基因组非编码区变异与转录因子调控关系的计算分析方法研究

61732012
2017
F0213.生物信息计算与数字健康
黄德双
重点项目
研究员
同济大学
270万元
序列特异性;深度学习;转录因子;基因组非编码区变异;结合位点
2018-01-01到2022-12-31
  • 中英文摘要
  • 结题摘要
  • 结题报告
  • 项目成果
  • 项目参与人
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序号 标题 类型 作者
1 Leaf Recognition Based on Capsule Network 会议论文 Yang Zheng
2 Person Reidentification by Multiscale Feature Representation Learning With Random Batch Feature Mask 期刊论文 Wu Yong;Zhang Kun;Wu Di;Wang Chao;Yuan Chang-An;Qin Xiao;Zhu Tao;Du Yu-Chuan;Wang Han-Li;Huang De-Shuang
3 DeepIDP-2L: protein intrinsically disordered region prediction by combining convolutional attention network and hierarchical attention network 期刊论文 Yi-Jun Tang;Yi-He Pang;Bin Liu
4 A Network-guided Association Mapping Approach from DNA Methylation to Disease 期刊论文 Yuan Lin;Huang De Shuang
5 iRO-3wPseKNC: identify DNA replication origins by three-window-based PseKNC 期刊论文 Liu Bin;Weng Fan;Huang De Shuang;Chou Kuo Chen
6 Discovery of Relationships Between Long Non-Coding RNAs and Genes in Human Diseases Based on Tensor Completion 期刊论文 Peng Chen;Zou Liang;Huang De-Shuang
7 A novel deep model with multi-loss and efficient training for person re-identification 期刊论文 Wu Di;Zheng Si Jia;Bao Wen Zheng;Zhang Xiao Ping;Yuan Chang An;Huang De Shuang
8 Fast sequence analysis based on diamond sampling 期刊论文 Gao Liangxin;Bao Wenzhen;Zhang Hongbo;Yuan Chang-An;Huang De-Shuang
9 Base-resolution prediction of transcription factor binding signals by a deep learning framework 期刊论文 Qinhu Zhang;Ying He;Siguo Wang;Zhanheng Chen;Zhenhao Guo;Zhen Cui;De-Shuang Huang
10 PL-search: a profile-link-based search method for protein remote homology detection 期刊论文 Jin Xiaopeng;Liao Qing;Liu Bin
11 Plant Leaf Recognition Network Based on Feature Learning and Metric Learning 会议论文 Hongwei Yang;Di Wu;Changan Yuan;Xiao Qin;Hongjie Wu;Xingming Zhao;Zhongqiu Zhao
12 Image co-segmentation via locally biased discriminative clustering 期刊论文 xianpeng liang;D.S Huang
13 A comprehensive review and evaluation of computational methods for identifying protein complexes from protein-protein interaction networks 期刊论文 Zhourun Wu;Qing Liao;Bin Liu
14 RMSCNN: A Random Multi-Scale Convolutional Neural Network for Marine Microbial Bacteriocins Identification 期刊论文 Zhen Cui;Zhan-Heng Chen;De-Shuang Huang;Valeriya Gribova;Filaretov Vladimir F;De-Shuang Huang
15 FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network 期刊论文 Shao Jiangyi;Yan Ke;Liu Bin
16 SelfAT-Fold: protein fold recognition based on residue-based and motif-based self-attention networks 期刊论文 Yi-He Pang;Bin Liu
17 Recurrent Neural Network for Predicting Transcription Factor Binding Sites 期刊论文 Shen Zhen;Bao Wenzheng;Huang De-Shuang
18 A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information 期刊论文 Yi Hai-Cheng;You Zhu-Hong;Huang De-Shuang;Li Xiao;Jiang Tong-Hai;Li Li-Ping
19 Drug–target interaction prediction based on graph neural network and recommendation system 会议论文 peng lei;changan yuan;hongjie wu;xingming zhao
20 Comprehensive evaluation of BERT model for DNA-language for prediction of DNA sequence binding specificities in fine-tuning phase 会议论文 Xianbao Tan;Changan Yuan;Changan Yuan;Xingming Zhao
21 Predicting in-Vitro Transcription Factor Binding Sites with Deep Embedding Convolution Network 会议论文 Yindong Zhang;Qinhu Zhang;Changan Yuan;Xiao Qin;Hongjie Wu;Xingming Zhao
22 BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models 期刊论文 Hong-Liang Li;Yi-He Pang;Bin Liu
23 Capsule Network for Predicting RNA-Protein Binding Preferences Using Hybrid Feature 期刊论文 Shen Zhen;Deng Su-Ping;Huang De-shuang
