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


Office: Room 407
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
2012 – present Deputy Director, Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
2011 - present Research Fellow, Institute of Statistical Science, Academia Sinica,
Taipei, Taiwan
2002 - 2011 Associate Research Fellow, Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
2007 - present Adjunct Associate Professor, Institute of Statistics, National Central University, Jhongli, Taiwan
2005 - present 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, BMC (BioMed Central) Research Notes (2008 - present)
  • Associate Editor, Computational Statistics (2004 - present)
  • Associate Editor, Computational Statistics and Data Analysis (2004 - present)
  • Statistics Consultant, Taiwanese Journal of Psychiatry (1996 - present)
  • Associate Editor, Statistica Sinica (2005 - 2008)
  • Associate Editor, Journal of the Korean Statistical Society (2002 - 2005)

Academic Society:

International Conference Organizer:

      Conference Chairman:
  • 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).

      Member of Scientific Program Committee:

  • 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: 1, Postdoctoral Fellows: 3.

RESEARCH FUNDING
  • 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
  • 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
  • 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.


PUBLICATION
Refereed Journal Articles:
  1. 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.

  2. 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.

  3. 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.

  4. 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..

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  21. 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.

  22. 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.

  23. 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.

  24. 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.

  25. 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.

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

  27. 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.

  28. 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.

  29. 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.

  30. 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.

  31. 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.

  32. 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.

  33. 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.

  34. 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.

  35. 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.

  36. 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.

  37. 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.

  38. 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.

  39. 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.

  40. 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).

  41. 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).

  42. 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.

  43. 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.

  44. 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.

  45. 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.

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

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

  48. 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.

  49. Book Chapters:

  50. 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.

  51. 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.

  52. 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.

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

  54. 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.

  55. Refereed Proceedings Articles:

  56. 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).

  57. 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.

  58. 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.

  59. Proceedings Articles:

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

  61. 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.

  62. Books:

  63. 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/