Jing Chen

Summary

Affiliation: Cincinnati Children's Hospital Medical Center
Country: USA

Publications

  1. pmc Overstaying their welcome: defective CX3CR1 microglia eyed in macular degeneration
    Jing Chen
    Department of Ophthalmology, Children s Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
    J Clin Invest 117:2758-62. 2007
  2. pmc Dissecting microregulation of a master regulatory network
    Amit U Sinha
    Department of Pediatrics, University of Cincinnati College of Medicine, Ohio, USA
    BMC Genomics 9:88. 2008
  3. pmc Disease candidate gene identification and prioritization using protein interaction networks
    Jing Chen
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH, USA
    BMC Bioinformatics 10:73. 2009
  4. pmc Improved human disease candidate gene prioritization using mouse phenotype
    Jing Chen
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, USA
    BMC Bioinformatics 8:392. 2007
  5. doi request reprint Integrative systems biology approaches to identify and prioritize disease and drug candidate genes
    Vivek Kaimal
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH, USA
    Methods Mol Biol 700:241-59. 2011
  6. doi request reprint Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge
    Ranga Chandra Gudivada
    Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45229 3039, USA
    J Biomed Inform 41:717-29. 2008
  7. pmc PhenoHM: human-mouse comparative phenome-genome server
    Divya Sardana
    Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA
    Nucleic Acids Res 38:W165-74. 2010
  8. doi request reprint Oral benzo[a]pyrene in Cyp1a1/1b1(-/-) double-knockout mice: Microarray analysis during squamous cell carcinoma formation in preputial gland duct
    Marina Galvez-Peralta
    Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati, OH 45267 0056, USA
    Int J Cancer 132:2065-75. 2013
  9. pmc Loss of the miR-144/451 cluster impairs ischaemic preconditioning-mediated cardioprotection by targeting Rac-1
    Xiaohong Wang
    Department of Pharmacology and Cell Biophysics, University of Cincinnati College of Medicine, Cincinnati, OH 45267 0575, USA
    Cardiovasc Res 94:379-90. 2012
  10. pmc GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
    Anil G Jegga
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA
    Nucleic Acids Res 35:D116-21. 2007