24 Locating transcription factor binding sites by fully convolutional neural network 期刊论文 Qinhu Zhang;Siguo Wang;Zhanheng Chen;Ying He;Qi Liu;De-Shuang Huang
25 Plant Leaf Recognition Based on Conditional Generative Adversarial Nets 会议论文 zhihao jiao
26 Improving Prediction of Self-interacting Proteins Using Stacked Sparse Auto-Encoder with PSSM profiles 期刊论文 Wang Yan-Bin;You Zhu-Hong;Li Li-Ping;Huang De-Shuang;Zhou Feng-Feng;Yang Shan
27 Integration of Multi-Omics Data for Gene Regulatory Network Inference and Application to Breast Cancer 期刊论文 Yuan Lin;Guo Le Hang;Yuan Chang An;Zhang Youhua;Han Kyungsook;Nandi Asoke K;Honig Barry;Huang De Shuang
28 DCDE: An Efficient Deep Convolutional Divergence Encoding Method for Human Promoter Recognition 期刊论文 Xu Wenxuan;Zhu Lin;Huang De Shuang
29 S2L-PSIBLAST: a supervised two-layer search framework based on PSI-BLAST for protein remote homology detection 期刊论文 Jin Xiaopeng;Liao Qing;Liu Bin
30 Omnidirectional Feature Learning for Person Re-Identification 期刊论文 Wu Di;Yang Hong Wei;Huang De Shuang;Yuan Chang An;Qin Xiao;Zhao Yang;Zhao Xin Yong;Sun Jian Hong
31 RNA-Protein Binding Sites Prediction via Multi Scale Convolutional Gated Recurrent Unit Networks 期刊论文 Zhen Shen;Su-Ping Deng;De-Shuang Huang
32 MSCHLMDA: Multi-Similarity Based Combinative Hypergraph Learning for Predicting MiRNA-Disease Association 期刊论文 Qingwen Wu;Yutian Wang;Zhen Gao;Jiancheng Ni;Chunhou Zheng
33 Attention Deep Model With Multi-Scale Deep Supervision for Person Re-Identification 期刊论文 Di Wu;Chao Wang;Yong Wu;De-Shuang Huang
34 Random occlusion recovery with noise channel for person re-identification 会议论文 Kun Zhang;Di Wu;Changan Yuan;Xiao Qin;Hongjie Wu;Xingming Zhao;Lijun Zhang;Yuchuan Du;Hanli Wang
35 Hierarchical Attention Network for Predicting DNA-Protein Binding Sites 会议论文 Wenbo Yu
36 Three-layer dynamic transfer learning language model for E. Coli promoter classification 会议论文 Ying He;Zhen Shen;Qinhu Zhang;Siguo Wang;Changan Yuan;Xiao Qin;Hongjie Wu;Xingming Zhao
37 A New Method Combining DNA Shape Features to Improve the Prediction Accuracy of Transcription Factor Binding Sites 会议论文 Siguo Wang;Zhen Shen;Ying He;Qinhu Zhang;Changan Yuan;Xiao Qin;Hongjie Wu;Xingming Zhao
38 A Deep Learning Model for RNA-Protein Binding Preference Prediction based on Hierarchical LSTM and Attention Network 期刊论文 Zhen Shen;Qinhu Zhang;Kyungsook Han;De-shuang Huang
39 Identification of Intrinsically Disordered Proteins and Regions by Length-Dependent Predictors Based on Conditional Random Fields 期刊论文 Liu Yumeng;Chen Shengyu;Wang Xiaolong;Liu Bin
40 RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins 期刊论文 Liu Yumeng;Wang Xiaolong;Liu Bin
41 一种基于深度学习的转录因子结合位点定位方法 专利 黄德双;徐尤红;元昌安
42 一种基于序列和形状信息深度融合的模体挖掘方法 专利 黄德双;张寅东
43 iLncRNAdis-FB: identify lncRNA-disease associations by fusing biological feature blocks through deep neural network 期刊论文 Hang Wei;Qing Liao;Bin Liu
44 NCBRPred: predicting nucleic acid binding residues in proteins based on multilabel learning 期刊论文 Jun Zhang;Qingcai Chen;Bin Liu
45 DeepSVM-fold: protein fold recognition by combining support vector machines and pairwise sequence similarity scores generated by deep learning networks 期刊论文 Liu Bin;Li Chen-Chen;Yan Ke
46 Modeling in-vivo protein-DNA binding by combining multiple-instance learning with a hybrid deep neural network 期刊论文 Zhang Qinhu;Shen Zhen;Huang De Shuang
47 ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm 期刊论文 Shao Jiangyi;Liu Bin
48 iCircDA-MF: identification of circRNA-disease associations based on matrix factorization 期刊论文 Wei Hang;Liu Bin
