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Chen-Hsiang Yeang Institute of Statistical Science Academia Sinica E-mail: chyeang@stat.sinica.edu.tw |
I am currently an associate research fellow at the Institute of Statistical Science of Academia Sinica. My research interests focus on several areas in computational biology and data science: 1)cancer genomics, 2)cancer treatment, 3)molecular evolution, 4)network topology, 5)machine learning. In cancer genomics, we developed statistical models and inference algorithms to integrate multiple types of molecular aberration data and applied them to large-scale cancer genomic data analysis (BMC Bioinformatics 2010, BMC Systems Biology 2011, Nucleic Acids Res. 2013, Scientific Reports 2018, BMC Bioinformatics 2019, Biology Open 2022, PLOS Digital Health 2022). In cancer treatment, we proposed several population dynamics models for a heterogeneous tumor and developed optimization algorithms for combinatorial treatments (PNAS 2012, Biology Direct 2016, J. Math. Biol. 2019). In molecular evolution, we investigated various problems including coevolution (Mol. Biol. Evol. 2007; PLoS Comp. Biol. 2007), biomolecular network evolutionary history (Genome. Biol. & Evol. 2012), and evolution of human populations (Scientific Reports 2019). In network topology, we detected recurrent motifs in distinct networks (ASONAM 2012) and analyzed the spatiotemporal gene expression patterns of developing mouse brains (Scientific Reports 2016). In machine learning, we constructed a probabilistic graphical model of quantum systems (ICMLA 2012) and clustered image data with a fixed embedding (ICMLA 2022).
Selected Publications
Journal Articles
K.L. Tiong et al. An integrated analysis of the cancer genome atlas data discovers a hierarchical association structure across thirty three cancer types. PLOS Digital Health 1(12):e0000151, 2022. [pdf].
K.L. Hsu et al. Cooperative stability renders protein complex formation more robust and controllable. Scientific Reports 12(1):10490, 2022. [pdf],[pubmed link].
K.L. Tiong et al. Characterization of gene cluster heterogeneity in single-cell transcriptomic data within and across cancer types. Biology Open 11(6):bio059256, 2022. [pdf],[pubmed link].
S. Padakanti et al. Genotypes of informative loci from 1000 Genomes data allude evolution and mixing of human populations. Scientific Reports 11(1):17741, 2021. [pdf],[pubmed link].
C.W. Yeh et al. The C-degron pathway eliminates mislocalized proteins and products of deubiquitinating enzymes. EMBO Journal 40:e105846, 2021. [pdf],[pubmed link].
C. Dai et al. Population histories of the United States revealed through fine-scale migration and haplotype analysis American Journal of Human Genetics 106(3):371-388, 2020. [pdf],[pubmed link].
A.R. Akhmetzhanov et al. Modelling bistable tumour population dynamics to design effective treatment strategies. Journal of Theoretical Biology 474:88-102, 2019. [pdf],[pubmed link].
K.L. Tiong, C.H. Yeang MGSEA -- a multivariate gene set enrichment analysis. BMC Bioinformatics 20(1):145, 2019. [pdf],[pubmed link].
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 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
Peer-reviewed Conference Papers
Y.B. Chen, K.L. Tiong, C.H. Yeang.
Clustering image data with a fixed embedding. Proceedings, 21st IEEE International Conference on Machine Learning and Applications (ICMLA),
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),
C.H. Yeang. A probabilistic graphical
model of quantum systems. Proceedings,
the 9th International Conference on Machine Learning and
Applications (ICMLA),
C.H. Yeang. Quantifying the strength
of natural selection of a motif sequence. Proceedings, the 10th Workshop on Algorithms in
Bioinformatics (WABI),
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),
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),
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),
L. Perez-Breva, L.E. Ortiz, C.H. Yeang, T. Jaakkola. Game theoretic
algorithms for protein-DNA binding. Proceedings, the 12th
Annual Conference on Neural Information Processing (NIPS),
J. Darot, C.H. Yeang, D. Haussler. Detecting the dependent evolution
of biosequences. Proceedings, the 10th Annual
International Conference of the Research in Computational Molecular Biology
(RECOMB),
C.H. Yeang and T. Jaakkola. Modeling the combinatorial functions of
multiple transcription factors. Proceedings, the 9th
Annual International Conference of the Research in Computational Molecular
Biology (RECOMB),
C.H. Yeang and M. Szummer. Continuous Markov random walks. Proceedings,
the 18th conference of uncertainty in artificial intelligence (UAI),
C.H. Yeang and T. Jaakkola. Physical network models and multi-source data
integration. Proceedings, the 7th conference on
research in computational biology (RECOMB),
C.H. Yeang and T. Jaakkola. Time-series analysis of gene expression
and location data. Proceedings, the 3rd IEEE conference
on bioinformatics and bioengineering (BIBE),
C.H. Yeang. An information geometric perspective on active learning.
Proceedings, the 13th European conference on machine learning
(ECML),
C.H. Yeang et al. Molecular classification of multiple tumor types.
Proceedings, the 9th conference on intelligent systems for molecular
biology (ISMB),
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.
Thesis
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.
Current and Past Collaborators
Ker-Chau Li, University of California, Los Angeles.
Pablo Tamayo, University of California, San Diego.
William Kim, University of California, San Diego.
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
Alex Yu, College of Life Science, National Taiwan University.
Ming Chen, Changhua Christian Hospital, Taiwan.
Na-Sheng Lin, Academia Sinica.
Arnold Levine,
Frank McCormick,
David Haussler,
Center for Molecular Science and Engineering, UC
Josh Stuart, Department of
Biomolecular Engineering, UC
Harry Noller,
Center for Molecular Biology of RNA, UC
Tommi Jaakkola, Electrical Engineering and Computer Science Department, MIT.
Trey
Ideker, Department of Bioengineering, UC
Martin Vingron, Max-Planck Institute for Molecular Genetics.
Current and Past Group Members
Chia Hsuan Fu, Institute of Statistical Science, Academia Sinica.
Yuli Tung, Institute of Statistical Science, Academia Sinica.
Dmytro Luzhbin, Institute of Statistical Science, Academia Sinica.
Kuan-Lun Hsu, Institute of Molecular Biology, Academia Sinica.
Yan-Bin Chen, Institute of Statistical Science, Academia Sinica.
Sridevi Padakanti, Institute of Statistical Science, Academia Sinica.
Roman Andreev, 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
Pinal Kanabar, Department of Biomolecular Engineering, UC
Jeremy Darot, European Bioinformatics Institute.