Journal: Briefings in Bioinformatics

Volume 23, Issue 3

0 -- 0Xiaozhe Wan, Xiaolong Wu, Dingyan Wang, Xiaoqin Tan, Xiaohong Liu, Zunyun Fu, Hualiang Jiang, Mingyue Zheng, Xutong Li. An inductive graph neural network model for compound-protein interaction prediction based on a homogeneous graph
0 -- 0Zimo Huang, Jun Wang, Zhongmin Yan, Maozu Guo 0001. Differentially expressed genes prediction by multiple self-attention on epigenetics data
0 -- 0Wei Liu, Hui Lin, Li Huang, Li Peng, Ting Tang, Qi Zhao, Li Yang. Identification of miRNA-disease associations via deep forest ensemble learning based on autoencoder
0 -- 0Cheng-Hong Yang 0001, Yu-Huei Cheng, Li-Yeh Chuang, Yu-Da Lin. Multiobjective optimization-driven primer design mechanism: towards user-specified parameters of PCR primer
0 -- 0Eric Van Buren, Ming Hu, Liang Cheng, John Wrobel, Kirk Wilhelmsen, Lishan Su, Yun Li, Di Wu. TWO-SIGMA-G: a new competitive gene set testing framework for scRNA-seq data accounting for inter-gene and cell-cell correlation
0 -- 0Lei Wang, Yaqin Tan, Xiaoyu Yang, Linai Kuang, Pengyao Ping. Review on predicting pairwise relationships between human microbes, drugs and diseases: from biological data to computational models
0 -- 0Xue Zhang, Chen Guang Liu, Shi-Hui Yang, Xia Wang, Feng-Wu Bai, Zhuo Wang. Benchmarking of long-read sequencing, assemblers and polishers for yeast genome
0 -- 0Kanghao Shao, Yunhao Zhang, Yuqi Wen, Zhongnan Zhang, Song He, Xiaochen Bo. DTI-HETA: prediction of drug-target interactions based on GCN and GAT on heterogeneous graph
0 -- 0Wenze Ding, Kenta Nakai, Haipeng Gong. Protein design via deep learning
0 -- 0Ruibo Zhang, Souparno Ghosh, Ranadip Pal. Predicting binding affinities of emerging variants of SARS-CoV-2 using spike protein sequencing data: observations, caveats and recommendations
0 -- 0Rashmie Abeysinghe, Yuntao Yang, Mason Bartels, W. Jim Zheng, Licong Cui. An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations
0 -- 0Qiongqiong Feng, Minghua Hou, Jun Liu, Kai-Long Zhao, Guijun Zhang. Construct a variable-length fragment library for de novo protein structure prediction
0 -- 0Qiang Kang, Jun Meng, Yushi Luan. RNAI-FRID: novel feature representation method with information enhancement and dimension reduction for RNA-RNA interaction
0 -- 0Weizhong Zhao, Shujie Luo, Haifang Wu, Xingpeng Jiang, Tingting He, Xiaohua Hu 0001. A multi-label learning framework for predicting antibiotic resistance genes via dual-view modeling
0 -- 0Xia-an Bi, Wenyan Zhou, Sheng Luo, Yuhua Mao, Xi Hu, Bin Zeng 0001, Luyun Xu. Feature aggregation graph convolutional network based on imaging genetic data for diagnosis and pathogeny identification of Alzheimer's disease
0 -- 0Peng Zhou 0003, Li Wen, Jing Lin, Li Mei, Qian Liu, Shuyong Shang, Juelin Li, Jianping Shu. Integrated unsupervised-supervised modeling and prediction of protein-peptide affinities at structural level
0 -- 0Ziwei Chen, Fuzhou Gong, Lin Wan, Liang Ma. BiTSC 2: Bayesian inference of tumor clonal tree by joint analysis of single-cell SNV and CNA data
0 -- 0Zi-Yi Yang, Zhaofeng Ye, Yijia Xiao, Chang-Yu Hsieh, Sheng-yu Zhang. SPLDExtraTrees: robust machine learning approach for predicting kinase inhibitor resistance
0 -- 0Gang Xu, Qinghua Wang, Jianpeng Ma. Expression of Concern to: OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors
0 -- 0Meidan Zhao, Pengqian Wang, Kai Zhang. Bioinformatics/network topology analysis of acupuncture in the treatment of COVID-19: response to methodological issues
0 -- 0Ju Xiang, Xiangmao Meng, Yichao Zhao, Fang-Xiang Wu, Min Li 0007. HyMM: hybrid method for disease-gene prediction by integrating multiscale module structure
0 -- 0Ye Hong, Dani Flinkman, Tomi Suomi, Sami Pietilä, Peter James, Eleanor Coffey, Laura L. Elo. Correction to: PhosPiR: an automated phosphoproteomic pipeline in R
0 -- 0Sare Amerifar, Mahammad Norouzi, Mahmoud Ghandi. A tool for feature extraction from biological sequences
0 -- 0Yixin Yan, Mengyun Yang, Haochen Zhao, Guihua Duan, Xiaoqing Peng, Jianxin Wang 0001. Drug repositioning based on multi-view learning with matrix completion
0 -- 0Wajdi Alghamdi, Muhammad Attique, Ebraheem Alzahrani, Malik Zaka Ullah, Yaser Daanial Khan. LBCEPred: a machine learning model to predict linear B-cell epitopes
0 -- 0Martin Bartas, Adriana Volná, Christopher A. Beaudoin, Ebbe Toftgaard Poulsen, Jirí Cerven, Václav Brázda, Vladimír Spunda, Tom L. Blundell, Petr Pecinka. Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA
0 -- 0Axel Kowald, Israel Barrantes, Steffen Möller, Daniel Palmer, Hugo Murua Escobar, Anne Schwerk, Georg Fuellen. Transfer learning of clinical outcomes from preclinical molecular data, principles and perspectives
0 -- 0Anqi Lin, Chang Qi, Ting Wei, Mengyao Li, Quan Cheng, Zaoqu Liu, Peng Luo, Jian Zhang. CAMOIP: a web server for comprehensive analysis on multi-omics of immunotherapy in pan-cancer
0 -- 0Xiaoyi Guo, Yizhang Jiang, Quan Zou. Structured Sparse Regularized TSK Fuzzy System for predicting therapeutic peptides
0 -- 0Tao Wang, Yongzhuang Liu, Quanwei Yin, Jiaquan Geng, Jin Chen 0004, Xipeng Yin, Yongtian Wang, Xuequn Shang, Chunwei Tian, Yadong Wang, Jiajie Peng. Correction to: Enhancing discoveries of molecular QTL studies with small sample size using summary statistic imputation
0 -- 0Hongchao Ji, Xue Lu, Zhenxiang Zheng, Siyuan Sun, Chris Soon Heng Tan. ProSAP: a GUI software tool for statistical analysis and assessment of thermal stability data
0 -- 0Yuanyuan Ma, Zexuan Sun, Pengcheng Zeng, Wenyu Zhang, Zhixiang Lin. JSNMF enables effective and accurate integrative analysis of single-cell multiomics data
0 -- 0Xiaocong Yang, Yang Liu 0236, Jianhong Gan, Zhixiong Xiao, Yang Cao. FitDock: protein-ligand docking by template fitting
0 -- 0Xiangwen Wang, Yonggang Lu, Xianghong Lin. Heterogeneous cryo-EM projection image classification using a two-stage spectral clustering based on novel distance measures
0 -- 0Xingyu Li, Xue Lin, Xueyin Mei, Pin Chen, Anna Liu, Weicheng Liang, Shan Chang, Jian Li. HLA3D: an integrated structure-based computational toolkit for immunotherapy
0 -- 0Haiyue Wang, Xiaoke Ma. Learning deep features and topological structure of cells for clustering of scRNA-sequencing data
0 -- 0Han-Jing Jiang, Yabing Huang, Qianpeng Li. Spectral clustering of single cells using Siamese nerual network combined with improved affinity matrix
0 -- 0Xuanjin Cheng, Yongxing Liu, Jiahe Wang, Yujie Chen, Andrew Gordon Robertson, Xuekui Zhang, Steven J. M. Jones, Stefan Taubert. cSurvival: a web resource for biomarker interactions in cancer outcomes and in cell lines
0 -- 0César R. García-Jacas, Sergio A. Pinacho-Castellanos, Luis A. García-González, Carlos A. Brizuela. Do deep learning models make a difference in the identification of antimicrobial peptides?