49 Predicting in-vitro Transcription Factor Binding Sites Using DNA Sequence plus Shape 期刊论文 Zhang Qinhu;Shen Zhen;Huang De-Shuang
50 DeepCRISPR: optimized CRISPR guide RNA design by deep learning 期刊论文 Chuai;Guohui;Ma;Hanhui;Yan;Jifang;Chen;Ming;Hong;Nanfang;Xue;Dongyu;Zhou;Chi;Zhu;Chenyu;Chen;Ke;Duan;Bin;Gu;Feng;Qu;Sheng;Huang;Deshuang;Wei;Jia;Liu;Qi;Chuai Guohui;Yan Jifang;Hong Nanfang;Xue Dongyu;Zhou Chi;Zhu Chenyu;Chen Ke;Duan Bin;Qu Sheng;Liu Qi;Huang Deshuang;Chen Ming;Wei Jia;Ma Hanhui;Gu Feng;Liu Q;Huang DS;Wei J
51 Convolutional Capsule-Based Network for Person Re-identification 会议论文 De-Shuang Huang;Andong Li
52 iPromoter-2L: a two-layer predictor for identifying promoters and their types by multi-window-based PseKNC 期刊论文 Liu;Bin;Yang;Fan;Huang;De-Shuang;Chou;Kuo-Chen;Liu Bin;Yang Fan;Chou Kuo-Chen;Huang De-Shuang;Liu B;Chou KC;Huang DS
53 Predicting transcription factor binding sites using DNA shape features based on shared hybrid deep learning architecture 期刊论文 Siguo Wang;De-Shuang Huang;Zhen Shen;Ying He;Zhen-Heng Chen;Jianqiang Li;De-Shuang Huang
54 Graph regularized L2,1-nonnegative matrix factorization for miRNA-disease association prediction 期刊论文 Zhen Gao;Yu-Tian Wang;Qing-Wen Wu;Jian-Cheng Ni;Chun-Hou Zheng
55 Capsule Network Based Modeling of Multi-omics Data for Discovery of Breast Cancer-Related Genes 期刊论文 Peng Chen;Zheng Yang;Huang De-shuang
56 iRO-PsekGCC: Identify DNA Replication Origins Based on Pseudo k-Tuple GC Composition 期刊论文 Bin Liu;Shengyu Chen;Ke Yan;Fan Weng
57 Deep learning-based methods for person re-identification: A comprehensive review 期刊论文 Wu Di;Zheng Si Jia;Zhang Xiao Ping;Yuan Chang An;Cheng Fei;Zhao Yang;Lin Yong Jun;Zhao Zhong Qiu;Jiang Yong Li;Huang De Shuang
58 A survey on deep learning in DNA/RNA motif mining 期刊论文 Ying He;Zhen Shen;Qinhu Zhang;Siguo Wang;De-Shuang Huang
59 IDP-Seq2Seq: identification of intrinsically disordered regions based on sequence to sequence learning 期刊论文 Yi-Jun Tang;Yihe Pang;Bin Liu
60 Predicting in-vitro DNA protein binding with a spatially aligned fusion of sequence and shape 期刊论文 Qinhu Zhang;Yindong Zhang;Siguo Wang;Zhan-Heng Chen;Valeriya V. Gribova;Vladimir Fedorovich Filaretov;De-shuang Huang
61 IEsGene-ZCPseKNC: Identify Essential Genes Based on Z Curve Pseudo k-Tuple Nucleotide Composition 期刊论文 Jiahai Chen;Yongmin Liu;Qing Liao;Bin Liu
62 ProtDec-LTR3.0: protein remote homology detection by incorporating profile-based features into Learning to Rank 期刊论文 Bin Liu;Yulin Zhu
63 IDRBP-PPCT: Identifying nucleic acid-binding proteins based on Position-Specific Score Matrix and Position-Specific Frequency Matrix Cross Transformation 期刊论文 Ning Wang;Jun Zhang;Bin Liu
64 License Plate Detection and Recognition Technology for Complex Real Scenarios 会议论文 Zhipeng Li;Fei Wang;Hamdan Taleb;Changan Yuan;Xiao Qin;Hongjie Wu;Xingming Zhao;Lijun Zhang
65 Using deep learning to predict transcription factor binding sites based on multiple-omics data, 会议论文 Youhong Xu;Changan Yuan;Hongjie Wu;Xingming Zhao
66 Motif Discovery via Convolutional Networks with K-mer Embedding 会议论文 Dailun Wang
67 Position Attention-Guided Learning for Infrared-Visible Person Re-identification 会议论文 Yong Wu;Sizhe Wan;Di Wu;Chao Wang;Changan Yuan;Xiao Qin;Hongjie Wu;Xingming Zhao
68 A deep model with combined losses for person re-identification 期刊论文 Wu Di;Zheng Si Jia;Yuan Chang An;Huang De Shuang
69 High-Order Convolutional Neural Network Architecture for Predicting DNA-Protein Binding Sites 期刊论文 Zhang Qinhu;Zhu Lin;Huang De Shuang
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