Journal: Briefings in Bioinformatics

Volume 24, Issue 3

0 -- 0Hui Zhang, Hongjia Li, Fa Zhang 0001, Ping Zhu. A strategy combining denoising and cryo-EM single particle analysis
0 -- 0Peilin Jia, Ruifeng Hu 0002, Zhongming Zhao. Benchmark of embedding-based methods for accurate and transferable prediction of drug response
0 -- 0Jiashu Liu, Cui-Xiang Lin, Xiaoqi Zhang, Zongxuan Li, Wenkui Huang, Jin Liu, Yuanfang Guan, Hong-Dong Li. Computational approaches for detecting disease-associated alternative splicing events
0 -- 0Jian Liu, Pingjing Li, Jialiang Sun, Jun Guo. LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data
0 -- 0Qi Lu, Ruihan Zhang, Hongyuan Zhou, Dongxuan Ni, Weilie Xiao, Jin Li. MetaHMEI: meta-learning for prediction of few-shot histone modifying enzyme inhibitors
0 -- 0Sikang Chen, Jian Gao, Jiexuan Chen, Yufeng Xie, Zheyuan Shen, Lei Xu, Jinxin Che, Jian Wu, Xiaowu Dong. ClusterX: a novel representation learning-based deep clustering framework for accurate visual inspection in virtual screening
0 -- 0Yi-Gang Chen, Yang-Chi-Dung Lin, Yijun Luo, Xiao-Xuan Cai, Peng Qiu, Shi-Dong Cui, Zhe Wang, Hsi-Yuan Huang, Hsien-Da Huang. Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis
0 -- 0Ruiqiang Lu, Jun Wang, Pengyong Li, Yuquan Li, Shuoyan Tan, Yiting Pan, Huanxiang Liu, Peng Gao, Guotong Xie, Xiaojun Yao. Improving drug-target affinity prediction via feature fusion and knowledge distillation
0 -- 0Zeinab Sherkatghanad, Moloud Abdar, Jérémy Charlier, Vladimir Makarenkov. Using traditional machine learning and deep learning methods for on- and off-target prediction in CRISPR/Cas9: a review
0 -- 0Wei Liu, Yu Yang, Xu Lu, Xiangzheng Fu, Ruiqing Sun, Li Yang, Li Peng. NSRGRN: a network structure refinement method for gene regulatory network inference
0 -- 0Lun Li, Bo Xu, Dongmei Tian, Anke Wang, Junwei Zhu, Cuiping Li 0004, Na Li, Wei Zhao, Leisheng Shi, Yongbiao Xue, Zhang Zhang 0002, Yiming Bao, Wenming Zhao, Shuhui Song. McAN: a novel computational algorithm and platform for constructing and visualizing haplotype networks
0 -- 0Ryuji Hamamoto, Ken Takasawa, Norio Shinkai, Hidenori Machino, Nobuji Kouno, Ken Asada, Masaaki Komatsu, Syuzo Kaneko. Analysis of super-enhancer using machine learning and its application to medical biology
0 -- 0Junwei Luo, Ting Guan, Guolin Chen, Zhonghua Yu, Haixia Zhai, Chaokun Yan, HuiMin Luo. SLHSD: hybrid scaffolding method based on short and long reads
0 -- 0Ajay Subbaroyan, Priyotosh Sil, Olivier C. Martin, Areejit Samal. Leveraging developmental landscapes for model selection in Boolean gene regulatory networks
0 -- 0Wei Xu, Teng Wang, Nan Wang, Haohong Zhang, Yuguo Zha, Lei Ji, Yuwen Chu, Kang Ning 0001. Artificial intelligence-enabled microbiome-based diagnosis models for a broad spectrum of cancer types
0 -- 0Bruna Moreira da Silva, David B. Ascher, Douglas E. V. Pires. epitope1D: accurate taxonomy-aware B-cell linear epitope prediction
0 -- 0Manuel Tognon, Rosalba Giugno, Luca Pinello. A survey on algorithms to characterize transcription factor binding sites
0 -- 0Long-Hao Jia, Yingjian Wu, Yanqi Dong, Jingchao Chen, Wei-Hua Chen, Xing-Ming Zhao. A survey on computational strategies for genome-resolved gut metagenomics
0 -- 0Kai-Li Chang, Jia Hong Chen, Tzu-Chieh Lin, Jun-Yi Leu, Cheng-Fu Kao, Jin Yung Wong, Huai-Kuang Tsai. Short human eccDNAs are predictable from sequences
0 -- 0Fengqi Ge, Chunxiang Peng, Xinyue Cui, Yuhao Xia, Guijun Zhang. Inter-domain distance prediction based on deep learning for domain assembly
0 -- 0Ge Zhang, Zhijie Gao, Chaokun Yan, Jianlin Wang, WenJuan Liang, Junwei Luo, HuiMin Luo. KGANSynergy: knowledge graph attention network for drug synergy prediction
