Chun-houh Chen, Research Fellow and Director
陳 君 厚 研 究 員 兼 所 長
Institute of Statistical Science, Academia Sinica
128 Academia Road Sec.2, Nankang, Taipei 115, Taiwan


Office: Room 209
Telephone: +886 2 27835611 ext 407
Facsimile:        +886 2 27831523
Email: cchen@stat.sinica.edu.tw
URL:      gap.stat.sinica.edu.tw/
EDUCATION
1987 - 1992 Ph.D. Department of Mathematics   (Program in Statistics)  
    University of California, Los Angeles USA
       
1987 - 1990 M.S. Department of Mathematics   (Program in Statistics)  
    University of California, Los Angeles USA
       
1980 - 1984 B.S. Department of Statistics  
    National Chung-Hsing University Taiwan
RESEARCH INTERESTS

Bioinformatics; Data/Information Visualization; Dimension Reduction; Matrix Visualization; Multivariate Statistical Methods; Pattern Recognition.

EXPERIENCE
2017 - present Director, Institute of Statistical Science, Academia Sinica,
Taipei, Taiwan
2017 - present Co-Director, Data Science Degree Program, National Taiwan University and Academia Sinica,
Taipei, Taiwan
2019 - present Co-Principal Investigator, Taiwan Biobank,
Taipei, Taiwan
2011 - present Research Fellow, Institute of Statistical Science, Academia Sinica,
Taipei, Taiwan
2016 - 2017 Director, Department of Academic Affairs and Instrument Service, Academia Sinica,
Taipei, Taiwan
2012 – 2016 Deputy Director, Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
2002 - 2011 Associate Research Fellow, Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
2007 - 2010 Adjunct Associate Professor, Institute of Statistics, National Central University, Jhongli, Taiwan
2005 - 2010 Core Faculty Member, Bioinformatics Ph.D. Program,
Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
1993 - 2002 Assistant Research Fellow, Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
1998 - 1999 Adjunct Assistant Professor, Graduate Institute of Epidemiology,
College of Public Health, National Taiwan University, Taipei, Taiwan
1994 - 1995 Adjunct Associate Professor, Institute of Mathematical Statistics,
National Chung-Cheng University, Chia-Yi, Taiwan
1992 - 1993 Assistant Professor, Department  of Statistics/Computer and Information Systems, George Washington University, Washington, D.C., U.S.A.
EDITORIAL AND OTHER ACADEMIC SERVICES

Editorships:

  • Associate Editor, Computational Statistics (2004 - 2020)
  • Associate Editor, Computational Statistics and Data Analysis (2004 - 2018)
  • Associate Editor, Journal of the Japan Statistical Society (2013 - 2016)
  • Statistics Consultant, Taiwanese Journal of Psychiatry (1996 - 2000)
  • Associate Editor, BMC (BioMed Central) Research Notes (2008 - 2016)
  • Associate Editor, Statistica Sinica (2005 - 2008)
  • Associate Editor, Journal of the Korean Statistical Society (2002 - 2005)

Academic Society:

  • Chairperson, Academic Committee, Chinese Statistical Association (Taiwan) (2017 - )
  • Council Member (elected), The International Statistical Institute (ISI) (2015 - 2019)
  • Chairperson, The Asian Regional Section (ARS) of The International Association for Statistical Computing (IASC) (2013 - 2015)
  • President, the Chinese Institute of Probability and Statistics (CIPS) (2013 - 2016)
  • Council Member, IASC (2011 - 2015)
  • BoD (Board of Directors) Member, the Asian Regional Section(ARS), IASC (2004 - 2013)

International Conference Organizer:

      Conference Chairman:
  • The 9th Conference of the Asian Regional Section of the IASC, December 17th ~ 19th, 2015, Singapore.
  • Statistical Computing Asia 2015, July 1~2, 2015, Taipei, Taiwan.
  • The 4th Workshop in Symbolic Data Analysis (SDA 2014), June 13th ~ 16th, 2014, Taipei, Taiwan.
  • ISI-ISM-ISSAS (Indian Statistical Institute, Institute of Statistical Mathematics, Institute of Statistical Science, Academia Sinica) Joint Conference 2013, January 31st ~ February 1st, 2013, Taipei, Taiwan.
  • Joint Meeting of the 2011 Taipei International Statistical Symposium and 7th Conference of the Asian Regional Section of the IASC (Joint2011), Taipei, Taiwan
  • Statistical Computation and Visualization 2008 (SCV2008), Taipei, Taiwan

      Member of International Organizing Committee:

  • Joint Meeting of the IASC Satellite Conference for the 59th ISI WSC and the 8th Conference of IASC-ARS, Seoul, Korea (2013).

      Consultative Members:

  • Joint Meeting of 10th Asian Regional Section (ARS) of the International Association for Statistical Computing (IASC) and the NZ Statistical Association (NZSA), December 10th ~ 14th, 2017, Auckland, New Zealand.
  • The 22nd International Conference on Computational Statistics (CompStat2016), August 23rd ~ 26th, 2016, Oviedo, Spain. (Consultative Member of SPC).
  • International conference on mathematics, statistics, and financial mathematics 2014 (ICMSFM2014) with IASC-ARS sessions, Petaling Jaya, Malaysia.

