| 0 | -- | 0 | Tian-Hao Li, Chun-Chun Wang, Li Zhang, Xing Chen 0001. SNRMPACDC: computational model focused on Siamese network and random matrix projection for anticancer synergistic drug combination prediction |
| 0 | -- | 0 | Mengjie Shao, Nanjiao Ying, Qian Liang, Nan Ma, Sebastian Leptihn, Yunsong Yu, Huan Chen, Chengzhi Liu, Xiaoting Hua. dif-mediated antibiotic resistance genes transfer in bacteria identified by pdifFinder |
| 0 | -- | 0 | Shehab Sarar Ahmed, Zaara Tasnim Rifat, M. Saifur Rahman, M. Sohel Rahman. Succinylated lysine residue prediction revisited |
| 0 | -- | 0 | Yanqiang Han, Zhilong Wang, An Chen, Imran Ali, Junfei Cai, Simin Ye, Zhiyun Wei, Jin-Jin Li. A deep transfer learning-based protocol accelerates full quantum mechanics calculation of protein |
| 0 | -- | 0 | Xiao Fan, Hongbing Pan, Alan Tian, Wendy K. Chung, Yufeng Shen. SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants |
| 0 | -- | 0 | Guo-Hua Yuan, Ying Wang, Guang-Zhong Wang, Li Yang. RNAlight: a machine learning model to identify nucleotide features determining RNA subcellular localization |
| 0 | -- | 0 | Haoran Gong, Jianguo Wen, Ruihan Luo, Yuzhou Feng, Jingjing Guo, Hongguang Fu, Xiaobo Zhou. Integrated mRNA sequence optimization using deep learning |
| 0 | -- | 0 | Jiayu Shang, Xubo Tang, Yanni Sun. PhaTYP: predicting the lifestyle for bacteriophages using BERT |
| 0 | -- | 0 | Lihua Wang, Tao Zhang, Lihong Yu, Chun-Hou Zheng 0001, Wenguang Yin, Junfeng Xia, Tiejun Zhang. Deleterious synonymous mutation identification based on selective ensemble strategy |
| 0 | -- | 0 | Zimeng Li, Shichao Zhu, Bin Shao, Xiangxiang Zeng, Tong Wang, Tie-Yan Liu. DSN-DDI: an accurate and generalized framework for drug-drug interaction prediction by dual-view representation learning |
| 0 | -- | 0 | Kai Wang. GPDOCK: highly accurate docking strategy for metalloproteins based on geometric probability |
| 0 | -- | 0 | Chun-Jie Liu, Fei-Fei Hu, Gui-Yan Xie, Ya-Ru Miao, Xin-Wen Li, Yan Zeng, An-Yuan Guo. GSCA: an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels |
| 0 | -- | 0 | Ke Han, Jianchun Wang, Yu Wang, Lei Zhang, Mengyao Yu, Fang Xie, Dequan Zheng, Yaoqun Xu, Yijie Ding, Jie Wan. A review of methods for predicting DNA N6-methyladenine sites |
| 0 | -- | 0 | Upendra Kumar Pradhan, Prabina Kumar Meher, Sanchita Naha, Soumen Pal, Ajit Gupta, Rajender Parsad. lDBPred: a novel computational model for discovery of DNA binding proteins in plants |
| 0 | -- | 0 | Weibin Huang, Yuhui Zhang, Songyao Chen, Haofan Yin, Guangyao Liu, Huaqi Zhang, Jiannan Xu, Jishang Yu, Yujian Xia, Yulong He, Changhua Zhang. Personalized immune subtypes based on machine learning predict response to checkpoint blockade in gastric cancer |
| 0 | -- | 0 | Softya Sebastian, Swarup Roy, Jugal Kalita. A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer's disease network |
| 0 | -- | 0 | Yetian Fan, April S. Chan, Jun Zhu, Suet Yi Leung, Xiaodan Fan. A Bayesian model for identifying cancer subtypes from paired methylation profiles |
| 0 | -- | 0 | Chonghao Wang, Jing Zhang, Werner Pieter Veldsman, Xin Zhou, Lu Zhang. A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants |
| 0 | -- | 0 | Yi-zhou He, Yue Yang, Xiao-Rui Su, Bo-Wei Zhao, Shengwu Xiong, Lun Hu. Incorporating higher order network structures to improve miRNA-disease association prediction based on functional modularity |
| 0 | -- | 0 | Haohong Zhang, Hui Chong, Qingyang Yu, Yuguo Zha, Mingyue Cheng, Kang Ning 0001. Tracing human life trajectory using gut microbial communities by context-aware deep learning |
| 0 | -- | 0 | Wayland Yeung, Zhongliang Zhou, Sheng Li 0001, Natarajan Kannan. Alignment-free estimation of sequence conservation for identifying functional sites using protein sequence embeddings |
| 0 | -- | 0 | Lifang Yang, Ye Yang, Luqi Huang, Xiuming Cui, Yuan Liu. From single- to multi-omics: future research trends in medicinal plants |
| 0 | -- | 0 | Zhenshuang Tang, Lilin Yin, Dong Yin, Haohao Zhang, Yuhua Fu, Guangliang Zhou, Yunxiang Zhao, Zhiquan Wang, Xiaolei Liu, Xinyun Li, Shuhong Zhao. Development and application of an efficient genomic mating method to maximize the production performances of three-way crossbred pigs |
| 0 | -- | 0 | Lu Yang, Jun Chen. Benchmarking differential abundance analysis methods for correlated microbiome sequencing data |
| 0 | -- | 0 | Zechen Wang, Liangzhen Zheng, Sheng Wang, Mingzhi Lin, ZhiHao Wang, Adams Wai-Kin Kong, Yuguang Mu, Yanjie Wei, Weifeng Li. A fully differentiable ligand pose optimization framework guided by deep learning and a traditional scoring function |
| 0 | -- | 0 | Xin Zhang, Lesong Wei, Xiucai Ye, Kai Zhang, Saisai Teng, Zhongshen Li, Junru Jin, Min-jae Kim, Tetsuya Sakurai, LiZhen Cui, Balachandran Manavalan, Leyi Wei. SiameseCPP: a sequence-based Siamese network to predict cell-penetrating peptides by contrastive learning |
| 0 | -- | 0 | Jing-Zhe Jiang, Wen-Guang Yuan, Jiayu Shang, Ying-Hui Shi, Li-Ling Yang, Min Liu, Peng Zhu, Tao Jin, Yanni Sun, Li-Hong Yuan. Virus classification for viral genomic fragments using PhaGCN2 |
| 0 | -- | 0 | Siqi Chen, Xuhua Yan, Ruiqing Zheng, Min Li 0007. Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data |
| 0 | -- | 0 | Xi-Liang Zhu, Lin-Xia Bao, Min-Qi Xue, Ying-Ying Xu. Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning |
| 0 | -- | 0 | Alessia Buratin, Stefania Bortoluzzi, Enrico Gaffo. Systematic benchmarking of statistical methods to assess differential expression of circular RNAs |
| 0 | -- | 0 | Lei Wang, Shao-Hua Shi, Hui Li, Xiangxiang Zeng, Su-You Liu, Zhao-Qian Liu, Yafeng Deng, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao 0001. Reducing false positive rate of docking-based virtual screening by active learning |
| 0 | -- | 0 | Guobo Xie, Rui-Bin Chen, Zhiyi Lin, Guosheng Gu, Jun-Rui Yu, Zhen-Guo Liu, Ji Cui, Lieqing Lin, Lang-Cheng Chen. Predicting lncRNA-disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation |
| 0 | -- | 0 | Jianbo Fu, Qingxia Yang, Yongchao Luo, Song Zhang, Jing Tang, Ying Zhang, Hongning Zhang, Hanxiang Xu, Feng Zhu 0004. Label-free proteome quantification and evaluation |
| 0 | -- | 0 | Yiming Xu, Bowen Zheng, Xiaohong Liu, Tao Wu, Jinxiu Ju, Shi-jie Wang, Yufan Lian, Hongjun Zhang, Tong Liang, Ye Sang, Rui Jiang 0001, Guangyu Wang, Jie Ren, Ting Chen 0006. Improving artificial intelligence pipeline for liver malignancy diagnosis using ultrasound images and video frames |