Collaborators

Detail Information

Publications40

  1. pmc Overstaying their welcome: defective CX3CR1 microglia eyed in macular degeneration
    Jing Chen
    Department of Ophthalmology, Children s Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
    J Clin Invest 117:2758-62. 2007
    ..In this issue of the JCI, the study by Combadière and colleagues shows that CX3C chemokine receptor 1-deficient (CX3CR1-deficient) mice have abnormal microglia that accumulate beneath the retina and contribute to the progression of AMD...
  2. pmc Dissecting microregulation of a master regulatory network
    Amit U Sinha
    Department of Pediatrics, University of Cincinnati College of Medicine, Ohio, USA
    BMC Genomics 9:88. 2008
    ..While it has been reported that some of the p53's functions are microRNA-mediated, it is not known as to how many other microRNAs might contribute to the p53-mediated tumorigenesis...
  3. pmc Disease candidate gene identification and prioritization using protein interaction networks
    Jing Chen
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH, USA
    BMC Bioinformatics 10:73. 2009
    ..In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN) analyses...
  4. pmc Improved human disease candidate gene prioritization using mouse phenotype
    Jing Chen
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, USA
    BMC Bioinformatics 8:392. 2007
    ....
  5. doi request reprint Integrative systems biology approaches to identify and prioritize disease and drug candidate genes
    Vivek Kaimal
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH, USA
    Methods Mol Biol 700:241-59. 2011
    ..We illustrate the method in detail using examples of two neurodegenerative diseases (Alzheimer's and Parkinson's) and one neuropsychiatric disease (Schizophrenia)...
  6. doi request reprint Identifying disease-causal genes using Semantic Web-based representation of integrated genomic and phenomic knowledge
    Ranga Chandra Gudivada
    Department of Biomedical Engineering, University of Cincinnati, Cincinnati, OH 45229 3039, USA
    J Biomed Inform 41:717-29. 2008
    ....
  7. pmc PhenoHM: human-mouse comparative phenome-genome server
    Divya Sardana
    Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA
    Nucleic Acids Res 38:W165-74. 2010
    ..The PhenoHM server can be accessed freely at http://phenome.cchmc.org...
  8. doi request reprint Oral benzo[a]pyrene in Cyp1a1/1b1(-/-) double-knockout mice: Microarray analysis during squamous cell carcinoma formation in preputial gland duct
    Marina Galvez-Peralta
    Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati, OH 45267 0056, USA
    Int J Cancer 132:2065-75. 2013
    ..The mechanism by which cancer-related genes are responsible for SCC tumor progression in the PGD remains to be elucidated...
  9. pmc Loss of the miR-144/451 cluster impairs ischaemic preconditioning-mediated cardioprotection by targeting Rac-1
    Xiaohong Wang
    Department of Pharmacology and Cell Biophysics, University of Cincinnati College of Medicine, Cincinnati, OH 45267 0575, USA
    Cardiovasc Res 94:379-90. 2012
    ..While a wealth of data has uncovered distinct microRNA (miR) expression alterations in hypertrophic and ischaemic/reperfused (I/R) hearts, little is known about miR regulation and response to ischaemic preconditioning (IPC)...
  10. pmc GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs
    Anil G Jegga
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA
    Nucleic Acids Res 35:D116-21. 2007
    ....
  11. pmc ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
    Jing Chen
    Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA
    Nucleic Acids Res 37:W305-11. 2009
    ..ToppGene ranked 19 of 20 (95%) candidate genes within the top 20%, while ToppNet ranked 12 of 16 (75%) candidate genes among the top 20%...
  12. pmc PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease
    Anil G Jegga
    Division of Biomedical Informatics, Cincinnati Children s Hospital Medical Center, Cincinnati, OH 45229, USA
    Nucleic Acids Res 35:D700-6. 2007
    ..PolyDoms will continue to be curated to improve its usefulness...
  13. pmc Deciphering gene expression program of MAP3K1 in mouse eyelid morphogenesis
    Chang Jin
    Department of Environmental Health, University of Cincinnati College of Medicine, 3223 Eden Avenue, Kettering Laboratory, Suite 410, P O Box 670056, Cincinnati, OH 45267 0056, USA
    Dev Biol 374:96-107. 2013
    ..Using LCM and expression array, our studies have uncovered novel molecular signatures of MAP3K1 in embryonic eyelid closure...
  14. pmc Oral benzo[a]pyrene-induced cancer: two distinct types in different target organs depend on the mouse Cyp1 genotype
    Zhanquan Shi
    Department of Environmental Health and Center for Environmental Genetics, University of Cincinnati Medical Center, Cincinnati, OH 45267 0056, USA
    Int J Cancer 127:2334-50. 2010
    ..This oral BaP mouse paradigm represents an example of "gene-environment interactions" in which the same exposure of carcinogen results in altered target organ and tumor type, as a function of just 1 or 2 globally absent genes...
  15. pmc Aging exacerbates depressive-like behavior in mice in response to activation of the peripheral innate immune system
    Jonathan P Godbout
    Department of Molecular Virology, Immunology and Medical Genetics, Institute for Behavioral Medicine, The Ohio State University, Columbus, OH, USA
    Neuropsychopharmacology 33:2341-51. 2008
