Jing Wu

Summary

Affiliation: Purdue University
Country: USA

Publications

  1. ncbi Improving the specificity of exon prediction using comparative genomics
    Jing Wu
    Department of Statistics, Purdue University, 150 N, University Street, West Lafayette, IN 47906, USA
    BMC Genomics 9:S13. 2008
  2. ncbi Coding exon detection using comparative sequences
    Jing Wu
    Department of Statistics, Purdue University, West Lafayette, Indiana 47906, USA
    J Comput Biol 13:1148-64. 2006
  3. ncbi Hidden Markov model and its applications in motif findings
    Jing Wu
    Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
    Methods Mol Biol 620:405-16. 2010
  4. ncbi Statistical methods in integrative analysis for gene regulatory modules
    Lingmin Zeng
    Purdue University
    Stat Appl Genet Mol Biol 7:Article 28. 2008
  5. ncbi Screen and clean: a tool for identifying interactions in genome-wide association studies
    Jing Wu
    Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
    Genet Epidemiol 34:275-85. 2010
  6. ncbi Computation-based discovery of cis-regulatory modules by hidden Markov model
    Jing Wu
    Department of Statistics, Purdue University, West Lafayette, Indiana 47907, USA
    J Comput Biol 15:279-90. 2008
  7. ncbi A small trypsin inhibitor from the frog of Odorrana grahami
    Jianxu Li
    Biotoxin Units of Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences CAS, Kunming 650223, Yunnan, China
    Biochimie 90:1356-61. 2008
  8. ncbi dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
    Seung Hee Bae
    Department of Computer Science, Indiana University Bloomington, IN 47404, USA
    Bioinformatics 23:2619-21. 2007
  9. ncbi Anti-infection peptidomics of amphibian skin
    Jianxu Li
    Biotoxin Units and gLaboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
    Mol Cell Proteomics 6:882-94. 2007
  10. ncbi Cryopreservation of human embryonic stem cells: a protocol by programmed cooling
    Peng-Fei Yang
    Institute of Cryomedicine and Food Refrigeration, Shanghai University of Science and Technology, and Laboratory of Tissue Engineer, The 9th People's Hospital, Shanghai, China
    Cryo Letters 27:361-8. 2006

Collaborators

  • Jun Xie
  • Nadine Melhem
  • Kathryn Roeder
  • Bernie Devlin
  • Lingmin Zeng
  • Laura Elnitski
  • Sun Kim
  • K F Chater
  • Yan Zhou
  • Haixu Tang
  • Jianxu Li
  • Xueqing Xu
  • Ren Lai
  • Wencheng Li
  • Seung Hee Bae
  • Peng-Fei Yang
  • Wei Xia Liu
  • Weihua Fu
  • Yipeng Wang
  • Huajie Zhu
  • Tongguang Liu
  • Govind Chandra
  • Keyun Zhang
  • Dongming Yang
  • Weiping Zhou
  • Xiufen Zhou
  • Yongtang Zheng
  • Chunhua Zhao
  • Seung-Hee Bae
  • Zixin Deng
  • Yemin Wang
  • Chunhua Xu
  • Meifeng Tao
  • Xinyi He
  • Huw H Rees
  • Weixin Tao
  • Yaping Zhang
  • Haining Yu
  • Zhao-Hua Chang
  • Yi-lin Cao
  • Hsiao-Chien Tsung
  • Tse-Chao Hua
  • Bo-Qin Qiang
  • Jian-Gang Yuan
  • Xiao-zhong Peng
  • Bo qin Qiang
  • Hongzhi Zhang
  • Zhao Zhao
  • Jian gang Yuan
  • Xiao zhong Peng
  • Wei-Xia Liu

