Jie Wu

Summary

Affiliation: Boston University
Country: USA

Publications

  1. ncbi request reprint Identification of functional links between genes using phylogenetic profiles
    Jie Wu
    Department of Biomedical Engineering, USA Bioinformatics Graduate Program, Boston University, 44 Cummington St, Boston, MA, 02215, USA
    Bioinformatics 19:1524-30. 2003
  2. ncbi request reprint Deciphering protein network organization using phylogenetic profile groups
    Jie Wu
    Department of Biomedical Engineering, Boston University, 24 Cummington St Boston, MA 02215, USA
    Genome Inform 16:142-9. 2005
  3. pmc Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression
    Jie Wu
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Genome Biol 7:R85. 2006
  4. pmc Gene annotation and network inference by phylogenetic profiling
    Jie Wu
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    BMC Bioinformatics 7:80. 2006
  5. pmc Comparative assessment of performance and genome dependence among phylogenetic profiling methods
    Evan S Snitkin
    Bioinformatics Graduate Program, Boston University, Boston, USA
    BMC Bioinformatics 7:420. 2006
  6. pmc VisANT: an online visualization and analysis tool for biological interaction data
    Zhenjun Hu
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    BMC Bioinformatics 5:17. 2004
  7. ncbi request reprint Towards zoomable multidimensional maps of the cell
    Zhenjun Hu
    Program in Bioinformatics and Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Nat Biotechnol 25:547-54. 2007
  8. pmc VisANT: data-integrating visual framework for biological networks and modules
    Zhenjun Hu
    Program in Bioinformatics and Systems Biology, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 33:W352-7. 2005
  9. ncbi request reprint Constructing networks with correlation maximization methods
    Joseph C Mellor
    Program in Bioinformatics, Boston University
    Genome Inform 15:149-59. 2004
  10. ncbi request reprint Stability of plasmid and expression of a recombinant gonadotropin-releasing hormone (GnRH) vaccine in Escherichia coli
    Jinshu Xu
    School of Pharmacy, Nanjing Medical University, 140 Hanzhong Road, Nanjing, People s Republic of China
    Appl Microbiol Biotechnol 73:780-8. 2006

