題目🌐：Differential Gene Expression Analysis Using Coexpression and RNA-Seq Data
時間：2013年12月3日 (周二) 13:30
地點🖊：意昂3娱乐244
演講人🈲：Tao Jiang (姜濤) 美國加州大學河濱分校計算機科學系教授
Abstract: As a fundamental tool for discovering genes involved in a disease or biological process, differential gene expression analysis plays an important role in genomics research. High throughput sequencing technologies such as RNA-Seq are increasingly being used for differential gene expression analysis which was dominated by the microarray technology in the past decade. However, inferring differential gene expression based on the observed difference of RNA-Seq read counts has unique challenges that were not present in microarray-based analysis. The differential expression estimation may be biased against low read count values such that the differential expression of genes with high read counts is more easily detected. The estimation bias may further propagate in downstream analyses at the systems biology level if it is not corrected. In this work, we propose a new efficient algorithm for detecting differentially expressed genes based on a markov random field (MRF) model, called MRFSeq, that uses additional coexpression data to enhance the prediction power. Our main technical contribution is a careful construction of the clique potential functions in the MRF so its maximum a posteriori (MAP) estimation can be reduced to the well-known maximum flow problem and thus solved in polynomial time. Our extensive experiments on simulated and real RNA-Seq datasets demonstrate that MRFSeq is more accurate and less biased against genes with low read counts than the existing methods based on RNA-Seq data alone. For example, on the well-studied MAQC dataset, MRFSeq improved the sensitivity from 11.6% to 38.8% for genes with low read counts.
演講人簡介：Tao Jiang, 男，美國加州大學河濱分校計算機科學系教授🙏🏼。1984年7月畢業於中國科學技術大學計算機科學系🤸，獲本科學位🙅♀️。1988年11月畢業於美國明尼蘇達大學，獲博士學位。1989年1月至2001年7月在加拿大麥克馬斯特大學 (McMaster University)先後擔任助理教授、副教授及教授職位，1999年至今任美國加州大學河濱分校教授。研究興趣包括組合算法、計算生物學👦、生物信息學、信息檢索等🗜。從事計算機算法和生物信息學研究多年，在計算機科學及生物信息領域期刊及會議上共發布學術論文240余篇🧎🏻♂️，學術專著一部。擔任ACM Fellow（此榮譽由Association for Computing Machinery，即計算機協會頒給全世界計算機相關領域有傑出貢獻之學者），以及American Association for the Advancement of Science (AAAS) Fellow🧖🏻，美國加州大學河濱分校講席教授（Presidential Chair Professor， 2007-2010）職位。