<Chinese Version>

Wei-Sheng Wu
Position

Associate Professor

Telephone number
+886-6-275-7575 ext. 62426
FAX
 +886-6-234-5482
E-mail
 wessonwu@mail.ncku.edu.tw
Lab
Systems Biology Lab (8F, EE Department Building, #1, Da-Tsuen Rd.,Tainan,Taiwan)  92803 & 92806 & 92879
Courses
 
2009 Spring Electricity and Life 2009 Fall Introduction of Systems Biology
2010 Spring Biological data integration and analysis

Electricity and Life

2010 Fall Introduction of Systems Biology
2011 Spring Biological data integration and analysis

Electricity and Life

2011 Fall Introduction of Systems Biology
2012 Spring Biological data integration and analysis

Electricity and Life

2012 Fall Introduction of Systems Biology
       
       

 

Educations
  • Ph.D., National Tsing Hua University (2001-2007)
  • M.S.,   National Tsing Hua University (1998-2000)
  • B.S.,    National Tsing Hua University (1994-1998)
Experiences
  • Assistant Professor, Department of Electrical Engineering, National Cheng Kung University (2009-2013)

  • Postdoc, Department of Ecology and Evolution, University of Chicago (2007-2009)

  • Assistant, Department of Electrical Engineering, National Tsing Hua University (2000-2001)

Specialities
  • Systems Biology
  • Gene Regulatory Networks
Honors
  • (2007)  Recipient of the Postdoctoral Research Abroad Program Fellowship
  • (2000)  An Honorary Member of the Phi Tau Phi Scholastic Honor Society

  • (2000)  Pan Wen-yuan Memorial Scholarship

  • (1999)  GARMIN Corporation’s Scholarship

  • (1997)  Yen Tjing Ling Industrial Development Foundation Yen’s Scholarship

  • (1996)  Mr. Tung-fu Chou and Mrs. Pin-juo Lin Chou Memorial Scholarship

  • (1994)  Mr. Tung-fu Chou and Mrs. Pin-juo Lin Chou Memorial Scholarship

    Reviewer for the following journals :
     
    • BMC Systems Biology (2009)

    • IJDMB: International Journal of Data Mining and Bioinformatics (2009)

    • AJC: Asian Journal of Control (2008)

    • EURASIP: Journal on Advances in Signal Processing (2002)

 

Patents
Publication List

 

Citation statistics of my papers by Google Scholar 

Citation statistics of my papers by ResearchGate 

 A. Journal Papers

(2001/9~2007/6) PhD Student (8 papers)

1. Chen BS*, Wang YC, Wu WS, Li WH (2005 June): A new measure of robustness of biochemical networks. Bioinformatics, 21(11):2698-2705. 
SCI, impact factor=5.04, Ranking 1% (1/92) in Computer Science & Interdisciplinary Application

2. Wu WS*, Li WH, Chen BS (2006 Sept.): Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics, 7:421.
SCI, impact factor=3.49, Ranking 11% (3/27) in Mathematical & Computational Biology

3. Chen BS*, Wu WS, Wu WS, Li WH (2007 Feb.): On the adaptive design rules of biochemical networks in evolution. Evolutionary Bioinformatics, 2:1-13.
SCI, impact factor=1.23, Ranking 70% (33/47) in Mathematical & Computational Biology

4. Wu WS*, Li WH, Chen BS (2007 June): Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics, 8:188.
SCI, impact factor=3.49, Ranking 11% (3/27) in Mathematical & Computational Biology

5. Chen BS*, Wu WS (2007 Sept.) Underlying principles of natural selection in network evolution: systems biology approach. Evolutionary Bioinformatics, 3:245-262.
SCI, impact factor=1,23, Ranking 70% (33/47) in Mathematical & Computational Biology

6. Wu WS*, Chen BS (2007 Oct.): Identifying stress transcription factors using gene expression and TF-gene association data. Bioinformatics and Biology Insights, 1:9-17.

7. Chen BS*, Wu WS (2008 Feb.): Robust filtering circuit design for gene networks under intrinsic and extrinsic molecular noises. Mathematical Biosciences, 211:342-355.
SCI, impact factor=1.19, Ranking 54% (38/71) in Biology

8. Wu WS*, Li WH, Chen BS (2008 Feb.): Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation. Gene Regulation and Systems Biology, 2:53-62.


 (2007/10~2009/1) Postdoctoral Fellow (3 papers)

9. Wu WS, Li WH* (2008 Sept.): Identifying gene regulatory modules of heat shock response in yeast. BMC Genomics, 9:439. (NSC-096-2917-I-564-122) (Highly accessed)
SCI, impact factor=4.18, Ranking 15% (21/138) in Biotechnology & Applied Microbiology

10.Wu WS, Li WH* (2008 Dec.): Systematic identification of yeast cell cycle transcription factors using multiple data sources. BMC Bioinformatics, 9:522. (NSC-096-2917-I-564-122)
SCI, impact factor=3.49, Ranking 11% (3/27) in Mathematical & Computational Biology

11.Lin Z^, Wu WS^, Liang H, Yoo Y, Li WH* (2010 Oct.): The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcription regulation. BMC Genomics, 11:581.   (^co-first author)
SCI, impact factor=3.76, Ranking 18% (28/152) in Biotechnology & Applied Microbiology


 (2009/2~2013/7) Assistant Professor (9 papers)

12.Wu WS* (2010 June): Identifying highly confident TF-gene regulatory relationships in yeast. International Journal of Systems and Synthetic Biology, 1(1):121-133. (Invited paper)

13.Lai F, Chang JS, Wu WS* (2010 Dec.): Identifying a transcription factor's regulatory targets from its binding targets. Gene Regulation and Systems Biology, 4:125-133.   (NSC-099-2628-B-006-015-MY3)

14.Wu WS* (2011 Jan.): Different functional gene clusters in yeast have different spatial distribution of the transcription factor binding sites. Bioinformatics and Biology Insights, 5:1-11. (NSC-099-2628-B-006-015-MY3)

15.Chang DTH, Huang CY, Wu CY, Wu WS* (2011 Jan.): YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. Nucl. Acids Res., 39(1):D647-D652. (NSC-099-2628-B-006-015-MY3)
Featured article in NAR (represents the top 5% of NAR papers in terms of originality, significance and scientific excellence!)

SCI, impact factor=7.48, Ranking 10% (27/283) in Biochemistry & Molecular Biology

16.Wu WS* (2011 June): A quantitative robustness measure for gene regulatory networks. International Journal of Computational Intelligence in Control, 3(1):1-8.  (Invited paper) (NSC-099-2628-B-006-015-MY3)

17.Wang H, Wang YH, Wu WS* (2011 Oct.): Yeast cell cycle transcription factors identification by variable selection criteria. Gene, 485:172-176. (NSC-099-2628-B-006-015-MY3)
SCI, impact factor=2.416, Ranking 53% (78/146) in Genetics & Heredity

18.Yang TH, Wu WS* (2012 Aug.): Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data. BMC Systems Biology, 6:102. (NSC-099-2628-B-006-015-MY3)
SCI, impact factor=3.15, Ranking 9% (4/47) in Mathematical & Computational Biology

 19.Chang DTH, Li WS, Bai YH, Wu WS* (2012 Dec.): YGA: identifying distinct biological features between yeast gene sets. Gene, 518:26-34. (NSC-099-2628-B-006-015-MY3)
SCI, impact factor=2.341, Ranking 53% (78/146) in Genetics & Heredity

 20.Xu SSD, Ying H, Carbonell P, Lee CH, Wu WS (2013 May): Fuzzy logic application in control theory and systems biology. Advances in Fuzzy Systems, vol. 2013, Article ID 504728, 1 page, 2013.


(2013/8~now) Associate Professor (12 papers)

21.Wang H, Chiu CC, Wu YC, Wu WS* (2013 Dec.): Shrinkage regression-based methods for microarray missing value imputation. BMC Systems Biology, 7(Suppl 6):S11. 
SCI, impact factor=2.982, Ranking 15% (7/47) in Mathematical & Computational Biology

22.Chiu CC, Chan SY, Wang CC,  Wu WS* (2013 Dec.): Missing value imputation for microarray data: a comprehensive comparison study and a web tool. BMC Systems Biology, 7(Suppl 6):S12.
SCI, impact factor=2.982, Ranking 15% (7/47) in Mathematical & Computational Biology 

23.Yang TH, Wu WS* (2013 Dec.): Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. BMC Systems Biology, 7(Suppl 6):S13.
SCI, impact factor=2.982, Ranking 15% (7/47) in Mathematical & Computational Biology 

24.Lai FJ, Chiu CC, Yang TH, Huang YM, Wu WS* (2013 Dec.): Identifying functional transcriptional factor binding sites in yeast by considering their positional preference in  
     the promoters
. PLOS ONE, 8(12):e83791.
     SCI, impact factor=3.73, Ranking 13% (7/56) in Multidisciplinary Sciences

25.Yang TH, Wang CC, Wang YC, Wu WS* (2014 Mar.): YTRP: a repository for yeast transcriptional regulatory pathways. Database, vol. 2014, Article ID bau014.
SCI, 2013impact factor=4.457, Ranking 10% (5/52) in Mathematical & Computational Biology

26.Yang TH, Chang HT, Hsiao ESL, Sun JL, Wang CC, Wu HY, Liao PC*, Wu WS* (2014 Dec.): iPhos: toolkit to streamline the alkaline phosphatase assisted comprehensive LC-MS phosphorproteome investigation. BMC Bioinformatics, 15(Suppl 16):S10.
SCI, 2013impact factor=2.672, Ranking 15% (8/52) in Mathematical & Computational Biology

27.Yang TH, Wang CC, Hung PC, Wu WS* (2014 Dec.): cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. BMC Systems Biology, 8(Suppl 4):S8.
SCI, 2013impact factor=2.672, Ranking 13% (7/52) in Mathematical & Computational Biology

28.Hung PC, Yang TH, Liaw HJ*, Wu WS* (2014 Dec.): YNA: an integrative gene mining platform for studying chromatin structure and its regulation in Yeast. BMC Genomics, 15(Suppl 9):S5.
SCI, 2013impact factor=4.041, Ranking 18% (29/165) in Biotechnology & Applied Microbiology

29.Lai FJ, Chang HT, Huang YM, Wu WS* (2014 Dec.): A comprehensive performance evaluation on the prediction results of existing cooperative transcription factors identification algorithms. BMC Systems Biology, 8(Suppl 4):S9.
SCI, 2013impact factor=2.672, Ranking 13% (7/52) in Mathematical & Computational Biology

30.Lai FJ, Jhu MH, Chiu CC, Huang YM, Wu WS* (2014 Dec.): Identifying cooperative transcription factors in yeast using multiple data sources. BMC Systems Biology, 8(Suppl 5):S2.
SCI, 2013impact factor=2.672, Ranking 13% (7/52) in Mathematical & Computational Biology

31. Wu WS, Wei ML, Yeh CM, DTH Chang* (2014 Dec.): A regulatory similarity measure using the location information of transcription factor binding sites in Saccharomyces cerevisiae. BMC Systems Biology, 8(Suppl 5):S9.
SCI, 2013impact factor=2.672, Ranking 13% (7/52) in Mathematical & Computational Biology

 

 

xx.Juang JN, Wu WS (201x xx.): A hybrid parameter estimation algorithm for S-system model of gene regulatory networks. Journal of the Astronautical Sciences, xx:xx.

 


B. Conference papers

See會議論文列表 from 2002/07 to 2013/07

a. 國際會議

13.Wang H, Chiu CC, Wu YC, Wu WS* (2013 Dec.): Shrinkage regression-based methods for microarray missing value imputation. In The 24rd International Conference on Genome Informatics (GIW): Biopolis, Singapore. (Oral) 

14.Chiu CC, Chan SY, Wang CC, Wu WS* (2013 Dec.): Missing value imputation for microarray data: a comprehensive comparison study and a web tool. In The 24rd International Conference on Genome Informatics (GIW): Biopolis, Singapore. (Oral) 

15.Yang TH, Wu WS* (2013 Dec.): Inferring functional transcription factor-gene binding pairs by integrating transcription factor binding data with transcription factor knockout data. In The 24rd International Conference on Genome Informatics (GIW): Biopolis, Singapore. (Oral) 

16.Chang DTH, Yeh CM, Wei ML, Wu WS* (2014 June): A metric for computing regulatory similarity of two genes. In The 11th IEEE International Conference on
     Control & Automation (ICCA)
: Taichung, Taiwan. (Invited talk)

17.Chiu CC, Wu WS* (2014 June): IMDE: an easy-to-use web server for missing data estimation. In The 11th IEEE International Conference on Control & Automation (ICCA): Taichung, Taiwan. (Invited talk)

 

b. 國內會議

17.Yang TH and Wu WS* (2013 Sept.): YTRPD: Yeast transcriptional regulatory pathway database. In 2013 Yeast Meeting: Taipei, Taiwan. (Poster)

18.Hong PC, Liao HJWu WS* (2013 Sept.): YNA: Yeast nucleosome atlas. In 2013 Yeast Meeting: Taipei, Taiwan. (Poster)

19.Lai FJ, Wu WS* (2013 Oct.): A novel method for functional transcription factor binding sites identification. In Symposium of Bioinformatics and Systems Biology in Taiwan. (Poster)

20.Hong PC, Liao HJWu WS* (2013 Nov.): YNA: Yeast nucleosome atlas. In International Symposium on Evolutionary Genomics and Bioinformatics: Taichung, Taiwan. (Poster)

21.Wang H, Chiu CC, Wu YC, Wu WS* (2013 Nov.): Shrinkage regression-based methods for microarray missing value imputation. In International Symposium on Evolutionary Genomics and Bioinformatics: Taichung, Taiwan. (Poster)

22.Wang CC, Wu WS* (2013 Nov.): YSGM: a web-based tool for mining yeast similar genes. In International Symposium on Evolutionary Genomics and Bioinformatics: Taichung, Taiwan. (Poster)

23.Wei ML, Chang DTH, Wu WS* (2013 Nov.): Probing the relations among various types of biologically-experimented depiction using Yeast. In International Symposium on Evolutionary Genomics and Bioinformatics: Taichung, Taiwan. (Poster)

24.Yang TH, Wu WS* (2013 Nov.): cisMEP: an integrated repository of genomic epigenetic profiles for cis-regulatory modules in Drosophila. In International Symposium on Evolutionary Genomics and Bioinformatics: Taichung, Taiwan. (The Best Student Oral Presentation Award)

 

 

C. Book Chapters

1.  Wu WS, Wang CH, Chiu MC, Chao CC* (2002): Stability analysis of the Turbo decoding algorithm using Max-Log-MAP. In Information, Coding and Mathematics. Edited by Farrell P, van Tilborg H, Blaum M. Boston: Kluwer; 257-278.

2.  Wu WS*, Li WH, Chen BS (2008): Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. In Analysis of Microarray Data: Network based Approaches. Edited by Emmert-Streib F, Dehmer M. NJ: Wiley; 331-354.

3.  Wu WS* (2015): Computational methods for identifying yeast cell cycle transcription factors and their regulatory targets. In Axx. Edited by xx. xx: Springer; xx-xx.

D. Presentations (including exhibitions)

1. 2004 (Jan.) Dept. of Ecology and Evolution, University of Chicago   Title: Quantitative modeling of cis-regulatory circuit

2. 2004 (Mar.) Dept. of Electrical Engineering, Chung Hua University   Title: Quantitative characterization of transcriptional regulatory networks in Saccharomyces cerevisiae cell cycle

3. 2005 (May) National Center for Theoretical Sciences   Title: Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle

4. 2006 (Oct.) IEEE SMC Conference   Title: Robust filtering circuit design for gene networks under intrinsic and extrinsic molecular noises

5. 2007 (Sept.) Dept. of Electrical Engineering, National Cheng Kung University   Title: Transcriptional regulatory networks of Saccharomyces cerevisiae

6. 2009 (Mar.) Genomic center, Academia Sinica   Title: Reconstruction of yeast gene regulatory networks

7. 2009 (Mar.) Dept. of Electrical Engineering, National Tsing Hua University   Title: Introduction to Systems Biology

8. 2009 (Nov.) Yang-Ming Institute of Biomedical Informatics   Title: xxxx

Projects
A. National Science Council Projects

1. (2008/01~2008/12) NSC-096-2917-I-564-122: Computational reconstruction of the gene regulatory network of the yeast stress response and its evolutionary process

2. (2009/08~2010/07) NSC-098-2218-E-006-235: Developing a robustness measure for gene regulatory networks

B. General Projects

Activity

 

Students

A. Students


B. Honors for Students

Holding or Attending National Conferences
  • (2006 Oct.) IEEE International Conference on Systems, Man, and Cybernetics: Taipei, Taiwan.
     

  • (2006 Dec.) Conference on Engineering Principles in Biological Systems: Cold Spring Harbor, New York, USA
International Teaching and Research Exchange
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