Collaborators

Detail Information

Publications43

  1. ncbi request reprint Identification of functional links between genes using phylogenetic profiles
    Jie Wu
    Department of Biomedical Engineering, USA Bioinformatics Graduate Program, Boston University, 44 Cummington St, Boston, MA, 02215, USA
    Bioinformatics 19:1524-30. 2003
    ..Function is then inferred at any desired level of confidence...
  2. ncbi request reprint Deciphering protein network organization using phylogenetic profile groups
    Jie Wu
    Department of Biomedical Engineering, Boston University, 24 Cummington St Boston, MA 02215, USA
    Genome Inform 16:142-9. 2005
    ..Our method is extendable to N-component clusters, and therefore serves as a general tool for high order protein function annotation...
  3. pmc Comparative sequence analysis reveals an intricate network among REST, CREB and miRNA in mediating neuronal gene expression
    Jie Wu
    Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Genome Biol 7:R85. 2006
    ..How these two classes of regulators act together to mediate neuronal gene expression is unclear...
  4. pmc Gene annotation and network inference by phylogenetic profiling
    Jie Wu
    Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    BMC Bioinformatics 7:80. 2006
    ..Current methods, though useful, perform at a level well below what is possible, largely because performance of the latter deteriorates rapidly as coverage increases...
  5. pmc Comparative assessment of performance and genome dependence among phylogenetic profiling methods
    Evan S Snitkin
    Bioinformatics Graduate Program, Boston University, Boston, USA
    BMC Bioinformatics 7:420. 2006
    ..Here we explore the application of phylogenetic profiling, a method that exploits the evolutionary co-occurrence of genes in the assignment of functional linkages, to eukaryotic genomes...
  6. pmc VisANT: an online visualization and analysis tool for biological interaction data
    Zhenjun Hu
    Bioinformatics Program, Boston University, Boston, MA 02215, USA
    BMC Bioinformatics 5:17. 2004
    ..This networked view of biology brings the potential for systematic understanding of living molecular systems...
  7. ncbi request reprint Towards zoomable multidimensional maps of the cell
    Zhenjun Hu
    Program in Bioinformatics and Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
    Nat Biotechnol 25:547-54. 2007
    ....
  8. pmc VisANT: data-integrating visual framework for biological networks and modules
    Zhenjun Hu
    Program in Bioinformatics and Systems Biology, Boston University, 44 Cummington Street, Boston, MA 02215, USA
    Nucleic Acids Res 33:W352-7. 2005
    ..VisANT is distributed freely via the web at http://visant.bu.edu and can also be downloaded for individual use...
  9. ncbi request reprint Constructing networks with correlation maximization methods
    Joseph C Mellor
    Program in Bioinformatics, Boston University
    Genome Inform 15:149-59. 2004
    ..We show how statistical strength and information are equivalent criteria in limiting cases, and demonstrate the application of these measures to simple systems of gene regulation...
  10. ncbi request reprint Stability of plasmid and expression of a recombinant gonadotropin-releasing hormone (GnRH) vaccine in Escherichia coli
    Jinshu Xu
    School of Pharmacy, Nanjing Medical University, 140 Hanzhong Road, Nanjing, People s Republic of China
    Appl Microbiol Biotechnol 73:780-8. 2006
    ..The amount of the fusion protein was also up to 40% of the total cell protein after the 50th generation. These data would be useful for the industrial production of the recombinant GnRH vaccine...
  11. pmc The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S10. 2008
    ..The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists...
  12. ncbi request reprint SARS coronavirus 7a protein blocks cell cycle progression at G0/G1 phase via the cyclin D3/pRb pathway
    Xiaoling Yuan
    Department of Pathophysiology, Beijing Institute of Radiation Medicine, No 27 Taiping road, Beijing 100850, China
    Virology 346:74-85. 2006
    ..Accumulation of hypo- or non-phosphorylated pRb thus prevents cell cycle progression at G0/G1 phase...
  13. ncbi request reprint Changes in muscarinic acetylcholine receptor expression in form deprivation myopia in guinea pigs
    Qiong Liu
    State Key Laboratory of Ophthalmology Zhongshan Ophthalmic Center, SunYat sen University, Guangzhou, China
    Mol Vis 13:1234-44. 2007
    ....
  14. ncbi request reprint Hydroxamic acid analogue histone deacetylase inhibitors attenuate estrogen receptor-alpha levels and transcriptional activity: a result of hyperacetylation and inhibition of chaperone function of heat shock protein 90
    Warren Fiskus
    Medical College of Georgia Cancer Center, Augusta, Georgia 30912, USA
    Clin Cancer Res 13:4882-90. 2007
    ..Here, we determined the effect of HA-HDIs on the levels and activity of ERalpha, as well as on the survival of ERalpha-expressing, estrogen-responsive human breast cancer MCF-7 and BT-474 cells...
  15. ncbi request reprint Inhibition effects on liver tumors of BALB/c mice bearing H22 cells by immunization with a recombinant immunogen of GnRH linked to heat shock protein 65
    Yin Zhang
    Life Sciences College, Nanjing Normal University, Wenyuan Road 1, Nanjing 210046, Jiangsu, People s Republic of China
    Vaccine 25:6911-21. 2007
    ....
  16. pmc Identification of a signalling molecule involved in bacterial intergeneric communication
    Hua Xie
    School of Dentistry, Meharry Medical College, Nashville, TN 37208, USA
    Microbiology 153:3228-34. 2007
    ..These results present a novel mechanism by which intergeneric communication in dental biofilms is accomplished...
