Publications (# corresponding author, * contribute equally)

2016

• 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
  Web Server
  

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

• CMsearch: Simultaneous Exploration of Protein Sequence Space and Structure Space Improves Not Only Protein Homology Detection But Also Protein Structure Prediction
  Xuefeng Cui, Zhiwu Lu, Sheng Wang, Jim Jing-Yan Wang, Xin Gao
  ISMB, 2016 (accepted)
  Bioinformatics, 2016 (accepted)
  

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

• Lynx: A Knowledge Base and an Analytical Workbench for Integrative Medicine
  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, Natalia Maltsev
  Nucleic Acids Research, 2016
  Web Server
  

2015

• 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)
  Software Download
  Supplemental Data
  

• 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)
  Software Download
  Supplemental Data
  

• Protein Homology Detection through Alignment of Markov Random Fields: using MRFalign
  Jianzhu Ma, Sheng Wang, Jinbo Xu
  SpringerBriefs in Computer Science, 2015
  

• Bermuda: De Novo Assembly of Transcripts with New Insights for Handling Uneven Coverage
  Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
  ACM-BCB, 2015
  

• Predicting Diverse M-best Protein Contact Maps
  Siqi Sun, Jianzhu Ma, Sheng Wang, Jinbo Xu
  BIBM, 2015
  

• Structure Learning Constrained by Node-Specific Degree Distribution
  Jianzhu Ma, Qingming Tang, Sheng Wang, Feng Zhao, Jinbo Xu
  UAI, 2015
  

2014

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

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

• An Integrative Computational Approach for Prioritization of Genomic Variants
  Inna Dubchak, Sandhya Balasubramanian, Sheng Wang, Cem Meyden, Dinanath Sulakhe, Alexander Poliakov, Daniela Bornigen, Bingqing Xie, Andrew Taylor, Jianzhu Ma, Alex Paciorkowski, Ghayda M Mirzaa, Paul Dave, Gady Agam, Jinbo Xu, Lihadh Al-Gazali, Christopher E Mason, M Elizabeth Ross, Natalia Maltsev, T Conrad Gilliam
  PLOS ONE, 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
  Web Server
  

2013

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

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

• RaptorX Server: A Resource for Template-based Protein Structure Modeling
  Morten Kallberg, Gohar Margaryan, Sheng Wang, Jianzhu Ma, Jinbo Xu
  Methods in Molecular Biology, 2013
  Web Server
  

• Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling
  Jianzhu Ma, Jian Peng, Sheng Wang*, Jinbo Xu
  AISTATS, 2013
  

before 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
  Web Server
  

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

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

• Incorporating Ab Initio Energy into Threading Approaches for Protein Structure Prediction
  Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Cheng Li, Wei-Mou Zheng, Dongbo Bu
  BMC Bioinformatics, 2011
  

• Fast Multiple Alignment of Protein Structures Using Conformational Letter Blocks
  Sheng Wang, Wei-Mou Zheng
  Open Bioinformatics Journal, 2009
  Software Download
  

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