Wei Sheng Wu

Summary

Publications

  1. pmc Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
    Bioinform Biol Insights 1:137-45. 2009
  2. pmc Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites
    Wei Sheng Wu
    Lab of Computational Systems Biology, Department of Electrical Engineering, National Cheng Kung University, Taiwan
    Bioinform Biol Insights 5:1-11. 2011
  3. pmc Identifying a Transcription Factor's Regulatory Targets from its Binding Targets
    Fred Lai
    Department of Engineering Science, National Cheng Kung University, Tainan, Taiwan
    Gene Regul Syst Bio 4:125-33. 2010
  4. pmc Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
    Gene Regul Syst Bio 2:53-62. 2008
  5. pmc Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
    BMC Bioinformatics 7:421. 2006
  6. pmc Systematic identification of yeast cell cycle transcription factors using multiple data sources
    Wei Sheng Wu
    Department of Evolution and Ecology, University of Chicago, Chicago, IL 60637, USA
    BMC Bioinformatics 9:522. 2008
  7. pmc Identifying gene regulatory modules of heat shock response in yeast
    Wei Sheng Wu
    Department of Evolution and Ecology, University of Chicago, Chicago, IL 60637, USA
    BMC Genomics 9:439. 2008
  8. pmc Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
    BMC Bioinformatics 8:188. 2007
  9. pmc The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation
    Zhenguo Lin
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    BMC Genomics 11:581. 2010
  10. pmc CoopTFD: a repository for predicted yeast cooperative transcription factor pairs
    Wei Sheng Wu
    Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
    Database (Oxford) 2016:. 2016