  17. ncbi request reprint Regulation of the Erk2-Elk1 signaling pathway and megakaryocytic differentiation of Bcr-Abl(+) K562 leukemic cells by Gab2
    Jay F Dorsey
    Molecular Oncology Program, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
    Blood 99:1388-97. 2002
    ..All of these changes are characteristics of megakaryocytic differentiation. Together, these results reveal Gab2 as a limiting signaling component for Erk MAP kinase activation and terminal differentiation of K562 CML cells...
  18. ncbi request reprint Immunization with a recombinant GnRH vaccine conjugated to heat shock protein 65 inhibits tumor growth in orthotopic prostate cancer mouse model
    Jinshu Xu
    School of Pharmacy, Nanjing Medical University, Nanjing, PR China
    Cancer Lett 259:240-50. 2008
    ..001). The conjugation of the recombinant GnRH peptide to Hsp65 could be considered a promising approach for the development of an efficacious vaccine against the prostate cancer...
  19. doi request reprint Morphological observation of nuclear sub-localization of human angiogenin in HUVECs
    Jie Wu
    Department of Medical Research, Guangzhou Liuhuaqiao Hospital, Liuhua road 111, Guangzhou, Guangdong Province, 510010, P R China
    Biotechnol Lett 30:989-93. 2008
    ..Recombinant angiogenin was found to mainly concentrate in the pars granulosa of the nucleus, where the protein accumulates to form ribonucleoprotein particles...
  20. pmc Nucleoprotein structure of the CD4 locus: implications for the mechanisms underlying CD4 regulation during T cell development
    Ming Yu
    Department of Immunobiology, Yale University Medical School, New Haven, CT 06520, USA
    Proc Natl Acad Sci U S A 105:3873-8. 2008
    ..Our data shed light on the molecular basis of CD4 regulation and provide a conceptual framework for understanding how the same regulatory elements can mediate both reversible and irreversible CD4 regulation...
  21. pmc OxyR is involved in coordinate regulation of expression of fimA and sod genes in Porphyromonas gingivalis
    Jie Wu
    School of Dentistry, Meharry Medical College, Nashville, TN 37208, USA
    FEMS Microbiol Lett 282:188-95. 2008
    ..These results suggest that OxyR plays an important role in regulation of expression of virulence genes in P. gingivalis...
  22. pmc Role of differential expression of streptococcal arginine deiminase in inhibition of fimA expression in Porphyromonas gingivalis
    Xinghua Lin
    School of Dentistry, Meharry Medical College, Nashville, TN 37208, USA
    J Bacteriol 190:4367-71. 2008
    ..In this study, we demonstrate the differential expression of arcA in two streptococcal species. The expression level of arcA in streptococci appears to be controlled by both cis and trans elements...
  23. ncbi request reprint [Genes related with male gonadal morphogenesis in mammals]
    Jie Wu
    Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
    Zhonghua Nan Ke Xue 14:356-9. 2008
    ..The functions of some genes, such as SRY, SOX9, SOX8, DAX1, and FGF9, have already been defined in male gonadal morphogenesis. This paper presents a review of the genes involved in the formation of the male gonad in mammals...
  24. doi request reprint Electric field-driven strategy for multiplexed detection of protein biomarkers using a disposable reagentless electrochemical immunosensor array
    Jie Wu
    Key Laboratory of Analytical Chemistry for Life Science Ministry of Education of China, Department of Chemistry, Nanjing University, Nanjing 210093, PR China
    Anal Chem 80:6072-7. 2008
    ....
  25. doi request reprint Discovering regulatory motifs in the Plasmodium genome using comparative genomics
    Jie Wu
    Department of Computer Sciences, University of California, Irvine, CA 92697, CODA Genomics, Laguna Hills, CA 92656, USA
    Bioinformatics 24:1843-9. 2008
    ....
  26. doi request reprint DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks
    Bing Xiong
    State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Pudong, Shanghai, China
    Bioinformatics 24:2117-8. 2008
    ..DrugViz represents a new tool for the analysis of data from chemogenomics, metabolomics and systems biology...
  27. ncbi request reprint Two approaches to construct mammalian expression vector of shRNA to reduce expression and replication of HBV in vitro
    Hong Bin Zhang
    Department of Medical Research, Guangzhou Liuhuaqiao Hospital, Liuhua road 111, Guangzhou, Guangdong Province, P R China
    Mol Biol Rep 35:465-72. 2008
    ..The pU6 derived plasmids might be a useful shRNA delivery system in mammalian cells. In addition, we found siRNA based on stealth 2311 was a potent RNAi target of HBV genome...
  28. ncbi request reprint A molecular epidemiological study targeting the glycoprotein gene of rabies virus isolates from China
    Sheng Li Meng
    Wuhan Institute of Biological Products, Wuhan 430060, China
    Virus Res 124:125-38. 2007
    ..The predicted glycoprotein sequences of these RABVs variants are presented and discussed with respect to the utility of the anti-rabies biologicals currently employed in China...
  29. ncbi request reprint Regulation of the mitogen-activated protein kinase signaling pathway by SHP2
    Jess M Cunnick
    H Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
    J Biol Chem 277:9498-504. 2002
    ....
  30. ncbi request reprint Potent inhibition of platelet-derived growth factor-induced responses in vascular smooth muscle cells by BMS-354825 (dasatinib)
    Zhengming Chen
    Molecular Oncology Program, SRB 3, H Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, and the Department of Interdisciplinary Oncology, University of South Florida College of Medicine, Tampa, FL 33612, USA
    Mol Pharmacol 69:1527-33. 2006
