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ORCIDIEEE Transactions on Computational Biology and Bioinformatics, Volume 23
Volume 23, Number 1, January - February 2026
- Sarwan Ali
, Prakash Chourasia, Bipin Koirala, Murray Patterson:
Nearest Neighbor CCP-Based Molecular Sequence Analysis. 1-13 - Faezeh Sadeghi, Mohammadreza Pourfard, Maryam Talebi Rostami, Seyed Ahmad Motamedi:
GEXPNET: A Novel Gene EXPression NETwork for Tumor Classification Using the ResNet-Based Deep Learning Approach. 14-26 - Somnath Mondal, Debarghya Datta, Soumajit Pramanik, Rukmankesh Mehra:
UniGEN-DDI: Computing Drug-Drug Interactions Using a Unified Graph Embedding Network. 27-38 - He Zhao, Tao Wang, Huan Xu, Guixia Liu:
GTLSTMEP: A Novel Model Based on Graph Transformer and bi-LSTM for Predicting Essential Proteins in Sampled Subgraphs. 39-52 - Tjeerd V. Olde Scheper, Alex Silverthorne, Holly Tonks, Karl J. Morten:
Allosteric Rate Control of Chaos Governs Reaction Rate Kinetics. 53-64 - Doruk Topcu, Ebru Akçapinar Sezer:
ASAP-ML: Antibiotic Susceptibility and Antibiogram Prediction With Machine Learning Methods. 65-74 - Beyza Kaya, Emre Sefer:
GAT-HiC: Efficient Reconstruction of 3D Chromosome Structure via Residual Graph Attention Neural Networks. 75-88 - Chen Song, Shidong Wu, Xiankun Zhang, Mengyu Li, Tao Li:
Sequence to Location: Protein Subcellular Localization Driven by Deep Pretrained Language Model. 89-100 - Juan Antonio Villatoro-García, Pablo Pedro Jurado-Bascón, Pedro Carmona-Saez:
Effect Size-Driven Pathway Meta-Analysis for Gene Expression Data. 101-111 - Lin Zhang, Feng Wang, Jiani Ma, Hui Liu:
scDBImpute: Dual-Branch Imputation for Single-Cell RNA-Seq Data Dropouts. 112-121 - Dayu Hu, Renxiang Guan, Zhibin Dong, Ke Liang, Jun Wang, Siwei Wang, Xinwang Liu:
Single-Cell Multi-View Clustering via Community Detection With Unknown Number of Clusters. 122-133 - Yangfeng Zhu, Yongxian Fan, Guicong Sun:
iDRKAN: Interpretable miRNA-Disease Association Prediction Based on Dual-Graph Representation Learning and Kolmogorov-Arnold Network. 151-162 - Weipeng Lv, Changkun Jiang, Jianqiang Li:
Spatial Hierarchical Protein-Protein Interaction Site Prediction Using Squeeze-and-Excitation Capsule Networks. 163-175 - Xiao Kang, Licai Zhang, Xinxing Yang, Lin Wang, Genke Yang, Jian Chu:
A Graph Attention Network-Based Spatial Decomposition Method for Drug Repositioning. 176-188 - Sa Li, Jonah Shader, Abhijeet Bhattacharya, Tianle Ma:
Integration of Multi-Omics Data With Topology Adaptive Graph Convolutional Network for Cancer Driver Gene Identification. 189-199 - Abdulyekeen T. Adebisi, Kalyana C. Veluvolu:
Graph Theory Approach for the Control of COVID-19 Diffusion. 200-210 - Yue Zhang, Yuting Bai, Endai Guo, Yi Liao, Kening Zhao, Weitian Huang, Hongmin Cai:
EPILOGUE: Multi-View Graph Contrastive Learning for Gene Function Prediction. 211-223 - Wenhao Zheng, Peidong Liu, Hanwen Zhang, Chenwei Sun, Xiong Deng, Xianggen Liu, Jiancheng Lv:
ProtoDiff: Prototypical Diffusion Model for Few-Shot Molecular Image Generation. 224-235 - Jian Zhong, Haochen Zhao, Guihua Duan, Shaokai Wang:
MMFF-DDI: A Multi-Modal Fusion Framework for Drug-Drug Interaction Event Prediction With Contrastive Learning. 236-246 - Buchao Zhan, Dongmei He, Xin Yang, Zilong Zhang, Shankai Yan:
FNatPred: A Data-Driven Approach for Distinguishing Between NAT and Tumor on the Fungal Microbiome. 247-258 - Yue Huang, Dandan Li, Weizhong Zhao, Xianjun Shen:
A Novel Drug Repositioning Method Using Meta-Path Aggregating via Hierarchical Attention Mechanism. 259-270 - Mijin Kwon, Young Min Woo, Woochang Hwang, Jong-Won Kim, Doheon Lee:
SOCAR: Network-Based Computational Framework to Overcome Acquired Tamoxifen Resistance of MCF7 Cells. 271-283 - Guosheng Gu, Haojie Han, Haowei Wu, Yuping Sun, Ping Liu, Guihua Jiang, Jiehang Deng, Guobo Xie, Jiazhou Chen:
H$^{3}$CDR : An Anti-Cancer Drug Response Prediction Model Driven by Heterogeneous and Homogeneous Hybrid Graph Neural Network. 284-296 - Yuanyuan Zhang, Wenying Li, Zhennuo Wang, Shuang Du, Shaoqiang Wang:
Synthetic Assessment of Transfer Learning Method From Cell Lines to Single-Cell on Drug Response Prediction. 297-312 - Hui Yang, Dangguo Shao, Jie Zhou, Lei Ma:
iDeep-Cancer: Predicting Cancer-Related circRNA-RBP Binding Sites Using a Hybrid Network Framework. 313-325 - Jinwei Wang, Zhenjie Luo, Aoyun Geng, Junlin Xu, Yajie Meng, Shankai Yan, Leyi Wei, Zilong Zhang, Qingchen Zhang, Quan Zou, Feifei Cui:
DeepNhKcr: Explainable Deep Learning Framework for the Prediction of Crotonylation Sites of Non-Histone Lysine in Plants Based on Pre-Trained Protein Language Model. 326-340 - Balaiah Kukkala, Akshay Deepak, Vikash Kumar, Aravind Prakash:
Multi-DeepProtGraphGO: Integrating GCN on PPI Networks With Sequence-Driven Convolutional Bi-LSTM and Attention for Protein Function Prediction. 341-352 - Patrik Waldmann, Yuhua Fan:
A Proximal Multi-Objective Optimization Method for Incorporation of Polygenic Breeding Values in Genomic Prediction. 353-361 - Shuwen Xiong, Feifei Cui, Zilong Zhang, Rao Zeng, Ran Su, Leyi Wei:
A Multi-Modal Contrastive Learning Framework for Cyclic Peptide Permeability Prediction. 362-373 - Hanwen Zhou, Wei Zhang, Zhaohong Deng, Guanjin Wang, Zhisheng Wei, Lei Wang, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu, Jing Wu:
SMENET: A Multi-View Semantic Model for Multi-Level Enzyme Function Prediction. 374-385 - Jeongho Park, Kyuri Jo:
DriverMONI: Cancer Driver Gene Prediction With Multimodal Deep Learning Integrating Multiomics Data and Condition-Specific Network Information. 386-394 - Jinmiao Song, Bin Xu, Lei Deng, Qimeng Yang, Qiguo Dai, Shengwei Tian:
HECLCDA:CircRNA-Drug Sensitivity Prediction via Heterogeneous Cross-Scale Contrastive Learning. 395-406 - Zhikai Lin, Jing Chen, Lianlian Wu, Kunhong Liu, Yong Xu, Song He, Xiaochen Bo:
MOCT: A Multi-Class Oblique Tree Algorithm for Synergistic Drug Combination Prediction. 407-418 - Jiahao Yuan, Shun Gao, Ziyuan Yan, Feifei Cui, Leyi Wei, Qingchen Zhang, Quan Zou, Zilong Zhang:
DeepR2OM: Accurate Recognition for RNA 2′-O-Methylation Sites in Human Genome Using Deep Learning. 419-431 - Fengfan Zhou, Xinqi Chen, Yusheng Jiang, Jinting Guan:
MISF: Multimodal Data Integration Through Adaptive Similarity Learning and Matrix Factorization. 432-443 - Benjun Tang, Xiuzhen Hu, Yuqian Yao, Shaohua Chen:
SG-DCNN: A Deep Learning Method Integrating Self-Attention Mechanism and Generative Adversarial Network for Predicting Ion-Ligand Binding Residues in Small Samples. 444-455 - Junqi Wu, Liyan Dong, Longyi Li, Hao Zhang:
GALA: Integrating Weighted Graph Walks and Latent-Space Adversarial Training for Single-Cell Batch Alignment. 456-468 - Pengli Lu, Zhong Yan, Fentang Gao:
Multi-Head Hypergraph Convolution With Feature Enhancement and Latent Representation Learning for miRNA-Disease Association Prediction. 469-482 - Hao Zhang, Xianghui Su, Shihua Fu, Jie Zhong, Feifei Yang:
Asynchronous Controllability of Non-Homogeneous Markov Switch Generalized Asynchronous Boolean Control Networks With Deterministic Dwell Time. 483-493 - Jinmiao Song, Yang Meng, Lei Deng, Qimeng Yang, Qiguo Dai, Shengwei Tian:
HHGSynergy: An Adaptive Heterogeneous Hypergraph Representation Learning Method for Anticancer Drug Synergy Prediction. 494-505 - Aishik Chanda, Ashmita Dey, Mrittika Chakraborty, Utsav Bandyopadhyay Maulik, Sanghamitra Bandyopadhyay:
Drug Effect Classification Using Frequency-Based Graph Traversal Approach. 506-517 - Zheng Zhang, Tong Luo, Xiangan Chen, Xiaofei Yang, Jihong Gong:
Multimodal Hypergraph Representation Learning for Drug Synergy Prediction. 518-527 - Binrui Wang, Yongping Du, Xingnan Jin, Zikai Wang:
Efficient Tuning Framework for Resource- Constrained Biomedical Question Answering. 528-538 - Sandhya Gubbala, Santhosh Amilpur, Chandra Mohan Dasari:
Dynamic Bernstein GCN for Pan-Cancer Subtype Classification Using RNA-Seq and CNV Data. 539-551 - Li Zhou, Dechen Xu, Feng Zhu, Jiahuan Jin, Zhengnan Zhao, Jie Li:
The Pathway-Informed Deep Learning Models in Cancer Research: A Survey. 134-150
Volume 23, Number 2, March - April 2026
- Min Li, Feng Luo, Yi-Ping Phoebe Chen:
Guest Editorial for the 21th Asia Pacific Bioinformatics Conference. 558-559 - Kai Zheng, Guihua Duan, Qichang Zhao, Mengyun Yang, Xiao Liang, Yiwei Liu, Jianxin Wang:
DLP: Duplex Link Prediction via Subspace Segmentation for Predicting Drug-MiRNA Associations. 560-568 - Wei Lan, Jianwei Chen, Mingyang Liu, Qingfeng Chen, Jin Liu, Jianxin Wang, Yi-Ping Phoebe Chen:
Deep Imputation Bi-Stochastic Graph Regularized Matrix Factorization for Clustering Single-Cell RNA-Sequencing Data. 569-578 - Gao-Fei Wang, Juan Wang, Shasha Yuan, Chun-Hou Zheng, Jin-Xing Liu:
MLRR-ATV: A Robust Manifold Nonnegative Low-Rank Representation With Adaptive Total-Variation Regularization for scRNA-seq Data Clustering. 579-588 - Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Nastaran Hajinazar, Mohammed Alser, Can Alkan, Onur Mutlu:
AirLift: A Fast and Comprehensive Technique for Remapping Alignments Between Reference Genomes. 589-597 - Tanveer Ahmad, Joseph Schuchart, Zaid Al-Ars, Christoph Niethammer, José Gracia, H. Peter Hofstee:
GenMPI: Cluster Scalable Variant Calling for Short/Long Reads Sequencing Data. 598-610 - Sha Tian, Ying Yang, Yushan Qiu, Quan Zou:
SMCC: A Novel Clustering Method for Single- and Multi-Omics Data Based on Co-Regularized Network Fusion. 611-618 - Kuiyang Che, Qiao Ning, Ruijie Li, Xirun Wei, Hui Li, Shikai Guo:
Cross Attention and Intra-Layer Attention in Heterogeneous Graph Neural Networks for Drug-Target Interaction Prediction. 619-630 - Manvel Gasparyan, Satya Tamby, Gubbi Vani HarshaRani, Upinder S. Bhalla, Ovidiu Radulescu:
Automated Hierarchical Block Decomposition of Biochemical Networks. 631-643 - Gopikrishna Deshpande, Bonian Lu, Nguyen Huynh, D. Rangaprakash:
Transfer Learning for Improving Neuroimaging-Based Diagnostic Classification. 644-657 - Ziyang Wang, Yangkun Zheng, Ridi Wen, Haoyu Hua, Xiaoli Lu, Xiaoping Min:
PocketStruct: Integrating Protein Pocket Structural Features for Protein-Peptide Binding Prediction. 658-669 - Xiaojian Ding, Pengcheng Shi, Xin Wang, Hui Cao:
Survival-Informed Multi-Omics Kernel Fusion for Cancer Subtyping. 670-681 - Xihong Yuan, Chizhuo Ma, Zhichao Lei, Chuzheng Wang:
DeepTESite: The Prediction of Protein Arginine Methylation Sites Using Amino Acids Sequence Symmetric Position Encodings Based on Transformer Encoder. 682-693 - Poorya Khajouie, Titli Sarkar, Krishna Rauniyar, Li Chen, Wu Xu, Vijay Raghavan:
SSE-TSR: An Approach to Integrate Secondary Structure Elements Into Triangular Spatial Relationships for Protein Classification. 694-703 - Qinghui Weng, Mingyi Hu, Guohao Peng, Wenwei Lu, Hongchao Wang, Jinlin Zhu:
Variational Bayesian Multi-Output Gaussian Process Regression for Metabolic Profiles Prediction With Microbiome Data. 704-716 - Chenfei Wang, Yunping Wang, Qinghan Xue, Zhiheng Zhou, Guiying Yan, Xingqin Qi:
Classification of Alzheimer's Disease by Modeling Brain Networks as Signed Networks Under Deep Learning Frameworks. 717-726 - Mahendra Kumar, Navin Chandra, Avinash Kumar, Nitin Chandra:
Binding Possibilities of Cro-, λ-, and Gal-Repressor Proteins With SARS-CoV-2 Genomes: A Computational Approach for Potential Drug/Vaccine Design. 727-736 - Büsra Özgöde Yigin, Gorkem Saygili, Pieter Spronck:
Confidence-Based Batch Ordering in Continual Learning: A Curriculum Learning Approach for Single-Cell RNA Sequencing Data. 737-747 - Md. Mustahid Hasan, Md. Ashikur Rahman, Md Mamun Ali, Kawsar Ahmed, Francis M. Bui, Sobhy M. Ibrahim, Imran Mahmud, Mohammad Ali Moni:
Deep_TPPred: Improved Prediction of Protein Toxicity Using Feature Fusion and Hybrid Neural Network Approach. 748-759 - Kaiwen Tan, Yun Bai, Yongbing Zhang, Zhenqiu Shu, Zhengtao Yu:
scDGCL: A Dual-Level and Graph-Constrained Contrastive Learning Method for Single-Cell RNA Sequencing Data Clustering. 760-773 - Yin Shen, Xuan Xu, Shuaibin Wang, Tong Chen, Zihao Zhang, Qiaoyu Sun, Xuan Sun, Zhen Liang, Junxiang Gao:
TransSE: A Transfer Learning-Based Predictive Model for Distinguishing Super Enhancers and Typical Enhancers. 774-787 - Bertil Schmidt, Felix Kallenborn, Alexander Wichmann, Alejandro Chacón, Christian Hundt:
gpuPairHMM: High-Speed Pair-HMM Forward Algorithm for DNA Variant Calling on GPUs. 788-794 - Yue Wang, Yanan Li, Changjiang Zhou, Xiao Ma, Ji Qi:
HFFST: A Hierarchical Feature Fusion Algorithm for Spatial Gene Expression Prediction Using Histopathology Images. 795-804 - Pragya, Jac Fredo Agastinose Ronickom:
Artificial Intelligence Driven Virtual Screening and Molecular Docking Approaches Identified LIFR, BTG2, EPHX2, and PAK3 as Targets and BI-2536, AP-24534, and AZ-628 as Repurposed Drugs for PDAC. 805-816 - Wenchuan Zhang, Yujian Lee, Ricky Yuen-Tan Hou, Weifeng Su, Hong Yan, Wentao Fan:
Bayesian Hyperspherical Graph Mixture-of-Experts Deciphers Cell-Cell Interaction in Spatial Transcriptomics. 817-830 - Haitao Ma, Zhenkang Hu, Jiale Tu, Xuxian Zhou, Yuhai Zhao, Changyong Yu:
Different Graph-Level Attention Based on Multi-Scale for Predicting lncRNA-Disease Associations. 831-842 - Shuangshuang Wang, Meiling Liu, Jiyun Zhou:
PEGN-PSP: Prediction of General Protein Phosphorylation Sites Using Protein Embeddings and Graph Neural Network. 843-852 - Sizhe Wang, Zhichao Zhou, Chen Li, Yudong Cai, Jiong Wang, Zhuangbiao Zhang, Ran Li, Zhannur Niyazbekova, Yu Jiang, Quanzhong Liu:
AGEP_TWAS: A Deep Learning-Based Framework for Predicting Gene Expression Levels in Tissues. 853-862 - Tanjin Taher Toma, Yibo Wang, Andreas Gahlmann, Scott T. Acton:
Deep Temporal Sequence Classification and Mathematical Modeling for Cell Tracking in Dense 3D Microscopy Videos of Bacterial Biofilms. 863-876 - Suprativ Saha, Rupak Bhattacharyya, Swarup Kumar Ghosh, Tanmay Bhattacharya:
Rule-Based Protein Classification Through Multi-Phase Feature Extraction Technique. 877-890 - Yue Yin, Jiaoyun Yang, Ning An:
SCImputation: Mitigating Feature Confounding From a Structural Causal Perspective for Data Imputation. 891-903
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last updated on 2026-06-11 23:11 CEST by the dblp team
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