      Member of Scientific Program Committee (SPC):

  • Data Science, Statistics and Visualisation 2021 (DSSV2021), July 7-9, 2021, Erasmus University Rotterdam, The Netherlands.
  • The 16th IMT-GT International Conference on Mathematics, Statistics and their Applications (ICMSA 2020), 23 & 24 November 2020 in Klang Valley, Malaysia.
  • 2020 Symbolic Data Analysis Workshop (SDA2020), June 11-12, 2020, Caserta, Italy.
  • Data Science, Statistics and Visualisation (DSSV2018), July 9-11, 2018, Vienna University of Technology, Austria.
  • The 61st World Statistics Congress (ISI2017), July 16th ~ 21st, 2017, Marrakech, Morocco. (Vice-Chair of SPC).
  • The 5th Workshop in Symbolic Data Analysis (SDA 2015), November 17th ~ 19th, 2015, Orléans, France.
  • IASC Satellite Conference 2015: Statistical Computing for Data Science, August 2nd ~ 4th, 2015, Búzios, Brazil.
  • 2014 Computer Graphics Workshop (CGW 2014), Taipei, Taiwan (2014).
  • The International Statistical Institute Regional Statistics Conference 2014 (ISI-RSC 2014), Kuala Lumpur, Malaysia (2014).
  • 2013 Computer Graphics Workshop (CGW 2013), Hsin-chu, Taiwan (2013).
  • The 2013 ICSA International Conference, Hong Kong  (2013)
  • 2012 Computer Graphics Workshop (CGW 2012), Puli, Taiwan (2012)
  • The 4th IEEE Pacific Visualization Symposium, Hong Kong  (2011)
  • 2011 Computer Graphics Workshop (CGW 2011), Taipei, Taiwan (2011)
  • The 3rd IEEE Pacific Visualization Symposium, Taipei, Taiwan (2010)
  • Joint meeting of 4th World Conference of IASC and 6th Conference of IASC-ARS, Yokohama, Japan (2008)
  • The IASC-ARS Special Conference, Seoul, Korea (2007)
  • Workshop on Data and Information Visualization, Berlin, Germany (2006)
  • The 4th Conference of IASC-ARS, Busan, Korea (2002)
TEACHING

Statistical Graphics and Data Visualization, Multivariate Analysis, Statistical Computing

GRADUATE STUDENTS AND POSTDOCTORAL FELLOWS

Graduated Master Students: 4, Ph.D. Students: 2, Postdoctoral Fellows: 10.

RESEARCH FUNDING
  • PI, Ministry of Science and Technology (MOST) individual projects: (2012-2022).
  • PI, Core Facility Component Project of Department of Life Sciences , National Science Council (NSC100-2319-B-010-002) (2011/05/01 - 2012/04/30): "Bioinformatics Consortium of Taiwan: Genomic Statistics for Life Science Studies Unit"
  • PI, Core Facility Component Project of National Research Program for Genomic Medicine (NRPGM), NSC (2008/05/01-2011/04/30): "Advanced bioinformatics core: Genomic Statistics for Complex Diseases"
  • PI, Program Project of Genomic and Proteomic Program, Academia Sinica (2005/01/01-2007/12/31): "Bioinformatic Study of Yeast Cis-regulatory Elements and Circuits"
  • PI, Program Project of Academia Sinica Theme Project (2002/01/01-2004/12/31): "Information Visualization of Bioinformatics" in "Development of Knowledge-based Human Biology Databases"
  • PI, National Science Council (NSC) individual projects: (1994-2008)
ACADEMIC VISITING
  • Department of Statistics, The University of Auckland, Auckland, New Zealand.
  • Network Information System Laboratory, Doshisha University, Kyoto, Japan.
  • Department of Statistics and Applied Probability, National University of Singapore, Singapore.
  • Department of Prob. and Mathematical Statistics, Charles University in Prague, Czech Republic
  • Center for Applied Statistics and Economics, Humboldt-Universität zu Berlin, Germany
  • Institute of Mathematical Statistics, Tokyo, Japan
  • Department of Statistics, SungKyunKwan University, Korea
  • Department of Statistics, Pukyong National University, Korea
  • National Center of Toxicology Research, Little Rock, Arkansas, USA
MAJOR AWARDS AND HONORS
  • Presented a Keynote Lecture at the 2019 Taiwan Econometric Research Annual Conference, Taipei, Taiwan (2019): “Matrix Visualization with Applications”
  • Presented a Keynote Lecture at the 2014 Korean Statistical Society Fall Conference, Seoul, Korea (October 31st ~ November 1st, 2014): “Matrix Visualization: New Generation of Exploratory Data Analysis”
  • ISI (The International Statistical Institute) Member, 2011.
  • Presented the Opening Keynote Lecture at the 16th Symposium of International Association for Statistical Computing (COMPSTAT 2004) at Prague, Czech Republic (August 23-27, 2004): “Matrix Visualization and Information Mining.


