ClEPaps: Fast Pair Alignment of protein Structures Based on conformational Letters. - Sheng Wang 001; Wei-Mou Zheng (J. Bioinform. Comput. Biol., 2008)

Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. - Sheng Wang 001; Jian Peng 001; Jinbo Xu (Bioinform., 2011)

Incorporating Ab Initio energy into threading approaches for protein structure prediction. - Mingfu Shao; Sheng Wang 001; Chao Wang; Xiongying Yuan; Shuai Li; Wei-Mou Zheng; Dongbo Bu (BMC Bioinform., 2011)

A conditional neural fields model for protein threading. - Jianzhu Ma; Jian Peng 001; Sheng Wang 001; Jinbo Xu (Bioinform., 2012)

Estimating the Partition Function of Graphical Models Using Langevin Importance Sampling. - Jianzhu Ma; Jian Peng 001; Sheng Wang 001; Jinbo Xu (AISTATS, 2013)

Protein threading using context-specific alignment potential. - Jianzhu Ma; Sheng Wang 001; Feng Zhao; Jinbo Xu (Bioinform., 2013)

Protein contact prediction by joint evolutionary coupling analysis across multiple families. - Jianzhu Ma; Sheng Wang 001; Jinbo Xu (CoRR, 2013)

Lynx: a database and knowledge extraction engine for integrative medicine. - Dinanath Sulakhe; Sandhya Balasubramanian; Bingqing Xie; Bo Feng; Andrew Taylor; Sheng Wang 001; Eduardo Berrocal; Utpal J. Dave; Jinbo Xu; Daniela Börnigen; T. Conrad Gilliam; Natalia Maltsev (Nucleic Acids Res., 2014)

MRFalign: Protein Homology Detection through Alignment of Markov Random Fields. - Jianzhu Ma; Sheng Wang 001; Zhiyong Wang 005; Jinbo Xu (PLoS Comput. Biol., 2014)

Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. - Qingming Tang; Sheng Wang 001; Jian Peng 001; Jianzhu Ma; Jinbo Xu (BCB, 2015)

Predicting diverse M-best protein contact maps. - Siqi Sun; Jianzhu Ma; Sheng Wang 001; Jinbo Xu (BIBM, 2015)

Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning. - Jianzhu Ma; Sheng Wang 001; Zhiyong Wang 005; Jinbo Xu (Bioinform., 2015)

Exploiting ontology graph for predicting sparsely annotated gene function. - Sheng Wang 001; Hyunghoon Cho; ChengXiang Zhai; Bonnie Berger; Jian Peng 001 (Bioinform., 2015)

Protein secondary structure prediction using deep convolutional neural fields. - Sheng Wang 001; Jian Peng 001; Jianzhu Ma; Jinbo Xu (CoRR, 2015)

AUC-maximized Deep Convolutional Neural Fields for Sequence Labeling. - Sheng Wang 001; Siqi Sun; Jinbo Xu (CoRR, 2015)

Protein Homology Detection Through Alignment of Markov Random Fields - Using MRFalign - Jinbo Xu; Sheng Wang 001; Jianzhu Ma (Springer, 2015)

Subtype Cell Detection with an Accelerated Deep Convolution Neural Network. - Sheng Wang 001; Jiawen Yao; Zheng Xu 005; Junzhou Huang (MICCAI (2), 2016)

Imaging Biomarker Discovery for Lung Cancer Survival Prediction. - Jiawen Yao; Sheng Wang 001; Xinliang Zhu; Junzhou Huang (MICCAI (2), 2016)

AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling. - Sheng Wang 001; Siqi Sun; Jinbo Xu (ECML/PKDD (2), 2016)

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 001; Sheng Wang 001; Jim Jing-Yan Wang; Xin Gao 001 (Bioinform., 2016)

AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. - Sheng Wang 001; Jianzhu Ma; Jinbo Xu (Bioinform., 2016)