| 0 | -- | 0 | Tim D. Rose, Nikolai Köhler, Lisa Falk, Lucie Klischat, Olga Lazareva, Josch K. Pauling. Lipid network and moiety analysis for revealing enzymatic dysregulation and mechanistic alterations from lipidomics data |
| 0 | -- | 0 | Zhenling Peng, Zixia Li, Qiaozhen Meng, Bi Zhao, Lukasz A. Kurgan. CLIP: accurate prediction of disordered linear interacting peptides from protein sequences using co-evolutionary information |
| 0 | -- | 0 | Chengqian Lu, Lishen Zhang, Min Zeng, Wei Lan, Guihua Duan, Jianxin Wang 0001. Inferring disease-associated circRNAs by multi-source aggregation based on heterogeneous graph neural network |
| 0 | -- | 0 | Kai Yu 0011, Zekun Liu, Haoyang Cheng, Shihua Li, Qingfeng Zhang, Jia Liu, Huai-Qiang Ju, Zhixiang Zuo, Qi Zhao, Shiyang Kang, Zexian Liu. dSCOPE: a software to detect sequences critical for liquid-liquid phase separation |
| 0 | -- | 0 | Sumeet Patiyal, Anjali Dhall, Khushboo Bajaj, Harshita Sahu, Gajendra P. S. Raghava. Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile |
| 0 | -- | 0 | Yang Yang, Yuwei Lu, Wenying Yan. A comprehensive review on knowledge graphs for complex diseases |
| 0 | -- | 0 | Yan Kang, Yulong Xu, Xinchao Wang, Bin Pu, Xuekun Yang, Yulong Rao, Jianguo Chen. HN-PPISP: a hybrid network based on MLP-Mixer for protein-protein interaction site prediction |
| 0 | -- | 0 | Bo Yang, Hailin Chen. Predicting circRNA-drug sensitivity associations by learning multimodal networks using graph auto-encoders and attention mechanism |
| 0 | -- | 0 | Jiacheng Lin, Lijun Wu, Jinhua Zhu, Xiaobo Liang, Yingce Xia, Shufang Xie 0003, Tao Qin, Tie-Yan Liu. R2-DDI: relation-aware feature refinement for drug-drug interaction prediction |
| 0 | -- | 0 | Marta Nazzari, Duncan Hauser, Marcel van Herwijnen, Mírian Romitti, Daniel J. Carvalho, Anna M. Kip, Florian Caiment. CODA: a combo-Seq data analysis workflow |
| 0 | -- | 0 | Hailin Feng, Dongdong Jin, Jian Li, Yane Li, Quan Zou, Tongcun Liu. Matrix reconstruction with reliable neighbors for predicting potential MiRNA-disease associations |
| 0 | -- | 0 | Ziyang Tang, Tonglin Zhang, Baijian Yang, Jing Su, Qianqian Song. spaCI: deciphering spatial cellular communications through adaptive graph model |
| 0 | -- | 0 | Hong Wang, Chong Dai, Yuqi Wen, Xiaoqi Wang, Wenjuan Liu, Song He, Xiaochen Bo, Shaoliang Peng. GADRP: graph convolutional networks and autoencoders for cancer drug response prediction |
| 0 | -- | 0 | Jun Liu, Kai-Long Zhao, Guijun Zhang. Improved model quality assessment using sequence and structural information by enhanced deep neural networks |
| 0 | -- | 0 | Nisha Bajiya, Anjali Dhall, Suchet Aggarwal, Gajendra P. S. Raghava. Advances in the field of phage-based therapy with special emphasis on computational resources |
| 0 | -- | 0 | Zerun Lin, Le Ou-Yang. Inferring gene regulatory networks from single-cell gene expression data via deep multi-view contrastive learning |
| 0 | -- | 0 | Peicong Lin, Yumeng Yan, Sheng-You Huang. DeepHomo2.0: improved protein-protein contact prediction of homodimers by transformer-enhanced deep learning |
| 0 | -- | 0 | Zhangxin Zhao, Qianjin Feng, Yu Zhang, Zhenyuan Ning. Adaptive risk-aware sharable and individual subspace learning for cancer survival analysis with multi-modality data |
