Xuefeng Cui

Release date : November 6, 2019 office viewed :

Dr. Xuefeng Cui

Position

Professor, School of Computer Science and Technology

Employment

l Professor, School of Computer Science and Technology, Shandong University, Qingdao, China, September 2019- present

l Assistant Professor, Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China, October 2016 - July 2019

l Post-Doc Fellow of Computer, Electrical and Mathematical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia, June 2014 - August 2016

Education

l Doctor of Philosophy of Mathematics in Computer Science at the University of Waterloo, Waterloo, Canada, 2014

l Master of Mathematics in Computer Science at the University of Waterloo, Waterloo, Canada, 2007

l Bachelor of Mathematics in Computer Science at the University of Waterloo, Waterloo, Canada, 2004

Research Interest

I am interested in discovering and solving computational problems that can benefit everyday life. This includes designing and applying deep learning methods (e.g., generative adversarial networks) and parallel computing (e.g., CUDA programming) for computational biology problems. Specifically, my recent research work mainly focuses on the following problems:

l Cryo-EM protein structure determination

l Neoantigen design for immunotherapy

l Antibiotic resistance gene discovery in metagenomes

Teaching

l Deep Learning in Computational Biology

l Parallel Algorithm and CUDA Programming

Selected Publications

l Yaosen Min, Shang Liu, and Xuefeng Cui Learning protein structural fingerprints under the label-free supervision of domain knowledge Published on IEEE International Conference on Bioinformatics and Biomedicine (IEEE-BIBM), Madrid, Spain, December 3-6, 2018

l Xuefeng Cui, Zhiwu Lu, Sheng Wang, Jim Jing-Yan Wang, and Xin Gao CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also structure prediction Published on Intelligent Systems for Molecular Biology (ISMB), Orlando, Florida, U.S.A, July 8-12, 2016

l Xuefeng Cui, Hammad Naveed, and Xin Gao Finding optimal interaction interface alignments between biological complexes Published on Intelligent Systems for Molecular Biology (ISMB), Dublin, Ireland, July 10-14, 2015

l Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li, and Xin Gao Compare local pocket and global protein structure models by small structure patterns Published on ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), Atlanta, U.S.A, September 9-12, 2015

l Xuefeng Cui, Tomas Vinar, Brona Brejova, Dennis Shasha, and Ming Li Homology search for genes Published on Intelligent Systems for Molecular Biology (ISMB), Vienna, Austria, July 21-25, 2007