0 -- 0Xiaoyu Guan, Yuqin Wang, Wei Shao 0005, Zhongnian Li, Shuo Huang, Daoqiang Zhang. S2Snet: deep learning for low molecular weight RNA identification with nanopore
0 -- 0Ping Xuan, XiangFeng Meng, Ling Gao, Tiangang Zhang, Toshiya Nakaguchi. Heterogeneous multi-scale neighbor topologies enhanced drug-disease association prediction
0 -- 0Zhihua Du, Yang-Han Wu, Yu-An Huang, Jie Chen, Gui-Qing Pan, Lun Hu, Zhu-Hong You, Jian-qiang Li. GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions
0 -- 0Ping Xuan, Meng Wang, Yong Liu, Dong Wang, Tiangang Zhang, Toshiya Nakaguchi. Integrating specific and common topologies of heterogeneous graphs and pairwise attributes for drug-related side effect prediction
0 -- 0Fei Wu, Yao-Zhong Liu, Binhua Ling. MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
0 -- 0Yaowen Gu, Si Zheng, Zidu Xu, Qijin Yin, Liang Li, Jiao Li. An efficient curriculum learning-based strategy for molecular graph learning
0 -- 0Naveen Duhan, Jeanette M. Norton, Rakesh Kaundal. deepNEC: a novel alignment-free tool for the identification and classification of nitrogen biochemical network-related enzymes using deep learning
0 -- 0Zhonghua Jiang, Yongmei Lu, Zhuochong Liu, Wei Wu, Xinyi Xu, András Dinnyés, Zhonghua Yu, Li Chen, Qun Sun. Mycobacterium tuberculosis based on a hierarchical attentive neural network utilizing genome-wide variants
0 -- 0Rongfan Tang, Pengcheng Chen, Zhe Wang, Lingling Wang, Haiping Hao, Tingjun Hou, Huiyong Sun. Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations
0 -- 0Paul R. Buckley, Chloe H. Lee, Ruichong Ma, Isaac Woodhouse, Jeongmin Woo, Vasily Tsvetkov, Dmitrii S. Shcherbinin, Agne Antanaviciute, Mikhail Shughay, Margarida Rei, Alison Simmons, Hashem Koohy. Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens
0 -- 0Yifan Shang, Xiucai Ye, Yasunori Futamura, Liang Yu, Tetsuya Sakurai. Multiview network embedding for drug-target Interactions prediction by consistent and complementary information preserving
0 -- 0Mengya Liu, Zhan-Li Sun, Zhigang Zeng, Kin-Man Lam 0001. MGF6mARice: prediction of DNA N6-methyladenine sites in rice by exploiting molecular graph feature and residual block
0 -- 0Liang Yu, Yujia Zheng, Bingyi Ju, Chunyan Ao, Lin Gao 0006. Research progress of miRNA-disease association prediction and comparison of related algorithms
0 -- 0Md. Solayman, Thomas Litfin, Jaswinder Singh, Kuldip K. Paliwal, Yaoqi Zhou, Jian Zhan. Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives
0 -- 0Fuxu Wang, Haoyan Wang, Lizhuang Wang, Haoyu Lu, Shizheng Qiu, Tianyi Zang, Xinjun Zhang, Yang Hu 0008. MHCRoBERTa: pan-specific peptide-MHC class I binding prediction through transfer learning with label-agnostic protein sequences
0 -- 0Anna Dal Molin, Enrico Gaffo, Valeria Difilippo, Alessia Buratin, Caterina Tretti Parenzan, Silvia Bresolin, Stefania Bortoluzzi. Correction to: CRAFT a bioinformatics software for custom prediction of circular RNA functions