SELECTED INVITED INTERNATIONAL PRESENTATIONS (Since 2004)
Invited Workshops (at least 3-hour lecture):
  1. “Statistical Graphics and Data Visualization,” Indian Statistical Institute, Kolkata, India (2020).
  2. “Statistical Graphics and Data Visualization,” Waseda University, Tokyo (2019).
  3. Two-day Workshop on “Matrix Visualization: Approaching Statistics and Statistical Approach," Institute for Statistics und Econometrics, Humboldt-Universität zu Berlin, Germany (2014).
  4. Ph.D. Course on “Matrix Visualization: Approaching Statistics and Statistical Approach,” Charles University in Prague, Czech Republic (2013).
  5. Two-month Workshop on “Some Extensions and Applications of Matrix Visualization Using GAP.", Institute of Statistical Mathematics, Tokyo, Japan (2011).
  6. "Information Visualization for High Dimensional Data:the Matrix Visualization Approach", Section on Statistical Computation, Korean Statistical Society, Korea, Seoul, Korea (2009).
  7. "Information Visualization for High Dimensional Data:the Matrix Visualization Approach", Busan & Kyungnam Branch of the Korean Statistical Society, Busan, Korea (2009).
  8. “Information Visualization for High Dimensional Biomedical Data: the Matrix Visualization Approach", International Conference of Bioinformatics (InCoB), Taipei, Taiwan (2008).
  9. “High dimensional data visualization: the matrix visualization approach", International Conference on the Frontiers of Statistics, Kunming, China (2007).
  10. Tutorial on “Matrix Visualization and Information Mining", The Fourth Asia Pacific Bioinformatics Conference, Taipei, Taiwan (2006).
  11. “GAP: Generalized Association Plots for Dimension Free Data Visualization", The 5th IASC Asian Conference on Statistical Computing, Hong Kong. (2005).
  12. Two-day Workshop on “Dimension Free Data Visualization and Information Mining", Institute of Statistical Mathematics, Tokyo, Japan (2004).
  13. “Data- and Information visualization: Generalized Association Plots", Institute for Statistics und Econometrics, Humboldt-Universität zu Berlin, Germany (2004).
Invited Talks:
  1. Invited Talk: “Matrix Visualization for Big Data,” Indian Statistical Institute, Kolkata, India (2020).
  2. Invited Talk: “Matrix Visualization: New Generation of Exploratory Data Analysis,” Waseda University, Tokyo (2019).
  3. Banquet Speech: Symposium in honor of Professor Higuchi's retirement from the director-general of The Institute of Statistical Mathematics. Hitotsubashi Hall, National Center of Sciences Building, Tokyo, Japan (2019).
  4. Keynote Lecture: “Matrix Visualization with Applications,” 2019 Taiwan Econometric Research Annual Conference, Taipei, Taiwan (2019).
  5. Invited Talk: “Matrix Visualization: New Generation of Exploratory Data Analysis,” Universiti Tunku Abdul Rahman (UTAR), Kuala Lumpur, Malaysia (2019).
  6. Banquet Speech: The IASC-ARS 25th Anniversary Conference and the CASC 2nd Annual Conference. Beijing, China (2018).
  7. Keynote Lecture: “Matrix Visualization: New Generation of Exploratory Data Analysis,” 2014 Korean Statistical Society Fall Conference, Seoul, Korea (2014).
  8. Invited Talk: “Examples of matrix visualization for exploratory data analysis (EDA),” The International Statistical Institute Regional Statistics Conference 2014 (ISI-RSC 2014), Kuala Lumpur, Malaysia (2014).
  9. Invited Talk: “Exploratory Data Analysis of Interval-­valued Symbolic Data with Matrix Visualization,” International conference on mathematics, statistics, and financial mathematics 2014 (ICMSFM2014) with IASC-ARS sessions, Petaling Jaya, Malaysia (2014).
  10. Invited Talk: “Matrix Visualization: Approaching Statistics and Statistical Approach,” Korean National Open University, Seoul, Korea (2014).
  11. Invited Talk: "Some Extensions of Matrix Visualization: the GAP Approach", Seoul National University, Seoul, Korea (2014).
  12. Invited Talk: “Matrix Visualization for Health Statistics: Phenotype, Environtype, and Genotype”, 5th Asia-Pacific Conference on Public Health, Seoul, Korea (10-11 April, 2014).
  13. Plenary Talk: “Visualization of Publication Profile for A Statistician”, Applicable Semiparametrics, Humboldt-Universität zu Berlin, Germany.
  14. Invited Talk: "Covariate-adjusted matrix visualization via correlation decomposition", Charles University in Prague, Czech Republic (2013).
  15. Invited Talk: "Matrix Visualization for Symbolic Data Analysis", The Technical University of Liberec, Czech Republic (2013).
  16. Invited Talk: "Matrix Visualization for High-Dimensional Data with a Cartography Link", Palacký University, Czech Republic (2013).
  17. Invited Talk: "Matrix visualization for high-dimensional categorical data structure", Masaryk University, Czech Republic (2013).
  18. NCTR Seminar Talk “A Brave New World of Biomedical Sciences: Statistics and Visualization ", National Center for Toxicological Research, FDA, USA (2012).
  19. Invited Talk: “Matrix Visualization: Approaching Statistics and Statistical Approach", National Center for Toxicological Research, FDA, USA (2012).
  20. Invited Talk: “Matrix Visualization: Approaching Statistics and Statistical Approach", National University of Singapore (Singapore) (2012).
  21. Invited Talk: “Matrix Visualization with Biomedical Research Applications", East Asia Regional Biometric Conference 2012, Seoul, Korea (2012).
  22. Invited Talk: “Matrix Visualization: Approaching Statistics and Statistical Approach", The 58th World Statistics Congress of the International Statistical Institute (ISI2011), Dublin, Ireland (2011).
  23. Invited Talk: “Matrix Visualization for Symbolic Data Analysis", 2nd Workshop in Symbolic Data Analysis, University of Namur, Namur, Belgium (2011).
  24. Invited Talk: “Matrix Visualization for High-Dimensional Categorical Data Structure with a Cartography Link", International Workshop on Information System for Social Innovation, Institute of Statistical Mathematics, Tokyo, Japan (2011).
  25. Invited Talk: “Matrix Visualization and its Extension to Symbolic Data Analysis", シンボリックデータ解析に関する講演会, Hokkaido University, Sapporo, Japan (2011).
  26. Invited Talk: “Matrix visualization with applications: EDA for the 21st century", Chinese Week of Humboldt-Universität zu Berlin, Humboldt-Universität zu Berlin, Berlin, Germany (2010).
  27. Invited Talk: “Matrix visualization with applications: EDA (exploratory data analysis) for the 21st century", Sungkyunkwan University, Suwon, Korea (2010).
  28. Invited Talk: “Selection of Proximity Measures for Matrix visualization of Binary Data", The 2nd International Conference on BioMedical Engineering and Informatics (BMEI'09), Tianjing, China (2009).
  29. Invited Talk: “Matrix visualization: EDA (exploratory data analysis) tools for the 21st century", 2009 meeting of Japanese Federation of Statistical Science Association (JFSSA), Kyoto, Japan (2009).
  30. Invited Talk: “Covariate-adjusted Matrix Visualization", The 1st Institute of Mathematical Statistics - Asia Pacific Rim Meeting, Seoul National University, Seoul, Korea (2009).
  31. Keynote Lecture: “Visual information mining of high-dimensional data structure with generalized association plots", Symposium on Large-scale Data Linkage, Data Mining and Statistical Methods, Tokyo, Japan (2008).
  32. Invited Talk: “Matrix Visualization for High Dimensional Biomedical Data with Categorical Nature", Workshop on Computational Biology and Statistics, UCLA, Los Angeles, USA (2008).
  33. Invited Talk: “Information Visualization for High Dimensional Categorical Data: the Matrix Visualization Approach", International Workshop on Information Visualization, Taipei, Taiwan (2008).
  34. Invited Talk: “Matrix Visualization for High-Dimensional Categorical Data Structure with a Cartography Link", 2007 Joint Statistical Meetings, Salt Lake City, USA (2007).
  35. Invited Talk: “Applications of Matrix Visualization for Information Mining", Royal Statistical Society Annual Conference 2006, Belfast, North Ireland (2006).
  36. Invited Talk: “Applications of Matrix Visualization for Information Mining", Korean Statistical Society 2006 Spring Conference, Daegu, Korea (2006).
  37. NCTR Seminar Talk: “Visualization and Information Mining for High Dimensional Biomedical Data", National Center for Toxicological Research, FDA, USA (2005).
  38. Keynote Lecture: “Dimension Free Data Visualization and Information Mining", 16th Symposium of International Association for Statistical Computing (COMPSTAT 2004), Prague, Czech Republic (2004).
PUBLICATION
Refereed Journal Articles:
  1. Yang, H. C., Chen, C. H., Wang, J. H., Liao, H. C., Yang, C. T., Chen, C. W., Lin, Y. C., Kao, C. H., Lu, M. Y. J., and Liao, J. C. (2020), Analysis of genomic distributions of SARS-CoV-2 reveals a dominant strain type with strong allelic associations, Proceedings of the National Academy of Sciences Nov 2020, 202007840; DOI: 10.1073/pnas.2007840117.

  2. Wu, H. M., Kao, C. H., and Chen, C. H.* (2020), Dimension reduction and visualization of symbolic interval-valued data using sliced inverse regression, Advances in Data Science: Symbolic, Complex and Network Data, Diday E, Guan R, Saporta G, Wang H (eds). London: Wiley-ISTE, 49-78.

  3. Wu, H. M, Tien, Y. J., Ho, M. R., Hwu, H. G., Lin, W. C., Tao, M. H., Chen, C. H.* (2018), Covariate-adjusted heatmaps for visualizing biological data via correlation decomposition, Bioinformatics, 34(20), 3529–3538.

  4. Yang, H. C., Chen, I. C., Tsay, Y. C., Li, Z. R., Chen, C. H., Hwu, H. G., and Chen, C. H. (2017), Using an Event-History with Risk-Free Model to Study the Genetics of Alcoholism, Scientific Reports, 7: 1975.

  5. Chatla, S.B., Chen, C. H., Shmuéli, G. (2017), Selected topics in statistical computing, Encyclopedia with Semantic Computing and Robotic Intelligence, March 2017, Vol. 01, No. 01, World Scientific Publishing Company.

  6. Kuo, Y. L., Chen, C. H., Chuang, T. H., Hua, W. K., Lin, W. J., Hsu, W. H., Chang, P. M. H., Hsu, S. L., Huang, T. H., Kao, C. Y., Huang, F. C. Y. (2015), Gene expression profiling and pathway network analysis predicts a novel anti-tumor function for a botanical-derived drug, PG2, Evidence-Based Complementary and Alternative Medicine (eCAM), 2015, Article ID 917345.

  7. Huang, C. C., Tien, Y. J., Chen, M. J., Chen, C. H., Ho, H. N., Yang, Y. S. (2015) Symptom patterns and phenotypic subgrouping of women with polycystic ovary syndrome: Association between endocrine characteristics and metabolic aberrations, Human Reproduction, 30(4), 937–946.

  8. Chen, T. C., Lin, K. T., Chen, C. H., Lee, S. A., Lee, P. Y., Liu, Y. W., Kuo, Y. L., Wang, F. S., Lai, J. M., Huang, F. C. Y. (2014), Using an in Situ Proximity Ligation Assay to Systematically Profile Endogenous Protein−Protein Interactions in a Pathway Network, Journal of Proteome Research, 2014, 13, 5339−5346.

  9. Kao, C. H., Nakano, J., Shieh, S. H., Tien, Y. J., Wu, H. M., Yang, C. K., and Chen, C. H.* (2014). Exploratory data analysis of interval-valued symbolic data with matrix visualization, Computational Statistics and Data Analysis, 79 (2014), 14-29.

  10. Chien, W. H., Gau, S. S. F., Chen, C. H., Tsai, W. C., Wu, Y. Y., Chen, P. H., Shang, C. Y., Chen, C. H. (2013) Increased gene expression of FOXP1 in patients with autism spectrum disorders. Molecular Autism, 4:23.

  11. Yang, H. C., Liu, C. M., Liu, Y. L., Chen, C. W., Chang, C. C., Fann, C. S. J., Chiou, J.-J., Yang, Y. C., Chen, C. H., Faraone, S. V., Tsuang, M. T. and Hwu, H. G. (2013). The DAO Gene Is Associated with Schizophrenia and Interacts with Other Genes in the Taiwan Han Chinese Population. PLoS ONE, 8:3.

  12. Chen, Y. C., Tien, Y. J., Chen, C. H., Beltran, F. N., Amor, E. C., Wang, R. J., Wu, D. J., Mettling, C., Lin, Y. L., and Yang, W. C. (2013). Morus alba and active compound oxyresveratrol exert anti-inflammatory activity via inhibition of leukocyte migration involving MEK/ERK signaling. BMC Complementary and Alternative Medicine, 13:45.

  13. Liu, C. H., Chen, T. C., Chau, G. Y., Jan, Y. H., Chen, C. H., Hsu, C. N., Lin, K. T., Juang, Y. L., Lu, P. J., Cheng, H. C., Chen, M. H., Chang, C. F., Ting, Y. S., Kao, C. Y., Hsiao, M., and Huang, F. C. Y. (2013). An analysis of protein-protein interactions in cross-talk pathways reveals CRKL as a novel prognostic marker in hepatocellular carcinoma. Molecular and Cellular Proteomics, 12, 1335-1349.

  14. Liu, C. C., Tien, Y. J., Chen, C. H., Chiu, Y. N., Chien, Y. L., Hsieh, M. H., Liu, C. M., Hwang, T. J., and Hwu, H. G. (2013). Development of a brief self-report questionnaire for screening putative pre-psychotic states. Schizophrenia Research, 143(1), 32-37.

  15. Kuo, Y. L., Chang, M. H. P., Liu, Y. W., Chen, P. H., Lee, P. Y., Liu, R. S., Lai, J. M., Tien, Y. J., Wu, Y. C., Su, L. J., Kao, C. Y., Chen, C. H.*, and Huang, F. C. Y.* (2012) In silico Therapeutic Drug Screening for Reversing the Lung Adenocarcinoma Overexpressed Gene Signatures. Open Access Scientific Reports, 1: 101. doi:10.4172/scientificreports.101.

  16. 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. accepted for publication by BMC Genomics.

  17. Tsai, C. A., Huang, C. H., Chang, C. W., and Chen, C. H. (2012). Recursive Feature Selection with Significant Variables of Support Vectors. to appear in Computational and Mathematical Methods in Medicine.

  18. Chang, C. T., Tsai, C. N., Tang, C. Y., Chen, C. H., Lian, J. H., Hu, C. Y., Tsai, C. L., Chao, A., Lai, C. H., Wang, T. H., and Lee, Y. S. (2012). Mixed Sequence Reader (MSR): a program for analyzing DNA sequences with heterozygous base calling. The Scientific World Journal, Volume 2012, Article ID 365104, 10 pages doi:10.1100/2012/365104.

  19. Liu, C. C., Chen, C. H., Hwu, H. G., Shiue, S. Y., Hua, M. S., Chen, C. H., Hwang, T. J., Liu, C. M., Hsieh, M. H., Liu, S. K., and Chen, W. J. (2012). Medium-term course and outcome of schizophrenia depicted by the sixth-month subtype after an acute episode. Journal of the Formosan Medical Association, 111, 265-274..

  20. Shaw, G. T. W., Shih, E. S. C., Chen, C. H,, and Hwang, M. J. (2011). Preservation of Ranking Order in the Expression of Human Housekeeping Genes. PLoS ONE 6(12): e29314. doi:10.1371/journal.pone.0029314.

  21. Lee, Y. S., Chao, A., Chen, C. H., Chou, T., Wang, S. M. M., and Wang, T. H. (2011). Analysis of Human Meiotic Recombination Events with A Parent-Sibling Tracing Approach, BMC Genomics, 12:434.

  22. Lai, C. Y., Yu, S. .L, Hsieh, M. H., Chen, C. H., Chen, H. Y., Wen, C. C., Huang, Y. H., Hsiao, P. C., Hsiao, C. K., Liu, C. M., Yang, P. C., Hwu, H. G., and Chen, W. J. (2011). MicroRNA expression aberration as potential peripheral blood biomarkers for schizophrenia, PLoS ONE, 2011; 6 (6):e21635.

  23. Yang, H. C., Lin, H. C., Kang, M., Chen, C. H., Lin, C. W., Li, L. H., Wu, J. Y., Chen, Y. T., Pan, W. H.  (2011). SAQC: SNP Array Quality Control, BMC Bioinformatics, 12:100.

  24. Yang, H. C., Chang, L. C., Huggins,R. M., Chen, C. H., and Mullighan, C. G. (2011). LOHAS: Loss-of-Heterozygosity Analysis Suite, Genetic Epidemiology, 35 (4), 247–260.

  25. Ho, M. R., Tsai, K. W., Chen, C. H., and Lin, W. C. (2011). dbDNV: a resource of duplicated-gene nucleotide variants in human genome, Nucleic Acids Research, 39, Database issue.

  26. Wu, H. M., Tien, Y. J., and Chen, C. H*. (2010). GAP: A graphical environment for matrix visualization and cluster analysis, Computational Statistics and Data Analysis, 54 (3), 767-778.

  27. Ho, M. R., Chen, C. H., and Lin, W. C. (2010). Gene-oriented ortholog database: a functional comparison platform for orthologous loci, Database: The Journal of Biological Databases and Curation, 2010:baq002.

  28. Hou, C. C., Chen, C. H., Yang, N. S., Chen, Y. P., Lo, C. P., Wang, S. Y., Tien, Y. J., Tsai, P. W., and Shyur, L. F. (2010). Comparative metabolomics approach coupled with cell- and gene-based assays for species classification and anti-inflammatory bioactivity validation of Echinacea plants, Journal of Nutritional Biochemistry, 21, 1045-1059.

  29. Zou, W., Lin, W. J., Foley, S. L., Chen, C. H., Nayak, R., and Chen, J. J. (2010). Evaluation of Pulsed-field Gel Electrophoresis Profiles for the Identification of Salmonella Serotypes, Journal of Clinical Microbiology, 48 (9), 3122-3126.

  30. Lin, S. H., Liu, C. M., Liu, Y. L., Fann, C. S. J., Hsiao, P. C., Wu, J. Y., Hung, S. I., Chen, C. H., Wu, H. M., Jou, Y. S., Liu, S. K., Hunag, T. J., Hsieh, M. H., Chang, C. C., Yang, W. C., Lin, J. J., Chou, F. H. C., Faraone, S. V., Tsuang, M. T., Hwu, H. G., and Chen, W. J. (2009). Clustering by neurocognition for fine-mapping of the schizophrenia susceptibility loci on chromosome 6p,  Genes, Brain and Behavior, 8 (8), 785-294.

  31. Chien, S. C., Young, P. H., Hsu, Y. J., Chen, C. H., Tien, Y. J., Shiu, S. Y., Li, T. H., Yang, C. W., Marimuthu, P., Tsai, L. F. L., Yang, W. C. (2009). Anti-diabetic properties of three common Bidens pilosa variants in Taiwan, Phytochemistry, 70 (10), 1246-1254.

  32. Lee, Y. S., Chen, C. H., Tsai, C. N., Chao, A., and Wang, T. H. (2009). Microarray Labeling Extension Values: Laboratory Signatures for Affymetrix GeneChips, Nucleic Acids Research, 37 (8), e61.

  33. Wang, C. Y., Staniforth, V., Chiao, M. T., Hou, C. C., Wu, H. M., Yeh, K. C., Chen, C. H., Hwang, P. I., Wen, T. N., Shyur, L. F., and Yang, N. S. (2008). Genomics and proteomics of immune modulatory effects of a butanol fraction of Echinacea purpurea in human dendritic cells, BMC Genomics, 9:479.

  34. Wu, T. T., Sun, W., Yuan, S. S., Chen, C. H., W., Li, K. C. (2008). A Method for Analyzing Censored Survival Phenotype with Gene Expression Data, BMC Bioinformatics, 9:417.

  35. Lee, Y. S., Chao, A., Chao, A. S., Chang, S. D., Chen, C. H., Wu, W. M., Wang, T. H., Wang, H. S. (2008). CGcgh: a tool for molecular karyotyping using DNA microarray-based comparative genomic hybridization (array-CGH),” Journal of Biomedical Science, 15 (6): 687-96.

  36. Liu, Y. L., Fann, C. S. J., Liu, C. M., Chen, W. J., Wu, J. Y., Hung, S. I., Chen, C. H., Jou, Y. S., Liu, S. K., Hwang, T. J., Hsieh, M. H., Chang, C. C., Yang, W. C., Lin, J. J., Chou, F. H. C., Faraone, S. V., Tsuang, M. T., and,Hwu, H. G. (2008). RASD2, MYH9, and CACNG2 Genes at Chromosome 22q12 Associated with the Subgroup of Schizophrenia with Non-deficit in Sustained Attention and Executive Function, Biological Psychiatry, 64 (9), 789–796.

  37. Ho, M. R., Jang, W. J., Chen, C. H., Ch’ang, L. Y., and Lin, W. C. (2008). Designating Eukaryotic Orthology via Transcription Units, Nucleic Acids Research, 36 (10), 3436-3442.

  38. Yeh, L. L., Hwu, H. G., Chen, C. H., Chen, C. H., Wu, A. C. C. (2008). Factors Related to Perceived Needs of Primary Caregivers of Patients with Schizophrenia, Journal of the Formosan Medical Association, 107 (8), 644-652.

