Publications (# corresponding author, * co-first author)

2019

• Structures and mechanism of transcription initiation by bacterial ECF factors
  Chengli Fang*, Lingting Li*, Liqiang Shen, Jing Shi, Sheng Wang#, Yu Feng#, Yu Zhang#
  Nucleic Acids Research, 2019
  

• Efficient and accurate prediction of transmembrane topology from amino acid sequence only
  Qing Wang*, Chongming Ni*, Zhen Li*, Xiufeng Li, Renmin Han, Feng Zhao, Jinbo Xu, Xin Gao#, Sheng Wang#
  bioRxiv, 2019
  Web Server
  Source Code
  Dataset
  

• Analysis of distance-based protein structure prediction by deep learning in CASP13
  Jinbo Xu#, Sheng Wang
  bioRxiv, 2019
  

• RET S409Y Germline Mutation and Associated Medullary Thyroid Carcinoma
  Xiaoping Qi, Baiye Jin, Pengfei Li, Sheng Wang, Yihua Zhao, Zhilie Cao, Xiuhua Yu, Xudong Fang, Jianqiang Zhao#
  Thyroid, 2019
  

• Searching and mapping genomic subsequences in nanopore raw signals through novel dynamic time warping algorithms
  Renmin Han*, Sheng Wang#*, Xin Gao#
  bioRxiv, 2019
  

2018

• A membrane burial potential with H-bonds and applications to curved membranes and fast simulations
  Zongan Wang, John Jumper, Sheng Wang, Karl Freed#, Tobin Sosnick#
  Biophysical Journal, 2018
  

• Marine microalgae bioengineered Schizochytrium sp. meal hydrolysates inhibits acute inflammation
  Xiaoli Wang, Heng Wang, Joseph F. Pierre, Sheng Wang, Huifang Huang, Jun Zhang, Shuangzhen Liang, Qingzhu Zeng, Chenqing Zhang, Meijuan Huang, Chengxu Ruan, Juan Lin, Hao Li#
  Scientific Reports, 2018
  

• PredMP: a web server for de novo prediction and visualization of membrane proteins
  Sheng Wang#*, Shiyang Fei*, Zongan Wang*, Yu Li, Jinbo Xu, Feng Zhao#, Xin Gao#
  Bioinformatics, 2018
  Web Server
  

• AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction
  Renmin Han, Xiaohua Wan, Lun Li, Albert Lawrence, Peng Yang, Yu Li, Sheng Wang, Fei Sun, Zhiyong Liu, Xin Gao#, Fa Zhang#
  Bioinformatics, 2018
  

• ComplexContact: a web server for inter-protein contact prediction using deep learning
  Hong Zeng*, Sheng Wang*, Tianming Zhou*, Feifeng Zhao, Xiufeng Li, Qing Wu#, Jinbo Xu#
  Nucleic Acids Research, 2018
  Web Server
  

• Protein threading using residue co-variation and deep learning
  Jianwei Zhu, Sheng Wang, Dongbo Bu#, Jinbo Xu#
  ISMB, 2018
  Bioinformatics, 2018
  

• WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets
  Sheng Wang#*, Zhen Li*, Yizhou Yu, Xin Gao#
  Quantitative Biology, 2018 (invited)
  

• Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources
  Dinanath Sulakhe#*, Mark D'Souza*, Sheng Wang, Sandhya Balasubramanian, Prashanth Athri, Bingqing Xie, Stefan Canzar, Gady Agam, T. Conrad Gilliam, Natalia Maltsev#
  Briefings in Bioinformatics, 2018
  

• Chiron: Translating nanopore raw signal directly into nucleotide sequence using deep learning
  Haotian Teng#*, Minh Duc Cao*, Michael B Hall, Tania Duarte, Sheng Wang, Lachlan J M Coin#
  GigaScience, 2018
  Source Code
  

• PredMP: A Web Resource for Computationally Predicted Membrane Proteins via Deep Learning
  Sheng Wang#*, Shiyang Fei*, Zongan Wang*, Yu Li, Feng Zhao#, Xin Gao#
  Biophysical Journal, 2018 (poster)
  

• DeepSimulator: a deep simulator for Nanopore sequencing
  Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang#, Xin Gao#
  Bioinformatics, 2018
  Source Code
  

• An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing
  Renmin Han, Yu Li, Xin Gao#, Sheng Wang#
  ECCB, 2018
  Bioinformatics, 2018
  Source Code
  

• Deep learning reveals many more inter-protein residue-residue contacts than direct coupling analysis
  Tianming Zhou*, Sheng Wang#*, Jinbo Xu#
  RECOMB, 2018
  

• RaptorXAngle: real-value and confidence prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning
  Yujuan Gao, Sheng Wang, Minghua Deng#, Jinbo Xu#
  APBC, 2018 (Best Paper Award)
  BMC Bioinformatics, 2018
  

2017

• A conserved salt bridge theft triggered by phosphorylation regulates the protein interactome
  John J. Skinner*, Sheng Wang*, Ji-Young Lee, Colin Ong, Ruth F Sommese, Sivaraj Sivaramakrishnan, Wolfgang Koelmel, Maria Hirschbeck, Hermann Schindelin, Caroline Kisker, Kristina Lorenz, Tobin R. Sosnick#, Marsha R Rosner#
  Proceedings of the National Academy of Sciences of USA, 2017
  

• Folding membrane proteins by deep transfer learning
  Sheng Wang*, Zhen Li*, Yizhou Yu, Jinbo Xu#
  Cell Systems, 2017
  

• Analysis of deep learning methods for blind protein contact prediction in CASP12
  Sheng Wang, Siqi Sun, Jinbo Xu#
  Proteins, 2017 (1st in CASP12 contact prediction)
  

• DEEPre: sequence-based enzyme EC number prediction by deep learning
  Yu Li, Sheng Wang, Ramzan Umarov, Bingqing Xie, Xin Gao#
  Bioinformatics, 2017
  Web Server
  

• The functional domain for BaxDelta2 aggregate-mediated caspase8-dependent cell death.
  Adriana Manas, Sheng Wang, Adam Nelson, Jiajun Li, Yu Zhao, Huaiyuan Zhang, Aislinn Davis, Bingqing Xie, Natalia Maltsev, Jialing Xiang#
  Experimental Cell Research, 2017
  

• De Novo Protein Structure Prediction by Big Data and Deep Learning
  Sheng Wang, Jinbo Xu#
  Biophysical Journal, 2017 (poster)
  

• Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks
  Mark D'Souza#, Dinanath Sulakhe, Sheng Wang, Bingqing Xie, Somaye Hashemifar, Andrew Taylor, Inna Dubchak, T Conrad Gilliam, Natalia Maltsev#
  Biological Networks and Pathway Analysis, 2017
  

• Pro-death Bax Has an Intrinsic Capability to Induce Aggregate-dependent Caspase 8-mediated Cell Death
  Adriana Manas, Sheng Wang, Jiajun Li, Adam Nelson, Aislinn Davis, Sydney Lamerand, Huaiyuan Zhang, Jialing Xiang#
  The FASEB Journal, 2017 (abstract)
  

• Folding Membrane Proteins by Contacts Inferred from Non-Membrane Proteins and Near-Atomic Level Refinement
  Sheng Wang*, Zongan Wang*, John Jumper, Karl Freed, Tobin Sosnick, Jinbo Xu#
  Biophysical Journal, 2017 (poster)
  

• A Phospho-Induced Theft of a Salt Bridge in RKIP Links Map Kinase and G Protein-Mediated Signaling
  Tobin Sosnick, John Skinner, Sheng Wang, Jiyoung Lee, Ruth Sommese, Sivaraj Sivaramakrishnan, Wolfgang Koelmel, Maria Hirschbeck, Hermann Schindelin, Caroline Kisker, Kristina Lorenz, Marsha Rosner#
  Biophysical Journal, 2017 (poster)
  

• Extracellular vesicles in gastrointestinal cancer in conjunction with microbiota: on the border of Kingdoms
  Natasha Barteneva#, Yeldar Baiken, Elizaveta Fasler-Kan, Kennet Alibek, Sheng Wang, Natalia Maltsev, Eugene Ponomarev, Zarina Sautbayeva, Sholpan Kauanova, Anna Moore, Christoph Beglinger, Ivan Vorobjev
  BBA Reviews on Cancer, 2017
  

• DeepBound: Accurate Identification of Transcript Boundaries via Deep Convolutional Neural Fields
  Mingfu Shao*#, Jianzhu Ma*, Sheng Wang*#
  ISMB, 2017
  Bioinformatics, 2017
  Source Code
  

• Predicting Membrane Protein Contacts from Non-Membrane Proteins by Deep Transfer Learning
  Zhen Li*, Sheng Wang*, Yizhou Yu, Jinbo Xu#
  RECOMB, 2017
  

• Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
  Sheng Wang*, Siqi Sun*, Zhen Li, Renyu Zhang, Jinbo Xu#
  PLOS Computational Biology, 2017 (Highly Cited Paper by WEB OF SCIENCE)
  

2016

• AUC-maximized Deep Convolutional Neural Fields for Protein Sequence Labeling
  Sheng Wang, Siqi Sun, Jinbo Xu#
  ECML/PKDD, 2016 (Best Poster Award in IJCAI BOOM 2016)
  Source Code
  

• AUCpreD: Proteome-level Protein Disorder Prediction by AUC-maximized Deep Convolutional Neural Fields
  Sheng Wang#, Jianzhu Ma, Jinbo Xu#
  ECCB, 2016
  Bioinformatics, 2016
  Software Download
  

• 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
  Source Code
  

• 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
  Bioinformatics, 2016
  

• Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields
  Sheng Wang#, Jian Peng, Jianzhu Ma, Jinbo Xu#
  Scientific Reports, 2016 (Highly Cited Paper by WEB OF SCIENCE)
  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 (Best Paper Award)
  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 (Warren DeLano Award in ISMB 3Dsig 2012)
  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 (Highly Cited Paper by WEB OF SCIENCE)
  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 (Hilary Booth Prize in BioInfoSummer07)