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Articles by W. Peng
Total Records ( 2 ) for W. Peng
  C Zang , D. E Schones , C Zeng , K Cui , K Zhao and W. Peng

Motivation: Chromatin states are the key to gene regulation and cell identity. Chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-Seq) is increasingly being used to map epigenetic states across genomes of diverse species. Chromatin modification profiles are frequently noisy and diffuse, spanning regions ranging from several nucleosomes to large domains of multiple genes. Much of the early work on the identification of ChIP-enriched regions for ChIP-Seq data has focused on identifying localized regions, such as transcription factor binding sites. Bioinformatic tools to identify diffuse domains of ChIP-enriched regions have been lacking.

Results: Based on the biological observation that histone modifications tend to cluster to form domains, we present a method that identifies spatial clusters of signals unlikely to appear by chance. This method pools together enrichment information from neighboring nucleosomes to increase sensitivity and specificity. By using genomic-scale analysis, as well as the examination of loci with validated epigenetic states, we demonstrate that this method outperforms existing methods in the identification of ChIP-enriched signals for histone modification profiles. We demonstrate the application of this unbiased method in important issues in ChIP-Seq data analysis, such as data normalization for quantitative comparison of levels of epigenetic modifications across cell types and growth conditions.

  Q. Simon , V. Bouquet , W. Peng , J.-M. Le Floch , F. Houdonougbo , S. Deputier , S. Weber , A. Dauscher , V. Madrangeas , D. Cros and M. Guilloux-Viry
  KTa1 − xNbxO3 (KTN) thin films were grown by pulsed laser deposition on sapphire and MgO substrates. Their structural and high frequency dielectric characteristics evidenced the strong influence of the substrate and suggested possible KTN/MgO interdiffusion that could be responsible for the lower dielectric losses obtained on this substrate. Both undoped and 6% MgO-doped KTN thin films were then grown on sapphire. Dielectric measurements performed at 12.5 GHz by a resonant cavity perturbation method evidenced reduction of losses by MgO-doping. Loss tangent (tan δ) was reduced by a factor of 3 in comparison with undoped films grown on sapphire.
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