0 -- 0Xia-an Bi, Lou Li, Zizheng Wang, Yu Wang, Xun Luo, Luyun Xu. IHGC-GAN: influence hypergraph convolutional generative adversarial network for risk prediction of late mild cognitive impairment based on imaging genetic data
0 -- 0Jing Wang, Qinglong Zhang, Junshan Han, Yanpeng Zhao, Caiyun Zhao, Bowei Yan, Chong Dai, Lianlian Wu, Yuqi Wen, Yixin Zhang, Dongjin Leng, Zhongming Wang, Xiaoxi Yang, Song He, Xiaochen Bo. Computational methods, databases and tools for synthetic lethality prediction
0 -- 0Le Huang, Yuchen Yang, Gang Li 0034, Minzhi Jiang, Jia Wen, Armen Abnousi, Jonathan D. Rosen, Ming Hu 0001, Yun Li. A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data
0 -- 0Wenjing Ma, Sumeet Sharma, Peng Jin, Shannon L. Gourley, Zhaohui S. Qin. LRcell: detecting the source of differential expression at the sub-cell-type level from bulk RNA-seq data
0 -- 0Matteo Tiberti, Thilde Terkelsen, Kristine Degn, Ludovica Beltrame, Tycho Canter Cremers, Isabelle da Piedade, Miriam Di Marco, Emiliano Maiani, Elena Papaleo. in silico saturation mutagenesis of protein structures and structural ensembles
0 -- 0Mingsheng Tang, Tong Wang, Xuefen Zhang. A review of SNP heritability estimation methods
0 -- 0Ping Xuan, Zhe Gong, Hui Cui 0002, Bochong Li, Tiangang Zhang. Fully connected autoencoder and convolutional neural network with attention-based method for inferring disease-related lncRNAs
0 -- 0Likun Jiang, Changzhi Jiang, Xinyu Yu, Rao Fu, Shuting Jin, Xiangrong Liu. DeepTTA: a transformer-based model for predicting cancer drug response
0 -- 0Sarah Mubeen, Alpha Tom Kodamullil, Martin Hofmann-Apitius, Daniel Domingo-Fernández. On the influence of several factors on pathway enrichment analysis
0 -- 0Dafei Xie, Song He, Lu Han, Lianlian Wu, Hai Huang, Huan Tao, Pingkun Zhou, Xunlong Shi, Hui Bai, Xiaochen Bo. Systematic optimization of host-directed therapeutic targets and preclinical validation of repositioned antiviral drugs
0 -- 0Ettayapuram Ramaprasad Azhagiya Singam, Martyn T. Smith, David McCoy, Alan E. Hubbard, Michele A. La Merrill, Kathleen A. Durkin. Predicting the binding of small molecules to nuclear receptors using machine learning
0 -- 0Zuguang Gu, Daniel Hübschmann. Improve consensus partitioning via a hierarchical procedure
0 -- 0Dietmar Fernández-Orth, Manuel Rueda, Babita Singh, Mauricio Moldes, Aina Jene, Marta Ferri, Claudia Vasallo, Lauren A. Fromont, Arcadi Navarro, Jordi Rambla. A quality control portal for sequencing data deposited at the European genome-phenome archive
0 -- 0Liangzhen Zheng, Jintao Meng, Kai Jiang, Haidong Lan, Zechen Wang, Mingzhi Lin, Weifeng Li, Hongwei Guo, Yanjie Wei, Yuguang Mu. Improving protein-ligand docking and screening accuracies by incorporating a scoring function correction term
0 -- 0Yu Liu. scDeconv: an R package to deconvolve bulk DNA methylation data with scRNA-seq data and paired bulk RNA-DNA methylation data