  39. Tien, Y. J., Lee, Y. S., Wu, H. M., and Chen, C. H*. (2008). Methods for Simultaneously Identifying Coherent Local Clusters with Smooth Global Patterns in Gene Expression Profiles, BMC Bioinformatics, 9:155.

  40. Chou, C. C., Hsiao, H. Y., Hong, Q. S., Chen, C. H., Peng, Y. W., Chen, H. W., and Yang, P. C. (2008). Single-Walled Carbon Nanotubes can Induce Pulmonary Injury in Mouse Model, Nano Letters, 8 (2), 437-445.

  41. Chen, J. J., Tsai, C. A., Tzeng, S., and Chen, C. H*. (2007). Gene Selection with Multiple Ordering Criteria, BMC Bioinformatics, 8:74.

  42. Chen, H. Y., Yu, S. L., Chen, C. H., Chang, G. C., Chen, C. Y., Yuan, A., Cheng, C. L., Wang, C. H., Terng, H. J., Kao, S. F., Chen, W. J., Chen, J. J. W., Yang, P. C. (2007). A Five-Gene Signature and Clinical Outcome in Non–Small-Cell Lung Cancer, The New England Journal of Medicine, 356:11-20.

  43. Sher, Y. P., Chou, C. C., Chou , R. H., Wu, H. M., Chang, W. W-S, Chen, C. H., Wu, C. W., Yang, P. C., Yu, C. L., and Peck, K. (2006). Human Kallikrein 8 Protease Confers a Favorable Clinical Outcome in Non–Small Cell Lung Cancer by Suppressing Tumor Cell Invasiveness, Cancer Research, 66, 11763-11770.

  44. Pan, W. H., Chang, Y. P., Yeh, N. H., Chen, C. H., and Tzeng, S. L. (2006). Evaluating the DOH (Department of Health) Food Guide Based on Taiwanese Food Choices, Nutritional Sciences Journal, 30 (3), 116-126.

  45. Chiu, M. J., Hua, M. S., Chen, T. F., Hwu, H. G., Kao, C. H., and Chen, C. H. (2006). Brain responses of explicit and implicit memory - an ERP study, NeuroReport, 17 (14), 1483~1486.

  46. Chen, J. J., Tsai, C. A., Moon, H., Ahn, H., and Chen, C. H. (2006). Decision threshold adjustment in class prediction, SAR and QSAR in Environmental Research, 17 (3), 337-352.

  47. Chou, C. C., Lee, T. T., Chen, C. H., Hsiao, H. Y., Lin, Y. L., Ho, M. S., Yang, P. C., and Peck, K. (2006). Design of microarray probes for virus identification and detection of emerging viruses at the genus level, BMC Bioinformatics, 7:232.

  48. Liu, Y. L., Fann, C. S. J., Liu, C. M., Chen, W. J., Wu, J. Y., Hung, S. I., Chen, C. H., Jou, Y. S., Liu, S. K., Hwang, T. J., Shieh, M. H., Ouyang, W. C., Chan, H. Y., Chen, J. J., Lin, C. Y., Lee, S. F. C., Hwu, H. G. (2006). A Single Nucleotide Polymorphism Fine Mapping Study of Chromosome 1q42.1 Reveals the Vulnerability Genes for Schizophrenia, GNPAT and DISC1: Association with Impairment of Sustained Attention, Biological Psychiatry, 60, 554-562.

  49. Pan, W. H., Lynn, K. S., Chen, C. H., Wu, Y. L., Lin, C. Y., and Chang, H. Y. (2006). Using endophenotypes for pathway clusters to map complex disease genes, Genetic Epidemiology, 30 (2):143-54.

  50. Lee, Y. S., Chen, C. H., Chao, A., Chen, E. S., Wei, M. L., Chen, L. K., Yang, K., Lin, M. C., Wang, Y. H., Liu, J. W., Eng, H. L., Chiang, P. C., Wu, T. S., Tsao, K. C., Huang, C. G., Tien, Y. J., Wang, T. H., Wang, H. S., Lee, Y. S. (2005). Molecular signature of clinical severity in recovering patients with severe acute respiratory syndrome coronavirus (SARS-CoV), BMC Genomics, 6:132.

  51. Chen, J. J. W., Lin, Y. C., Yao, P. L., Yuan, A., Chen, H. Y., Shun, C. T., Tsai, M. F., Chen, C. H., and Yang, P. C. (2005). Tumor-Associated Macrophages: The Double Edged Sword in Cancer Progression, Journal of Clinical Oncology, 23, 1-12.

  52. Tsai, C. A., Lee, T. C., Ho, I. C., Yang, U. C., Chen, C. H., and Chen, J. J. (2005). Multi-class Clustering and Prediction in the Analysis of Microarray Data, Mathematical Biosciences, 193 (1): 79-100.

  53. Chen, C. H., and Li, K. C. (2004). A Three-way Classification Strategy for Reducing Class-Abundance: the Zip Code Recognition Example, Optimality, J. Rojo & V. Perez-Abreu, Editors. I.M.S. Lecture Notes-Monograph Series, 44, 63-86.

  54. Tsai, C. A., Chen, C. H., Lee, T. C., Ho, I. C., Yang, U. C., and Chen, J. J. (2004). Gene selection for sample classifications in microarray experiments, DNA and Cell Biology, 23, 607-614.