    ..These results suggest that BMS-354825 is a potent inhibitor of PDGF-stimulated VSMC activities and a potential agent for the development of a new therapy for vascular obstructive diseases such as restenosis...
  31. ncbi request reprint Construction and activity of a novel GHRH analog, Pro-Pro-hGHRH(1-44)-Gly-Gly-Cys
    Song Shan Tang
    Laboratory of Minigene Pharmacy, Biopharmaceutical College, Jiangsu Key Laboratory of Drug Delivery System, China Pharmaceutical University, Nanjing, China
    Acta Pharmacol Sin 25:1464-70. 2004
    ..To construct another growth hormone releasing hormone (GHRH) analog, Pro-Pro-hGHRH(1-44)-Gly-Gly-Cys peptide and to compare its activity with that of Pro-Pro-hGHRH(1-44)OH peptide...
  32. ncbi request reprint Facile synthesis of chromeno[4,3-b]quinolin-6-ones from unexpected reactions of aryl isocyanides with 4-chloro-2-oxo-2H-chromene-3-carbaldehyde
    Jie Wu
    Department of Chemistry, Fudan University, 220 Handan Road, Shanghai, 200433, China
    Org Biomol Chem 4:1348-51. 2006
    ..An unexpected reaction of aryl isocyanides with 4-chloro-2-oxo-2H-chromene-3-carbaldehyde leads to chromeno[4,3-b]quinolin-6-ones in good yields...
  33. ncbi request reprint [Construction of phage antibody library for Fab fragment from a convalescent patient infected with SARS coronavirus]
    Jie Wu
    Institute of Cancer Molecular Biology, Guangzhou Command General Hospital, Guangzhou 510010, China
    Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi 20:592-4. 2004
    ..To construct the phage antibody library for Fab fragment from a convalescent patient infected with SARS coronavirus...
  34. pmc The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Nat Biotechnol 24:1151-61. 2006
    ..This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings...
  35. ncbi request reprint Electrophysiological, pharmacological, and molecular evidence for alpha7-nicotinic acetylcholine receptors in rat midbrain dopamine neurons
    Jie Wu
    Division of Neurology, Barrow Neurological Institute, 350 West Thomas Road, Phoenix, AZ 85013 4496, USA
    J Pharmacol Exp Ther 311:80-91. 2004
    ....
  36. ncbi request reprint A role for Grb2-associated binder-1 in growth hormone signaling
    Sung Oh Kim
    Department of Medicine, Division of Endocrinology and Metabolism, University of Alabama, Birmingham, Alabama 35294, USA
    Endocrinology 143:4856-67. 2002
    ..Our results suggest selective involvement of Gab1 in GH-induced ERK activation and implicate the Gab1 PH domain as critical in this involvement...
  37. ncbi request reprint Cloning, expression, and purification of a highly immunogenic recombinant gonadotropin-releasing hormone (GnRH) chimeric peptide
    Jinshu Xu
    The Biopharmaceutical College, China Pharmaceutical University, Nanjing, PR China
    Protein Expr Purif 50:163-70. 2006
    ..Further, immunization of female mice with the recombinant chimeric peptide resulted in generation of high-titer antibodies specific for GnRH. The results showed that GnRH3-hinge-MVP could be considered as a candidate anti-GnRH vaccine...
  38. ncbi request reprint Interaction between tyrosine kinase Etk and a RUN domain- and FYVE domain-containing protein RUFY1. A possible role of ETK in regulation of vesicle trafficking
    Jianbo Yang
    Department of Laboratory Medicine and Pathology and Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, USA
    J Biol Chem 277:30219-26. 2002
    ..Our data suggest that Etk may be involved in regulation of endocytosis through its interaction with an endosomal protein RUFY1...
  39. ncbi request reprint Long-lasting specific antibodies against P277 induced by mucosal administration of P277 repeat sequences carried by Hsp65 in the absence of adjuvants
    Liang Jin
    Minigene Pharmacy Laboratory, Biopharmaceutical College, China Pharmaceutical University, Tongjia Xiang 24, Nanjing 210009, PR China
    Vaccine 25:2043-50. 2007
    ..Specific antibodies were successfully induced and lasted for more than 20 weeks in animals immunized with the fusion protein via intranasal route even in the absence of adjuvants...
  40. pmc Regulated surface expression and shedding support a dual role for semaphorin 4D in platelet responses to vascular injury
    Li Zhu
    Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
    Proc Natl Acad Sci U S A 104:1621-6. 2007
    ..As thrombus formation continues, sema4D is shed from the platelet surface and becomes available to interact with receptors on endothelial cells and monocytes, as well as continuing to interact with platelets...
  41. pmc Porphyromonas gingivalis short fimbriae are regulated by a FimS/FimR two-component system
    Jie Wu
    School of Dentistry, Meharry Medical College, Nashville, TN, USA
    FEMS Microbiol Lett 271:214-21. 2007
    ..Unlike the regulatory mechanism of FimA by FimR, this regulation of the mfa1 gene is accomplished by FimR directly binding to the promoter region of mfa1...
  42. ncbi request reprint Optimization of triaryl bis-sulfones as cannabinoid-2 receptor ligands
    Brian J Lavey
    Department of Chemistry, Schering Plough Research Institute, 2015 Galloping Hill Road, Kenilworth, NJ 07033 0539, USA
    Bioorg Med Chem Lett 17:3760-4. 2007
    ..A compound with excellent CB2 activity, selectivity for CB2 over CB1, and in vivo plasma levels was identified...
  43. ncbi request reprint Time-course of changes to nitric oxide signaling pathways in form-deprivation myopia in guinea pigs
    Jie Wu
    State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat Sen University, 54 Xianlie Road, Guangzhou, Guangdong, China
    Brain Res 1186:155-63. 2007
    ..Our main observations were a change in NOS activity and an up-regulation in cGMP concentrations in posterior ocular tissues during the development of myopia. The function of elevated NOS activity may be mediated by cGMP...