Sheng Wang

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 32

Top Topics

Sequence Labeling

Protein Structure

Top Venues

Nucleic Acids Res.

Publications

Zechen Wang, Sheng Wang, Yangyang Li, Jingjing Guo, Yanjie Wei, Yuguang Mu, Liangzhen Zheng, Weifeng Li
A new paradigm for applying deep learning to protein-ligand interaction prediction. Briefings Bioinform. 25 (3) (2024)
Yatong Han, Yingfeng Lu, Xu Yan, Hannah Cui, Shenghui Cheng, Jiayou Zheng, Yuzhe Zhou, Sheng Wang, Zhen Li
Atom-ProteinQA: Atom-level protein model quality assessment through fine-grained joint learning. Comput. Methods Programs Biomed. 249 (2024)
Ruiyi Zhang, Yunan Luo, Jianzhu Ma, Ming Zhang, Sheng Wang
scPretrain: multi-task self-supervised learning for cell-type classification. Bioinform. 38 (6) (2022)
Xu Yan, Yingfeng Lu, Zhen Li, Qing Wei, Xin Gao, Sheng Wang, Song Wu, Shuguang Cui
PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms. J. Chem. Inf. Model. 62 (11) (2022)
Zhihao Yuan, Xu Yan, Yinghong Liao, Ruimao Zhang, Sheng Wang, Zhen Li, Shuguang Cui
InstanceRefer: Cooperative Holistic Understanding for Visual Grounding on Point Clouds through Instance Multi-level Contextual Referring. ICCV (2021)
Yu Li, Sheng Wang, Chongwei Bi, Zhaowen Qiu, Mo Li, Xin Gao
DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing. Bioinform. 36 (8) (2020)
Renmin Han, Sheng Wang, Xin Gao
Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing. Bioinform. 36 (5) (2020)
Sheng Wang, Shiyang Fei, Zongan Wang, Yu Li, Jinbo Xu, Feng Zhao, Xin Gao
PredMP: a web server for de novo prediction and visualization of membrane proteins. Bioinform. 35 (4) (2019)
Zhen Li, Chongming Ni, Jinbo Xu, Xin Gao, Shuguang Cui, Sheng Wang
Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers. BCB (2019)
Dinanath Sulakhe, Mark D'Souza, Sheng Wang, Sandhya Balasubramanian, Prashanth Athri, Bingqing Xie, Stefan Canzar, Gady Agam, T. Conrad Gilliam, Natalia Maltsev
Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. Briefings Bioinform. 20 (5) (2019)
Zhen Li, Chongming Ni, Jinbo Xu, Xin Gao, Shuguang Cui, Sheng Wang
Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers. BCB (2019)
Renmin Han, Xiaohua Wan, Lun Li, Albert F. Lawrence, Peng Yang, Yu Li, Sheng Wang, Fei Sun, Zhiyong Liu, Xin Gao, Fa Zhang
AuTom-dualx: a toolkit for fully automatic fiducial marker-based alignment of dual-axis tilt series with simultaneous reconstruction. Bioinform. 35 (2) (2019)
Yu Li, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, Xin Gao
DeepSimulator: a deep simulator for Nanopore sequencing. Bioinform. 34 (17) (2018)
Hong Zeng, Sheng Wang, Tian-Ming Zhou, Feifeng Zhao, Xiufeng Li, Qing Wu, Jinbo Xu
ComplexContact: a web server for inter-protein contact prediction using deep learning. Nucleic Acids Res. 46 (Webserver-Issue) (2018)
Sheng Wang, Zhen Li, Yizhou Yu, Xin Gao
WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets. Quant. Biol. 6 (4) (2018)
Tian-Ming Zhou, Sheng Wang, Jinbo Xu
Deep Learning Reveals Many More Inter-protein Residue-Residue Contacts than Direct Coupling Analysis. RECOMB (2018)
Renmin Han, Yu Li, Xin Gao, Sheng Wang
An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing. Bioinform. 34 (17) (2018)
Jianwei Zhu, Sheng Wang, Dongbo Bu, Jinbo Xu
Protein threading using residue co-variation and deep learning. Bioinform. 34 (13) (2018)
Yu Li, Sheng Wang, Ramzan Umarov, Bingqing Xie, Ming Fan, Lihua Li, Xin Gao
DEEPre: sequence-based enzyme EC number prediction by deep learning. Bioinform. 34 (5) (2018)
Yujuan Gao, Sheng Wang, Minghua Deng, Jinbo Xu
RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. BMC Bioinform. (4) (2018)
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. PLoS Comput. Biol. 13 (1) (2017)
Sheng Wang, Zhen Li, Yizhou Yu, Jinbo Xu
Folding membrane proteins by deep transfer learning. CoRR (2017)
Zhen Li, Sheng Wang, Yizhou Yu, Jinbo Xu
Predicting membrane protein contacts from non-membrane proteins by deep transfer learning. CoRR (2017)
Zhen Li, Sheng Wang, Yizhou Yu, Jinbo Xu
Folding Membrane Proteins by Deep Transfer Learning. RECOMB (2017)
Mingfu Shao, Jianzhu Ma, Sheng Wang
DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. Bioinform. 33 (14) (2017)
Xuefeng Cui, Zhiwu Lu, Sheng Wang, Jim Jing-Yan Wang, Xin Gao
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. Bioinform. 32 (12) (2016)
Sheng Wang, Wei Li, Renyu Zhang, Shiwang Liu, Jinbo Xu
CoinFold: a web server for protein contact prediction and contact-assisted protein folding. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Sheng Wang, Wei Li, Shiwang Liu, Jinbo Xu
RaptorX-Property: a web server for protein structure property prediction. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
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
Lynx: a knowledge base and an analytical workbench for integrative medicine. Nucleic Acids Res. 44 (Database-Issue) (2016)
Sheng Wang, Jianzhu Ma, Jinbo Xu
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. Bioinform. 32 (17) (2016)
Sheng Wang, Siqi Sun, Jinbo Xu
AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling. ECML/PKDD (2) (2016)
Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang, Jinbo Xu
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. CoRR (2016)
Qingming Tang, Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. BCB (2015)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. Bioinform. 31 (21) (2015)
Sheng Wang, Siqi Sun, Jinbo Xu
AUC-maximized Deep Convolutional Neural Fields for Sequence Labeling. CoRR (2015)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
Protein Contact Prediction by Integrating Joint Evolutionary Coupling Analysis and Supervised Learning. RECOMB (2015)
Siqi Sun, Jianzhu Ma, Sheng Wang, Jinbo Xu
Predicting diverse M-best protein contact maps. BIBM (2015)
Sheng Wang, Jian Peng, Jianzhu Ma, Jinbo Xu
Protein secondary structure prediction using deep convolutional neural fields. CoRR (2015)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. RECOMB (2014)
Dinanath Sulakhe, Sandhya Balasubramanian, Bingqing Xie, Bo Feng, Andrew Taylor, Sheng Wang, Eduardo Berrocal, Utpal J. Dave, Jinbo Xu, Daniela Börnigen, T. Conrad Gilliam, Natalia Maltsev
Lynx: a database and knowledge extraction engine for integrative medicine. Nucleic Acids Res. 42 (Database-Issue) (2014)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. PLoS Comput. Biol. 10 (3) (2014)
Jianzhu Ma, Sheng Wang, Zhiyong Wang, Jinbo Xu
MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. CoRR (2014)
Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling. AISTATS (2013)
Jianzhu Ma, Sheng Wang, Feng Zhao, Jinbo Xu
Protein threading using context-specific alignment potential. Bioinform. 29 (13) (2013)
Jianzhu Ma, Sheng Wang, Jinbo Xu
Protein contact prediction by joint evolutionary coupling analysis across multiple families. CoRR (2013)
Jianzhu Ma, Jian Peng, Sheng Wang, Jinbo Xu
A conditional neural fields model for protein threading. Bioinform. 28 (12) (2012)
Sheng Wang, Jian Peng, Jinbo Xu
Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Bioinform. 27 (18) (2011)
Mingfu Shao, Sheng Wang, Chao Wang, Xiongying Yuan, Shuai Li, Wei-Mou Zheng, Dongbo Bu
Incorporating Ab Initio energy into threading approaches for protein structure prediction. BMC Bioinform. 12 (S-1) (2011)
Sheng Wang, Wei-Mou Zheng
ClEPaps: Fast Pair Alignment of protein Structures Based on conformational Letters. J. Bioinform. Comput. Biol. 6 (2) (2008)