| 0 | -- | 0 | Muhammad Nabeel Asim, Muhammad Ali Ibrahim, Ahtisham Fazeel, Andreas Dengel 0001, Sheraz Ahmed. DNA-MP: a generalized DNA modifications predictor for multiple species based on powerful sequence encoding method |
| 0 | -- | 0 | Zixi Zheng, Yanyan Tan, Hong Wang, Shengpeng Yu, Tianyu Liu, Cheng Liang. CasANGCL: pre-training and fine-tuning model based on cascaded attention network and graph contrastive learning for molecular property prediction |
| 0 | -- | 0 | Yao Lu, Zhiqiang Pang, Jianguo Xia. Comprehensive investigation of pathway enrichment methods for functional interpretation of LC-MS global metabolomics data |
| 0 | -- | 0 | George Minadakis, Marios Tomazou, Nikolas Dietis, George M. Spyrou. Vir2Drug: a drug repurposing framework based on protein similarities between pathogens |
| 0 | -- | 0 | Shu-Guang Ge, Jian Liu, Yuhu Cheng, Xiaojing Meng, Xuesong Wang 0001. Multi-view spectral clustering with latent representation learning for applications on multi-omics cancer subtyping |
| 0 | -- | 0 | Qilong Wu, Sheng-You Huang. HCovDock: an efficient docking method for modeling covalent protein-ligand interactions |
| 0 | -- | 0 | Shujun He, Baizhen Gao, Rushant Sabnis, Qing Sun. RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning |
| 0 | -- | 0 | Ilias Moutsopoulos, Eleanor C. Williams, Irina Mohorianu. bulkAnalyseR: an accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data |
| 0 | -- | 0 | Zhi Jian Zhou, Chen-Hui Yang, Sheng-Bao Ye, Xiao-Wei Yu, Ye Qiu, Xing-Yi Ge. VirusRecom: an information-theory-based method for recombination detection of viral lineages and its application on SARS-CoV-2 |
| 0 | -- | 0 | Jiung-Wen Chen, Lisa Shrestha, George Green, André Leier, Tatiana T. Marquez-Lago. The hitchhikers' guide to RNA sequencing and functional analysis |
| 0 | -- | 0 | Risa Karakida Kawaguchi, Ziqi Tang, Stephan Fischer, Chandana Rajesh, Rohit Tripathy, Peter K. Koo, Jesse Gillis. Learning single-cell chromatin accessibility profiles using meta-analytic marker genes |
| 0 | -- | 0 | Qitong Yuan, Keyi Chen, Yimin Yu, Nguyen-Quoc-Khanh Le, Matthew Chin Heng Chua. Prediction of anticancer peptides based on an ensemble model of deep learning and machine learning using ordinal positional encoding |
| 0 | -- | 0 | Kanggeun Lee, Dongbin Cho, Jinho Jang, Kang Choi, Hyoung-oh Jeong, Jiwon Seo, Won-Ki Jeong, Semin Lee. RAMP: response-aware multi-task learning with contrastive regularization for cancer drug response prediction |
| 0 | -- | 0 | Marwan Abdellah, Juan Jose Garcia-Cantero, Nadir Román Guerrero, Alessandro Foni, Jay S. Coggan, Corrado Calì, Marco Agus, Eleftherios Zisis, Daniel Keller, Markus Hadwiger, Pierre J. Magistretti, Henry Markram, Felix Schürmann. in silico neuroscience |
| 0 | -- | 0 | Yue-Hua Feng, Shao-Wu Zhang 0001, Yi-Yang Feng, Qing-Qing Zhang, Ming-Hui Shi, Jian-Yu Shi. A social theory-enhanced graph representation learning framework for multitask prediction of drug-drug interactions |
| 0 | -- | 0 | Mengqi Luo, Shangfu Li, Yuxuan Pang, Lantian Yao, Renfei Ma, Hsi-Yuan Huang, Hsien-Da Huang, Tzong-Yi Lee. Extraction of microRNA-target interaction sentences from biomedical literature by deep learning approach |
