Junwen Wang

Summary

Affiliation: University of Pennsylvania
Country: USA

Publications

  1. pmc Generalizations of Markov model to characterize biological sequences
    Junwen Wang
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 6021, USA
    BMC Bioinformatics 6:219. 2005
  2. ncbi request reprint A mammalian promoter model links cis elements to genetic networks
    Junwen Wang
    Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, 19104 6021, USA
    Biochem Biophys Res Commun 347:166-77. 2006
  3. pmc Basonuclin regulates a subset of ribosomal RNA genes in HaCaT cells
    Shengliang Zhang
    Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 2:e902. 2007
  4. pmc Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
    Saran Vardhanabhuti
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 6021, USA
    Nucleic Acids Res 35:3203-13. 2007
  5. pmc YY1 controls Igκ repertoire and B-cell development, and localizes with condensin on the Igκ locus
    Xuan Pan
    Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
    EMBO J 32:1168-82. 2013
  6. ncbi request reprint Transcriptional genomics associates FOX transcription factors with human heart failure
    Sridhar Hannenhalli
    Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    Circulation 114:1269-76. 2006
  7. pmc MetaProm: a neural network based meta-predictor for alternative human promoter prediction
    Junwen Wang
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Genomics 8:374. 2007
  8. pmc Mouse ribosomal RNA genes contain multiple differentially regulated variants
    Hung Tseng
    Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 3:e1843. 2008
  9. pmc PU.1 can recruit BCL6 to DNA to repress gene expression in germinal center B cells
    Fang Wei
    Department of Animal Biology and Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Mol Cell Biol 29:4612-22. 2009
  10. pmc Search for basonuclin target genes
    Junwen Wang
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Biochem Biophys Res Commun 348:1261-71. 2006

Collaborators

Detail Information

Publications12

  1. pmc Generalizations of Markov model to characterize biological sequences
    Junwen Wang
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 6021, USA
    BMC Bioinformatics 6:219. 2005
    ..However, this neither takes into account the joint dependency of multiple neighboring nucleotides, nor does it consider the long range dependency with gap > 0...
  2. ncbi request reprint A mammalian promoter model links cis elements to genetic networks
    Junwen Wang
    Penn Center for Bioinformatics and Department of Genetics, University of Pennsylvania, Philadelphia, 19104 6021, USA
    Biochem Biophys Res Commun 347:166-77. 2006
    ..The discovered links between promoter elements and gene function allows us to infer genetic networks from promoter elements. The web server for the PSPA promoter predictor is available at /PSPA...
  3. pmc Basonuclin regulates a subset of ribosomal RNA genes in HaCaT cells
    Shengliang Zhang
    Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 2:e902. 2007
    ..In conclusion, our results demonstrate basonuclin's functional association with rDNA promoters and its interaction with Pol I in vivo. Our data also suggest that basonuclin-Pol I complex transcribes a subset of rDNA...
  4. pmc Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
    Saran Vardhanabhuti
    Penn Center for Bioinformatics, Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104 6021, USA
    Nucleic Acids Res 35:3203-13. 2007
    ..We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and position specificity, in addition to the evolutionary conservation, in discovering cis-regulatory motifs...
  5. pmc YY1 controls Igκ repertoire and B-cell development, and localizes with condensin on the Igκ locus
    Xuan Pan
    Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
    EMBO J 32:1168-82. 2013
    ..Knock-down of a condensin subunit protein or YY1 reduced rearrangement of Igκ Vκ genes suggesting a direct role for YY1-condensin complexes in Igκ locus structure and rearrangement...
  6. ncbi request reprint Transcriptional genomics associates FOX transcription factors with human heart failure
    Sridhar Hannenhalli
    Department of Genetics and Penn Center for Bioinformatics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
    Circulation 114:1269-76. 2006
    ..We developed and applied a computational approach called transcriptional genomics to test the hypothesis that a discrete set of cardiac TFs is associated with human heart failure...
  7. pmc MetaProm: a neural network based meta-predictor for alternative human promoter prediction
    Junwen Wang
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    BMC Genomics 8:374. 2007
    ..Furthermore, most PPPs are trained and tested on the most-upstream promoters; their performances on alternative promoters have not been assessed...
  8. pmc Mouse ribosomal RNA genes contain multiple differentially regulated variants
    Hung Tseng
    Department of Dermatology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
    PLoS ONE 3:e1843. 2008
    ..Thus, the mouse rDNA array likely consists of genetically distinct variants, and some are regulated tissue-specifically. Our results provide the first molecular evidence for cell-type-specific regulation of a subset of rDNA...
  9. pmc PU.1 can recruit BCL6 to DNA to repress gene expression in germinal center B cells
    Fang Wei
    Department of Animal Biology and Mari Lowe Center for Comparative Oncology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
    Mol Cell Biol 29:4612-22. 2009
    ..The recruitment of BCL6 to promoter regions by PU.1 represents a new regulatory mechanism that expands the number of genes regulated by this important transcriptional repressor...
  10. pmc Search for basonuclin target genes
    Junwen Wang
    Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA
    Biochem Biophys Res Commun 348:1261-71. 2006
    ..Our results suggest that basonuclin, like MYC, may coordinate transcriptional activities among the three RNA polymerases. But basonuclin regulates a distinctive set of pathways, which differ from that regulated by MYC...
  11. ncbi request reprint NdPASA: a novel pairwise protein sequence alignment algorithm that incorporates neighbor-dependent amino acid propensities
    Junwen Wang
    Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA
    Proteins 58:628-37. 2005
    ..6%. NdPASA is most effective for aligning query sequences with template sequences whose structure is known. NdPASA can be accessed online at http://astro.temple.edu/feng/Servers/BioinformaticServers.htm...
  12. pmc A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer
    David J Hunter
    Channing Laboratory, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
    Nat Genet 39:870-4. 2007
    ..Our summary results from the GWAS are available online in a form that should speed the identification of additional risk loci...