University of Michigan, Ann Arbor

Transcription

1 Zing Tsung-Yeh Tsai is a bioinformatics research fellow in the University of Michigan, focusing on functional genomics, in particular interested in understanding gene regulation and evolutionary mechanism through machine learning and data science. He has interdisciplinary education and research experience which are listed as follows: 10 years research experience in bioinfomatics and regulatory genomics Expertise in machine learning, statistics, and genomics 16 journal papers and 2 manuscripts in revision 5 scholarships and 6 awards in presentation/publication Bioinfomatics PhD in Academia Sinica, the national academy of Taiwan Biomedical Engineering BS/MS in NTU, the #1 university in Taiwan CONTACT ME ttsai@umich.edu RESEARCH EXPERIENCE BIOINFORMATICS RESEARCH FELLOW 2016-CURRENT University of Michigan, Ann Arbor Michigan, US Investigating how environmental toxicants influence development process across multiple tissues (Contributing in the Bioinformatics Working Group of the nationwide TaRGET project) Analyzing multi-omics data (RNA-seq, ChIP-seq, ATAC-seq, WGBS) in studies related to epigenomics and pirna system POSTDOCTORAL RESEARCHER Michigan State University Michigan, US Demarcated genic boundaries through large scale data integration using human and plant data Investigated contributions of conservation, sequence and biochemical characteristics in defining functional regions in the human genome POSTDOCTORAL FELLOW (THE ALTERNATIVE MILITARY SERVICE) Academia Sinica Conducted genome-wide identification and functional analysis of enhancer RNAs in mouse Investigated the evolution trend and potential function of human long non-coding RNA DOCTORAL RESEARCH Academia Sinica Characterized chromatin accessibility features of transcription factor binding region to develop a computational framework for identification of functional transcription factor binding site Discovered the potential roles of non-b DNA structures play in post-transcriptional regulation Revealed the difference in evolutionary roles of new genes from different origins Investigated the impact of trans-regulation on the evolutionary rates of metazoan proteins MASTER RESEARCH Reconstructed gene network of human diseases by integrating omics data Page 1 of 6

2 Inferred regulatory relationship between transcription factor and target gene by statistical model UNDERGRADUATE RESEARCH Applied heuristic algorithms to optimize ecology model under extreme climate events EDUCATION PHD, BIOINFORMATICS Academia Sinica, Taiwan International Graduate Program Diploma conferred by National Yang-Ming University Toward a Better Understanding of Transcription Factor Binding: Strategies, Features, and Applications MS, BIOMEDICAL ENGINEERING A Statistical Approach to Estimating Transcription Factor Activity for Identifying Regulatory Relationship BS, BIOENVIRONMENTAL SYSTEMS ENGINEERING Application of Simulated Annealing Algorithm to Optimize Water Quality Model under Climate Change SKILLS & QUALIFICATION SCIENTIFIC PROGRAMMING Expert in Perl and R Competent in Python, Matlab, VB6, C++, JAVA Linux environment with computer clusters and large data sets Parallel computing using PBS and version control by GitHub STATISTICAL MODELING/MACHINE LEARNING Clustering, Classification, and Regression models Graphic model such as Hidden Markov Model and Bayesian Network Optimization algorithms BIOINFORMATICS NGS data analysis RNA-seq, bisulfite sequencing, ChIP-seq, Hi-C, ATAC-seq Sequence analysis multiple sequence alignment and motif finding Functional genomics Gene Ontology analysis, Network analysis, GWAS analysis, and Evolutionary analysis AWARD & SCHOLARSHIP 1. ASBMB Special Symposium Third Prize Poster Award, St. Louis, MO, USA, The Postdoctoral Research Abroad Program, Ministry of Science and Technology, TW, The Outstanding Publication Award, National Yang-Ming University, TW, Page 2 of 6