    ..These results provide the first evidence that age-associated reactivity of the brain cytokine system could play a pathophysiological role in the increased prevalence of depression observed in the elderly...
  16. pmc Identification of a NF-κB cardioprotective gene program: NF-κB regulation of Hsp70.1 contributes to cardioprotection after permanent coronary occlusion
    Michael E Wilhide
    Department of Pharmacology and Cell Biophysics, University of Cincinnati College of Medicine, Cincinnati, OH 45267 0575, USA
    J Mol Cell Cardiol 51:82-9. 2011
    ..The significance of the research is that understanding the gene network regulated by NF-κB after ischemic insult may lead to identification of therapeutic targets more appropriate for clinical development...
  17. pmc MicroRNA-494 targeting both proapoptotic and antiapoptotic proteins protects against ischemia/reperfusion-induced cardiac injury
    Xiaohong Wang
    Department of Pharmacology and Cell Biophysics, University of Cincinnati College of Medicine, 231 Albert Sabin Way, Cincinnati, OH 45267 0575, USA
    Circulation 122:1308-18. 2010
    ..Recently, we and others observed that miR-494 was downregulated in murine I/R-injured and human infarcted hearts. However, the functional consequence of miR-494 in response to I/R remains unknown...
  18. pmc Identification of IFRD1 as a modifier gene for cystic fibrosis lung disease
    YuanYuan Gu
    Division of Molecular Immunology, Cincinnati Children s Hospital Research Foundation and the University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
    Nature 458:1039-42. 2009
    ..These data indicate that IFRD1 modulates the pathogenesis of cystic fibrosis lung disease through the regulation of neutrophil effector function...
  19. pmc Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays
    Marina Bibikova
    Genetic Analysis, Illumina, Inc, 9885 Towne Center Drive, San Diego, CA 92121, USA
    Am J Pathol 165:1799-807. 2004
    ..The DASL assay system should prove useful for high-throughput expression profiling of archived clinical samples...
  20. ncbi request reprint Neutron fluence-to-dose conversion coefficients for embryo and fetus
    Jing Chen
    Radiation Protection Bureau, Health Canada 6302D1, 775 Brookfield Road, Ottawa K1A 1C1, Canada
    Radiat Prot Dosimetry 110:693-8. 2004
    ..The results indicate that for neutrons <10 MeV more protection should be given to pregnant women in the first trimester due to the higher absorbed dose per unit neutron fluence to the fetus...
  21. ncbi request reprint Positive and negative regulatory roles of the WW-like domain in TEL-PDGFbetaR transformation
    Jing Chen
    Division of Hematology, Brigham and Women s Hospital, 75 Francis St, Boston, MA 02115, USA
    Blood 104:535-42. 2004
    ..Therefore, the WW-like domain in the context of TELPDGFbetaR may have both positive and negative regulatory roles in kinase activation...
  22. ncbi request reprint Radiation quality of photons in small and large receptors--a microdosimetric analysis
    Jing Chen
    Radiation Protection Bureau, Health Canada, 775 Brookfield Road, Ottawa K1A 1C1, Canada
    Radiat Prot Dosimetry 118:238-42. 2006
    ..The values of y(D) suggest that, for both small and large receptors, conventional X rays should be about twice as effective as gamma rays from 60Co...
  23. pmc Functional reconstruction of rabbit corneal epithelium by human limbal cells cultured on amniotic membrane
    Yiqin Du
    Peking University Stem Cell Research Center, Beijing China
    Mol Vis 9:635-43. 2003
    ..To investigate the phenotype of fetal and adult human limbal cells cultured on human amniotic membrane and the ability of cultured adult human limbal cells to repair limbal stem cell deficiency in a rabbit model...
  24. ncbi request reprint Estimate of annual average radon concentration in the normal living area from short-term tests
    Jing Chen
    Radiation Protection Bureau, 6302D1, Health Canada, 775 Brookfield Road, Ottawa K1A 1C1, Canada
    Health Phys 85:740-4. 2003
    ..The annual average radon level can be estimated by multiplying the result of a short-term screening test with the appropriate estimate factor given in this study...
  25. ncbi request reprint Mobilization of hematopoietic stem cells during homeostasis and after cytokine exposure
    Janis L Abkowitz
    Department of Medicine, Division of Hematology, University of Washington, Box 357710, Seattle, WA 98195 7710, USA
    Blood 102:1249-53. 2003
    ....
  26. ncbi request reprint Identification and characterization of a novel human testis-specific Golgi protein, NYD-SP12
    Min Xu
    Laboratory of Reproductive Medicine, Center of Human Functional Genomics, Nanjing Medical University, People s Republic of China
    Mol Hum Reprod 9:9-17. 2003
    ..In conclusion, the results suggest that NYD-SP12 is involved in spermatogenesis, and that NYD-SP12-encoded protein might function in the Golgi apparatus...
  27. doi request reprint Identification of SVM-based classification model, synthesis and evaluation of prenylated flavonoids as vasorelaxant agents
    Xiaowu Dong
    ZJU ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
    Bioorg Med Chem 16:8151-60. 2008
    ..Structure-activity relationship (SAR) analysis revealed that flavanone derivatives showed the most potent activities, while flavone and chalcone derivatives exhibited medium activities...
  28. ncbi request reprint Acute lung injury induced by chlorine inhalation in C57BL/6 and FVB/N mice
