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Articles by K. Huang
Total Records ( 3 ) for K. Huang
  C Taslim , J Wu , P Yan , G Singer , J Parvin , T Huang , S Lin and K. Huang

Motivation: Antibody-based Chromatin Immunoprecipitation assay followed by high-throughput sequencing technology (ChIP-seq) is a relatively new method to study the binding patterns of specific protein molecules over the entire genome. ChIP-seq technology allows scientist to get more comprehensive results in shorter time. Here, we present a non-linear normalization algorithm and a mixture modeling method for comparing ChIP-seq data from multiple samples and characterizing genes based on their RNA polymerase II (Pol II) binding patterns.

Results: We apply a two-step non-linear normalization method based on locally weighted regression (LOESS) approach to compare ChIP-seq data across multiple samples and model the difference using an Exponential-NormalK mixture model. Fitted model is used to identify genes associated with differential binding sites based on local false discovery rate (fdr). These genes are then standardized and hierarchically clustered to characterize their Pol II binding patterns. As a case study, we apply the analysis procedure comparing normal breast cancer (MCF7) to tamoxifen-resistant (OHT) cell line. We find enriched regions that are associated with cancer (P < 0.0001). Our findings also imply that there may be a dysregulation of cell cycle and gene expression control pathways in the tamoxifen-resistant cells. These results show that the non-linear normalization method can be used to analyze ChIP-seq data across multiple samples.

  J.Q. Liu , J.F. Wang , Y.F. Liu , K. Huang , X.J. Hu , Y.M. Zhang , Y. Xu , K. Xu and H. Yang

The threading dislocation density of hydride vapor phase epitaxy (HVPE)-grown thick GaN layers was measured by high-resolution X-ray diffraction (HR-XRD). Three models were compared, namely mosaic model, Kaganer model and modified Kaganer model. X-ray rocking curves (XRC) of (0 0 0 2), (1 0 1¯ 5), (1 0 1¯ 4), (1 0 1¯ 3), (1 0 1¯ 2), (1 0 1¯ 1) and (1 0 1¯ 0) planes were recorded for quantitative analysis. The screw-, edge-, and mixed-type threading dislocation densities were simulated from the XRD line profile by using the three models. The dislocation density was also measured by atomic force microscopy (AFM), wet chemical etching and cathodoluminescence (CL). The results showed that the Kaganer model was more physically precise and well explained the rocking curve broadening for HVPE-grown high-quality GaN compared with the mosaic model. Assuming a randomly distributed threading dislocation configuration, we modified the Kaganer model. Based on the modified Kaganer model, the edge and screw threading dislocation densities in HVPE-grown GaN thick films ranging from 20 μm up to 700 μm were analyzed. It was shown that screw-type dislocation density decreased more rapidly than edge-type dislocation with increase in film thickness.

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