Sheng Wang, PhD

Research Fellow Toyota Technological Institute at Chicago Research Professional Department of Human Genetics, University of Chicago Email: wangsheng <at> ttic <dot> edu wangsheng <at> uchicago <dot> edu

Short Biography

• Currently, I am a joint research scientist at Department of Human Genetics in University of Chicago, and Toyota Technological Institute at Chicago. I obtained my Ph.D. under the supervision of Wei-Mou Zheng from Institute of Theoretical Physics, Chinese Academy of Sciences. I got my Bachelor degree in School of Life Sciences and Biotechnology, Shanghai Jiao Tong University.
  

• My research interest lies in protein-related computational biology and bioinformatics. In particular, I apply statistics and machine learning algorithms to study the protein sequence/structure alignment, protein homology search and protein structure prediction. My current research interests are also focused on structure-based computational immunology and system biology.
  

• Please view my full publications and citations at Google Scholar. Please review my codes at GitHub.
  

Selected Publications (# corresponding author, * contribute equally)

• CoinFold: a Web Server for Protein Contact Prediction and Contact-assisted Protein Folding
  Sheng Wang#, Wei Li, Renyu Zhang, Shiwang Liu, Jinbo Xu
  Nucleic Acids Research, 2016
  

• RaptorX-Property: a Web Server for Protein Structure Property Prediction
  Sheng Wang#, Wei Li, Shiwang Liu, Jinbo Xu
  Nucleic Acids Research, 2016
  

• Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields
  Sheng Wang#, Jian Peng, Jianzhu Ma, Jinbo Xu
  Scientific Reports, 2016
  

• Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning
  Jianzhu Ma, Sheng Wang*, Zhiyong Wang, Jinbo Xu
  RECOMB, 2015
  Bioinformatics, 2015
  

• DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields
  Sheng Wang#, Shunyan Weng, Jianzhu Ma, Qingming Tang
  International Journal of Molecular Sciences, 2015 (invited)
  

• AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multi-Task Learning Framework under the Conditional Neural Fields Model
  Jianzhu Ma, Sheng Wang#
  BioMed Research International, 2015 (invited)
  

• Algorithms, Applications and Challenges of Protein Structure Alignment
  Jianzhu Ma, Sheng Wang#
  Advances in Protein Chemistry and Structural Biology, 2014 (invited)
  

• MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
  Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
  RECOMB, 2014
  PLOS Computational Biology, 2014
  

• Lynx: a Database and Knowledge Extraction Engine for Integrative Medicine
  Dinanath Sulakhe, Sandhya Balasubramanian, Bingqing Xie, Bo Feng, Andrew Taylor, Sheng Wang, Eduardo Berrocal, Utpal Dave, Jinbo Xu, Daniela Bornigen, T. Conrad Gilliam, Natalia Maltsev
  Nucleic Acids Research, 2014
  

• Protein Structure Alignment beyond Spatial Proximity
  Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
  Scientific Reports, 2013
  

• Protein Threading Using Context-Specific Alignment Potential
  Jianzhu Ma, Sheng Wang, Jinbo Xu
  ISMB, 2013
  Bioinformatics, 2013
  

• Template-based Protein Structure Modeling using the RaptorX Web Server
  Morten Kallberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu, Jinbo Xu
  Nature Protocols, 2012
  

• A Conditional Neural Fields Model for Protein Threading
  Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
  ISMB, 2012
  Bioinformatics, 2012
  

• Alignment of Distantly-related Protein Structures: Algorithm, Bound and Implications to Homology Modeling
  Sheng Wang, Jian Peng, Jinbo Xu
  Bioinformatics, 2011
  

• CLEPAPS: Fast Pair Alignment of Protein Structures based on Conformational Letters
  Sheng Wang, Wei-Mou Zheng
  Journal of Bioinformatics and Computational Biology, 2008
  

Research Highlights

• Oral presentation on Research in Computational Molecular Biology (RECOMB), 2015.
  

• Oral presentation on Research in Computational Molecular Biology (RECOMB), 2014.
  

• Oral presentation on Artificial Intelligence and Statistics (AISTAT), 2013.
  

• Oral presentation on Intelligent Systems for Molecular Biology (ISMB), 2013.
  

• Oral presentation on Intelligent Systems for Molecular Biology (ISMB), 2012.
  

• Our server RaptorX attends a Protein Strcuture Prediction Marathon: CAMEO.
  

• Check our performance of structure prediction
  

Awards

• In ISMB 3DSIG 2014, I won the Warren DeLano Award for our team work MRFalign.
  

• In RECOMB 2014, I won the Best Paper Award for our team work entitled MRFalign.
  

• In ISMB 3DSIG 2012, I won the Warren DeLano Award for my work DeepAlign.
  

• In BioInfoSummer07, I won the Hilary Booth Prize for Best talk for my work CLEPAPS.