| 0 | -- | 0 | Wujuan Zhong, Aparna Chhibber, Lan Luo, Devan V. Mehrotra, Judong Shen. A fast and powerful linear mixed model approach for genotype-environment interaction tests in large-scale GWAS |
| 0 | -- | 0 | Yuanyuan Chen, Hao Zhang, Xiao Sun 0006. Improving the performance of single-cell RNA-seq data mining based on relative expression orderings |
| 0 | -- | 0 | Xinyi Xu, Xiangjie Li. Structure-preserved dimension reduction using joint triplets sampling for multi-batch integration of single-cell transcriptomic data |
| 0 | -- | 0 | Chun-Qiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-bin Shen. Leveraging scaffold information to predict protein-ligand binding affinity with an empirical graph neural network |
| 0 | -- | 0 | Mei Li, Xiangrui Cai, Sihan Xu, Hua Ji. Metapath-aggregated heterogeneous graph neural network for drug-target interaction prediction |
| 0 | -- | 0 | Huiyu Li, Chen Shen, Gongji Wang, Qinru Sun, Kai Yu, Zefeng Li, Xinggong Liang, Run Chen, Hao Wu, Fan Wang, Zhenyuan Wang, Chunfeng Lian. BloodNet: An attention-based deep network for accurate, efficient, and costless bloodstain time since deposition inference |
| 0 | -- | 0 | Sayed-Rzgar Hosseini, Xiaobo Zhou. CCSynergy: an integrative deep-learning framework enabling context-aware prediction of anti-cancer drug synergy |
| 0 | -- | 0 | Kai Zheng 0020, Xin-Lu Zhang, Lei Wang 0121, Zhu-Hong You, Bo-Ya Ji, Xiao Liang, Zheng-Wei Li. SPRDA: a link prediction approach based on the structural perturbation to infer disease-associated Piwi-interacting RNAs |
| 0 | -- | 0 | Jing Liu, Xinghua Tang, Xiao Guan. Grain protein function prediction based on self-attention mechanism and bidirectional LSTM |
| 0 | -- | 0 | Gabriel Cia, Fabrizio Pucci, Marianne Rooman. Critical review of conformational B-cell epitope prediction methods |
| 0 | -- | 0 | Yongchao Luo, Panpan Wang, Minjie Mou, Hanqi Zheng, Jiajun Hong, Lin Tao, Feng Zhu 0004. A novel strategy for designing the magic shotguns for distantly related target pairs |
| 0 | -- | 0 | Hai Yang 0002, Lipeng Gan, Rui Chen, Dongdong Li, Jing Zhang, Zhe Wang. From multi-omics data to the cancer druggable gene discovery: a novel machine learning-based approach |
| 0 | -- | 0 | Xue Li, Peifu Han, Wenqi Chen, Changnan Gao, Shuang Wang, Tao Song 0001, Muyuan Niu, Alfonso Rodríguez-Patón. MARPPI: boosting prediction of protein-protein interactions with multi-scale architecture residual network |
| 0 | -- | 0 | Xiayang Li, Moxuan Chen, Huaming Wu. Multiple errors correction for position-limited DNA sequences with GC balance and no homopolymer for DNA-based data storage |
| 0 | -- | 0 | Khandakar Tanvir Ahmed, Sze Cheng, Qian Li, Jeongsik Yong, Wei Zhang 0076. Incomplete time-series gene expression in integrative study for islet autoimmunity prediction |
| 0 | -- | 0 | Wenchuang He, Kunli Xiang, Caijin Chen, Jie Wang, Zhiqiang Wu. Master graph: an essential integrated assembly model for the plant mitogenome based on a graph-based framework |
| 0 | -- | 0 | Yang Yue, Yongxuan Liu, Luoying Hao, Huangshu Lei, Shan He 0001. Improving therapeutic synergy score predictions with adverse effects using multi-task heterogeneous network learning |
| 0 | -- | 0 | Giulia Pais, Giulio Spinozzi, Daniela Cesana, Fabrizio Benedicenti, Alessandra Albertini, Maria Ester Bernardo, Bernhard Gentner, Eugenio Montini, Andrea Calabria. ISAnalytics enables longitudinal and high-throughput clonal tracking studies in hematopoietic stem cell gene therapy applications |
| 0 | -- | 0 | Han Yu, Xiaozhou Luo. IPPF-FE: an integrated peptide and protein function prediction framework based on fused features and ensemble models |
| 0 | -- | 0 | Min Li 0007, Baoying Zhao, Rui Yin, Chengqian Lu, Fei Guo, Min Zeng. GraphLncLoc: long non-coding RNA subcellular localization prediction using graph convolutional networks based on sequence to graph transformation |
| 0 | -- | 0 | Shuaiqun Wang, Kai Zheng, Wei Kong, Ruiwen Huang, Lulu Liu, Gen Wen, Yaling Yu. Multimodal data fusion based on IGERNNC algorithm for detecting pathogenic brain regions and genes in Alzheimer's disease |
| 0 | -- | 0 | Jing Wang, Junfeng Xia, Haiyun Wang, Yansen Su, Chun-Hou Zheng 0001. scDCCA: deep contrastive clustering for single-cell RNA-seq data based on auto-encoder network |
| 0 | -- | 0 | Wenxuan Deng, Bolun Li, Jiawei Wang, Wei Jiang 0019, Xiting Yan, Ningshan Li, Milica Vukmirovic, Naftali Kaminski, Jing Wang, Hongyu Zhao. A novel Bayesian framework for harmonizing information across tissues and studies to increase cell type deconvolution accuracy |
| 0 | -- | 0 | Bihan Shen, Fangyoumin Feng, Kunshi Li, Ping Lin, Liangxiao Ma, Hong Li. A systematic assessment of deep learning methods for drug response prediction: from in vitro to clinical applications |
| 0 | -- | 0 | Zheng Zhang, Shengquan Chen, Zhixiang Lin. RefTM: reference-guided topic modeling of single-cell chromatin accessibility data |
| 0 | -- | 0 | Erik Christensen, Ping Luo, Andrei L. Turinsky, Mia Husic, Alaina Mahalanabis, Alaine Naidas, Juan Javier Díaz-Mejía, Michael Brudno, Trevor J. Pugh, Arun K. Ramani, Parisa Shooshtari. Evaluation of single-cell RNAseq labelling algorithms using cancer datasets |
| 0 | -- | 0 | Zhiqiang Hu, Wenfeng Liu, Chenbin Zhang, Jiawen Huang, Shaoting Zhang, Huiqun Yu, Yi Xiong, Hao Liu, Song Ke, Liang Hong. SAM-DTA: a sequence-agnostic model for drug-target binding affinity prediction |
| 0 | -- | 0 | Ze-Qun Zhang, Junlin Xu, Yanan Wu, Nian-Nian Liu, Ying-Long Wang, Ying Liang. CapsNet-LDA: predicting lncRNA-disease associations using attention mechanism and capsule network based on multi-view data |
| 0 | -- | 0 | Cheng-Hong Yang 0001, Ming-Feng Hou, Li-Yeh Chuang, Cheng-San Yang, Yu-Da Lin. Dimensionality reduction approach for many-objective epistasis analysis |
| 0 | -- | 0 | Jingxuan Zhao, Jianqiang Sun, Stella C. Shuai, Qi Zhao, Jianwei Shuai. Predicting potential interactions between lncRNAs and proteins via combined graph auto-encoder methods |
| 0 | -- | 0 | Yimeng Wang, Mengting Huang, Hua Deng, Weihua Li 0005, Zengrui Wu, Yun Tang, Guixia Liu. Identification of vital chemical information via visualization of graph neural networks |
| 0 | -- | 0 | Andrew Cheng, Guanyu Hu, Wei Vivian Li. Benchmarking cell-type clustering methods for spatially resolved transcriptomics data |
| 0 | -- | 0 | . Correction to: VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants |
| 0 | -- | 0 | Lishen Zhang, Chengqian Lu, Min Zeng, Yaohang Li, Jianxin Wang 0001. CRMSS: predicting circRNA-RBP binding sites based on multi-scale characterizing sequence and structure features |
| 0 | -- | 0 | Hongwei Chen, Yunpeng Cai, Chaojie Ji, Gurudeeban Selvaraj, Dongqing Wei, Hongyan Wu. AdaPPI: identification of novel protein functional modules via adaptive graph convolution networks in a protein-protein interaction network |
| 0 | -- | 0 | Tianyuan Liu, Bohao Zou, Manman He, Yongfei Hu, Yiying Dou, Tianyu Cui, Puwen Tan, Shaobin Li, Shuan Rao, Yan Huang, Sixi Liu, Kaican Cai, Dong Wang 0011. LncReader: identification of dual functional long noncoding RNAs using a multi-head self-attention mechanism |
| 0 | -- | 0 | Qi Liang, Wenxiang Zhang, Hao Wu, Bin Liu 0014. LncRNA-disease association identification using graph auto-encoder and learning to rank |
| 0 | -- | 0 | Bailing Zhou, Maolin Ding, Jing Feng, Baohua Ji, Pingping Huang, Junye Zhang, Xue Yu, Zanxia Cao, Yuedong Yang, Yaoqi Zhou, Jihua Wang. EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning |
| 0 | -- | 0 | Lei Sun, Gongming Wang, Zhihua Zhang. SimCH: simulation of single-cell RNA sequencing data by modeling cellular heterogeneity at gene expression level |
| 0 | -- | 0 | Donghyo Kim, Doyeon Ha, Kwanghwan Lee, Heetak Lee, Inhae Kim, Sanguk Kim. An evolution-based machine learning to identify cancer type-specific driver mutations |
| 0 | -- | 0 | Huan Hu, Zhen Feng, Hai Lin, JunJie Zhao, Yaru Zhang, Fei Xu, Lingling Chen, Feng Chen, Yunlong Ma, Jianzhong Su, Qi Zhao, Jianwei Shuai. Modeling and analyzing single-cell multimodal data with deep parametric inference |
| 0 | -- | 0 | Dong Wang, Zhenxing Wu, Chao Shen, Lingjie Bao, Hao Luo, Zhe Wang 0041, Hucheng Yao, De-Xin Kong, Cheng Luo, Tingjun Hou. Learning with uncertainty to accelerate the discovery of histone lysine-specific demethylase 1A (KDM1A/LSD1) inhibitors |
| 0 | -- | 0 | Anna Dal Molin, Caterina Tretti Parenzan, Enrico Gaffo, Cristina Borin, Elena Boldrin, Lueder H. Meyer, Geertruij te Kronnie, Silvia Bresolin, Stefania Bortoluzzi. KMT2A::AFF1 rearrangements by the new software CircFusion |
| 0 | -- | 0 | Simon Orozco-Arias, Luis Humberto López-Murillo, Mariana S. Candamil-Cortes, Maradey Arias, Paula A. Jaimes, Alexandre Rossi Paschoal, Reinel Tabares-Soto, Gustavo A. Isaza, Romain Guyot. Inpactor2: a software based on deep learning to identify and classify LTR-retrotransposons in plant genomes |
| 0 | -- | 0 | Xing Chen 0001, Li Huang. Computational model for disease research |
| 0 | -- | 0 | Wengang Wang, Hailin Chen. Predicting miRNA-disease associations based on lncRNA-miRNA interactions and graph convolution networks |
| 0 | -- | 0 | Wayland Yeung, Zhongliang Zhou, Liju Mathew, Nathan Gravel, Rahil Taujale, Brady O'boyle, Mariah Salcedo, Aarya Venkat, William Lanzilotta, Sheng Li 0001, Natarajan Kannan. Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies |
| 0 | -- | 0 | Kaili Wang, Renyi Zhou, Yifan Wu, Min Li 0007. RLBind: a deep learning method to predict RNA-ligand binding sites |
| 0 | -- | 0 | Wubin Ding, Diljeet Kaur, Steve Horvath, Wanding Zhou. Comparative epigenome analysis using Infinium DNA methylation BeadChips |
| 0 | -- | 0 | Kuo Yang, Yuxia Yang, Shuyue Fan, Jianan Xia, Qiguang Zheng, Xin Dong, Jun Liu, Qiong Liu, Lei Lei, Yingying Zhang, Bing Li, Zhuye Gao, Runshun Zhang, Baoyan Liu, Zhong Wang, Xuezhong Zhou. DRONet: effectiveness-driven drug repositioning framework using network embedding and ranking learning |
| 0 | -- | 0 | Bo Song, Hao Li, Mengyun Jiang, Zhongtian Gao, Suikang Wang, Lei Gao, Yunsheng Chen, Wujiao Li. trans-splicing of spliced leader sequences |
| 0 | -- | 0 | Yishu Wang, Juan Qi, Dongmei Ai. DPADM: a novel algorithm for detecting drug-pathway associations based on high-throughput transcriptional response to compounds |
| 0 | -- | 0 | Eva María Trinidad, Enrique Vidal 0002, Esther Coronado, Anna Esteve-Codina, Victoria Castel, Adela Cañete Nieto, Marta Gut, Simon Heath, Jaime Font de Mora. Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA |
| 0 | -- | 0 | Wei Lan, Yi Dong, Hongyu Zhang, Chunling Li, Qingfeng Chen, Jin Liu 0012, Jianxin Wang 0001, Yi-Ping Phoebe Chen. Benchmarking of computational methods for predicting circRNA-disease associations |
| 0 | -- | 0 | Yifang Wei, Lingmei Li, Xin Zhao, Haitao Yang, Jian Sa, Hongyan Cao, Yuehua Cui. Cancer subtyping with heterogeneous multi-omics data via hierarchical multi-kernel learning |
| 0 | -- | 0 | Wenjie Du, Xiaoting Yang, Di Wu, Fenfen Ma, Baicheng Zhang, Chaochao Bao, Yaoyuan Huo, Jun Jiang, Xin Chen, Yang Wang 0015. Fusing 2D and 3D molecular graphs as unambiguous molecular descriptors for conformational and chiral stereoisomers |
| 0 | -- | 0 | Hai-Yun Wang, Jian-ping Zhao 0001, Chun-Hou Zheng 0001, Yan-Sen Su. scGMAAE: Gaussian mixture adversarial autoencoders for diversification analysis of scRNA-seq data |
| 0 | -- | 0 | Siqin Zhang, Kuo Yang, Zhenhong Liu, Xinxing Lai, Zhen Yang, Jianyang Zeng, Shao Li. DrugAI: a multi-view deep learning model for predicting drug-target activating/inhibiting mechanisms |
| 0 | -- | 0 | Nishant Kumar, Sumeet Patiyal, Shubham Choudhury, Ritu Tomer, Anjali Dhall, Gajendra P. S. Raghava. DMPPred: a tool for identification of antigenic regions responsible for inducing type 1 diabetes mellitus |
| 0 | -- | 0 | Jiayin Zhou, Wen Song, Qichao Tu. To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities |
| 0 | -- | 0 | Fang Ge, Chen Li 0021, Shahid Iqbal, Muhammad Arif 0012, Fuyi Li, Maha A. Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-jun Yu. VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants |
| 0 | -- | 0 | Qiao Liu, Wanwen Zeng, Wei Zhang, Sicheng Wang, Hongyang Chen, Rui Jiang 0001, Mu Zhou, Shaoting Zhang. Deep generative modeling and clustering of single cell Hi-C data |
| 0 | -- | 0 | Xiaosa Zhao, Jun Wu 0020, Xiaowei Zhao, Minghao Yin. Multi-view contrastive heterogeneous graph attention network for lncRNA-disease association prediction |
| 0 | -- | 0 | Yanan Tian, Xiaorui Wang, Xiaojun Yao, Huanxiang Liu, Ying Yang. Predicting molecular properties based on the interpretable graph neural network with multistep focus mechanism |
| 0 | -- | 0 | Yu Zhao, Bing He, Zhimeng Xu, Yidan Zhang, Xuan Zhao, Zhi-an Huang, Fan Yang 0081, Liang Wang, Lei Duan, Jiangning Song, Jianhua Yao 0001. Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire |
| 0 | -- | 0 | Lingling Wang, Lei Xu 0035, Zhe Wang 0041, Tingjun Hou, Haiping Hao, Huiyong Sun. Cooperation of structural motifs controls drug selectivity in cyclin-dependent kinases: an advanced theoretical analysis |
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