Sheng Wang, PhD

Research Scientist King Abdullah University of Science and Technology (KAUST) Email: wangsheng <at> ttic <dot> edu realbigws <at> gmail <dot> com Curriculum Vitae: Full version Sketch version

Recent News

• A new server, PredMP, for de novo prediction and visualization of membrane proteins has been accepted by Bioinformatics. Congratulations to Shiyang Fei and Zongan Wang.

• A new algorithm, continuous wavelet Dynamic Time Warping (cwDTW), for end-to-end mapping in ultra-long nanopore sequencing has been accepted for presentation at ECCB 2018. Congratulations to Renmin Han.

• Our Research Article "Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model" has been selected as the winner of the PLOS Computational Biology Research Prize 2018 in the category Breakthrough in Advance. Each year only one paper receives this prize.

• A Web Server for inter-protein contact prediction using deep learning has been accepted by Nucleic Acids Research. Congratulations to Tian-ming Zhou.

• A deep simulator for Nanopore sequencing has been accepted by Bioinformatics. Congratulations to Yu Li.

• Our paper on protein contact map prediction by Ultra-Deep Learning model was awarded 'Highly Cited Paper' by WEB OF SCIENCE.

• Our team work DeepThreader has been accepted by ISMB 2018.

• Our work RaptorX-Angle won the Best Paper Award in APBC 2018.

• Our work on the protein interfacial contact prediction has been accepted by RECOMB 2018.

• Our paper on the salt-bridge competition triggered by phosphorylation has been accepted by PNAS.

• We were invited to write the CASP 2016 special issue paper for PROTEINS journal.

• Our paper on folding membrane proteins by deep transfer learning has been accepted by Cell Systems and RECOMB 2017.

• A Deep Learning approach for identification of transcript boundaries from RNA-seq has been accepted by ISMB 2017.

• Our RaptorX-Contact ranked 1st in contact prediction in the worldwide protein structure prediction (CASP) round XII (2016).

• Our RaptorX Server was reported in Science magazine.

Short Biography

• I'm now a Research Scientist at King Abdullah University of Science and Technology (KAUST). Previously, I was a joint Research Professional 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 the pipeline that initiates from machine learning models to computational biology algorithms and terminates at applications in biological problems. Specifically, my research interests focus on the data analysis and interpretation with respect to DNA, RNA, and protein. In the past years, I have devoted myself to studying models and algorithms for learning from big and imbalanced data, which are then applied for predicting protein structure and function. My current research interests are also focused on machine-learning-based next generation sequencing and structure-based protein function analysis.
  

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

Selected Top15 Publications (# corresponding author, * co-first author)

• 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
  

• 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
  

• 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
  

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

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

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

• AUC-maximized Deep Convolutional Neural Fields for Protein Sequence Labeling
  Sheng Wang, Siqi Sun, Jinbo Xu#
  ECML/PKDD, 2016
  

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

• 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
  

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

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

Research Highlights

• Oral presentation on Rocky Mountain Bioinformatics Conference (Rocky), 2016.
  

• Oral presentation on European Conference on Computational Biology (ECCB), 2016.
  

• Oral presentation on European Conference on Machine Learning (ECML), 2016.
  

• Oral presentation on Workshop on Biomedical infOrmatics with Optimization and Machine learning (BOOM) of International Joint Conference on Artificial Intelligence (IJCAI), 2016.
  

• 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 APBC 2018, I won the Best Paper Award for our team work entitled RaptorX-Angle.
  

• In the year 2017, I was selected as Top10 reviewers for the journal Molecular Biosystems.
  

• In CASP12 2016, our team RaptorX-Contact was officially ranked 1st in contact prediction.
  

• In IJCAI BOOM 2016, I won the Best Poster Award for my work DeepCNF-AUC.
  

• 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.