Journal: Briefings in Bioinformatics

Volume 26, Issue 5

0 -- 0Hongxu Zhu, Amir Asiaee, Leila Azinfar, Jun Li, Han Liang, Ehsan Irajizad, Kim-Anh Do, James P. Long. in-silico perturbation methods in identifying differentially expressed genes
0 -- 0Yinyin Gong, Rui Li 0019, Yan Liu 0032, Jilong Wang 0002, Danny Z. Chen, Chee-Keong Kwoh 0001. DeepPhosPPI: a deep learning framework with attention-CNN and transformer for predicting phosphorylation effects on protein-protein interactions
0 -- 0Yu Wang, Haichun Yang, Ruining Deng, Yuankai Huo, Qi Liu 0024, Yu Shyr, Shilin Zhao. stImage: a versatile framework for optimizing spatial transcriptomic analysis through customizable deep histology and location informed integration
0 -- 0Rami Zakh, Alexander Churkin, Marina Parr, Tamir Tuller, Ohad Etzion, Harel Dahari, Danny Barash. The bioinformatics of the finding that the hepatitis delta virus RNA editing mechanism by a conformational switch exists in genotype 7 in addition to genotype 3
0 -- 0Linyang Jiang, Xiaodi Yang, Xiaokun Guo, Dianke Li, Jiajun Li, Stefan Wuchty, Wenyu Shi, Ziding Zhang. Graph neural network integrated with pretrained protein language model for predicting human-virus protein-protein interactions
0 -- 0Yingxuan Ren, Fengtao Ren, Bo Yang 0041. Multi-layer matrix factorization for cancer subtyping using full and partial multi-omics dataset
0 -- 0John Lee, Canh Hao Nguyen, Hiroshi Mamitsuka. Beyond rigid docking: deep learning approaches for fully flexible protein-ligand interactions
0 -- 0Geng-Ming Hu, Hsin Wei Chen, Chi-Ming Chen. Mapping cancer heterogeneity: a consensus network approach to subtypes and pathways
0 -- 0Guosheng Gu, Haowei Wu, Haojie Han, Zhiyi Lin, Yuping Sun, Guobo Xie, Qing Su, Zhenguo Liu. MVSGDR: multi-view stacked graph convolutional network for drug repositioning
0 -- 0Youna Cho, Erin Kim, Minyoung Kim, Mina Rho. DeepMobilome: predicting mobile genetic elements using sequencing reads of microbiomes
0 -- 0Yanwen Shao, Zhihao Guo, Jinpeng Chen, Runsheng Li. SLRanger: an integrated approach for spliced leader detection and operon prediction using long RNA reads
0 -- 0Hao Wang, Guoqing Hu, Stephen S.-T. Yau. Energy entropy vector: a novel approach for efficient microbial genomic sequence analysis and classification
0 -- 0Junxin Li, Chao Zhang, Wei Xia, Hei Wun Kan, Kaifang Huang, Sai Li, Mark Akinola Ige, Qiuliyang Yu, Jiawei Zhao, Xiaochun Wan, John Z. H. Zhang, Haiping Zhang. Significantly enhancing human antibody affinity via deep learning and computational biology-guided single-point mutations
0 -- 0Kailun Bai, Belaid Moa, Xiaojian Shao, Xuekui Zhang. scSorterDL: a deep neural network-enhanced ensemble LDAs for single cell classifications
0 -- 0Junlei Yu, Wenjia Gao, Siqi Chen 0001, Ronglin Lu, Jianbo Qiao, Junru Jin, Leyi Wei, Hua Shi, Zilong Zhang, Feifei Cui, Xinbo Jiang, Zhongmin Yan. MCAMEF-BERT: an efficient deep learning method for RNA N7-methylguanosine site prediction via multi-branch feature integration
0 -- 0Yaowu Zhang, Xiu Jin, Xiaodan Zhang. GCNMF-SDA: predicting snoRNA-disease associations based on graph convolution and non-negative matrix factorization
0 -- 0Shenjie Wang, Xiaonan Wang, Xiaoyan Zhu, Xuwen Wang, Yuqian Liu, Minchao Zhao, Zhili Chang, Yang Shao, Haitao Zhang, Shuanying Yang, Jiayin Wang. TMBquant: an explainable AI-powered caller advancing tumor mutation burden quantification across heterogeneous samples
0 -- 0Xiang Li, Wei Peng, Xiaolei Zhu 0001. Predicting nucleic acid binding sites by attention map-guided graph convolutional network with protein language embeddings and physicochemical information
0 -- 0Carolin Charlotte Wendling, Marie Vasse, Sébastien Wielgoss. Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world
0 -- 0Huayu Zhong, Juanji Wang, Xiaoxiao Liu, Xiaoyun Wei, Chengcheng Zhou, Taiyan Zou, Xin Han, Lingyun Mo, Wenling Qin, Yonghong Zhang. A multi-dimensional computational framework of drug-induced hepatotoxicity: integrating molecular structure features with disease pathogenesis