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 001; T. Conrad Gilliam; et al. (Nucleic Acids Res., 2016)

RaptorX-Property: a web server for protein structure property prediction. - Sheng Wang 001; Wei Li; Shiwang Liu; Jinbo Xu (Nucleic Acids Res., 2016)

CoinFold: a web server for protein contact prediction and contact-assisted protein folding. - Sheng Wang 001; Wei Li; Renyu Zhang; Shiwang Liu; Jinbo Xu (Nucleic Acids Res., 2016)

Seq2seq Fingerprint: An Unsupervised Deep Molecular Embedding for Drug Discovery. - Zheng Xu 005; Sheng Wang 001; Feiyun Zhu; Junzhou Huang (BCB, 2017)

Deep learning based multi-label classification for surgical tool presence detection in laparoscopic videos. - Sheng Wang 001; Ashwin Raju; Junzhou Huang (ISBI, 2017)

ProSNet: integrating homology with molecular networks for protein function prediction. - Sheng Wang 001; Meng Qu; Jian Peng 001 (PSB, 2017)

Folding Membrane Proteins by Deep Transfer Learning. - Zhen Li 026; Sheng Wang 001; Yizhou Yu; Jinbo Xu (RECOMB, 2017)

DeepBound: accurate identification of transcript boundaries via deep convolutional neural fields. - Mingfu Shao; Jianzhu Ma; Sheng Wang 001 (Bioinform., 2017)

Predicting membrane protein contacts from non-membrane proteins by deep transfer learning. - Zhen Li 026; Sheng Wang 001; Yizhou Yu; Jinbo Xu (CoRR, 2017)

Robust Contextual Bandit via the Capped-$ ell_{2}$ norm. - Feiyun Zhu; Xinliang Zhu; Sheng Wang 001; Jiawen Yao; Junzhou Huang (CoRR, 2017)

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model. - Sheng Wang 001; Siqi Sun; Zhen Li 026; Renyu Zhang; Jinbo Xu (PLoS Comput. Biol., 2017)

Network-assisted target identification for haploinsufficiency and homozygous profiling screens. - Sheng Wang 001; Jian Peng 001 (PLoS Comput. Biol., 2017)

Adaptive Graph Convolutional Neural Networks. - Ruoyu Li 002; Sheng Wang 001; Feiyun Zhu; Junzhou Huang (AAAI, 2018)

Seq3seq Fingerprint: Towards End-to-end Semi-supervised Deep Drug Discovery. - Xiaoyu Zhang; Sheng Wang 001; Feiyun Zhu; Zheng Xu 005; Yuhong Wang; Junzhou Huang (BCB, 2018)

Robust Contextual Bandit via the Capped- ℓ _2 ℓ 2 Norm for Mobile Health Intervention. - Feiyun Zhu; Xinliang Zhu; Sheng Wang 001; Jiawen Yao; Zhichun Xiao; Junzhou Huang (MLMI@MICCAI, 2018)

Large-scale integration of heterogeneous pharmacogenomic data for identifying drug mechanism of action. - Yunan Luo; Sheng Wang 001; Jinfeng Xiao; Jian Peng 001 (PSB, 2018)

Annotating gene sets by mining large literature collections with protein networks. - Sheng Wang 001; Jianzhu Ma; Michael Ku Yu; Fan Zheng; Edward W. Huang; Jiawei Han 001; Jian Peng 001; Trey Ideker (PSB, 2018)

Deep Learning Reveals Many More Inter-protein Residue-Residue Contacts than Direct Coupling Analysis. - Tianming Zhou; Sheng Wang 001; Jinbo Xu (RECOMB, 2018)

An accurate and rapid continuous wavelet dynamic time warping algorithm for end-to-end mapping in ultra-long nanopore sequencing. - Renmin Han; Yu Li 006; Xin Gao 001; Sheng Wang 001 (Bioinform., 2018)

DeepSimulator: a deep simulator for Nanopore sequencing. - Yu Li 006; Renmin Han; Chongwei Bi; Mo Li 005; Sheng Wang 001; Xin Gao 001 (Bioinform., 2018)

DEEPre: sequence-based enzyme EC number prediction by deep learning. - Yu Li 006; Sheng Wang 001; Ramzan Umarov; Bingqing Xie; Ming Fan 003; Lihua Li 002; Xin Gao 001 (Bioinform., 2018)

Protein threading using residue co-variation and deep learning. - Jianwei Zhu; Sheng Wang 001; Dongbo Bu; Jinbo Xu (Bioinform., 2018)

RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. - Yujuan Gao; Sheng Wang 001; Minghua Deng; Jinbo Xu (BMC Bioinform., 2018)

ComplexContact: a web server for inter-protein contact prediction using deep learning. - Hong Zeng; Sheng Wang 001; Tianming Zhou; Feifeng Zhao; Xiufeng Li; Qing Wu; Jinbo Xu (Nucleic Acids Res., 2018)

PRIM: An Efficient Preconditioning Iterative Reweighted Least Squares Method for Parallel Brain MRI Reconstruction. - Zheng Xu 005; Sheng Wang 001; Yeqing Li; Feiyun Zhu; Junzhou Huang (Neuroinformatics, 2018)

WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets. - Sheng Wang 001; Zhen Li 026; Yizhou Yu; Xin Gao 001 (Quant. Biol., 2018)

Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers. - Zhen Li 026; Chongming Ni; Jinbo Xu; Xin Gao 001; Shuguang Cui; Sheng Wang 001 (BCB, 2019)

SMILES-BERT: Large Scale Unsupervised Pre-Training for Molecular Property Prediction. - Sheng Wang 001; Yuzhi Guo; Yuhong Wang; Hongmao Sun; Junzhou Huang (BCB, 2019)

Graph Convolutional Nets for Tool Presence Detection in Surgical Videos. - Sheng Wang 001; Zheng Xu 005; Chaochao Yan; Junzhou Huang (IPMI, 2019)

Exploring the functional impact of alternative splicing on human protein isoforms using available annotation sources. - Dinanath Sulakhe; Mark D'Souza; Sheng Wang 001; Sandhya Balasubramanian; Prashanth Athri; Bingqing Xie; Stefan Canzar; Gady Agam; T. Conrad Gilliam; Natalia Maltsev (Briefings Bioinform., 2019)

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 F. Lawrence; Peng Yang 010; Yu Li 006; Sheng Wang 001; Fei Sun; Zhiyong Liu 002; Xin Gao 001; Fa Zhang 001 (Bioinform., 2019)

PredMP: a web server for de novo prediction and visualization of membrane proteins. - Sheng Wang 001; Shiyang Fei; Zongan Wang; Yu Li 006; Jinbo Xu; Feng Zhao; Xin Gao 001 (Bioinform., 2019)

Identification of pathways associated with chemosensitivity through network embedding. - Sheng Wang 001; Edward W. Huang; Junmei Cairns; Jian Peng 001; Liewei Wang; Saurabh Sinha (PLoS Comput. Biol., 2019)

Re-balancing Variational Autoencoder Loss for Molecule Sequence Generation. - Chaochao Yan; Sheng Wang 001; Jinyu Yang; Tingyang Xu; Junzhou Huang (BCB, 2020)

Protein Ensemble Learning with Atrous Spatial Pyramid Networks for Secondary Structure Prediction. - Yuzhi Guo; Jiaxiang Wu 001; Hehuan Ma; Sheng Wang 001; Junzhou Huang (BIBM, 2020)

Improving Molecular Property Prediction on Limited Data with Deep Multi-Label Learning. - Hehuan Ma; Chaochao Yan; Yuzhi Guo; Sheng Wang 001; Yuhong Wang; Hongmao Sun; Junzhou Huang (BIBM, 2020)

PointASNL: Robust Point Clouds Processing Using Nonlocal Neural Networks With Adaptive Sampling. - Xu Yan 005; Chaoda Zheng; Zhen Li 026; Sheng Wang 001; Shuguang Cui (CVPR, 2020)

Label-Driven Reconstruction for Domain Adaptation in Semantic Segmentation. - Jinyu Yang; Weizhi An; Sheng Wang 001; Xinliang Zhu; Chaochao Yan; Junzhou Huang (ECCV (27), 2020)

An Efficient Hybrid Model for Kidney Tumor Segmentation in CT Images. - Xu Yan 005; Kun Yuan 004; Weibing Zhao; Sheng Wang 001; Zhen Li 026; Shuguang Cui (ISBI, 2020)

Characterizing Label Errors: Confident Learning for Noisy-Labeled Image Segmentation. - Minqing Zhang; Jiantao Gao; Zhen Lyu; Weibing Zhao; Qin Wang 011; Weizhen Ding; Sheng Wang 001; Zhen Li 026; Shuguang Cui (MICCAI (1), 2020)

Bagging MSA Learning: Enhancing Low-Quality PSSM with Deep Learning for Accurate Protein Structure Property Prediction. - Yuzhi Guo; Jiaxiang Wu 001; Hehuan Ma; Sheng Wang 001; Junzhou Huang (RECOMB, 2020)

DeepSimulator1.5: a more powerful, quicker and lighter simulator for Nanopore sequencing. - Yu Li 006; Sheng Wang 001; Chongwei Bi; Zhaowen Qiu; Mo Li 005; Xin Gao 001 (Bioinform., 2020)

Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing. - Renmin Han; Sheng Wang 001; Xin Gao 001 (Bioinform., 2020)

A Web-Based Protocol for Interprotein Contact Prediction by Deep Learning. - Xiaoyang Jing; Hong Zeng; Sheng Wang 001; Jinbo Xu (Protein-Protein Interaction Networks, 2020)

PSSM-Distil: Protein Secondary Structure Prediction (PSSP) on Low-Quality PSSM by Knowledge Distillation with Contrastive Learning. - Qin Wang 011; Boyuan Wang; Zhenlei Xu; Jiaxiang Wu 001; Peilin Zhao; Zhen Li 026; Sheng Wang 001; Junzhou Huang; Shuguang Cui (AAAI, 2021)

Shallow Feature Matters for Weakly Supervised Object Localization. - Jun Wei 006; Qin Wang 011; Zhen Li 026; Sheng Wang 001; S. Kevin Zhou; Shuguang Cui (CVPR, 2021)

InstanceRefer: Cooperative Holistic Understanding for Visual Grounding on Point Clouds through Instance Multi-level Contextual Referring. - Zhihao Yuan; Xu Yan 005; Yinghong Liao; Ruimao Zhang; Sheng Wang 001; Zhen Li 026; Shuguang Cui (ICCV, 2021)

Adaptive Residue-wise Profile Fusion for Low Homologous Protein Secondary Structure Prediction Using External Knowledge. - Qin Wang 011; Jun Wei 006; Boyuan Wang; Zhen Li 026; Sheng Wang 001; Shuguang Cui (IJCAI, 2021)

tFold-TR: Combining Deep Learning Enhanced Hybrid Potential Energy for Template-Based Modelling Structure Refinement. - Liangzhen Zheng; Haidong Lan; Tao Shen; Jiaxiang Wu 001; Sheng Wang 001; Wei Liu 005; Junzhou Huang (CoRR, 2021)

EBM-Fold: Fully-Differentiable Protein Folding Powered by Energy-based Models. - Jiaxiang Wu 001; Shitong Luo; Tao Shen; Haidong Lan; Sheng Wang 001; Junzhou Huang (CoRR, 2021)

Adaptive Residue-wise Profile Fusion for Low Homologous Protein SecondaryStructure Prediction Using External Knowledge. - Qin Wang 011; Jun Wei 006; Boyuan Wang; Zhen Li 026; Sheng Wang 001; Shuguang Cui (CoRR, 2021)

Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning. - Yuzhi Guo; Jiaxiang Wu 001; Hehuan Ma; Sheng Wang 001; Junzhou Huang (J. Comput. Biol., 2021)

EPTool: A New Enhancing PSSM Tool for Protein Secondary Structure Prediction. - Yuzhi Guo; Jiaxiang Wu 001; Hehuan Ma; Sheng Wang 001; Junzhou Huang (J. Comput. Biol., 2021)

Contact-Distil: Boosting Low Homologous Protein Contact Map Prediction by Self-Supervised Distillation. - Qin Wang 011; Jiayang Chen; Yuzhe Zhou; Yu Li 006; Liangzhen Zheng; Sheng Wang 001; Zhen Li 026; Shuguang Cui (AAAI, 2022)

Weakly Supervised Object Localization Through Inter-class Feature Similarity and Intra-class Appearance Consistency. - Jun Wei 006; Sheng Wang 001; S. Kevin Zhou; Shuguang Cui; Zhen Li 026 (ECCV (30), 2022)

Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures. - Shitong Luo; Yufeng Su; Xingang Peng; Sheng Wang 001; Jian Peng 001; Jianzhu Ma (NeurIPS, 2022)

Prior knowledge facilitates low homologous protein secondary structure prediction with DSM distillation. - Qin Wang 011; Jun Wei 006; Yuzhe Zhou; Mingzhi Lin; Ruobing Ren; Sheng Wang 001; Shuguang Cui; Zhen Li 026 (Bioinform., 2022)

PointSite: A Point Cloud Segmentation Tool for Identification of Protein Ligand Binding Atoms. - Xu Yan 005; Yingfeng Lu; Zhen Li 026; Qing Wei; Xin Gao 001; Sheng Wang 001; Song Wu; Shuguang Cui (J. Chem. Inf. Model., 2022)

Molecule Sequence Generation with Rebalanced Variational Autoencoder Loss. - Chaochao Yan; Jinyu Yang; Hehuan Ma; Sheng Wang 001; Junzhou Huang (J. Comput. Biol., 2023)

A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function. - Zechen Wang; Liangzhen Zheng; Sheng Wang 001; Mingzhi Lin; Zhihao Wang; Adams Wai-Kin Kong; Yuguang Mu; Yanjie Wei; Weifeng Li (Briefings Bioinform., 2023)

A physics-informed convolutional neural network for the simulation and prediction of two-phase Darcy flows in heterogeneous porous media. - Zhao Zhang 006; Xia Yan; Piyang Liu; Kai Zhang; Renmin Han; Sheng Wang 001 (J. Comput. Phys., 2023)

A new paradigm for applying deep learning to protein-ligand interaction prediction. - Zechen Wang; Sheng Wang 001; Yangyang Li; Jingjing Guo; Yanjie Wei; Yuguang Mu; Liangzhen Zheng; Weifeng Li (Briefings Bioinform., 2024)

Atom-ProteinQA: Atom-level protein model quality assessment through fine-grained joint learning. - Yatong Han; Yingfeng Lu; Xu Yan 005; Hannah Cui; Shenghui Cheng; Jiayou Zheng; Yuzhe Zhou; Sheng Wang 001; Zhen Li 026 (Comput. Methods Programs Biomed., 2024)

Hotspot-Driven Peptide Design via Multi-Fragment Autoregressive Extension. - Jiahan Li; Tong Chen; Shitong Luo; Chaoran Cheng; Jiaqi Guan; Ruihan Guo; Sheng Wang 001; Ge Liu; Jian Peng 001; Jianzhu Ma (CoRR, 2024)

Group Ligands Docking to Protein Pockets. - Jiaqi Guan; Jiahan Li; Xiangxin Zhou; Xingang Peng; Sheng Wang 001; Yunan Luo; Jian Peng 001; Jianzhu Ma (ICLR, 2025)