Sheng Wang

About

Sheng Wang worked as a Research Scientist at Prof. Xin Gao's Structural and Functional Bioinformatics Group at King Abdullah University of Science and Technology (KAUST). Sheng got his Ph.D. in Bioinformatics from the Institute of Theoretical Physics at the Chinese Academy of Sciences in 2010. He was then a postdoc fellow at Toyota Technological Institute in Chicago during 2010 and 2014. During 2014 and 2017, he was a research professional at the Department of Human Genetics at the University of Chicago. Since March 2017, he joined the SFB group as a research scientist. Currently, Sheng is a Research Expert in Tencent AI Lab, Shenzhen, China.

Research Interests

​Sheng's research interest lies in protein-related computational biology and bioinformatics. In particular, he applies machine learning algorithms to study the protein sequence/structure alignment, protein homology search, and protein structure prediction. His current research interests are also focused on machine-learning-based next-generation sequencing and structure-based computational immunology.

Selected Publications

​1. Sheng Wang, Jianzhu Ma, and Jinbo Xu. AUCpreD: Proteome-level Protein Disorder Prediction by AUC-maximized Deep Convolutional Neural Fields. Bioinformatics, 2016.
2. Sheng Wang, Wei Li, Renyu Zhang, Shiwang Liu, and Jinbo Xu. CoinFold: a web server for protein contact prediction and contact-assisted protein folding. Nucleic Acids Research, 2016.
3. Sheng Wang, Wei Li, Shiwang Liu, and Jinbo Xu. RaptorX-Property: a web server for protein structure-property prediction. Nucleic Acids Research, 2016.
4. Xuefeng Cui, Zhiwu Lu, Sheng Wang, Jim Jing-Yan Wang, and Xin Gao. CMsearch: a simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. Bioinformatics, 2016.
5. Sheng Wang, Jian Peng, Jianzhu Ma, and Jinbo Xu. Protein Secondary Structure Prediction using Deep Convolutional Neural Fields. Scientific Reports, 2016.
6. Dinanath Sulakhe, Bingqing Xie, Andrew Taylor, Mark D’Souza, Sandhya Balasubramanian, Somaye Hashemifar, Steven White, Utpal J. Dave, Gady Agam, Jinbo Xu, Sheng Wang, T. Conrad Gilliam, and Natalia Maltsev. Lynx: A Knowledge Base and an Analytical Workbench for Integrative Medicine. Nucleic Acids Research, 2016.
7. Jianzhu Ma*, Sheng Wang*, Zhiyong Wang, and Jinbo Xu. Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinformatics, 2015.
8. Jianzhu Ma, Sheng Wang, Zhiyong Wang, and Jinbo Xu. MRFalign: protein homology detection through alignment of Markov Random Fields. PLoS Computational Biology, 2014.
9. Dinanath Sulakhe, Sandhya Balasubramanian, Bingqing Xie, Bo Feng, Andrew Taylor, Sheng Wang, Eduardo Berrocal, Utpal Dave, Jinbo Xu, Daniela Bornigen, T. Conrad Gilliam, and Natalia Maltsev. Lynx: a database and knowledge extraction engine for integrative medicine. Nucleic Acids Research, 2014.
10. Sheng Wang, Jian Peng, Jianzhu Ma, and Jinbo Xu. Protein structure alignment beyond spatial proximity. Scientific Reports, 2013.
11. Jianzhu Ma, Sheng Wang, Feng Zhao, and Jinbo Xu. Protein threading using context-specific alignment potential, Bioinformatics, 2013.
12. Morten Kollberg,     Haipeng Wang,    Sheng Wang, Jian Peng, Zhiyong Wang, HuiLu and Jinbo Xu. Template-based protein structure modeling using the RaptorX web server. Nature Protocols, 2012.
13. Jianzhu Ma, Jian Peng, Sheng Wang, and Jinbo Xu. A Conditional Neural Fields model for protein threading. Bioinformatics, 2012.
14. Sheng Wang, Jian Peng, and Jinbo Xu. Alignment of distantly-related protein structures: algorithm, bound and implications to homology modeling. Bioinformatics, 2011.

Education Profile

• ​Ph.D., Bioinformatics, Institute of Theoretical Physics, Chinese Academy of Sciences, China, 2010.
• B.Sc., Biotechnology, School of Life Sciences, Shanghai Jiao Tong University, China, 2005.

Professional Memberships

• 2017-now: Research Scientist, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia 2014-2016: Research.
• Professional, Department of Human Genetics, University of Chicago, Chicago, IL,2010-2014: Postdoctoral Research Fellow, Toyota.
• Technological Institute of Chicago, Chicago, IL, USA.
• ​International Society for Computational Biology (ISCB) Member.
• Biophysical Society (BPS) Member.

Awards and Distinctions

• ​In CASP12 2016, our team RaptorX-Contact was Officially Ranked First in contact prediction.
• In IJCAI BOOM 2016, I won the Best Poster Award for my work entitled AUC-maximized Deep Convolutional Neural Fields for Protein Sequence Labeling.
• In ISMB 3DSIG 2014, I won the Warren DeLano Award for Structural Bioinformatics and Computational Biophysics for our team work entitled MRFalign: protein homology detection through alignment of Markov Random Fields. 
• In RECOMB 2014, I won the Best Paper Award for our team work entitled MRFalign: Protein Homology Detection through Alignment of Markov Random Fields, which is implemented as a software MRFalign.
• In ISMB 3DSIG 2012, I won the Warren DeLano Award for Structural Bioinformatics and Computational Biophysics for my work entitled protein structure alignment beyond spatial proximity, which is implemented as a software DeepAlign.
• In BioInfoSummer 2007, I won the Hilary Booth Prize for Best Talk for my work entitled protein structure alignment based on conformational letters, which is implemented as CLEPAPS.