Browsing by Author "Wu, X."
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- A Bayesian Assignment Method for Ambiguous Bisulfite Short ReadsTran, H.; Wu, X.; Tithi, S.; Sun, M.-A.; Xie, H.; Zhang, L. (PLOS, 2016-03-24)DNA methylation is an epigenetic modification critical for normal development and diseases. The determination of genome-wide DNA methylation at single-nucleotide resolution is made possible by sequencing bisulfite treated DNA with next generation high-throughput sequencing. However, aligning bisulfite short reads to a reference genome remains challenging as only a limited proportion of them (around 50–70%) can be aligned uniquely; a significant proportion, known as multireads, are mapped to multiple locations and thus discarded from downstream analyses, causing financial waste and biased methylation inference. To address this issue, we develop a Bayesian model that assigns multireads to their most likely locations based on the posterior probability derived from information hidden in uniquely aligned reads. Analyses of both simulated data and real hairpin bisulfite sequencing data show that our method can effectively assign approximately 70% of the multireads to their best locations with up to 90% accuracy, leading to a significant increase in the overall mapping efficiency. Moreover, the assignment model shows robust performance with low coverage depth, making it particularly attractive considering the prohibitive cost of bisulfite sequencing. Additionally, results show that longer reads help improve the performance of the assignment model. The assignment model is also robust to varying degrees of methylation and varying sequencing error rates. Finally, incorporating prior knowledge on mutation rate and context specific methylation level into the assignment model increases inference accuracy. The assignment model is implemented in the BAM-ABS package and freely available at https://github.com/zhanglabvt/BAM_ABS.
- Control of thermal runaway in microwave resonant cavitiesWu, X.; Thomas, J. R.; Davis, William A. (American Institute of Physics, 2002-09-15)This article reports direct experimental evidence of the so-called "S curve" of temperature versus electrical field strength when materials with positive temperature dependence of dielectric loss are heated in a microwave resonant cavity applicator. A complete discussion of how the experimental results were achieved is presented. From the experimental results, we believe the S curve theory provides an incomplete explanation of thermal runaway in microwave heating. To understand microwave heating in a resonant cavity, cavity effects must be considered. To explain the experimental results, a theoretical model based on single-mode waveguide theory is developed. Finally, a method to control thermal runaway is described. (C) 2002 American Institute of Physics.
- Mammalian Brain Development is Accompanied by a Dramatic Increase in Bipolar DNA MethylationSun, M.-A.; Sun, Z.; Wu, X.; Rajaram, V.; Keimig, D.; Lim, J.; Zhu, H.; Xie, H. (Nature Publishing Group, 2016-09-02)