0 -- 0Yi-Yang Feng, Hui Yu, Yue-Hua Feng, Jian-Yu Shi. Directed graph attention networks for predicting asymmetric drug-drug interactions
0 -- 0Fei Liu 0006, Monika Heiner, David R. Gilbert. Hybrid modelling of biological systems: current progress and future prospects
0 -- 0Mengya Chai, YaJuan Guo, Liu Yang, Jianhui Li, Shuo Liu, Lei Chen, Yuelei Shen, Yi Yang, Youchun Wang, Lida Xu, Changyuan Yu. A high-throughput single cell-based antibody discovery approach against the full-length SARS-CoV-2 spike protein suggests a lack of neutralizing antibodies targeting the highly conserved S2 domain
0 -- 0Yueming Yin, Haifeng Hu 0004, Zhen Yang 0001, Feihu Jiang, Yihe Huang, Jiansheng Wu. AFSE: towards improving model generalization of deep graph learning of ligand bioactivities targeting GPCR proteins
0 -- 0Liheng Luo, Michael Gribskov, Sufang Wang. Bibliometric review of ATAC-Seq and its application in gene expression
0 -- 0Yachen Liu, Yalan Lin, Wenxian Yang, Yuxiang Lin, Yujuan Wu, Zheyang Zhang, Nuoqi Lin, Xianlong Wang, Mengsha Tong, Rongshan Yu. Application of individualized differential expression analysis in human cancer proteome
0 -- 0Jing Liu, Xinghua Tang, Shuanglong Cui, Xiao Guan. Predicting the function of rice proteins through Multi-instance Multi-label Learning based on multiple features fusion
0 -- 0Mariella Bonomo, Raffaele Giancarlo, Daniele Greco, Simona E. Rombo. Topological ranks reveal functional knowledge encoded in biological networks: a comparative analysis
0 -- 0Talal Ahmed, Mark A. Carty, Stephane Wenric, Jonathan R. Dry, Ameen A. Salahudeen, Aly A. Khan, Eric Lefkofsky, Martin C. Stumpe, Raphael Pelossof. Privacy preserving validation for multiomic prediction models
0 -- 0Rakesh Kaundal, Cristian D. Loaiza, Naveen Duhan, Nicholas Flann. deepHPI: a comprehensive deep learning platform for accurate prediction and visualization of host-pathogen protein-protein interactions
0 -- 0Yulian Ding, Xiujuan Lei, Bo Liao, Fang-Xiang Wu. MLRDFM: a multi-view Laplacian regularized DeepFM model for predicting miRNA-disease associations
0 -- 0Muhammad Toseef, Xiangtao Li, Ka Chun Wong. Reducing healthcare disparities using multiple multiethnic data distributions with fine-tuning of transfer learning
0 -- 0Han-Yuan Zhang, Lei Wang, Zhu-Hong You, Lun Hu, Bo-Wei Zhao, Zheng-Wei Li, Yang-Ming Li. iGRLCDA: identifying circRNA-disease association based on graph representation learning
0 -- 0Yongqing Zhang, Qiang Zhang, Jiliu Zhou, Quan Zou 0001. A survey on the algorithm and development of multiple sequence alignment
0 -- 0Zhenxing Wu, Dejun Jiang, Jike Wang, Xujun Zhang, Hongyan Du, Lurong Pan, Chang-Yu Hsieh, Dongsheng Cao 0001, Tingjun Hou. Knowledge-based BERT: a method to extract molecular features like computational chemists
0 -- 0Ying Yang, Sha Tian, Yushan Qiu, Pu Zhao, Quan Zou 0001. MDICC: novel method for multi-omics data integration and cancer subtype identification