0 -- 0Yue Cao, Shila Ghazanfar, Pengyi Yang, Jean Y. H. Yang. Benchmarking of analytical combinations for COVID-19 outcome prediction using single-cell RNA sequencing data
0 -- 0Koushik Mallick, Sikim Chakraborty, Saurav Mallik, Sanghamitra Bandyopadhyay. A scalable unsupervised learning of scRNAseq data detects rare cells through integration of structure-preserving embedding, clustering and outlier detection
0 -- 0Mingliang Dou, Jiaqi Ding, Genlang Chen, Junwen Duan, Fei Guo 0001, Jijun Tang. IK-DDI: a novel framework based on instance position embedding and key external text for DDI extraction
0 -- 0Niloofar Yousefi, Mehdi Yazdani-Jahromi, Aida Tayebi, Elayaraja Kolanthai, Craig J. Neal, Tanumoy Banerjee, Agnivo Gosai, Ganesh Balasubramanian, Sudipta Seal, Özlem Özmen Garibay. BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing
0 -- 0Hongning Zhang, Mingkun Lu, Gaole Lin, Lingyan Zheng, Wei Zhang, Zhijian Xu, Feng Zhu 0004. SoCube: an innovative end-to-end doublet detection algorithm for analyzing scRNA-seq data
0 -- 0Daoyu Duan, Wen Tang, Runshu Wang, Zhenxing Guo, Hao Feng 0005. Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods
0 -- 0Zhenhua Yu 0002, Furui Liu, Fangyuan Shi, Fang Du. rcCAE: a convolutional autoencoder method for detecting intra-tumor heterogeneity and single-cell copy number alterations
0 -- 0Yan Wang, Chenxu Xuan, Hanwen Wu, Bai Zhang, Tao Ding, Jie Gao. P-CSN: single-cell RNA sequencing data analysis by partial cell-specific network
0 -- 0An-phi Nguyen, Stefania Vasilaki, María Rodríguez Martínez. FLAN: feature-wise latent additive neural models for biological applications
0 -- 0Prem Singh Bist, Hilal Tayara, Kil To Chong. Sars-escape network for escape prediction of SARS-COV-2
0 -- 0Bing Li, Tian Wang, Min Qian, Shuang Wang. MKMR: a multi-kernel machine regression model to predict health outcomes using human microbiome data
0 -- 0Yang Li, Zihou Guo, Keqi Wang, Xin Gao, Guohua Wang. End-to-end interpretable disease-gene association prediction
0 -- 0Marek Justyna, Maciej Antczak, Marta Szachniuk. Machine learning for RNA 2D structure prediction benchmarked on experimental data
0 -- 0Zhenjiao Du, Xingjian Ding, Yixiang Xu, Yonghui Li. UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity
0 -- 0Teng Liu, Zhao-Yu Fang, Xin Li, Li-ning Zhang, Dong-Sheng Cao 0001, Ming-Zhu Yin. Graph deep learning enabled spatial domains identification for spatial transcriptomics
0 -- 0Weihe Dong, Qiang Yang, Jian Wang, Long Xu, Xiaokun Li, Gongning Luo, Xin Gao. Multi-modality attribute learning-based method for drug-protein interaction prediction based on deep neural network
0 -- 0Yan Liu, Guo Wei, Chen Li, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-jun Yu. TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level
0 -- 0Mengsha Tong, Yuxiang Lin, Wenxian Yang, Jinsheng Song, Zheyang Zhang, Jiajing Xie, Jingyi Tian, Shijie Luo, Chenyu Liang 0004, Jialiang Huang, Rongshan Yu. Prioritizing prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer
0 -- 0Ying Liao, Yisha Xiang, Mingjie Zheng 0004, Jun Wang. DeepMiceTL: a deep transfer learning based prediction of mice cardiac conduction diseases using early electrocardiograms
0 -- 0Feng Chen, Yubo Bai, Chunhe Li. Estimation of non-equilibrium transition rate from gene expression data
0 -- 0Federico Gossi, Pushpak Pati, Panagiotis Chouvardas, Adriano Luca Martinelli, Marianna Kruithof-de Julio, Maria Anna Rapsomaniki. Matching single cells across modalities with contrastive learning and optimal transport
0 -- 0Guangshuai Wang, Tao Wu, Wei Ning, Kaixuan Diao, Xiaoqin Sun, Jinyu Wang, Chenxu Wu, Jing Chen, Dongliang Xu, Xue-Song Liu. TLimmuno2: predicting MHC class II antigen immunogenicity through transfer learning