    Xiaohua Tian
    Section of Pulmonary Diseases, Critical Care and Environmental Medicine, Department of Medicine, Tulane University Health Sciences Center, Louisiana, USA
    Inhal Toxicol 20:783-93. 2008
    ..Characterization of such responses in these mice will allow testing of therapeutic agents to treat chlorine-induced lung injury...
  29. doi request reprint Genome-wide mapping of allele-specific protein-DNA interactions in human cells
    Nathaniel D Maynard
    Ludwig Institute for Cancer Research, University of California, San Diego, 9500 Gilman Ave, La Jolla, California 92037, USA
    Nat Methods 5:307-9. 2008
    ..ChIP-SNP will facilitate the study of mechanisms of allele-specific gene expression...
  30. ncbi request reprint Novel leptin receptor mutation in NOD/LtJ mice suppresses type 1 diabetes progression: II. Immunologic analysis
    Chul Ho Lee
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
    Diabetes 55:171-8. 2006
    ....
  31. ncbi request reprint Variants in mitochondrial tRNAGlu, tRNAArg, and tRNAThr may influence the phenotypic manifestation of deafness-associated 12S rRNA A1555G mutation in three Han Chinese families with hearing loss
    Wie yen Young
    Institute of Otolaryngology, Chinese PLA General Hospital, Beijing, China
    Am J Med Genet A 140:2188-97. 2006
    ..Therefore, these mtDNA mutations may have a potential modifier role in increasing the penetrance and expressivity of the deafness-associated 12S rRNA A1555G mutation in those Chinese pedigrees...
  32. ncbi request reprint Transplantation of rat islets transduced with human heme oxygenase-1 gene using adenovirus vector
    Yongxiang Li
    Department of Urology and Center of Renal Transplantation, Shanghai Organ Transplant and Research Center, Shanghai First People s Hospital, China
    Pancreas 33:280-6. 2006
    ....
  33. ncbi request reprint Identification of two novel DSRAD mutations in two Chinese families with dyschromatosis symmetrica hereditaria
    Jianyun Lu
    Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, People s Republic of China
    Arch Dermatol Res 298:357-60. 2006
    ..This study should be useful for genetic counseling and prenatal diagnosis for affected families and in expanding the database on DSRAD gene mutations in DSH...
  34. ncbi request reprint Prohibitin suppresses renal interstitial fibroblasts proliferation and phenotypic change induced by transforming growth factor-beta1
    Wei Guo
    Department of Nephrology, Children s Hospital of Fudan University, 183 Feng Lin Road, Shanghai, 200032, P R China
    Mol Cell Biochem 295:167-77. 2007
    ..Therefore, over-expression of PHB suppresses renal interstitial fibroblasts proliferation and cell phenotypic change induced by TGF-beta1, which indicates PHB as a potential therapeutic target to halt the progression of TIF...
  35. ncbi request reprint Pocket v.2: further developments on receptor-based pharmacophore modeling
    Jing Chen
    Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Stable and Unstable Species, College of Chemistry, and Center for Theoretical Biology, Peking University, Beijing 100871, P R China
    J Chem Inf Model 46:2684-91. 2006
    ..For different proteins accommodating the same ligand, Pocket v.2 gives similar pharmacophore models, which opens the possibility to classify proteins with their binding features...
  36. ncbi request reprint "Agouti NOD": identification of a CBA-derived Idd locus on Chromosome 7 and its use for chimera production with NOD embryonic stem cells
    Jing Chen
    The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine 04609 1500, USA
    Mamm Genome 16:775-83. 2005
    ..CBALs- Tyr(+)/Lt blastocysts produced approximately 50% live-born mice, of which approximately 11% were chimeric. Presumably because of high genomic instability, no germline transmission was observed...
  37. ncbi request reprint Association of HLA-DRB1, DQB1 alleles with chronic urticaria
    Jing Chen
    Department of Dermatology, Union Hospital, Tongji Medical College, Huangzhong University of Science and Technology, Wuhan 430022, China
    J Huazhong Univ Sci Technolog Med Sci 25:354-6. 2005
    ..It was suggested that CU was found strongly associated with HLA-DRB1 * 12, * 0901 and HLA-DQB1 * 05, the former might be the genetic markers for susceptibility to CU, but the latter might play a resistive role...
  38. ncbi request reprint Novel leptin receptor mutation in NOD/LtJ mice suppresses type 1 diabetes progression: I. Pathophysiological analysis
    Chul Ho Lee
    The Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA
    Diabetes 54:2525-32. 2005
    ....
  39. ncbi request reprint A dynamin-3 spliced variant modulates the actin/cortactin-dependent morphogenesis of dendritic spines
    Noah W Gray
    Molecular Neuroscience Program and Graduate School, Mayo Clinic, Rochester, MN 55905, USA
    J Cell Sci 118:1279-90. 2005
    ....
  40. ncbi request reprint Regulation of transcription of the murine gamma-glutamyl hydrolase gene. Delineation of core promoter A and the role of LYF-1, E2F and ETS-1 in determining tumor-specific expression
    Naoko Masumoto
    Program in Molecular Pharmacology and Experimental Therapeutics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Gene 291:169-76. 2002
    ..This is an interesting finding in light of our earlier results which located promoter B and two associated alternates of exon 1 of this gene on chromosome 17...