0 -- 0Anna Torkamannia, Yadollah Omidi, Reza Ferdousi. A review of machine learning approaches for drug synergy prediction in cancer
0 -- 0Wenjian Xu, Haochen He, Zhengguang Guo, Wei Li. Evaluation of machine learning models on protein level inference from prioritized RNA features
0 -- 0Yanqing Yang, Deshan Zhou, XinBen Zhang, Yulong Shi, Jiaxin Han, Liping Zhou, Leyun Wu, Minfei Ma, Jintian Li, Shaoliang Peng, Zhijian Xu, Weiliang Zhu. D3AI-CoV: a deep learning platform for predicting drug targets and for virtual screening against COVID-19
0 -- 0Shengpeng Yu, Hong Wang, Tianyu Liu, Cheng Liang, Jiawei Luo 0001. A knowledge-driven network for fine-grained relationship detection between miRNA and disease
0 -- 0Yidi Deng, Jarny Choi, Kim-Anh Lê Cao. Sincast: a computational framework to predict cell identities in single-cell transcriptomes using bulk atlases as references
0 -- 0Jing Li, Ya-Nan Wu, Sen Zhang, Xiao-Ping Kang, Tao Jiang. Deep learning based on biologically interpretable genome representation predicts two types of human adaptation of SARS-CoV-2 variants
0 -- 0Renan Andrades, Mariana Recamonde Mendoza. Machine learning methods for prediction of cancer driver genes: a survey paper
0 -- 0Xiaoman Wang, Lifei Ma, Xiaoya Pei, Heping Wang, Xiaoqiang Tang, Jian-Fei Pei, Yang-Nan Ding, Siyao Qu, Zi-Yu Wei, Hui-Yu Wang, Xiaoyue Wang, Gong-Hong Wei, De-Pei Liu, Houzao Chen. Comprehensive assessment of cellular senescence in the tumor microenvironment
0 -- 0Xiao-Rui Su, Lun Hu, Zhuhong You, Pengwei Hu, Bo-Wei Zhao. Attention-based Knowledge Graph Representation Learning for Predicting Drug-drug Interactions
0 -- 0Keilash Chirom, Md. Zubbair Malik, Irengbam Rocky Mangangcha, Pallavi Somvanshi, R. K. Brojen Singh. Network medicine in ovarian cancer: topological properties to drug discovery
0 -- 0Mingsheng Tang, Tingting Hou, Xiaoran Tong, Xiaoxi Shen, Xuefen Zhang, Tong Wang, Qing Lu. Fast heritability estimation based on MINQUE and batch training
0 -- 0Liwen Xu, Shiwei Zhu, Yujia Lan, Min Yan, Zedong Jiang, Jiali Zhu, Gaoming Liao, Yanyan Ping, Jinyuan Xu, Bo Pang, Yunpeng Zhang, Yun Xiao 0001, Xia Li 0004. Revealing the contribution of somatic gene mutations to shaping tumor immune microenvironment
0 -- 0Miao-Hsia Lin, Pei-Shan Wu, Tzu-Hsuan Wong, I-Ying Lin, Johnathan Lin, Jürgen Cox, Sung-Huan Yu. Benchmarking differential expression, imputation and quantification methods for proteomics data
0 -- 0Amelia Villegas-Morcillo, Angel M. Gomez, Victoria E. Sánchez. An analysis of protein language model embeddings for fold prediction
0 -- 0Yusong Liu, Tongxin Wang, Ben Duggan, Michael F. Sharpnack, Kun Huang 0001, Jie Zhang 0010, Xiufen Ye, Travis S. Johnson. SPCS: a spatial and pattern combined smoothing method for spatial transcriptomic expression
0 -- 0Haohuai He, Guanxing Chen, Calvin Yu-Chian Chen. 3DGT-DDI: 3D graph and text based neural network for drug-drug interaction prediction