  55. Chou, C. C., Chen, C. H., Lee, T. T., and Peck, K. (2004). Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression, Nucleic Acids Research, 32 (12).

  56. Hwu, H. G., Chen, C. H., Hwang, T. J., Liu, C. M., Cheng, J. J., Lin, S. K., Liu, S. K., Chen, C. H., Chi, Y. Y., OuYoung, C. W., Lin, H. N., and Chen, W. J. (2002). Symptom Patterns and Subgrouping of Schizophrenic Patients: Significance of Negative Symptoms Assessed on Admission, Schizophrenia Research, 56, 105-119 (1 July 2002).

  57. Chen, C. H. (2002). Generalized Association Plots for Information Visualization: The applications of the convergence of iteratively formed correlation matrices, Statistica Sinica, 12, 1-23.

  58. Chen, C. H., and Li, K. C. (2001). Generalization of Fisher's Linear Discriminant Analysis via the Approach of Sliced Inverse Regression, Journal of the Korean Statistical Society, 30, 193-217.

  59. Chen, C. H*., and Chen, J. A. (2000). Interactive Diagnostic Plots for Multidimensional Scaling with Applications in Psychosis Disorder Data Analysis, Statistica Sinica, 10, 665-691.

  60. Li, K. C., Lue, H. H., and Chen, C. H. (2000). Interactive Tree-Structured Regression via Principal Hessian Directions, Journal of the American Statistical Association, 95, 547-560.

  61. Li, K. C., Wang, J. L., and Chen, C. H. (1999). Dimension Reduction for Censored Regression Data, Annals of Statistics, 27, 1-23.

  62. Chen, C. H., and Li, K. C. (1998). Can SIR be as Popular as Multiple Linear Regression? Statistica Sinica, 8, 289-316.

  63. Lin A. S., Chen, C. H., Hwu H. G., Lin H. N., and Chen J. A. (1998). Psychopathological Dimensions in Schizophrenia: A Correlational Approach to Items of the SANS and SAPS, Psychiatry Research, 77, 121-130.

    64. Book Chapters:

  64. Chen, J. J. and Chen, C. H. (2010). Microarray Gene Expression, Encyclopedia of Biopharmaceutical Statistics, 3rd Edition (S. Chow ed.), Marcel Dekker, Inc., New York, 780-794.

  65. Wu, H. M., Tzeng, S. L., and Chen, C. H*. (2008). Matrix Visualization, Handbook of Computational Statistics: Data Visualization, Chen CH, Härdle W, Unwin A (eds). Berlin: Springer-Verlag, 681-708.

  66. Unwin, A., Chen, C. H., and Härdle, W. (2008). Introduction, Handbook of Computational Statistics: Data Visualization, Chen CH, Härdle W, Unwin A (eds). Berlin: Springer-Verlag, 3-12.

  67. Chen, C. H. (2005). Sliced Inverse Regression, Encyclopedia of Statistics in Behavioral Sciences, Eds. B. Everitt and D. C. Howell, Wiley, 4, 1856-1863.

  68. Chen, J. J. and Chen, C. H. (2003). Microarray Gene Expression, Encyclopedia of Biopharmaceutical Statistics, 2nd Edition (S. Chow ed.), Marcel Dekker, Inc., New York, 599-613.

    69. Refereed Proceedings Articles:

  69. Liu, C. H., Chen, T. C., Chen, C. H., Kao, C. Y., Huang, C.Y. (2013) Differential network biology reveals a positive correlation between a novel protein-protein interaction and cancer cells migration, Conf Proc IEEE Eng Med Biol Soc. 2013;2013:2700-3. doi: 10.1109/EMBC.2013.6610097.

  70. Tzeng, S. L., Wu, H. M., and Chen, C. H*. (2009). Selection of Proximity Measures for Matrix Visualization of Binary Data, Proceedings of the 2009 2nd International Conference on BioMedical Engineering and Informatics (BMEI 2009), 1932-1940, Tianjin, China (available in  IEEE Xplore Digital Library).

  71. Chen, C. H*., Hwu, H. G., Jang, W. J., Kao, C. H., Tien, Y. J., Tzeng, S., and Wu, H. M. (2004). Matrix Visualization and Information Mining, Proceedings in Computational Statistics 2004 (Compstat 2004), 85-100, Physika Verlag, Heidelberg.

  72. Chang, S. C., Chen, C. H*., Chi, Y. Y., and Ouyoung, C. W. (2002). Relativity and Resolution for High Dimensional Information Visualization with Generalized Association Plots (GAP), Section for Invited Papers, Proceedings in Computational Statistics 2002 (Compstat 2002), 55-66Berlin, Germany.

    73. Proceedings Articles:

  73. Chen, C. H. (1999). Extensions of Generalized Association Plots, 1999 Proceedings of the Section on Statistical Graphics of the American Statistical Association, 111-116.

  74. Chen, C. H. (1996). The Properties and Applications of the Convergence of Correlation Matrices, 1996 Proceedings of the Section on Statistical Graphics of the American Statistical Association, 49-54.

    75. Books:

  75. Handbook of Computational Statistics: Data Visualization. Chen CH, Härdle W, Unwin A (eds). Berlin: Springer-Verlag, 2008.

SOFTWARE RELEASED
  • GAP: A graphical environment for matrix visualization and cluster analysis

           http://www.hmwu.idv.tw/GAPSoftware/