Collaborators

Detail Information

Publications22

  1. pmc Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
    Bioinform Biol Insights 1:137-45. 2009
    ..Second, there may exist extensive regulatory cross-talk among different stress responses. In conclusion, this study proposes a network of the regulators of stress responses and their mechanism of action...
  2. pmc Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites
    Wei Sheng Wu
    Lab of Computational Systems Biology, Department of Electrical Engineering, National Cheng Kung University, Taiwan
    Bioinform Biol Insights 5:1-11. 2011
    ..The spatial distributions of binding sites for many TFs derived from my analyses are valuable prior information for TFBS prediction algorithm because different regions of a promoter can assign different possibilities for TFBS occurrence...
  3. pmc Identifying a Transcription Factor's Regulatory Targets from its Binding Targets
    Fred Lai
    Department of Engineering Science, National Cheng Kung University, Tainan, Taiwan
    Gene Regul Syst Bio 4:125-33. 2010
    ..Finally, we showed that RETEA performs better than three published methods (MA-Network, TRIA and Garten et al's method)...
  4. pmc Reconstructing a network of stress-response regulators via dynamic system modeling of gene regulation
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
    Gene Regul Syst Bio 2:53-62. 2008
    ..Second, there may be regulatory cross-talks among different stress responses. In conclusion, this study proposes a network of stress-response regulators and the details of their actions...
  5. pmc Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan
    BMC Bioinformatics 7:421. 2006
    ..By organizing the genome into TRMs, a living cell can coordinate the activities of many genes and carry out complex functions. Therefore, identifying TRMs is helpful for understanding gene regulation...
  6. pmc Systematic identification of yeast cell cycle transcription factors using multiple data sources
    Wei Sheng Wu
    Department of Evolution and Ecology, University of Chicago, Chicago, IL 60637, USA
    BMC Bioinformatics 9:522. 2008
    ..To understand the cell cycle process, it is important to identify the cell cycle transcription factors (TFs) that regulate the expression of cell cycle-regulated genes...
  7. pmc Identifying gene regulatory modules of heat shock response in yeast
    Wei Sheng Wu
    Department of Evolution and Ecology, University of Chicago, Chicago, IL 60637, USA
    BMC Genomics 9:439. 2008
    ..By organizing the genome into GRMs, a living cell can coordinate the activities of many genes in response to various internal and external stimuli. Therefore, identifying GRMs is helpful for understanding gene regulation...
  8. pmc Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data
    Wei Sheng Wu
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
    BMC Bioinformatics 8:188. 2007
    ..However, the binding of a TF to a gene does not necessarily imply regulation. Thus, it is important to develop methods to identify regulatory targets of TFs from ChIP-chip data...
  9. pmc The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation
    Zhenguo Lin
    Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    BMC Genomics 11:581. 2010
    ..In this study, we reexamined the spatial distribution of TFBSs, investigated various promoter features that may affect the distribution, and studied the effect of TFBS distribution on transcriptional regulation...
  10. pmc CoopTFD: a repository for predicted yeast cooperative transcription factor pairs
    Wei Sheng Wu
    Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
    Database (Oxford) 2016:. 2016
    ..Database URL: http://cosbi.ee.ncku.edu.tw/CoopTFD/ or http://cosbi2.ee.ncku.edu.tw/CoopTFD/. ..
  11. doi request reprint YGA: identifying distinct biological features between yeast gene sets
    Darby Tien Hao Chang
    Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
    Gene 518:26-34. 2013
    ..YGA can be accessed from the following web pages: http://cosbi.ee.ncku.edu.tw/yga/ and http://yga.ee.ncku.edu.tw/...
  12. doi request reprint Yeast cell cycle transcription factors identification by variable selection criteria
    Hsiuying Wang
    Institute of Statistics, National Chiao Tung University, Hsinchu, Taiwan
    Gene 485:172-6. 2011
    ..The biological significance of our predictions is shown by four lines of indirect evidence derived from the protein-protein interaction data, TF mutant data, ChIP-chip data and the results of the previous computational studies...
  13. ncbi request reprint A new measure of the robustness of biochemical networks
    Bor Sen Chen
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, 300, Taiwan, ROC
    Bioinformatics 21:2698-705. 2005
    ..Since most biochemical networks in nature operate close to the steady state, we consider only the robustness measurement of a biochemical network at the steady state...
  14. pmc Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data
    Tzu Hsien Yang
    Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
    BMC Syst Biol 6:102. 2012
    ..Even if the identified TF knockout targets are true, the molecular mechanisms of how a TF regulates its TF knockout targets remain unknown by this kind of statistical approaches...
  15. pmc YPA: an integrated repository of promoter features in Saccharomyces cerevisiae
    Darby Tien Hao Chang
    Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
    Nucleic Acids Res 39:D647-52. 2011
    ..Compared to other established yeast promoter databases, YPA collects not only TFBSs but also many other promoter features to help biologists study transcriptional regulation...
  16. pmc Combined Interactions of Plant Homeodomain and Chromodomain Regulate NuA4 Activity at DNA Double-Strand Breaks
    Wen Pin Su
    Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan
    Genetics 202:77-92. 2016
    ..Our results suggest that multivalent interactions between the PHD, chromodomain, and methylated H3K4 and H3K36 act in a combinatorial manner to recruit NuA4 and regulate the NuA4 activity at the DSB site. ..
  17. pmc YTRP: a repository for yeast transcriptional regulatory pathways
    Tzu Hsien Yang
    Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan and Institute of Biomedical Informatics, National Yang Ming University, Taipei, Taiwan
    Database (Oxford) 2014:bau014. 2014
    ..Database URL: http://cosbi3.ee.ncku.edu.tw/YTRP/...
  18. doi request reprint Robust filtering circuit design for stochastic gene networks under intrinsic and extrinsic molecular noises
    Bor Sen Chen
    Lab of Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
    Math Biosci 211:342-55. 2008
    ..The robust gene network design principles have not only yielded a comprehensive design theory of robust gene networks, but also gained valuable insights into the molecular noise filtering of gene networks from the systematic perspective...
  19. pmc Detecting Cooperativity between Transcription Factors Based on Functional Coherence and Similarity of Their Target Gene Sets
    Wei Sheng Wu
    Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
    PLoS ONE 11:e0162931. 2016
    ..In summary, our study suggests that new algorithms based on novel rationales are worthy of developing for detecting previously unidentifiable cooperative TF pairs. ..
  20. pmc YCRD: Yeast Combinatorial Regulation Database
    Wei Sheng Wu
    Department of Electrical Engineering, National Cheng Kung University, Tainan, Taiwan
    PLoS ONE 11:e0159213. 2016
    ..We believe that YCRD will be a valuable resource for yeast biologists to study combinatorial regulation of gene expression. YCRD is available at http://cosbi.ee.ncku.edu.tw/YCRD/ or http://cosbi2.ee.ncku.edu.tw/YCRD/. ..
  21. pmc Identifying functional transcription factor binding sites in yeast by considering their positional preference in the promoters
    Fu Jou Lai
    Department of Engineering Science, National Cheng Kung University, Tainan, Taiwan
    PLoS ONE 8:e83791. 2013
    ..The FPC is implemented as a web tool at http://santiago.ee.ncku.edu.tw/FPC/. ..
  22. pmc On the adaptive design rules of biochemical networks in evolution
    Bor Sen Chen
    Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 300, Taiwan
    Evol Bioinform Online 3:27-39. 2007
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