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清华大学曾坚阳教授学术报告

来源: 点击: 时间:2019年07月09日 16:14

报告题目 Machine Learning for Modeling 3D Genome Structure

报告时间:7月9日 下午4:00

报告地点:校本部计算机楼313

报告人曾坚阳教授(清华大学)

Abstract

Decoding the spatial organizations of chromosomes has crucial implications for studying eukaryotic gene regulation. Recently, Chromosomal conformation capture based technologies, such as Hi-C, have been widely used to uncover the interaction frequencies of genomic loci in high-throughput and genome-wide manner and provide new insights into the folding of three-dimensional (3D) genome structure. In this project, we develop a novel manifold learning based framework, called GEM (Genomic organization reconstructor based on conformational Energy and Manifold learning), to reconstruct the threedimensional organizations of chromosomes by integrating Hi-C data with biophysical feasibility. Unlike previous methods, which explicitly assume specific relationships between Hi-C interaction frequencies and spatial distances, our model directly embeds the neighboring affinities from Hi-C space into 3D Euclidean space. Extensive validations demonstrated that GEM not only greatly outperformed other state-of-art modeling methods but also provided a physically and physiologically valid 3D representations of the organizations of chromosomes. Furthermore, we for the first time apply the modeled chromatin structures to recover long-range genomic interactions missing from original Hi-C datale.

Biography

曾坚阳,清华大学交叉信息研究院,长聘副教授,博士生导师,入选中组部“青年千人计划”。于1999年和2002年分别获得浙江大学的学士和硕士学位。2011年,在美国杜克大学(Duke University)获得计算机科学博士学位。2011年至2012年期间,在杜克医学院从事博士后研究。于2006年获得国际会议PDCAT'05的最佳论文奖。于2012年被卡内基梅隆大学(Carnegie Mellon University)评为Finalist for a Lane Fellowship in Computational Biology。获得“全国大学生挑战杯优秀指导教师”的称号。相关研究成果被生物信息领域的核心期刊GPB(Genomics, Proteomics and Bioinformatics)评为2018年度“中国生物信息学十大进展”。

目前主要研究方向包括计算生物学、机器学习和大规模数据分析。已在国际核心期刊和会议上发表论文50余篇,其中通讯作者论文包括《自然通讯》(Nature Communications)、《细胞》杂志子刊《细胞系统》(Cell Systems)、Nucleic Acids Research、Bioinformatics、计算生物学和人工智能领域的国际一流会议RECOMB、ISMB和AAAI等,合作作者论文包括《自然》(Nature)期刊等。在计算生物学领域和人工智能的国际一流会议ISMB、RECOMB、IJCAI上担任程序委员会委员。

联系方式:0731-88879336 地址:湖南省长沙市岳麓区中南大学计算机楼

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