0 -- 0Feng Zhang, Huiyuan Jiao, Yihao Wang, Chen Yang, Linying Li, Zhiming Wang, Ran Tong, Junmei Zhou, Jianfeng Shen, Lingjie Li. InferLoop: leveraging single-cell chromatin accessibility for the signal of chromatin loop
0 -- 0Hailin Wei, Tong Han, Taiwen Li, Qiu Wu, Chenfei Wang. SCREE: a comprehensive pipeline for single-cell multi-modal CRISPR screen data processing and analysis
0 -- 0Martin Bishop. Editorial
0 -- 0Kaixuan Xiao, Yu Wang, Kangning Dong, Shihua Zhang. SmartGate is a spatial metabolomics tool for resolving tissue structures
0 -- 0Yijia Li, Jonathan Nguyen, David C. Anastasiu, Edgar A. Arriaga. CosTaL: an accurate and scalable graph-based clustering algorithm for high-dimensional single-cell data analysis
0 -- 0Ruyi Chen, Fuyi Li, Xudong Guo, Yue Bi, Chen Li 0021, Shirui Pan, Lachlan J. M. Coin, Jiangning Song. ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species
0 -- 0Tong Zhang, Shao-Wu Zhang, Ming-Yu Xie, Yan Li. A novel heterophilic graph diffusion convolutional network for identifying cancer driver genes
0 -- 0. Correction to: Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design
0 -- 0Hongli Gao, Bin Zhang 0042, Long Liu, Shan Li, Xin Gao, Bin Yu 0007. A universal framework for single-cell multi-omics data integration with graph convolutional networks
0 -- 0Tao Wu, Yao Dai, Yue Xu, Jie Zheng, Shuting Chen, Yinuo Zhang, Peng Tian, Xiaoqi Zheng, Haiyun Wang. ExosomePurity: tumour purity deconvolution in serum exosomes based on miRNA signatures
0 -- 0Joshua Teitz, Jörg Sander 0001, Hassan Sarker, Carlos Fernandez-Patron. Potential of dissimilarity measure-based computation of protein thermal stability data for determining protein interactions
0 -- 0Xiaoqiang Huang, Jun Zhou, Dongshan Yang, Jifeng Zhang, Xiaofeng Xia, Yuqing Eugene Chen, Jie Xu. Decoding CRISPR-Cas PAM recognition with UniDesign
0 -- 0Ying-Ying Zhang, De-Min Liang, Pu-Feng Du. iEssLnc: quantitative estimation of lncRNA gene essentialities with meta-path-guided random walks on the lncRNA-protein interaction network
0 -- 0Yuting Zhou, Yongquan Jiang, Yan Yang. AGAT-PPIS: a novel protein-protein interaction site predictor based on augmented graph attention network with initial residual and identity mapping
0 -- 0Fatemeh Farhadi, Mohammad Allahbakhsh, Ali Maghsoudi, Nadieh Armin, Haleh Amintoosi. DiMo: discovery of microRNA motifs using deep learning and motif embedding
0 -- 0Sumit Mukherjee, Matan Drory Retwitzer, Sara M. Hubbell, Michelle M. Meyer, Danny Barash. A computational approach for the identification of distant homologs of bacterial riboswitches based on inverse RNA folding
0 -- 0. Correction to: Quantum computing algorithms: getting closer to critical problems in computational biology
0 -- 0Yushan Qiu, Chang Yan, Pu Zhao, Quan Zou 0001. SSNMDI: a novel joint learning model of semi-supervised non-negative matrix factorization and data imputation for clustering of single-cell RNA-seq data
0 -- 0Qianmu Yuan, Junjie Xie, Jiancong Xie, Huiying Zhao, Yuedong Yang. Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion
0 -- 0Hongjia Liu, Huamei Li, Amit Sharma, Wenjuan Huang, Duo Pan, Yu Gu, Lu Lin, Xiao Sun 0006, Hongde Liu. scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets
0 -- 0Yuanchun Zhao, Xingqi Chen, Jiajia Chen, Xin Qi. Decoding Connectivity Map-based drug repurposing for oncotherapy
0 -- 0Anna Klimovskaia Susmelj, Yani Ren, Yann Vander Meersche, Jean-Christophe Gelly, Tatiana Galochkina. Poincaré maps for visualization of large protein families
0 -- 0Ke Shen, Ahmad Ud Din, Baivab Sinha, Yi Zhou, Fuliang Qian, Bairong Shen. Translational informatics for human microbiota: data resources, models and applications
