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CV Chien-Wei Lin

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Chien-Wei Lin

This document is a CV for Chien-Wei (Masaki) Lin, a PhD candidate in Biostatistics at the University of Pittsburgh. It summarizes his education, research interests in statistical genetics and neuroscience, publications, teaching experience, and skills. His research focuses on developing statistical methods for analyzing high-throughput omics data, with a particular interest in integrating multi-omics datasets. He has over 15 peer-reviewed publications and has presented his work at several conferences.

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Chien-Wei (Masaki) Lin 1 CHIEN-WEI (MASAKI) LIN 2715 MURRAY AVE., APT 607, PITTSBURGH, PA 15217 : (412)-944-7488 : masaki396@gmail.com http://www.pitt.edu/~chl169/ Education University of Pittsburgh Pittsburgh, PA, US Ph.D. in Biostatistics (GPA: 3.96/4.00) Sep 2012 Expected in Jun 2017 - Dissertation: Power calculation and Experimental design in RNA-Seq and Methyl-Seq - Advisor: George C. Tseng National Chiao Tung University Hsinchu, Taiwan M.S. in Statistics (GPA: 4.00/4.00) Sep 2005 Jun 2007 - Dissertation: A goodness-of-fit test for Archimedean copula models in the presence of right censoring - Advisor: Weijing Wang National Tsing Hua University Hsinchu, Taiwan B.S. in Applied Mathematics Sep 2000 Jun 2005 Research Interest My research interest is in both methodology and collaborative research. I have many collaboration experiences with researchers in psychiatric field, specifically focus on brain disorders. I have been inspired by many of those interesting biological questions and developed statistical methods to solve real-world problems. I am particularly interested in working on high-throughput multi-omics data and developing integrative methods to identify disease-related biomarkers and to solve supervised/unsupervised statistical machine learning problems. I am also interested in techniques about how to handle Big Data (e.g., Apache Spark) and topics in integrating multi-omics data and brain imaging data. Scholarship and Award International Biometric Society Eastern North American Region (ENAR) Distinguished Student Paper Award 2016 - SeqDesign: A framework for RNA-Seq genome-wide power calculation and experimental design issues. University of Pittsburgh Best ENAR Presentation Award 2014/2016 Health Disparities Poster Competition Award 2015 Statistical and Applied Mathematical Sciences Institute (SAMSI) Challenges in Computational Neuroscience (CCNS) Transition Workshop Travel Award 2016 - Exchange and connect results spanned by the CCNS program CCNS Opening Workshop Travel Award 2015 - Overview of methodology and applications in computational neuroscience CCNS Summer School Travel Award 2015 - An in-depth course training in computation neuroscience Professor Chen Wen-Chens Memorial Foundation Chen Wen-Chen Memorial Scholarship in Statistical Sciences 2007
Chien-Wei (Masaki) Lin 2 The National Tsing Hua University/The National Chiao Tung University Academic Achievement Award 2003/2006 Publication Methodology........ Power and Sample Size Calculation in NGS Data [1] Lin, C.-W.* , Liao, G.* , Lee, M. L. T., Park, Y., & Tseng, G. C. (2017). SeqDesign: A framework for RNA-Seq genome-wide power calculation and experimental design issues. Submitted to JASA. Meta-analysis and Integrative Analysis [2] Kim, S., Lin, C.-W., & Tseng, G. C. (2016). MetaKTSP: A Meta-Analytic Top Scoring Pair Method for Robust Cross-Study Validation of Omics Prediction Analysis. Bioinformatics, 32(March), btw115. [3] Yang, H.-C., Lin, C.-W., Chen, C.-W., & Chen, J. (2014). Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics. BMC Genomics, 15(1), 319. [4] Yang, H.-C., Wang, P.-L., Lin, C.-W., Chen, C.-H., & Chen, C.-H. (2012). Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations. BMC Genomics, 13(1), 346. Statistical Metabolomics [5] Liang, Y. J., Lin, Y. T., Chen, C. W., Lin, C. W., Chao, K. M., Pan, W. H., & Yang, H. C. (2016). SMART: Statistical Metabolomics Analysis - An R Tool. Analytical Chemistry, 88(12), 63346341. Bioinformatics [6] Yang, H.-C., Lin, H.-C., Kang, M., Chen, C.-H., Lin, C.-W., Li, L.-H., Pan, W.-H. (2011). SAQC: SNP array quality control. BMC Bioinformatics, 12, 100. Survival Analysis [7] Emura, T., Lin, C. W., & Wang, W. (2010). A goodness-of-fit test for Archimedean copula models in the presence of right censoring. Computational Statistics and Data Analysis, 54(12), 30333043. Game Theory [8] Wang, B. C.* , Lin, C. W.* , Chen, K. T., & Chen, L. J. (2012). An analytical model for generalized ESP games. Knowledge-Based Systems, 34, 114127. Collaboration/Application.................................................................................................................. [9] McKinney, B. C.* , Lin, C.-W.* , Oh, H., Tseng, G. C., Lewis, D. A., & Sibille, E. (2017). DNA Methylation in the Human Frontal Cortex Reveals a Putative Mechanism for Age-by-Disease Interactions. Submitted to Biological Psychiatry. [10] Belzeaux, R., Lin, C.-W., Ding, Y., Bergon, A., Ibrahim, E. C., Turecki, G., Sibille, E. (2016). Predisposition to treatment response in major depressive episode: A peripheral blood gene coexpression network analysis. Journal of Psychiatric Research, 81, 119126. [11] Diniz, B. S., Reynolds, C. F., Sibille, E., Lin, C.-W., Tseng, G., Lotrich, F., Butters, M. A. (2016). Enhanced Molecular Aging in Late-Life Depression: the Senescent Associated Secretory Phenotype. The American Journal of Geriatric Psychiatry. [12] Grubisha, M. J.* , Lin, C.-W.* , Tseng, G. C., Penzes, P., Sibille, E., & Sweet, R. A. (2016). Age-dependent increase in Kalirin-9 and Kalirin-12 transcripts in human orbitofrontal cortex. European Journal of Neuroscience, 44(7), 24832492. [13] Diniz, B. S., Lin, C. W., Sibille, E., Tseng, G., Lotrich, F., Aizenstein, H. J., Butters, M. A. (2016). Circulating biosignatures of late-life depression (LLD): Towards a comprehensive, data-driven approach to understanding LLD pathophysiology. Journal of Psychiatric Research, 82, 17. [14] McKinney, B. C., Lin, C.-W., Oh, H., Tseng, G. C., Lewis, D. A., & Sibille, E. (2015). Hypermethylation of BDNF and SST Genes in the Orbital Frontal Cortex of Older Individuals: A Putative Mechanism for Declining Gene Expression with Age. Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology, 40(11), 260413.
Chien-Wei (Masaki) Lin 3 [15] Lin, C. W., Chang, L. C., Tseng, G. C., Kirkwood, C. M., Sibille, E. L., & Sweet, R. A. (2015). VSNL1 co- expression networks in aging include calcium signaling, synaptic plasticity, and Alzheimers disease pathways. Frontiers in Psychiatry, 6(MAR), 30. [16] Nikolova, Y. S., Iruku, S. P., Lin, C.-W., Conley, E. D., Puralewski, R., French, B., Sibille, E. (2015). FRAS1-related extracellular matrix 3 (FREM3) single-nucleotide polymorphism effects on gene expression, amygdala reactivity and perceptual processing speed: An accelerated aging pathway of depression risk. Frontiers in Psychology, 6(September), 1377. [17] Chang, L. C., Jamain, S., Lin, C. W., Rujescu, D., Tseng, G. C., & Sibille, E. (2014). A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies. PLoS ONE, 9(3), e90980. Methodology in Preparation....................................................................................................................................................................... [18] Lin, C.-W.* , Liu, P.* , Park, Y., & Tseng, G. C. (2017). MethylSeqDesign: A framework for Methyl-Seq genome-wide power calculation and experimental design issues. [19] Lin, C. W.* , Cahill, K. M.* , & Tseng, G. C. (2017) Meta analytic framework of tree methods. [20] Lin, C. W.* , Zeng, X.* , & Tseng, G. C. (2017) Parameter estimation scheme in clustering algorithms via stability analysis. [21] Ma, T., Huo, Z., Kuo, A., Zeng, X., Zhu, L., Fang, A., Wang, L., Lin, C. W., Rahman, T., Liu, S., Park, Y., Kim, S., Li, J., Chang, L. C., Song, C., & Tseng, G. C. (2017) MetaOmics - a Comprehensive Software Suite with Interactive Visualization for Transcriptomic Meta-Analysis. [22] Zeng, X., Fang, A., Lin, C. W., Ma, T., & Tseng, G. C. (2017) Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis. Collaboration/Application in Preparation........................................................... [23] Lin, C.-W., Chang, L. C., Ma, T., Oh, H., Tseng, G. C., Lewis, D. A., & Sibille, E. (2017). Genetic Modulation of Brain Molecular Aging. Conference Proceedings [24] Lin, C. W., Chen, K. T., Chen, L. J., King, I., & Lee, J. H. M. (2008). An analytical approach to optimizing the utility of ESP games. In Proceedings - 2008 IEEE/WIC/ACM International Conference on Web Intelligence, WI 2008 (pp. 184187). Working Experience Academia Sinica Taipei, Taiwan Research Assistant in Institute of Statistical Science Mar 2009 July 2012 - Advisor: Hsin-Chou Yang Research Assistant in Institute of Information Science Oct 2007 Mar 2009 - Advisor: Sheng-Wei Chen (a.k.a. Kuan-Ta Chen) *Remark: The working period from Oct 2007 to Oct 2011 was a replacement of required military service. Teaching Experience Guest Lecturer.. BIOST 2094 (Biostatistics, University of Pittsburgh) Statistical Computing in R/Advanced R Computing Mar 2015/Spring 2017 - Numerical methods in optimization problems, ggplot2, Graphical interface: tcltk, shiny. BIOST 2055/HUGEN 2070 (University of Pittsburgh) Introductory High-throughput Genomic Data Analysis I: Oct 2014/Mar 2015 Data Mining and Applications/Bioinformatics in Human Genetics
Chien-Wei (Masaki) Lin 4 - Differential and isoform analysis of RNA-Seq data. - Served as Teaching Assistant in BIOST 2055. Oral and Poster Presentations Oral Presentation... ENAR Baltimore, MD/Austin, TX SeqDesign: A framework for RNA-Seq genome-wide power Mar 2014/Mar 2016 calculation and experimental design issues. Contributed. Poster Presentation. Deans Days Competition, GSPH, University of Pittsburgh Pittsburgh, PA DNA Methylation in the Human Frontal Cortex Reveals a Apr 2016 Putative Mechanism for Age-by-Disease Interactions. Pittsburgh ASA banquet Pittsburgh, PA SeqDesign: A framework for RNA-Seq genome-wide power Apr 2015/Mar 2016 calculation and experimental design issues. Joint Statistical Meetings (JSM) Seattle, WA Comparative Pathway Integrator: a framework of meta- Aug 2015 of multiple transcriptomic studies for consensual and differential pathway analysis. Health Disparities Poster Competition, University of Pittsburgh Pittsburgh, PA Genetic Modulation of Brain Molecular Aging. Apr 2015 Deans Days Competition, GSPH, University of Pittsburgh Pittsburgh, PA Genetic Modulation of Brain Molecular Aging. Apr 2013/Apr 2014/Apr 2015 ICHG and ASHG Annual Meeting Montreal, Canada An integrative pathway analysis using gene expression, Oct 2011 single-nucleotide polymorphism and environmental factor successfully predicts disease status of hypertension. (Presented by Dr. Hsin-Chou Yang) Skills Statistical Software Proficient in R, SAS, Stata Bioinformatics Tools NCBI database, FASTSNP, Bioconductor, UCSC Genome Browser, Ensemble Database, HELIXTREE, PARTEK, SAS GENETICS Operating System Windows, Mac OS, Linux Languages Proficient in Chinese, Japanese, English

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CV Chien-Wei Lin

  • 1. Chien-Wei (Masaki) Lin 1 CHIEN-WEI (MASAKI) LIN 2715 MURRAY AVE., APT 607, PITTSBURGH, PA 15217 : (412)-944-7488 : masaki396@gmail.com http://www.pitt.edu/~chl169/ Education University of Pittsburgh Pittsburgh, PA, US Ph.D. in Biostatistics (GPA: 3.96/4.00) Sep 2012 Expected in Jun 2017 - Dissertation: Power calculation and Experimental design in RNA-Seq and Methyl-Seq - Advisor: George C. Tseng National Chiao Tung University Hsinchu, Taiwan M.S. in Statistics (GPA: 4.00/4.00) Sep 2005 Jun 2007 - Dissertation: A goodness-of-fit test for Archimedean copula models in the presence of right censoring - Advisor: Weijing Wang National Tsing Hua University Hsinchu, Taiwan B.S. in Applied Mathematics Sep 2000 Jun 2005 Research Interest My research interest is in both methodology and collaborative research. I have many collaboration experiences with researchers in psychiatric field, specifically focus on brain disorders. I have been inspired by many of those interesting biological questions and developed statistical methods to solve real-world problems. I am particularly interested in working on high-throughput multi-omics data and developing integrative methods to identify disease-related biomarkers and to solve supervised/unsupervised statistical machine learning problems. I am also interested in techniques about how to handle Big Data (e.g., Apache Spark) and topics in integrating multi-omics data and brain imaging data. Scholarship and Award International Biometric Society Eastern North American Region (ENAR) Distinguished Student Paper Award 2016 - SeqDesign: A framework for RNA-Seq genome-wide power calculation and experimental design issues. University of Pittsburgh Best ENAR Presentation Award 2014/2016 Health Disparities Poster Competition Award 2015 Statistical and Applied Mathematical Sciences Institute (SAMSI) Challenges in Computational Neuroscience (CCNS) Transition Workshop Travel Award 2016 - Exchange and connect results spanned by the CCNS program CCNS Opening Workshop Travel Award 2015 - Overview of methodology and applications in computational neuroscience CCNS Summer School Travel Award 2015 - An in-depth course training in computation neuroscience Professor Chen Wen-Chens Memorial Foundation Chen Wen-Chen Memorial Scholarship in Statistical Sciences 2007
  • 2. Chien-Wei (Masaki) Lin 2 The National Tsing Hua University/The National Chiao Tung University Academic Achievement Award 2003/2006 Publication Methodology........ Power and Sample Size Calculation in NGS Data [1] Lin, C.-W.* , Liao, G.* , Lee, M. L. T., Park, Y., & Tseng, G. C. (2017). SeqDesign: A framework for RNA-Seq genome-wide power calculation and experimental design issues. Submitted to JASA. Meta-analysis and Integrative Analysis [2] Kim, S., Lin, C.-W., & Tseng, G. C. (2016). MetaKTSP: A Meta-Analytic Top Scoring Pair Method for Robust Cross-Study Validation of Omics Prediction Analysis. Bioinformatics, 32(March), btw115. [3] Yang, H.-C., Lin, C.-W., Chen, C.-W., & Chen, J. (2014). Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics. BMC Genomics, 15(1), 319. [4] Yang, H.-C., Wang, P.-L., Lin, C.-W., Chen, C.-H., & Chen, C.-H. (2012). Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations. BMC Genomics, 13(1), 346. Statistical Metabolomics [5] Liang, Y. J., Lin, Y. T., Chen, C. W., Lin, C. W., Chao, K. M., Pan, W. H., & Yang, H. C. (2016). SMART: Statistical Metabolomics Analysis - An R Tool. Analytical Chemistry, 88(12), 63346341. Bioinformatics [6] Yang, H.-C., Lin, H.-C., Kang, M., Chen, C.-H., Lin, C.-W., Li, L.-H., Pan, W.-H. (2011). SAQC: SNP array quality control. BMC Bioinformatics, 12, 100. Survival Analysis [7] Emura, T., Lin, C. W., & Wang, W. (2010). A goodness-of-fit test for Archimedean copula models in the presence of right censoring. Computational Statistics and Data Analysis, 54(12), 30333043. Game Theory [8] Wang, B. C.* , Lin, C. W.* , Chen, K. T., & Chen, L. J. (2012). An analytical model for generalized ESP games. Knowledge-Based Systems, 34, 114127. Collaboration/Application.................................................................................................................. [9] McKinney, B. C.* , Lin, C.-W.* , Oh, H., Tseng, G. C., Lewis, D. A., & Sibille, E. (2017). DNA Methylation in the Human Frontal Cortex Reveals a Putative Mechanism for Age-by-Disease Interactions. Submitted to Biological Psychiatry. [10] Belzeaux, R., Lin, C.-W., Ding, Y., Bergon, A., Ibrahim, E. C., Turecki, G., Sibille, E. (2016). Predisposition to treatment response in major depressive episode: A peripheral blood gene coexpression network analysis. Journal of Psychiatric Research, 81, 119126. [11] Diniz, B. S., Reynolds, C. F., Sibille, E., Lin, C.-W., Tseng, G., Lotrich, F., Butters, M. A. (2016). Enhanced Molecular Aging in Late-Life Depression: the Senescent Associated Secretory Phenotype. The American Journal of Geriatric Psychiatry. [12] Grubisha, M. J.* , Lin, C.-W.* , Tseng, G. C., Penzes, P., Sibille, E., & Sweet, R. A. (2016). Age-dependent increase in Kalirin-9 and Kalirin-12 transcripts in human orbitofrontal cortex. European Journal of Neuroscience, 44(7), 24832492. [13] Diniz, B. S., Lin, C. W., Sibille, E., Tseng, G., Lotrich, F., Aizenstein, H. J., Butters, M. A. (2016). Circulating biosignatures of late-life depression (LLD): Towards a comprehensive, data-driven approach to understanding LLD pathophysiology. Journal of Psychiatric Research, 82, 17. [14] McKinney, B. C., Lin, C.-W., Oh, H., Tseng, G. C., Lewis, D. A., & Sibille, E. (2015). Hypermethylation of BDNF and SST Genes in the Orbital Frontal Cortex of Older Individuals: A Putative Mechanism for Declining Gene Expression with Age. Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology, 40(11), 260413.
  • 3. Chien-Wei (Masaki) Lin 3 [15] Lin, C. W., Chang, L. C., Tseng, G. C., Kirkwood, C. M., Sibille, E. L., & Sweet, R. A. (2015). VSNL1 co- expression networks in aging include calcium signaling, synaptic plasticity, and Alzheimers disease pathways. Frontiers in Psychiatry, 6(MAR), 30. [16] Nikolova, Y. S., Iruku, S. P., Lin, C.-W., Conley, E. D., Puralewski, R., French, B., Sibille, E. (2015). FRAS1-related extracellular matrix 3 (FREM3) single-nucleotide polymorphism effects on gene expression, amygdala reactivity and perceptual processing speed: An accelerated aging pathway of depression risk. Frontiers in Psychology, 6(September), 1377. [17] Chang, L. C., Jamain, S., Lin, C. W., Rujescu, D., Tseng, G. C., & Sibille, E. (2014). A conserved BDNF, glutamate- and GABA-enriched gene module related to human depression identified by coexpression meta-analysis and DNA variant genome-wide association studies. PLoS ONE, 9(3), e90980. Methodology in Preparation....................................................................................................................................................................... [18] Lin, C.-W.* , Liu, P.* , Park, Y., & Tseng, G. C. (2017). MethylSeqDesign: A framework for Methyl-Seq genome-wide power calculation and experimental design issues. [19] Lin, C. W.* , Cahill, K. M.* , & Tseng, G. C. (2017) Meta analytic framework of tree methods. [20] Lin, C. W.* , Zeng, X.* , & Tseng, G. C. (2017) Parameter estimation scheme in clustering algorithms via stability analysis. [21] Ma, T., Huo, Z., Kuo, A., Zeng, X., Zhu, L., Fang, A., Wang, L., Lin, C. W., Rahman, T., Liu, S., Park, Y., Kim, S., Li, J., Chang, L. C., Song, C., & Tseng, G. C. (2017) MetaOmics - a Comprehensive Software Suite with Interactive Visualization for Transcriptomic Meta-Analysis. [22] Zeng, X., Fang, A., Lin, C. W., Ma, T., & Tseng, G. C. (2017) Comparative Pathway Integrator: a framework of meta-analytic integration of multiple transcriptomic studies for consensual and differential pathway analysis. Collaboration/Application in Preparation........................................................... [23] Lin, C.-W., Chang, L. C., Ma, T., Oh, H., Tseng, G. C., Lewis, D. A., & Sibille, E. (2017). Genetic Modulation of Brain Molecular Aging. Conference Proceedings [24] Lin, C. W., Chen, K. T., Chen, L. J., King, I., & Lee, J. H. M. (2008). An analytical approach to optimizing the utility of ESP games. In Proceedings - 2008 IEEE/WIC/ACM International Conference on Web Intelligence, WI 2008 (pp. 184187). Working Experience Academia Sinica Taipei, Taiwan Research Assistant in Institute of Statistical Science Mar 2009 July 2012 - Advisor: Hsin-Chou Yang Research Assistant in Institute of Information Science Oct 2007 Mar 2009 - Advisor: Sheng-Wei Chen (a.k.a. Kuan-Ta Chen) *Remark: The working period from Oct 2007 to Oct 2011 was a replacement of required military service. Teaching Experience Guest Lecturer.. BIOST 2094 (Biostatistics, University of Pittsburgh) Statistical Computing in R/Advanced R Computing Mar 2015/Spring 2017 - Numerical methods in optimization problems, ggplot2, Graphical interface: tcltk, shiny. BIOST 2055/HUGEN 2070 (University of Pittsburgh) Introductory High-throughput Genomic Data Analysis I: Oct 2014/Mar 2015 Data Mining and Applications/Bioinformatics in Human Genetics
  • 4. Chien-Wei (Masaki) Lin 4 - Differential and isoform analysis of RNA-Seq data. - Served as Teaching Assistant in BIOST 2055. Oral and Poster Presentations Oral Presentation... ENAR Baltimore, MD/Austin, TX SeqDesign: A framework for RNA-Seq genome-wide power Mar 2014/Mar 2016 calculation and experimental design issues. Contributed. Poster Presentation. Deans Days Competition, GSPH, University of Pittsburgh Pittsburgh, PA DNA Methylation in the Human Frontal Cortex Reveals a Apr 2016 Putative Mechanism for Age-by-Disease Interactions. Pittsburgh ASA banquet Pittsburgh, PA SeqDesign: A framework for RNA-Seq genome-wide power Apr 2015/Mar 2016 calculation and experimental design issues. Joint Statistical Meetings (JSM) Seattle, WA Comparative Pathway Integrator: a framework of meta- Aug 2015 of multiple transcriptomic studies for consensual and differential pathway analysis. Health Disparities Poster Competition, University of Pittsburgh Pittsburgh, PA Genetic Modulation of Brain Molecular Aging. Apr 2015 Deans Days Competition, GSPH, University of Pittsburgh Pittsburgh, PA Genetic Modulation of Brain Molecular Aging. Apr 2013/Apr 2014/Apr 2015 ICHG and ASHG Annual Meeting Montreal, Canada An integrative pathway analysis using gene expression, Oct 2011 single-nucleotide polymorphism and environmental factor successfully predicts disease status of hypertension. (Presented by Dr. Hsin-Chou Yang) Skills Statistical Software Proficient in R, SAS, Stata Bioinformatics Tools NCBI database, FASTSNP, Bioconductor, UCSC Genome Browser, Ensemble Database, HELIXTREE, PARTEK, SAS GENETICS Operating System Windows, Mac OS, Linux Languages Proficient in Chinese, Japanese, English