3 4. Poster Presentation Award, International Symposium on Evolutionary Genomics and Bioinfo., TW, Postdoctoral Research Fellowship, Academia Sinica, TW, Poster Presentation Award, International Symposium on Evolutionary Genomics and Bioinfo., TW, The Best Presentation Award, the 11th Bioinformatics and Systems Biology in Taiwan, TW, The Best Oral Presentation Award, International Sym. on Evolutionary Genomics and Bioinfo., TW, Presidential Awards,, TW, 2004 & Scholarship from Chi-Shin Agricultural Research Foundation, TW, JURNAL PAPERS 1. Wang T, Pehrsson EC, et al., Tsai ZT-Y, et al.:the NIEHS TaRGET II Consortium and environmental epigenomics. Nature Biotechnology 2018.(in press) (Contributions: Bioinformatics Working Group) 2. Tsai ZT-Y, Lloyd PJ, Shiu S-H: Defining functional, genic regions in the human genome through integration of biochemical, evolutionary and genetic evidence. Molecular Biology and Evolution 2017, DOI: /molbev/msx101 (Contributions: conceived study, designed and performed computational analysis, wrote manuscript) 3. Liu WH*, Tsai ZT-Y*, Tsai H-K: Comparative genomic analyses highlight the contribution of pseudogenized protein-coding genes to human lincrnas. BMC Genomics 2017, 18:786 (co-first authors, in press) (Contributions: designed computational analysis, wrote manuscript) 4. Lloyd PJ, Tsai ZT-Y, Sowers RP, Panchy NL, Shiu S-H: Defining the functional significance of intergenic transcribed regions based on heterogeneous features of phenotype genes and pseudogenes. Molecular Biology and Evolution 2017 (in press) (Contributions: conceived study, designed and performed computational analysis) 5. Huang J-H, Kwan S-Y, Tsai ZT-Y, Tsai H-K: Expansion of transcription factor binding sites for introducing lineage-specific motifs in the promoter regions. Nucleic Acids Research 2017 (submitted)(contributions: conceived study, designed and performed computational analysis, wrote manuscript) 6. Tsai ZT-Y, Shiu S-H, Tsai H-K: Contribution of sequence motif, chromatin state, and DNA structure features to predictive models of transcription factor binding. PLoS Computational Biology 2015, 11(8):e (Contributions: conceived study, designed and performed computational analysis, wrote manuscript) 7. Liu M-J, Seddon AE, Tsai ZT-Y, Major IT, Floer M, Howe GA, Shiu S-H: Determinants of nucleosome positioning and their influence on plant gene expression. Genome Research 2015; 25: (Contributions: designed and performed computational analysis) 8. Cheng J-H, Pan DZ-C, Tsai ZT-Y, Tsai H-K: Genome-wide analysis of enhancer RNA in gene regulation across 12 mouse tissues. Scientific Reports 2015, 5:12648; doi: /srep (Contributions: conceived study, wrote manuscript) 9. Hung C-L, Cheng H-H, Hsieh W-C, Tsai ZT-Y, Tsai H-K, Chu C-H, Hsieh W-P, Chen Y-F, Tsou Y, Lai C-H, and Wang W-C: The CrdRS two-component system responds to nitrosative stress in Helicobacter pylori. Molecular Microbiology (Contributions: designed and performed computational analysis) 10. Tsai ZT-Y, Chu W-Y, Cheng, J.H., Tsai H-K: Associations between intronic non-b DNA structures and exon skipping. Nucleic Acids Research 2014, 42(2), (Contributions: conceived study, designed and performed computational analysis, wrote manuscript) 11. Lin C-H, Tsai ZT-Y, Wang D: Role of antisense RNAs in evolution of yeast regulatory complexity. Genomics 2013, 102(5-6), (Contributions: conceived study, wrote manuscript) Page 3 of 6

4 12. Chen, Y.C., Cheng, J.H., Tsai ZT-Y, Tsai, H.K., and Chuang, T.C. The impact of trans-regulation on the evolutionary rates of metazoan proteins, Nucleic Acid Research 2013, 41:13, pages (Contributions: designed and performed computational analysis) 13. Tsai ZT-Y, Tsai H-K, Cheng J-H, Lin C-H, Tsai Y-F,Wang D: Evolution of cis-regulatory elements in yeast de novo and duplicated new genes. BMC Genomics 2012, 13:717. (Contributions: conceived study, designed and performed computational analysis, wrote manuscript) 14. Chiang S, Swamy KBS, Hsu T-W, Tsai ZT-Y, Lu HH-S, Wang D, Tsai H-K: Analysis of the association between transcription factor binding site variants and distinct accompanying regulatory motifs in yeast. Gene 2012, 491: (Contributions: designed and performed computational analysis) 15. Swamy KBS, Cho C-Y, Chiang S, Tsai ZT-Y, Tsai H-K: Impact of DNA-binding position variants on yeast gene expression. Nucleic Acids Research 2009, 37: (Contributions: designed and performed computational analysis) 16. Tsai K-N, Chan E-C, Tsai ZT-Y, Chen K-T, Chen C-Y, Hung K, Chen C-M: Cytotoxic effect of recombinant Mycobacterium tuberculosis CFP-10/ESAT-6 protein on the crucial pathways of WI-38 cells. Journal of biomedicine & biotechnology 2009, 2009: (Contributions: designed and performed computational analysis) 17. Tsai K-N, Tsai ZT-Y, Chen C-M: A new approach to deciphering pathways of enterovirus 71-infected cells: an integration of microarray data, gene ontology, and pathway database. Biomedical Engineering - Applications, Basis & Communications 2006, 18: (Contributions: designed and performed computational analysis) ORAL PRESENTATIONS/INVITED TALKS 1. Advance the understanding of regulatory genomics by data integration. Seminar, Nov. 13, 2017, National Central University, Taiwan. 2. Advance the understanding of regulatory genomics by data integration. Seminar, Nov. 8, 2017, National Taiwan University, Taiwan. 3. Advance the understanding of regulatory genomics by data integration. TIGP Seminar, Oct. 19, 2017, Academia Sinica, Taiwan. 4. Advance the understanding of regulatory genomics by data integration. Webinar, Sep. 22, 2017, Harvard Medical School, MA, USA. 5. Defining functional genic regions in the human genome. Seminar Talk, Sep. 20, 2016, Cold Spring Harbor Laboratory, NY, USA. 6. Defining functional genic regions in the human genome. Seminar Talk, Sep. 15, 2016, University of Washington, WA, USA. 7. Defining functional genic regions in the human genome. Seminar Talk, Sep. 13, 2016, University of Michigan Ann Arbor, MI, USA. 8. Defining functional genic regions in the human genome. Seminar Talk, Sep. 9, 2016, Broad Institute, MA, USA. 9. Integrating heterogeneous data to advance the understanding of regulatory genomics. Seminar Talk, Mar. 23, 2016, National Cheng Kung University, Taiwan. 10. Defining functional regions.in human genomes through integration of heterogeneous data. Cell and Molecular Biology Research Forum, March 16, 2016, Michigan State University, USA. 11. Integrating heterogeneous data to advance the understanding of gene regulation. Seminar Talk, Dec. 9, 2015, National Central University, Taiwan. Page 4 of 6

5 12. Contribution of sequence motif, chromatin state, and DNA structure features to predictive models of transcription factor binding. Gene Expression in Development and Disease (GEDD) Research Forum, June 16, 2015, Michigan State University, USA. 13. Computational studies of gene regulation in the post- Next Generation Sequencing era. Seminar Talk, June 4, 2014, Department of Computer Science and Information Engineering, National Taiwan Normal University, Taiwan. 14. The regulatory genomics in the era of Next-Generation Sequencing. Seminar Talk, May 22, 2014, Department of Medical Informatics, Tzu Chi University, Taiwan. 15. Tsai ZT-Y, Chu W-Y, Cheng, J.H., Tsai H-K: Associations between intronic non-b DNA structures and exon skipping. The 11th Bioinformatics and Systems Biology in Taiwan, Oct. 2013, National Yang-Ming University, Taiwan. (The Best Presentation Award) 16. Evolution of cis-regulatory features in yeast de novo genes. Centre for Genomic Regulation and Academia Sinica Exchange Workshop, Nov. 29, 2012, Academia Sinica, Taiwan. 17. Tsai ZT-Y, Tsai H-K, Wang D: Evolution of cis-regulatory features in yeast de novo genes. International Symposium on Evolutionary Genomics and Bioinformatics (ISEGB 2012), Oct. 2012, National Sun Yat-Sen University, Taiwan. (The Best Oral Presentation Award) 18. Tsai ZT-Y, Huang, GT-W, and Tsai H-K: Simultaneous identification for synergistic transcription factors and their transcription factor binding sites. The Fourth International Workshop on Intelligent Informatics in Biology and Medicine (IIBM 2011), June 2011, Seoul, Korea. TEACHING EXPERIENCE INSTRUCTOR, INTRODUCTION TO REGULATORY GENOMICS 2014 CBiG14 summer courses, Introduce regulatory genomics challenge in DREAM9 and background knowledge INSTRUCTOR, SIMULATION AND MODELING 2014 Popular Science Lectures, National Taiwan Normal University Popular science lectures for teachers in senior high school Title: Applications of simulation models in climate change and gene expression TEACHING ASSISTANT, BIOLOGICAL COMPUTING 2009 Bioinformatics, TIGP, Academia Sinica Taught data structure and algorithms, advance algorithms in bioinformatics, and Python programming SOFTWARES & DATABASES Database: Drug-resistance associated single nucleotide variations in Helicobacter pylori Developed in Perl, R, and PHP Database: Regulatory network of two-component systems in Helicobacter pylori Developed in Perl, PHP, and the Cytoscape package AHPZing, a user-friendly analytic hierarchy process tool for decision making Page 5 of 6

6 Developed in Microsoft Visual Basic 6.0. Download: REFEREE FOR JOURNALS & CONFERENCES Nucleic Acids Research Scientific Report Bioinformatics PLOS ONE BMC Research Notes Genomics Proteomics and Bioinformatics Journal of Biomedicine and Biotechnology Journal of Information Science and Engineering Asia Pacific Bioinformatics Conference SCIENTIFIC SOCIETIES American Society for Biochemistry and Molecular Biology (ASBMB) Taiwan Society of Evolution and Computational Biology (TSECB) REFERENCE Maureen Sartor Dep. Comp. Med. and Bioinfo., U of Michigan, Ann Arbor sartorma@umich.edu Dana Dolinoy Envir. Health and Nutri. Sciences, U of Michigan, Ann Arbor ddolinoy@umich.edu Shin-Han Shiu Plant Biology Department, Michigan State University shius@msu.edu Wen-Hsiung Li Biodiversity Research Center, Academia Sinica whli@gate.sinica.edu.tw Huai-Kuang Tsai Institute of Information Science, Academia Sinica hktsai@iis.sinica.edu.tw Chien-Yu Chen chienyuchen@ntu.edu.tw Page 6 of 6