0 -- 0Camilo Rebolledo, Juan Pablo Silva, Nicolás Saavedra, Vinicius Maracaja-Coutinho. in silico characterization
0 -- 0Hang Zhao, Pin-yuan Dai, Xiao-jin Yu, Jieyu He, Chao Zhao, Li-hong Yin. Evaluation of graphical models for multi-group metabolomics data
0 -- 0Yongfan Ming, Wenkang Wang, Rui Yin 0002, Min Zeng, Li Tang, Shizhe Tang, Min Li 0007. A review of enzyme design in catalytic stability by artificial intelligence
0 -- 0Qikai Niu, Hongtao Li, Lin Tong, Sihong Liu, Wenjing Zong, Siqi Zhang, Siwei Tian, Jingai Wang, Jun Liu, Bing Li, Zhong Wang, Huamin Zhang. TCMFP: a novel herbal formula prediction method based on network target's score integrated with semi-supervised learning genetic algorithms
0 -- 0Mohammad Rizwan Alam, Kyung Jin Seo, Jamshid Abdul-Ghafar, Kwangil Yim, Sung-Hak Lee, Hyun-Jong Jang, Chan Kwon Jung, Yosep Chong. Recent application of artificial intelligence on histopathologic image-based prediction of gene mutation in solid cancers
0 -- 0Yiyou Song, Yue Wang, Xuan Wang, Daiyun Huang, Anh Nguyen, Jia Meng. Multi-task adaptive pooling enabled synergetic learning of RNA modification across tissue, type and species from low-resolution epitranscriptomes
0 -- 0Xin-Fei Wang, Changqing Yu, Zhu-Hong You, Li-ping Li, Wenzhun Huang, Zhong-Hao Ren, Yue-Chao Li, Weixiao Meng 0001. A feature extraction method based on noise reduction for circRNA-miRNA interaction prediction combining multi-structure features in the association networks
0 -- 0Minghao Jiang, Shiyan Zhang, Hongxin Yin, Zhiyi Zhuo, Guoyu Meng. A comprehensive benchmarking of differential splicing tools for RNA-seq analysis at the event level
0 -- 0Xin Wang, Xin Gao, Guohua Wang, Dan Li. miProBERT: identification of microRNA promoters based on the pre-trained model BERT
0 -- 0Jun Wang 0035, Xi Chen, Zhengtian Wu, Maozu Guo 0001, Guoxian Yu. Cooperative driver pathways discovery by multiplex network embedding
0 -- 0Zheng Ye, Shaohao Li, Xue Mi, Baoyi Shao, Zhu Dai, Bo Ding, Songwei Feng, Bo Sun, Yang Shen, Zhongdang Xiao. STMHCpan, an accurate Star-Transformer-based extensible framework for predicting MHC I allele binding peptides
0 -- 0Meng Wang, Lukasz A. Kurgan, Min Li. A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction
0 -- 0Akshay Khanduja, Manish Kumar, Debasisa Mohanty. ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes
0 -- 0Fatima Noor, Muhammad Asif, Usman Ali Ashfaq, Muhammad Qasim, Muhammad Tahir Ul Qamar. Machine learning for synergistic network pharmacology: a comprehensive overview
0 -- 0Jing Jiang, Junlin Xu, Yuansheng Liu, Bosheng Song, Xiulan Guo, Xiangxiang Zeng, Quan Zou 0001. Dimensionality reduction and visualization of single-cell RNA-seq data with an improved deep variational autoencoder
0 -- 0Ke Xu, Chinwang Cheong, Werner P. Veldsman, Aiping Lyu, William K. Cheung, Lu Zhang. Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute
0 -- 0Zengrui Guan, Zhenran Jiang. Transformer-based anti-noise models for CRISPR-Cas9 off-target activities prediction
0 -- 0Kechi Fang, Chuan Li, Jing Wang. An automatic immunofluorescence pattern classification framework for HEp-2 image based on supervised learning
0 -- 0Xiao Wang, Lijun Han, Rong Wang, Haoran Chen. DaDL-SChlo: protein subchloroplast localization prediction based on generative adversarial networks and pre-trained protein language model
0 -- 0Jiaqi Luo, Xueying Wang, Yiping Zou, Lingxi Chen, Wei Liu, Wei Zhang, Shuai Cheng Li. Quantitative annotations of T-Cell repertoire specificity
0 -- 0Pablo Acera Mateos, You Zhou, Kathi Zarnack, Eduardo Eyras. Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning