Comp. Biol. 2007; Mol. Biol. Evol. 2007).

Physical Network Model (JCB 2004; Genome Biol. 2005). The Java plug-in of Cytoscape (written by Craig Mak at Trey Ideker's group) is also available at the supplementary website of the Genome Biology paper.


Curriculum Vitae


Current and Past Collaborators

Ker-Chau Li, Academia Sinica.

Pablo Tamayo, University of California, San Diego.

William Kim, Broad Institute.

Carlo Ratti, Massachusetts Institute of Technology.

Sherry Hsueh-Chi Yen, Academia Sinica.

Shen-Ju Chou, Academia Sinica.

Ben-Yang Liao, National Health Research Institute.

Henry Horng-Shing Lu, National Chiao-Tung University.

Shyh-Dar Li, Ontario Institute of Cancer Research.

Kuo-I Lin, Academia Sinica.

Robert Beckman, Daiichi Sankyo Pharma Development.

Gunter Schemmann, Cancer Institute of New Jersey.

Alex Yu, College of Life Science, National Taiwan University.

Ming Chen, Changhua Christian Hospital, Taiwan.

Na-Sheng Lin, Academia Sinica.

Arnold Levine, Simons Center for Systems Biology, Institute for Advanced Study.

Frank McCormick, University of California, San Francisco.

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.


Current and Past Group Members

Sridevi Padakanti, Institute of Statistical Science, Academia Sinica.

Yu-Wei Lin, Institute of Statistical Science, Academia Sinica.

Khong-Loon Tiong, Institute of Statistical Science, Academia Sinica.

Min-Chin Lin, Institute of Statistical Science, Academia Sinica.

Andrei Akhmetzhanov, Institute of Statistical Science, Academia Sinica.

Hung-Chun Wang, Institute of Statistical Science, Academia Sinica.

Chih-Hung Cheng, Institute of Statistical Science, Academia Sinica.

Andrew Woolston, Institute of Statistical Science, Academia Sinica.

Mirrian Ho, Genome Research Center, Academia Sinica.

Chih-Hsu Lin, Institute of Statistical Science, Academia Sinica.

Mariya Simak, The International Graduate Program, Academia Sinica.

Nardnisa Sintupisut, Institute of Statistical Science, Academia Sinica.

Andy Chen, Institute of Statistical Science, Academia Sinica.

Summit Suen, Institute of Statistical Science, Academia Sinica.

I-Feng Lan, College of Life Science, National Taiwan University.

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

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

Jeremy Darot, European Bioinformatics Institute.