Detail Information

Publications16

  1. ncbi Improving the specificity of exon prediction using comparative genomics
    Jing Wu
    Department of Statistics, Purdue University, 150 N, University Street, West Lafayette, IN 47906, USA
    BMC Genomics 9:S13. 2008
    ..Computational gene prediction tools routinely generate large volumes of predicted coding exons (putative exons). One common limitation of these tools is the relatively low specificity due to the large amount of non-coding regions...
  2. ncbi Coding exon detection using comparative sequences
    Jing Wu
    Department of Statistics, Purdue University, West Lafayette, Indiana 47906, USA
    J Comput Biol 13:1148-64. 2006
    ..Last, shortHMM is also capable of finding new potential exons...
  3. ncbi Hidden Markov model and its applications in motif findings
    Jing Wu
    Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
    Methods Mol Biol 620:405-16. 2010
    ..We then introduce the application of HMM to a complex system in which an HMM is combined with Bayesian inference to identify transcription factor binding sites and cis-regulatory modules...
  4. ncbi Statistical methods in integrative analysis for gene regulatory modules
    Lingmin Zeng
    Purdue University
    Stat Appl Genet Mol Biol 7:Article 28. 2008
    ..The multiple data sources provide information of transcriptional regulation from different aspects. Therefore, the integrative analysis offers a fine prediction on transcriptional regulatory code and infers potential regulatory networks...
  5. ncbi Screen and clean: a tool for identifying interactions in genome-wide association studies
    Jing Wu
    Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
    Genet Epidemiol 34:275-85. 2010
    ..When the method is applied to data obtained from the Wellcome Trust Case Control Consortium study of Type 1 Diabetes it uncovers evidence supporting interaction within the HLA class II region as well as within Chromosome 12q24...
  6. ncbi Computation-based discovery of cis-regulatory modules by hidden Markov model
    Jing Wu
    Department of Statistics, Purdue University, West Lafayette, Indiana 47907, USA
    J Comput Biol 15:279-90. 2008
    ..The executable codes of our programs and module predictions across the fly Drosophila genome are available at www.stat.purdue.edu/~ jingwu/module/...
  7. ncbi A small trypsin inhibitor from the frog of Odorrana grahami
    Jianxu Li
    Biotoxin Units of Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences CAS, Kunming 650223, Yunnan, China
    Biochimie 90:1356-61. 2008
    ..In addition to its unique six-residue loop, the overall structure and precursor of OGTI are different from those of other serine protease inhibitors. It is also one of the smallest serine protease inhibitors ever found...
  8. ncbi dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
    Seung Hee Bae
    Department of Computer Science, Indiana University Bloomington, IN 47404, USA
    Bioinformatics 23:2619-21. 2007
    ..RESULTS: By modifying our previous REFINEMENT approach, we developed dPattern that searches for occurrences of TFBSs in the promotor regions of up/down regulated or random genes...
  9. ncbi Anti-infection peptidomics of amphibian skin
    Jianxu Li
    Biotoxin Units and gLaboratory of Molecular Immunopharmacology, Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China
    Mol Cell Proteomics 6:882-94. 2007
    ..With respect to the development of antibiotics, these peptides provide potential new templates to explore further...
  10. ncbi Cryopreservation of human embryonic stem cells: a protocol by programmed cooling
    Peng-Fei Yang
    Institute of Cryomedicine and Food Refrigeration, Shanghai University of Science and Technology, and Laboratory of Tissue Engineer, The 9th People's Hospital, Shanghai, China
    Cryo Letters 27:361-8. 2006
    ..They retained the properties of pluripotent cells, had a normal karyotype and showed histochemical staining for alkaline phosphatase...
  11. ncbi Glucocorticoid and growth factor synergism requirement for Notch4 chromatin domain activation
    Jing Wu
    Department of Pharmacology, University of Wisconsin School of Medicine, Madison, WI 53706, USA
    Mol Cell Biol 27:2411-22. 2007
    ..These results establish the molecular basis for a novel AP-1/GR-Notch4 axis in vascular endothelium...
  12. ncbi A genetic and bioinformatic analysis of Streptomyces coelicolor genes containing TTA codons, possible targets for regulation by a developmentally significant tRNA
    Wencheng Li
    State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
    FEMS Microbiol Lett 266:20-8. 2007
    ..Possible reasons for this, and the role and evolution of the observed distribution of TTA codons among Streptomyces genes were discussed...
  13. ncbi Molecular determinants of NOTCH4 transcription in vascular endothelium
    Jing Wu
    Molecular and Cellular Pharmacology Program, Department of Pharmacology, University of Wisconsin Medical School, 1300 University Ave, 383 Medical Sciences Center, Madison, WI 53706, USA
    Mol Cell Biol 25:1458-74. 2005
    ..These results reveal an AP-1-Notch4 pathway, which we propose to be crucial for transducing angiogenic signals and to be deregulated upon aberrant signal transduction in cancer...
  14. ncbi Functional and biochemical characterization of a recombinant Arabidopsis thaliana 3-deoxy-D-manno-octulosonate 8-phosphate synthase
    Jing Wu
    Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA
    Biochem J 381:185-93. 2004
    ..8 microM for D-arabinose 5-phosphate and kcat=5.9 s(-1) at 37 degrees C. On the basis of the characterization of A. thaliana KDOPS and phylogenetic analysis, plant KDOPSs may represent a new, distinct class of KDOPSs...
  15. ncbi [PIV: a computer-aided portal image verification system]
    Weihua Fu
    Department of Radiotherapy Oncology, Cancer Institute (Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100021
    Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 19:664-6. 2002
    ..Semi-automatic register methods make verification more accurate than view-box method. It can provide useful quantitative errors for regular fields. PIV is flexible and accurate. It is an effective tool for portal field verification...
  16. ncbi [Cloning and expression of human calcyclin binding protein (hCacyBP) gene]
    Wei Xia Liu
    Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10005, China
    Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 34:181-6. 2002
    ..The results of immunohistochemistrial staining showed that the location of CacyBP in BT325 cell line before and after differentiation changed from cytoplasm into nucleus and perinucleus cytoplasm...