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ORCIDIEEE Transactions on Computational Biology and Bioinformatics, Volume 22
Volume 22, Number 1, 2025
- Front Cover. 1-
- Phasit Charoenkwan, Nalini Schaduangrat, Mohammad Ali Moni
, Watshara Shoombuatong:
iMRSA-Fuse: A Fast and Accurate Computational Approach for Predicting Anti-MRSA Peptides by Fusing Multi-View Information. 2-12 - Tazin Rahman, Oieswarya Bhowmik, Ananth Kalyanaraman:
An Efficient Parallel Sketch-Based Algorithmic Workflow for Mapping Long Reads. 13-26 - Haosheng Zhou, Wei Lin, Sergio R. Labra, Stuart A. Lipton, Jeremy A. Elman, Nicholas J. Schork, Aaditya V. Rangan:
Detecting Boolean Asymmetric Relationships With a Loop Counting Technique and its Implications for Analyzing Heterogeneity Within Gene Expression Datasets. 27-38 - Bryan A. Dawkins, Brett A. McKinney:
Multivariate Optimization of k for k-Nearest-Neighbor Feature Selection With Dichotomous Outcomes: Complex Associations, Class Imbalance, and Application to RNA-Seq in Major Depressive Disorder. 39-51 - C. Vishnuppriya, TamilPavai Gurusamy:
Performance Comparison Between Deep Neural Network and Machine Learning Based Classifiers for Huntington Disease Prediction From Human DNA Sequence. 52-63 - Snehalika Lall, Sumanta Ray, Sanghamitra Bandyopadhyay:
Enhancing Single-Cell RNA-Seq Data Completeness With a Graph Learning Framework. 64-72 - Jia Wang, Zhenjing Yu, Jianqiang Li:
LHPre: Phage Host Prediction With VAE-Based Class Imbalance Correction and Lyase Sequence Embedding. 73-84 - Mir Tanveerul Hassan, Hilal Tayara, Kil To Chong:
iAnOxPep: A Machine Learning Model for the Identification of Anti-Oxidative Peptides Using Ensemble Learning. 85-96 - Flora Rajaei, Cristian Minoccheri, Emily Wittrup, Richard C. Wilson, Brian D. Athey, Gilbert S. Omenn, Kayvan Najarian:
AI-Based Computational Methods in Early Drug Discovery and Post Market Drug Assessment: A Survey. 97-115 - Orhun Vural, Leon Jololian, Lurong Pan:
DeepLigType: Predicting Ligand Types of Protein-Ligand Binding Sites Using a Deep Learning Model. 116-123 - Longfei Ma, Cong Su, Jun Wang, Xin Li, Rong Sun, Guoxian Yu:
AN-IHP: Incompatible Herb Pairs Prediction by Attention Networks. 124-135 - Warith Eddine Djeddi, Sadok Ben Yahia, Gayo Diallo:
Optimizing Global Network Alignment With a Genetic Algorithm: Leveraging Pre-Trained Embeddings for Protein Sequences and Gene Ontology Terms. 136-150 - Shifei Ding, Chuangui Cao, Fan Sun, Xuan Li, Xindong Wu:
Predicting microRNA-Disease Associations Through Multi-View Feature Fusion and Matrix Completion on Graph Convolutional Networks. 151-159 - Ming-Yu Xie, Shaowu Zhang, Tong Zhang, Yan Li, Xiaodong Cui:
MTGCL: Multi-Task Graph Contrastive Learning for Identifying Cancer Driver Genes From Multi-Omics Data. 160-170 - Jared K. Slone, Anja Conev, Maurício Menegatti Rigo, Alexandre Reuben, Lydia E. Kavraki:
TCR-pMHC Binding Specificity Prediction From Structure Using Graph Neural Networks. 171-179 - Anushree Tripathi, Richa Dhanuka, Jyoti Prakash Singh:
A Review of RNA Structure Prediction: Exploring the Potential of Computational Approaches. 180-191 - Xin He, Junliang Shang, Daohui Ge, Feng Li, Jin-Xing Liu:
RPMVCDA: Random Perturbation and Multi-View Graph Convolutional Networks for CircRNA-Disease Association Prediction. 192-202 - Ruijie Li, Qiao Ning, Yaomiao Zhao, Shikai Guo, Hui Li:
MHMDA: "Similarity-Association-Similarity" Metapaths and Heterogeneous-Hyper Network Learning for MiRNA-Disease Association Prediction. 203-215 - Wei Wang, Shitong Wan, Hu Jin, Dong Liu, Hongjun Zhang, Yun Zhou, Xianfang Wang:
ResaPred: A Deep Residual Network With Self-Attention to Predict Protein Flexibility. 216-227 - Mirko Coggi, Guido Walter Di Donato, Marco Domenico Santambrogio:
A Novel Methodology for a Comprehensive Analysis of Genomic Sequence-to-Graph Alignment Tools. 228-239 - Anushri Pal, Mahendra D. Chordia:
Effect of Atomic Size and Stereochemistry of Halogenated Hydantoin Derivatives on Main Protease Inhibition Activities of SARS-CoV-2: Rationalization Through Computational Studies. 240-249 - Xiaoxiao Liu, Hui Lv:
Disturbance Observer-Based Adaptive Synchronization of Heterogeneous Chaotic Systems With Uncertainties via DNA Strand Displacement. 250-260 - Junxiu Liu, Jufang Dai, Qiang Fu, Min Su, Yuling Luo, Sheng Qin, Su Yang, Lingxi Ma:
Enhancing the Robustness of Random Boolean Networks by Epigenetic Regulation. 261-270 - Zhenqiu Shu, Min Xia, Kaiwen Tan, Zhengtao Yu, Xiaojun Wu:
sigRGCN: A Robust Residual Graph Convolutional Network for scRNA-Seq Data Clustering. 271-284 - Pranab Das, Dilwar Hussain Mazumder:
MLCNNF: A Multi-Label Convolutional Neural Network Framework for Predicting Adverse COVID Drug Reactions From the Chemical Structure. 285-297 - Guiyun Chen, Xiaoyan Hong, Lei Zhang, Longzhen Ding, Lihua Li, Chunjuan Jiang, Jianming Ni, Kai Miao, Xiang Pan:
UPSST: Unsupervised Pathology Domain Identification by Integrating Tissue Morphology, Imputing and Clustering of Spatial Transcriptomics With GAT. 298-309 - Poornima Singh Thakur, Shubhangi Chaturvedi, Ayan Seal, Pritee Khanna, Tanuja Sheorey, Aparajita Ojha:
An Ultra Lightweight Interpretable Convolution-Vision Transformer Fusion Model for Plant Disease Identification: ConViTX. 310-321 - Zhipeng Hu, Gaoshi Li, Xinlong Luo, Jiafei Liu, Jingli Wu, Wei Peng, Xiaoshu Zhu:
Using Multi-Feature Weak Consensus Model to Discover Essential Proteins. 322-332 - Zhifeng Hao, Jianming Zhan, Yuan Fang, Min Wu, Ruichu Cai:
GNNSynergy: A Multi-View Graph Neural Network for Predicting Anti-Cancer Drug Synergy. 333-342 - Md Shazid Islam, Arindam Dutta, Calvin-Khang Ta, Kevin Rodriguez, Christian Michael, Mark S. Alber, G. Venugopala Reddy, Amit K. Roy-Chowdhury:
DEGAST3D: Learning Deformable 3D Graph Similarity to Track Plant Cells in Unregistered Time Lapse Images. 343-354 - Cheng Cai, Zhaohong Deng, Andong Li, Yun Zuo, Haoran Chen, Zhisheng Wei, Lei Wang, Xiaoyong Pan, Hong-Bin Shen, Dong-Jun Yu:
CATransUnetLBP: Accurate Prediction of Protein-Ligand Binding Pockets Using a Hybrid Network. 355-367 - Hui Liu, Xiuyu Li, Xinyu Fan, Zhaolin Lu, Lin Zhang:
ESNet: End-to-End Chromosome Instance Segmentation Method Based on Edge Supervised Network. 368-374 - Aditya Malusare, Vaneet Aggarwal:
Improving Molecule Generation and Drug Discovery With a Knowledge-Enhanced Generative Model. 375-381 - Xinrong Yang, Haitao Li:
Robust Output Tracking of Boolean Control Networks Subject to Stochastic Function Perturbations. 382-389 - 2024 Reviewers List*. 390-393
Volume 22, Number 2, 2025
- Da Yan, Ariful Azad, Jie Hou, Jake Y. Chen:
Guest Editorial for Selected Papers From BIOKDD 2023. 394-396 - Lei Zhang, Junyong Zhu, Sheng Wang, Jie Hou, Dong Si, Renzhi Cao:
AnglesRefine: Refinement of 3D Protein Structures Using Transformer Based on Torsion Angles. 397-408 - Ghulam Murtaza, Justin Wagner, Justin M. Zook, Ritambhara Singh:
GrapHiC: An Integrative Graph Based Approach for Imputing Missing Hi-C Reads. 409-419 - Zhipeng Cai, Alexander Zelikovsky:
Guest Editorial Introduction to the Special Section on Bioinformatics Research and Applications. 420-421 - Xuehua Bi, Chunyang Jiang, Cheng Yan, Kai Zhao, Linlin Zhang, Jian-Xin Wang:
ESGC-MDA: Identifying miRNA-Disease Associations Using Enhanced Simple Graph Convolutional Networks. 422-432 - Jingjing Zhang, Zhen Ju, Huiling Zhang, Haiping Zhang, Rui Zhou, Godfrey Chi-Fung Chan, Jintao Meng, Wenhui Xi, Yanjie Wei:
CircRNA Profiles Analysis of Neuroblastoma for Identification of Drug Targets. 433-443 - Shaokai Wang, Ming Zhu, Bin Ma:
NeoMS: Mass Spectrometry-Based Method for Uncovering Mutated MHC-I Neoantigens. 444-454 - Gabriel Siqueira, Alexsandro Oliveira Alexandrino, Andre Rodrigues Oliveira, Géraldine Jean, Guillaume Fertin, Zanoni Dias:
Partition Based Algorithms for Rearrangement Distances With Flexible Intergenic Regions. 455-468 - Ming Chen, Yunhan Pan, Xiujuan Lei, Chunyan Ji, Yinglong Dai, Yi Pan:
MKMGCN-DDI: Predicting Drug-Drug Interactions via Magnetic Graph Convolutional Network With Multiple Kernels. 469-480 - Chu-Ting Yu, Bo Tian, Qian-Qian Meng, Zhe-Ran Chen, Ya-Nan Pang, Xun Zhang, Yan Bian, Si-Wei Zhou, Meijuan Hao, Ye Gao, Lei Xin, Han Lin, Wei Wang, Luo-Wei Wang:
Development and Validation of a Comprehensive Analysis of the Competing Endogenous circRNA/miRNA/mRNA Network for the Identification of Immune-Related Targets in Esophageal Squamous Cell Carcinoma. 481-492 - Adam A. Butchy, Niloofar Arazkhani, Cheryl A. Telmer, Natasa Miskov-Zivanov:
Automating Knowledge-Driven Model Recommendation: Methodology, Evaluation, and Key Challenges. 493-502 - Venkatesan Saravanan, Bharath Kumar Chagaleti, Shakthi Devi Packiapalavesam, Muthu Kumaradoss Kathiravan:
Ligand-Based Pharmacophore Modeling and Quantum Computational Approaches for the Development of hCA XII Inhibitor. 503-513 - Xiangyu Meng, Xue Li, Qing Yang, Huanhuan Dai, Lian Qiao, Hongzhen Ding, Long Hao, Xun Wang:
Gene-MOE: A Sparsely Gated Cancer Diagnosis and Prognosis Framework Exploiting Pan-Cancer Genomic Information. 514-527 - Chaolu Meng, Yunyun Shi, Quan Zou, Ruijun Liu:
HodgeRankWeight: An Integration Algorithm for Feature Ranking Based on Weight Quantization. 528-536 - Jiawei Sun, Weiye Qian, Nan Ma, Wenjia Liu, Zhiyuan Yang:
Datt-AVP: Antiviral Peptide Prediction by Sequence-Based Dual Channel Network With Attention Mechanism. 537-544 - Yanxin Chen, Qiao Ning, Yitong Zhang, Hui Li, Shikai Guo:
Dual-Network Cross-Learning for Metabolite-Disease Association Prediction. 545-556 - Yuehao Wang, Pengli Lu:
ICDNSGA: Identification of Potential circRNA-Disease Associations Based on Improved Non-Dominated Sorting Genetic Algorithm. 557-569 - Kazuhiro Ikkyu, Itoshi Nikaido:
The Effect of Multi-Task Learning on the Prediction of Neoantigen-MHC Class II Binding. 570-580 - Wenkang Wang, Yunyan Shuai, Yiming Li, Min Zeng, Min Li:
Enhancing Protein Function Prediction Through the Fusion of Multi-Type Biological Knowledge With Protein Language Model and Graph Neural Network. 581-590 - Guobo Xie, Weijun Li, Guosheng Gu, Zhiyi Lin, Dayin Li:
A miRNA-Disease Association Prediction Method Integrating Graph Matrix Factorization With L$_{21}$ Similarity Constraint and Network Projection Fusion. 591-602 - Qiang Zhang, Feng Yang, Weihong Huang, Jing Feng, Juan Liu:
TRGOA: Topological-Aware Residue-Gene Ontology Attention Network for Protein Function Prediction. 603-613 - María A Valdez-Cabrera, Amy Willis:
Distances Between Extension Spaces of Phylogenetic Trees. 614-627 - Saikat Biswas, Vibhanshu Ranjan, Pabitra Mitra, Krothapalli Sreenivasa Rao:
Self Supervised Prediction of Genetic Associations in Comorbid Diseases With Masked Autoencoder Using Hypergraph Representations. 628-639 - Bin Pu, Haining Wang, Zhaozhao Xu, Fangyuan Yang, Xiangqiong Wu, Jianguo Chen:
TS-RePSO: A Three-Stage Feature Selection Method Combing ReliefF and PSO in Bioinformatics. 640-652 - Qifeng Tian, Jian Zhao, Zhe He, Jinhui Meng, Xiaoyu Liu, Mengfeng Hu, Jinhan Liu, Huawei Feng, Li Zhang, Hongsheng Liu:
Enhancing Chemical Prediction in Plasma Protein Binding: A Deep Learning Model Combining Molecular Descriptors and Fingerprint Representation With Attention Mechanisms. 653-660 - Wanwan Shi, Yahui Long, Jiawei Luo, Ying Liu, Zehao Xiong, Bo Wang, Zhongyuan Xu:
scGANCL: Bidirectional Generative Adversarial Network for Imputing scRNA-Seq Data With Contrastive Learning. 661-671 - Yiran Huang, Qiulong Pu, Wei Lan, Cuiyu Huang, Cheng Zhong:
SMDPG: Identifying Metabolite-Disease Associations via Optimized Negative Sampling and Sparse Graph Convolutional Network. 672-683 - Michael Maxfield, Jingcheng Xu, Cécile Ané:
A Dissimilarity Measure for Semidirected Networks. 684-696 - Cheng Wang, Yang Liu, Shitao Song, Kun Cao, Xiaoyan Liu, Gaurav Sharma, Maozu Guo:
DHAG-DTA: Dynamic Hierarchical Affinity Graph Model for Drug-Target Binding Affinity Prediction. 697-709 - Sarah Alver, Fletcher G. W. Christensen, James H. Degnan:
Improvement to GLASS/Maximum Tree Method of Species Tree Inference Using Measurement Error Modified Single Linkage Clustering. 710-720 - Xiaomei Li, Lin Liu, Jiuyong Li, Thuc Duy Le:
Stable Breast Cancer Prognosis. 721-731 - Chaoyu Wen, Li Cai, Chunyan Li, Jin Li:
TrustworthyCPI: Trustworthy Compound-Protein Interaction Prediction. 732-743 - Wenzhi Liu, Pengli Lu, Jiejun Zhou:
Enhancing Disease-Metabolite Associations Prediction With Weighted Graph Convolutional Networks Based on Community-Driven Link Completion. 744-756 - Zihao Gao, Huifang Ma, Yike Wang, Zhixin Li, Liang Chang:
DAISY: Dual-Granularity Contrastive Learning for Disease Similarity Prediction. 757-768 - Yunjie Ma, Fei Wang, Qiyu Feng, Zuocheng Wang, Luyu Xie:
HeMDAP: Heterogeneous Graph Self-Supervised Learning for MiRNA-Disease Association Prediction. 769-780 - Yan Liu, Guo Wei, Jia-Shun Wu, Chen Li, He Yan, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu:
MUSIC-GCN: A Novel Multi-Tasking Pipeline for Analyzing Single-Cell Transcriptomic Data Using Residual Graph Convolution Network. 781-789 - Yiren Wang, Hongning Wang, Arindam Kumar Das, M. P. Anantram:
A ML Framework for Genetic Sequence Identification Using 2D Electrical Conductance Probability Distributions from Mixed Data Sets. 790-799 - Wencan Zhu, Céline Lévy-Leduc, Nils Ternès:
Variable Selection in High-Dimensional Logistic Regression Models Using a Whitening Approach. 800-807 - Lu Chen, Yu Wang, Yu-Cheng Gu, Yan Zhou, Bing Xia:
SVCPI: A Soft Voting Ensemble-Based Model for Compound-Protein Interaction Prediction. 808-816 - Yuansheng Liu, Tao Tang, Zexuan Zhu, Xiangxiang Zeng, Quan Zou, Keqin Li:
Quality Scores Compression of Genomic Sequencing Data: A Comprehensive Review and Performance Evaluation. 817-831 - Lishuang Li, Jing Hao, Hongbin Lu, Jingyao Tang:
Document-Level Biomedical Relation Extraction via Knowledge-Enhanced Graph and Dynamic Generative Adversarial Networks. 832-841 - Jin Liu, Junbin Mao, Hanhe Lin, Hulin Kuang, Shirui Pan, Xusheng Wu, Shan Xie, Fei Liu, Yi Pan:
Multi-Modal Multi-Kernel Graph Learning for Autism Prediction and Biomarker Discovery. 842-854 - Xiaoping Min, Jiajun Zou, Jun Xie, Qianli Yang, Yiyang Liao, Junjie Ying, Xiaocheng Jin, Xiaoli Lu, Jun Zhang, Hai Yu, Shengxiang Ge, Ningshao Xia:
Equivariant Interaction-Aware Graph Network for Predicting the Binding Affinity of Protein-Ligand. 855-866 - Yaoyao Li, Yajie Yan, Xiguo Yuan:
COPCNVBD: An Integrated Approach for Somatic Copy Number Variation and Breakpoint Detection Using Whole Genome Sequencing Data. 867-876 - Yingqing Lin, Zhihui He, Cheng Liu, Dazhi Jiang:
ICE: A Driver Genes Identification Method With Improved Cross-Entropy Measure. 877-889 - Zhaoke Huang, Zelin Li, Hong Yan:
A Fusion Model With Effective Multi-Scale Parallel Transformer for Cellular Segmentation. 890-898 - Jarno N. Alanko, Elena Biagi, Simon J. Puglisi:
Finimizers: Variable-Length Bounded-Frequency Minimizers for $k$-mer Sets. 899-910 - Lei Wang, Xun Huang, Xueming Liu:
Predicting miRNA-Disease Associations via Meta-Path Embedding. 911-922 - Yordy S. Cangrejo-Useda, Rodrigo Perez-Gala, Lina M. Vera-Cala, Carlos Jaime Barrios Hernández, Erika P. Ardila-Sandoval, Cristian E. Cadena-Caballero, Fernando Ramirez Alatriste, Francisco Martinez-Perez:
PRKN Gene Introns in Families From Order Primates Show Common Open Reading Frames. 923-932 - Xiao-Na Huang, Wen-Jia Shi:
Design Principles of Regulatory Networks: Finding Network Topologies That Can Achieve Dual Function of Adaptation and Timeliness. 933-945 - Zhixiang Ren, Yiming Ren, Pengfei Liu, Qi Shu, Huijuan Ma, Huan Xu:
Discovery of Bioactive Constituents for Colitis From Traditional Chinese Medicine Prescription via Deep Neural Network. 946-955 - Tianshan Zhang, Bei Jiang, Guang Yang, Zhijie Bao, Jiajie Peng:
Predicting CRISPR Cas9 Off-Target Activities With a Two-Stage Deep Learning Framework. 956-962 - Shiyang Wang, Myeonghun Cho, Jiahui Kang, Kyungsook Han:
Predicting Cancer Metastasis From DNA Methylation and Gene Expression Profiles. 963-970
Volume 22, Number 3, 2025
- Zicheng Wang, Fei Fan, Yanfeng Wang, Junwei Sun:
Q-S Synchronization of Biological Chaotic Circuits Based on DNA Strand Displacement and its Application in Biological Information Secure Communication. 971-983 - Ahmad Firoz, Adeel Malik, Nitin Mahajan, Le Thi Phan, Hani S. H. Mohammed Ali, Chang-Bae Kim, Balachandran Manavalan:
TP-ML: A Machine-Learning-Based Tool to Identify Threonine Proteases Using Sequence-Derived Optimal Features. 984-996 - Rupali Patua, Anup Kumar Halder, Soma Dasgupta, Piyali Chatterjee, Mita Nasipuri, Subhadip Basu:
PCPredG: Protein Complex Prediction Using Graphlet Features. 997-1008 - Jiahui Zhang, Shuai Zhang, Xuqiang Li, Di Wu, Sihan Wang, Limin Li, Wenjie Du, Yang Wang:
IIB-DDI: Invariant Information Bottleneck Theory for Out-of-Distribution Drug-Drug Interaction Prediction. 1009-1022 - Dingkun Liu, Hongjie Zhou, Yilu Qu, Huimei Zhang, Yongdong Xu:
UMMAN: Unsupervised Multi-Graph Merge Adversarial Network for Disease Prediction Based on Intestinal Flora. 1023-1033 - Faranak Darabi, Zohre Beiki, Fatemeh Kazemi HassanAbadi:
A Boolean System for Breast Cancer Detection Using MicroRNA-Based Logic Gates. 1034-1040 - Shun Gao, Yan Xia, Xingfeng Li, Feifei Cui, Qingchen Zhang, Quan Zou, Zilong Zhang:
ACP-ESM2: Enhancing Anticancer Peptide Prediction With Pre-Trained Protein Language Models. 1041-1051 - Congzhi Song, Xuan Liu, Zhankun Xiong, Luotao Liu, Wen Zhang:
GNNDRP: Graph Neural Network With Multi-Task Learning for Drug Response Prediction. 1052-1059 - Juan Manuel López-Correa, Caroline König, Alfredo Vellido:
Dimensionality Reduction-Based Analysis of the Molecular Dynamics of G Protein-Coupled Receptors. 1060-1071 - Haisong Feng, Xiaosong Wang, Fan Lin:
MDSGCN: Predicting Multiple Types of Mutation-Drug Association Through Signed Graph Convolution Network. 1072-1085 - Xiang Lin, Jianlan Ren, Le Gao, Junwen Wang, Zhi Wei:
scDILT: A Model-Based and Constrained Deep Learning Framework for Single-Cell Data Integration, Label Transferring, and Clustering. 1086-1094 - Yongqing Zhang, Zhigan Zhou, Maocheng Wang, Xinyu Mao, Zixuan Wang, Quan Zou:
A Multi-Omics Data Integration Framework for Gene Regulatory Network Inference Based on Contrastive Learning. 1095-1106 - Yong Wang, Chi Huang, Jie Zhong, Qinyao Pan, Ning Li, Yaqi Wang:
Asymptotic Synchronization Analysis in Drive-Response Markovian Jump Boolean Networks. 1107-1117 - Shuqi Li, Shufang Xie, Hongda Sun, Yuhan Chen, Tao Qin, Tianjun Ke, Rui Yan:
MIN: Multi-Channel Interaction Network for Drug-Target Interaction With Protein Distillation. 1118-1127 - Yier Ma, Takeyuki Tamura:
RatGene: Gene Deletion-Addition Algorithms Using Growth to Production Ratio for Growth-Coupled Production in Constraint-Based Metabolic Networks. 1128-1140 - Changyong Yu, Xuxian Zhou, Xinyao Chen, Haitao Ma, Yuhai Zhao:
gShapeLnoc: A Graph Network Incorporating Shapelet Embedding Model for LncRNA Subcellular Localization. 1141-1151 - Xuncai Zhang, Baonan Qi, Ying Niu:
Optimization of Highly Robust DNA Storage Schemes Based on Specific Base Sequences. 1152-1163 - Jun Bai, Zhenzi Li, Bo Zhao, Chen Li, Chenghua Lin, Wenge Rong:
Rectifying and Discriminating Hard Negatives for Biomedical Retrieval Question Answering. 1164-1175 - Shunjie Chen, Pei Wang, Jinhu Lü:
$k$-Shape Clustering Enhances Group Lasso for Gene Selection and Sample Classification. 1176-1188 - Congzhou Chen, Mingyuan Ma, Jinyan Nie, Lingfeng Wang, Jin Xu:
PNAGMDA: A Principal Neighborhood Aggregation Based Graph Neural Network for miRNA-Disease Association Prediction. 1189-1200 - Wenyue Zhan, Weiyang Chen, Yi Pan:
Automated Recognition and Analysis of Escape Response in Caenorhabditis Elegans. 1201-1210 - Ziqi Zhang, Guanqing Yu, Zhaohong Deng, Chenxi Luo, Cheng Cai, Wei Zhang, Fuping Hu, Kup-Sze Choi, Zhisheng Wei, Lei Wang, Jing Wu:
SEFP: Structure-Based Enzyme Function Prediction. 1211-1221 - Shengji Jia, Muhong Gao:
A New Genomic Wave Adjustment Method for DNA Copy Number Variation Detection. 1222-1233 - Zeyu Wang, Tianyi Jiang, Jinhuan Wang, Jiafei Shao, Bin Wei, Qi Xuan, Hong Wang:
Molecular Connectivity Index-Based Data Augmentation for Molecular Property Prediction. 1234-1247 - Dongdong Zhao, Qiben Xu, Fan Li, Yiheng Mao, Jianwen Xiang, Huanhuan Li:
NegSPQ: Similar Patient Query Based on Negative Representation of Genomic Data. 1248-1262
Volume 22, Number 4, 2025
- Jianlin Cheng, Jing He, Mehmet Koyutürk:
Guest Editorial for Special Section on ACM BCB 2023. 1263-1264 - Julia Zheng, Yuya Nishida, Alicja Okrasinska, Gregory M. Bonito, Elizabeth A. C. Heath-Heckman, Kevin J. Liu:
The Impact of Species Tree Estimation Error on Cophylogenetic Reconstruction. 1265-1277 - Mengzhen Li, Mustafa Coskun, Mehmet Koyutürk:
Topological-Similarity Based Canonical Representations for Biological Link Prediction. 1278-1287 - Lorenzo Di Rocco, Umberto Ferraro Petrillo:
Efficient and Scalable Alignment-Free Distributed Genotyping of SNPs and Short Indels. 1288-1298 - Zhuoping Zhou, Boning Tong, Davoud Ataee Tarzanagh, Bojian Hou, Andrew J. Saykin, Qi Long, Li Shen:
MG-TCCA: Tensor Canonical Correlation Analysis Across Multiple Groups. 1299-1310 - Nandini Amit Gadhia, Michalis Smyrnakis, Po-Yu Liu, Damer Blake, Melanie Hay, Anh Nguyen, Dominic Richards, Dong Xia, Ritesh Krishna:
A Novel Approach to Differential Expression Analysis of Co-Occurrence Networks for Small-Sampled Microbiome Data. 1311-1322 - Md Alamin, Kevin J. Liu:
Phylogenetic Placement of Aligned Genomes and Metagenomes With Non-Tree-Like Evolutionary Histories. 1323-1334 - Sahand Hamzehei, Jun Bai, Gianna Raimondi, Rebecca Tripp, Linnaea Ostroff, Sheida Nabavi:
Advanced Feature Extraction and Outlier Detection for 3D Biological/Biomedical Image Registration. 1335-1346 - Kowshika Sarker, Ruoqing Zhu, Hannah D. Holscher, Chengxiang Zhai:
Integrating Prior Knowledge From Genome-Scale Metabolic Model With Metabolomics for Diet Assessment. 1347-1357 - Biing-Feng Wang, Chih-Yu Li, Wen-Horng Sheu:
Faster Algorithms for Constructing Frequency Difference Consensus Trees. 1358-1368 - Ying Wang, Yun Tie, Dalong Zhang, Chenxu Quan:
A Novel Vision Neural Network for Pan-Cancer Classification by Constructing Somatic Mutation Map With Feature Selection Optimization. 1369-1377 - Junlei Zhou, Ruixiang Li, Fangyuan Shi, Xianhao Huo, Fang Du, Zhenhua Yu:
scCMP: A Deep Learning Method for Identifying Clonal Mutational Profiles From Single-Cell Genomic Data. 1378-1387 - Karim Youssef, Yusuf Elnady, Eli Tilevich, Wu-chun Feng:
Scalable and Maintainable Distributed Sequence Alignment Using Spark. 1388-1400 - Fei Han, Yutao Liang, Qinghua Ling, Henry Han:
An Improved Conditional Wasserstein GAN With Gradient Penalty for Gene Expression Profiling Data Augmentation Based on Data Segmentation and Depth Feature Constraint. 1401-1414 - Ziwei Yang, Takeyuki Tamura:
DBgDel: Database-Enhanced Gene Deletion Framework for Growth-Coupled Production in Genome-Scale Metabolic Models. 1415-1427 - Xiaosong Wang, Xiaodi Li, Ying Xiang, Tao Xu, Zhenyu Yue, Lichuan Gu:
MDAGCN: Predicting Mutation-Drug Associations Through Signed Graph Convolutional Networks via Graph Sampling. 1428-1440 - Lin Gan, Xinyi Wang, Yi Zhou, Min Zhu:
Protein-Binding RNA Prediction Based on Integrated Sequence-Structure-Function Pre-Training. 1441-1452 - Douglas Raymond Beahm, Thomas M. Deangelo, Shouka Tavakolian, Rahul Sarpeshkar:
Six Fundamental Behaviors of Immune-Pathogen Feedback Circuits. 1453-1466 - Bin Wang, Hongye Yang, Jiarui Liang, Songhui Rao, Ting Yan, Yuhui Liu, Xinyun Li, Jie Xiang, Huiqing Wang, Yu Xia, Ying Li:
SSRAAI: Learning Sequence and Structural Representations to Predict Antibody-Antigen Interactions. 1467-1478 - Miguel A. Andrade-Navarro, Pablo Mier:
Xsurvey: Web Tool to Query the Set of Homorepeats of all Reference Proteomes. 1479-1480 - Liugen Wang, Bai Zhang, Hanwen Wu, Yongle Shi, Xiang Chen, Yibing Ma, Jie Gao:
Microbe-Drug Association Prediction Model Based on Adaptive Network Fusion of Structural-Topological Information With Integration Strategy. 1481-1493 - Xiaoyi Guo, Yijie Ding, Quan Zou:
Kernelized Fuzzy System for Predicting Therapeutic Peptides via Deep Stacked Encoder. 1494-1504 - Xuhui Zhu, Mingyuan Bi, Junliang Shang, Yan Sun, Feng Li, Yuanyuan Zhang, Ling-Yun Dai, Sheng-Jun Li, Jinxing Liu:
MPSO-CD: A Multi-Objective Particle Swarm Optimization Community Detection Method for Identifying Disease Modules. 1505-1516 - Mingquan Liu, Shuting Jin, Houtim Lai, Longyue Wang, Jianmin Wang, Zhixiang Cheng, Xiangxiang Zeng:
Molecular Dynamics-Powered Hierarchical Geometric Deep Learning Framework for Protein-Ligand Interaction. 1517-1527 - Lijia Ma, Wenxiang Zhou, Yuan Bai, Min Fang, Minfeng Xiao, Jian-Qiang Li:
BERTPVP: Identifying and Classifying Phage Virion Proteins Using Bidirectional Encoder Representations-Based Transformers. 1528-1541 - Wenzheng Bao, Bin Yang, Baitong Chen:
TAPE_selection: Organelle Proteins Classification With TAPE Feature Selection. 1542-1552 - Xin Huang, Mengjun Li, Yang Zhou, Xinyu He:
Multiomics Data Integration of Lipid Metabolism in Hepatocellular Carcinoma Studies Using Bioinformatics Networks Based on Vertical and Horizontal Comparisons. 1553-1563 - Hui Fang, Danyang Chen, Chunyan Tang, Min Li, Cheng Zhong:
DualF-PBR: Dual-Extracting Protein Sequence Features for Predicting Plant Resistance Proteins. 1564-1573 - Da-Bin Lee, Kyu-Baek Hwang:
Pre-Training and Ensembling of Deep Neural Networks for Target Gene Expression Prediction From Landmark Genes. 1574-1586 - Benjamin S. Mashford, Tim Hewitt, Maryam May, Aaron Chuah, Dan Andrews:
Comparison of Deep-Learning Models for Classification of Cellular Phenotype From Flow Cytometry Data. 1587-1592 - Eleanor Wedell, Chengze Shen, Tandy J. Warnow:
BSCAMPP: Batch-Scaled Phylogenetic Placement on Large Trees. 1593-1605 - Shenjian Gu, Matee Ullah, Jiangning Song, Dong-Jun Yu:
PScL-SDNNMAE: Protein Subcellular Localization Prediction Using Classical and Masked Autoencoder-Based Multi-View Features With Ensemble Feature Selection. 1606-1614 - Cheng Cheng, Xiaohong Zhang, Mianyang Yu, Yuqin Xia, Weiwei Xue:
Multiscale Motif-Aware Relation Graph Structure for Drug-Target Binding Affinity Prediction. 1615-1628 - M. Hasan Celik, Onurcan Ersen, Taj Saleh, Alper Dokay, Ahmet Enis Guven, Ali Cakmak:
MetaboliticsDB: A Database of Metabolomics Analyses. 1629-1640 - Yanfei Li, Renhong Cheng, Jinmao Wei:
Predicting Drug-Protein Interactions Based on Similarity Reconstruction and Adaptive Combination Algorithm. 1641-1652 - Tao Zhang, Baoqi Huang, Bing Jia, Fei Hao, Dongjun Liu, Haodong Cen:
Screening and Predicting Multi-Omics T-ALL Core Genes Based on PU Learning. 1653-1661 - Fangting Li, Ying Yin, Xin Wang, Changyong Yu, Yuhai Zhao, Ye Tian:
GPU-Powered Evolutionary Auxiliary Multitasking for Fast SNP Interaction Detection. 1662-1673 - Qianqian Wang, Xiongjie Xiao, Zhiwei Miao, Xu Zhang, Daiwen Yang, Bin Jiang, Maili Liu:
Prediction of Protein B-Factor Profiles Based on Bidirectional Long Short-Term Memory Network. 1674-1681 - Adyasha Sahu, Sukadev Meher:
A Modified Relation and Margin-Based Deep Learning Network for Automatic Breast Cancer Detection. 1682-1689 - Gustavo Taiji Naozuka, Heber L. Rocha, Thiago J. Pereira, Gustavo Barbosa Libotte, Regina C. Almeida:
Connecting Different Approaches for Cell Cycle Modeling: Learning Ordinary Differential Equations from Individual-Based Models. 1690-1702 - Qing Li, Jiayi Bian, Janith Weeraman, Zilong Zhang, Albert Leung, Qi-Xuan Ding, Thierry Chekouo, Lang Wu, Jun Yan, Jingjing Wu, Quan Long:
Autoencoder-Transformed Transcriptome Improves Genotype-Phenotype Association Studies. 1703-1715 - Fengsheng Wang, Jianbo Qiao, Xu Guo, Leyi Wei:
MC-MSTLoc: Self-Supervised Pre-Training for Imbalanced Multi-Label Protein Subcellular Localization Prediction Using Immunofluorescence Images. 1716-1726 - Shunbao Li, Kang Liu, Po Yang:
An Interpretable Deep Learning Approach for Alzheimer's Disease Diagnosis Using Gene Expression Data. 1727-1739 - Wenhui Ge, Yang Tan, Huiqun Yu, Guisheng Fan, Mingchen Li:
SRPM-Sol: A Structure Robust Protein Multimodal Model for Solubility Prediction. 1740-1751 - Alejandro Rodríguez-Sánchez, Jesus Gonzalez-Lopez, Alejandro Gonzalez-Martinez:
Study on Robustness of Denoising and Clusterization Algorithms for the Computation of Microbiome Data. 1752-1765 - Sakshi Ranjan, Dheeraj Mishra, Sanjay Kumar Singh:
Mitigating Catastrophic Forgetting in Molecular Property Prediction via Refresh Learning and Pareto Optimization. 1766-1777 - Mingcan Wang, Zhiqiong Wang, Luxuan Qu, Kaifu Long, Junchang Xin:
BFMDDT: A Decision-Tree-Based Gene Regulatory Network Inference From Multi-Type Datasets. 1778-1788 - Jingyuan Zhou, Dengwei Zhao, Hao Qian, Shikui Tu, Lei Xu:
Multi-Objective Structure-Based Drug Design Using Causal Discovery. 1789-1800 - Sayantika Chatterjee, Stuti Jain, Kriti Kumar, Emilie Chouzenoux, Angshul Majumdar:
Deep Probabilistic Matrix Factorization on Graphs: Application to Drug Repositioning in Antimicrobial Resistance. 1801-1811 - Kuan Xu, Kuo Yang, Chongyu Wang, Xinyan Wang, Hanyu Yuan, Qiang Zhu, Jian Yu, Xuezhong Zhou:
CPOne: Enhancing Prediction of Compound-Protein Interactions Through One-Shot Meta Learning. 1812-1821 - Dafne Lozano-Paredes, Luis Bote-Curiel, María Sabater-Molina, Concha Bielza, Juan-Ramón Gimeno-Blanes, Sergio Muñoz-Romero, Francisco Javier Gimeno-Blanes, Pedro Larrañaga, José Luis Rojo-Álvarez:
Discovering Genetic Variants in Hypertrophic Cardiomyopathy With Multiple Machine Learning Techniques. 1822-1835 - Yang Wang, Yanjiao Zeng, Dongning Liu, Zhuowei Wang:
Enhancement of Convolutional Neural Network for Protein-Protein Interaction Prediction Using Sequence Feature Extension. 1836-1849 - Yingying Chen, Gaoshi Li, Tianyi Liu, Rui Zhou, Yuqing Mao, Jingli Wu, Jiafei Liu, Haize Hu, Ke Wu, Qiyong Zhu:
A Deep Learning Framework for Identifying Cancer Driver Genes Based on Transformer and Graph Convolutional Network. 1850-1860 - Ping Li, Yuqing Qian, Junhai Xu, Yijie Ding, Fei Guo:
Prediction of ncRNA-Disease Association Based on Correntropy Induced Loss Matrix Factorization Model. 1861-1874 - Fateme Keikha, Lingyu Li, Wai-Ki Ching, Zhi-Ping Liu:
NetWalkRank: Cancer Driver Gene Prioritization in Multiplex Gene Regulatory Networks by a Random Walk Approach. 1875-1887 - Yangruirui Zhou, Christopher A. Voigt, Douglas Densmore:
Constraint-Based Sub-Graph Partitioning for Multi-Cellular Biological Networks. 1888-1901 - Peidong Zhang, Jianzhu Ma, Ting Chen:
Escaping the Drug-Bias Trap: Using Debiasing Design to Improve Interpretability and Generalization of Drug-Target Interaction Prediction. 1902-1911 - Sien Feng, Xinyi Qin, Lu Zhang, Xueyun Cheng, Yijun Wang, Chuang Dai:
ProMethylNet: Protein Methylation Site Prediction Based on Multimodal Feature Fusion and Deep Learning. 1912-1923 - Daniel Gonzalo Alonso-Reyes, Virginia Helena Albarracin:
Arche: An Advanced Flexible Tool for High-Throughput Annotation of Functions on Microbial Contigs. 1924-1934 - Songwei Ai, Yiwei Zhou, Wenkui Zou, Emeli Chatterjee, Guoping Li, Jifan Shi, Junjie Xiao, Juan Zhao:
diffMIN: Reconstructing Sample-Specific Differential Gene Regulatory Networks Based on Mutual Information. 1935-1946 - Bartlomiej Szawulak, Piotr Formanowicz:
Graphlet Degree Distribution Sensibility in Petri Net-Based Models of Biological Systems. 1947-1952
Volume 22, Number 5, 2025
- Yajun An, Rushi Lan, Huan Lin, Yumeng Wang, Huahu Deng, Zhenbing Liu, Lin Wang, Zaiyi Liu, Cheng Lu, Huihua Yang, Xipeng Pan:
Multimodal Fusion Framework Based on Low-Rank Interaction for Tumor Prognostic Prediction. 1953-1966 - Mei Ma, Xiujuan Lei:
BiAtt-GVAE: Molecular Design for Specific Target via Graph Variational Autoencoder Based on Bi-Channel Interactive Attention Network. 1967-1978 - Yongrui Fu, Yun Xiong, Siwei Zhang, Kangxiang Jia:
Molecular Property Prediction Based on Motif-Centric Multi-Grain Pretaining and Finetuning Strategy. 1979-1990 - Zhijian Huang, Rongtao Zheng, Siyuan Shen, Kai Chen, Min Wu, Lei Deng:
CircGO: Predicting circRNA Functions Through Self-Supervised Learning of Heterogeneous Networks. 1991-2000 - Prajna Bhat, Nagamma Patil:
Integrating Evolutionary and Structural Properties for Protein Interaction Site Prediction Using Graph and Temporal Convolutions. 2001-2012 - Xue Li, Lifeng Yang, Fa Jiang, Xiong Jiao:
Identifying Functional Modules for Axillary Lymph Node Metastasis in Breast Cancer. 2013-2019 - Xue Liu, Dan Sun:
Enhancing Molecular Contrastive Prediction by Recognizing Metric Distribution Separation. 2020-2030 - Xiangzhe Yuan, Chonghao Wang, Shuqin Zhu, Lu Zhang:
DBNX: A Machine Learning Method for Ensembling Polygenic Risk Scores and Non-Genetic Factors. 2031-2042 - Narmina Baghirova, Esther Galby, Martin Milanic:
Perfect phylogenies via the Minimum Uncovering Branching Problem: Efficiently Solvable Cases. 2043-2056 - Haochen Zhao, Bowei Li, Guihua Duan, Jian-xin Wang:
Probiotic-Disease Association Prediction via Cross-Modal Feature Aggregation. 2057-2067 - Deyou Tang, Biyao Lv, Rong Zhao, Pingjian Zhang, Chao Liu:
BTR-MCL: A Bioinformatics Tool Recommendation Method With Multi-View Contrastive Learning. 2068-2081 - Yun Zhou, Haoyu Cui, Wenbo Cai, Dong Liu, Wei Wang:
FSKansformer: An ncRNA-Protein Interaction Prediction Model Based on Feature Salience and Kansformer. 2082-2092 - Jingjing Hou, Zixin Li, Mengjun Yang, Binjie Wang, Bing Wang, Xiaohui Yang:
DGCA-DTA: A Deep Graph Neural Network Based on Co-Attention for Drug Target Affinity Prediction. 2093-2104 - Chengang Liu, Ying Chen, Xi Wu:
Collaborative Attention Contrast Learning for Cancer Subtype Identification Based on Multi-Omics Data. 2105-2116 - Pengyuan Nie, Mengxuan Lin, Jinzhong Ning, Zhihao Yang, Lei Wang:
Bi-Encoder-Based Approach to Biomedical Document-Level Entity Recognition and Relation Extraction. 2117-2128 - Meiling Wang, Wei Shao, Daoqiang Zhang, Qingshan Liu:
Deep Ring-Wise Block Network for Joint Association Analysis and Alzheimer's Disease Diagnosis With Interpretability. 2129-2142 - Ruimeng Li, Qinke Peng, Haozhou Li, Zeyuan Zeng, Tian Han:
Compound Interaction Presentation Learning for MHC-Peptide Binding Affinity Prediction. 2143-2151 - Kai Wang, Aijie Song, Fei Liu, Xiaoli Luan, Xinglong Wang, Jingwen Zhou:
PLMAM-PLA: A Method Using Pretrained Language Models and Attention Mechanisms for Protein-Ligand Binding Affinity Prediction. 2152-2163 - Jingli Wu, Xiaopeng Wei, Gaoshi Li, Jiafei Liu, Chang He, Xi Wu:
scPEGEnhanced Graph Convolutional Sparse Subspace Clustering Method for scRNA-Seq Data. 2164-2172 - Joan Carles Pons, Pau Vives López, Yukihiro Murakami, Leo van Iersel:
Fence Decompositions and Cherry Covers in Non-Binary Phylogenetic Networks. 2173-2183 - Jieqiong Wu, Penghao Wang, Yanfen Zheng, Bin Wang, Qiang Zhang, Pan Zheng:
Stable DNA Storage Encoding Scheme Based on Repeating Substring Tree. 2184-2193 - Luís Cunha, Thiago Lopes, Uéverton S. Souza, Leonard Bohnenkämper, Marília D. V. Braga, Jens Stoye:
Closing the Complexity Gap of the Double Distance Problem. 2194-2205 - Rui Zhou, Gaoshi Li, Yuqing Mao, Tianyi Liu, Yingying Chen, Jingli Wu, Jiafei Liu, Haize Hu, Ke Wu, Qiyong Zhu:
Identifying Cancer Driver Genes Using a Neural Network Framework With Cross-Attention Mechanism. 2206-2215 - Shivani Saxena, Ahsan Z. Rizvi:
Stacked Graph Attention Network With Temporal Modeling for lncRNA-miRNA Association Network. 2216-2229 - Sihan Wang, Shuai Zhang, Zhuo Chen, Xuqiang Li, Jianmin Wang, Wenjie Du, Yang Wang:
TRGH-PPI: Effective and Generalized Prediction of Protein-Protein Interactions Through Transformer and Graph. 2230-2240 - Peisheng Yang, Changxiang He, Ping Zhang, Xiaofei Qin, Qingqian Zhang, Die Li:
MHGCN: A Multi-Channel Hybrid Graph Convolutional Neural Network for Cancer Drug Response Prediction. 2241-2251 - Ziwei Yang, Takeyuki Tamura:
DeepGDel: Deep Learning-Based Gene Deletion Prediction Framework for Growth-Coupled Production in Genome-Scale Metabolic Models. 2252-2266 - Pei-Yuan Lai, Man-Sheng Chen, De-Zhang Liao, Chang-Dong Wang, Min Chen, Lin Mei:
Knowledge-Aware Synergistic Discovery of Drug Combinations: A Large Language Model Perspective. 2267-2279 - Wen-Horng Sheu, Biing-Feng Wang:
A Kernelization Algorithm for Finding a Perfect Phylogeny From Mixed Tumor Samples. 2280-2292 - Radhika Gupta, Manisha Ganguly, Prerona Jana, Amlan Roychowdhury, Ditipriya Hazra:
Two Birds With One Stone: Targeting Wild Type and Drug Resistant Mutant ALK Using Brute Force Screening, MD Simulation and NCI. 2293-2299 - Xiangrun Zhou, Guixia Liu, Chenjing Han, Ji Lv:
ABPDB: A Database of Antibacterial Peptides. 2300-2306 - Vincent Huang, Yongliang Zeng, Selim Yahia-Messaoud, Wenming Yang, Dong-Qing Wei:
MGOL: Molecule Generation With Ordering Loss. 2307-2312 - Hao Chen, Zhenran Jiang:
CrisprDA: A Data Augmentation Method Enhancing the Efficiency of sgRNA on-Target Activity Prediction. 2313-2319 - Lifeng Yan, Zhan Zhao, Zekun Yin, Tong Zhang, Yang Yang, Fangjin Zhu, Xiaohui Duan, Bertil Schmidt, Weiguo Liu:
RabbitBAM: Accelerating BAM File Manipulation on Multi-Core Platforms. 2320-2326
Volume 22, Number 6, 2025
- Ion I. Mandoiu, Marmar R. Moussa, Sanguthevar Rajasekaran, Pavel Skums, Sharma V. Thankachan, Alex Zelikovsky:
Editorial: Special Section on Computational Advances in Bio and Medical Sciences. 2327-2329 - Siqi Chen, Wenkang Wang, Ruiqing Zheng, Min Li:
SpaNN: Spatial Transcriptomic Data Enhancement Using Deep Neural Network. 2330-2340 - Mohsen Sharifitabar, Shiva Kazempour, Seiied-Mohammad-Javad Razavian, Sogand Sajedi, Soroosh Solhjoo, Habil Zare:
ZiPo: A Deep Neural Network to De-Noise Single-Cell RNA Sequencing Data. 2341-2352 - Xihan Qin, Li Liao:
Biologically Supervised Graph Embedding for Disease Comorbidity Prediction: A Versatile Framework for Various Embedding Techniques and Classifiers. 2353-2361 - Marmar Moussa, Charles H. Street:
Inference of Tumor Progression Patterns in Colon Cancer Using Optimal Cell Order Analysis in Single Cell Resolution. 2362-2373 - Wei Peng, Zhipeng Cai, Alexander Zelikovsky:
Guest Editorial: Introduction to the Special Section on Bioinformatics Research and Applications. 2374-2376 - Yunhai Li, Pengpai Li, Duanchen Sun, Zhi-Ping Liu:
PGDTA: Predicting Drug-Target Affinity Using Three-Dimensional Structure of Protein Pocket and Graph Neural Network. 2377-2386 - Jialiang Sun, Jun Guo, Jian Liu:
A Deep Learning Framework for Chromatin Loop De Novo Prediction With Enhanced Feature Extraction. 2387-2397 - Wuguo Tang, Qichang Zhao, Jian-xin Wang:
LLMDTA: Improving Cold-Start Prediction in Drug-Target Affinity With Biological LLM. 2398-2409 - Xiao Liang, Haochen Zhao, Jianxin Wang:
Enhancing Antimicrobial Peptide Function Prediction via Knowledge Transfer on Protein Language Models. 2410-2419 - Kang Jiang, Rwan Ahmed, Petros Papagerakis, Fang-Xiang Wu:
DIC: Deep Imputing and Clustering Single Cell RNA Sequencing Data. 2420-2429 - Wei Peng, Xinyue Xu, Jiangzhen Lin, Gong Chen, Wei Dai, Xiaodong Fu, Li Liu, Lijun Liu, Ning Yu:
Predicting Anti-Cancer Drug Response Based on Hypergraph Representation Learning. 2430-2441 - Mingkai Wang, Yang Yang, Zekun Yin, Lifeng Yan, Tong Zhang, Fangjin Zhu, Xin Li, Xiaohui Duan, Bertil Schmidt, Weiguo Liu:
RabbitTrim: An Efficient and Versatile Trimmer on Multi-Core Platforms. 2442-2452 - Saeed Ahmed, Nalini Schaduangrat, Ittipat Meewan, Watshara Shoombuatong:
DeepHDAC3i: Leveraging an Interpretable Deep Learning-Based Framework for the Accelerated Discovery of HDAC3 Inhibitors. 2453-2464 - Arijit De, Aritro Santra, Mona Tiwari, Ananda S. Chowdhury:
Predicting Genetic Markers for Brain Tumors Using a Composite Loss. 2465-2476 - Ziping Ma, Weiqing Min, Huanpu Zhang, Yulei Huang, Shuqiang Jiang:
SSC-PPI: A Subspace Structure Consistency-Based Method for Protein-Protein Interactions Prediction. 2477-2490 - Daanish Mahajan, Chirag Jain, Navin Kashyap:
On the Coverage Required for Diploid Genome Assembly. 2491-2502 - Jinlong Hu, Jiacheng Liu, Shoubin Dong, Bin Liao, Junjie Liang, Vasant G. Honavar:
DGX: Uncovering General Behavior of Deep Graph Models With Model-Level Explanation. 2503-2514 - Qiao Ning, Chaorui Guo, Ming Wu, Xiang Li, Hui Li, Shikai Guo:
Prediction of miRNA-Disease Association Based on Biodiversity Association Network. 2515-2525 - Haoran Liu, Xiaoli Lin, Jing Hu, Mengyao Wang, Jun Pang, Xiaolong Zhang:
An Efficient Targeted Drug Design Method Using Framework of Multiscale Encoder-Decoder. 2526-2539 - Jie Yang, Xijie Lan, Guoyin Wang, Zhong Chen, Yuwen Chen, Di Wu:
A Hybrid Ensemble End-to-End Neural Network for Accurate Protein-Protein Interactions Prediction. 2540-2553 - Wenbo Wang, Junlin Wang, Yi Shang:
AF2Ring: A Memory Efficient Method for Predicting Quaternary Structure of Cyclic Protein Oligomers. 2554-2561 - Liangwen He, Zhaohong Deng, Fuping Hu, Zhongyu Wang, Yun Zuo, Lin Zhu, Haoran Chen, Xiaoyong Pan, Zhisheng Wei, Lei Wang, Hong-Bin Shen, Dong-Jun Yu, Jing Wu:
DMMAFS: Protein Function Prediction Based on Multi-Modal Multi-Attention Fusion Features. 2562-2574 - Fairuz Shadmani Shishir, Bishnu Sarker, Farzana Rahman, Sumaiya Shomaji:
A Deep Learning Framework for Protein-to-Metal Binding Prediction Using Protein Language Models. 2575-2585 - Kai Zheng, Guihua Duan, Mengyun Yang, Wei Wu, Yaohang Li, Jian-Xin Wang:
LRTM: Left-Right Transition Matrices for Molecular Association Prediction. 2586-2595 - Phuc-Xuan-Quynh Nguyen, Hoai-Nhan Tran, Cheng Yan, Jian-xin Wang:
Predict MiRNA-Disease Associations Using a Variant of Deep Forest Model and Improving Feature Vectors by Graph Convolutional Network. 2596-2607 - William Howard-Snyder, Will Dumm, Mary Barker, Ognian Milanov, Claris Winston, David H. Rich, Marc A. Suchard, Frederick A. Matsen IV:
The Structure of Deviations From Maximum Parsimony for Densely-Sampled Data and Applications for Clade Support Estimation. 2608-2618 - Yan-Ru Ju, Long-Shang Cho, Chin Lung Lu:
A More Efficient Dynamic Programming Algorithm for Designing a Coding Sequence by Jointly Optimizing Its Structural Stability and Codon Usage. 2619-2629 - Hamza Faquir, Manuel Pájaro, Irene Otero-Muras:
A Computational Framework for Optimal and Model Predictive Control of Stochastic Gene Regulatory Networks. 2630-2641 - Jordan R. Ubbens, Ian Stavness, Andrew G. Sharpe:
GPFN: Prior-Data Fitted Networks for Genomic Prediction. 2642-2649 - Shivani Saxena, Ahsan Z. Rizvi:
A Novel Kernel-Based Hilbert Space Framework for Predictive Modeling of lncRNA-miRNA-Disease Interaction Networks. 2661-2672 - Jiejin Deng, Huimin Yu, Jing Zhang, Mingyu Lu, Yi-Jia Zhang:
HIN-MTDTI: Heterogeneous Information Networks for Multitask Drug-Target Interaction Prediction. 2673-2684 - Hangjun Che, Wei Guo, Man-Fai Leung, Yuting Cao, Cheng Liu:
Robust Diverse Multi-View Learning for Cancer Subtyping. 2685-2696 - Ning Ai, Haoliang Yuan, Zhonghua Lu, Yong Liang, Qi Hong Lai, Loi Lei Lai, Hongmin Cai, Dong Ouyang:
A Simplified Input Strategy for Predicting Multi-Type Associations in miRNA-LncRNA-Disease Network via Stacked Deep Matrix Factorization. 2697-2711 - Xiaohan Zou, Weihua Zheng, Shunfang Wang:
scDVAE:Single-Cell Data Clustering Based on Variational Autoencoder With Disentangled Latent Representations. 2712-2723 - Xiaoyi Yin, Yue Zhao, Xin Liu, Zhen Cui, Tong Zhang:
Deciphering the Structural Code of Proteins With Deep Graph Learning. 2724-2735 - Jian Liu, Jianghua Mao, Yuqi Wang, Hao He, Ye Jiang, Feibiao Dong, Minghui Shen, Ruiyan Sun, Lei Gao:
An Efficient and Explainable Ensemble-learning Framework for Early Lung Cancer Biomarkers Detection. 2736-2749 - Xiong Li, Chuang Chen, Yixin Li, Yangkai Lin, Juan Zhou, Xiao Chen, Xuan Feng, Yuchao Luo, Haowen Chen:
A Cell-Cell Interaction Network Based Method for Identifying Lymph Node Metastasis and Characterizing Lung Cancer Progression. 2750-2763 - Hassan Raza, Muhammad Junaid Ali Asif Raja, Rikza Mubeen, Zaheer Masood, Muhammad Asif Zahoor Raja:
Stochastic-Deterministic Modeling of Immune Responses and Tumor Evolution Under Therapeutic Influence: Intelligent Predictive Supervised Exogenous Networks. 2764-2773 - Elahe Khayatian, Louxin Zhang:
Simple k-RF Metrics for Comparison of Labeled DAGs. 2774-2785 - Min Xia, Qinghan Long, Zhenqiu Shu, Hongbin Wang, Zhengtao Yu:
scSAG$^{2}$E: Sparse Autoencoders With Gene Graph Embedding for scRNA-Seq Data Clustering. 2786-2800 - Zhongpan Wu, Abel Beyene, Karim Hammad, Ebrahim Ghafar-Zadeh, Sebastian Magierowski:
Toward an Embedded SoC for Mobile DNA Sequencing Applications. 2801-2816 - Wei Zheng, Jianyong Sun, Haotian Zhang:
Nature-Inspired Meta-Heuristic Algorithms for Detecting Protein Complexes in Protein-Protein Interaction Networks: A Survey. 2817-2832 - Li Pan, Chenyang Xiao, Jinliang Yang, Yancheng Fang, Bo Yang, Wenbin Li:
A Granularity-Related Network Refinement Method Based on Module Division and Biological Information for Identifying Essential Proteins. 2833-2845 - Yun Qin, Fei Zhu, Bo Xi, Yuping Duan:
TransDNA: A Deep Transfer Learning Network for Sequence Reconstruction in DNA-Based Data Storage. 2846-2857 - Prashanth Choppara, Bommareddy Lokesh:
Q-BAFNet: A Hybrid Quantum Classical Approach for Drug-Target Binding Affinity Prediction. 2858-2871 - Fuchuan Qu, Yijin Zhao, Tao Huang, Xinyan Wang, Jun Zhang, Junjie Chen:
HiPHD: Hierarchical Classification for Protein Remote Homology Detection by Incorporating Protein Sequential and Structural Information. 2872-2881 - Wei Zhang, Ruochen Yu, Chengjie Ding, Mingfeng Jiang, Qi Dai:
STAD-CoAtt: Integration of Evolving Gene Graphs in the Assessment of Neuropathological Stages Using Spatiotemporal Representations of Brain Transcriptomics Data. 2882-2894 - Huixiu Xu, Xin Tong, Haitao Jiang, Lusheng Wang, Binhai Zhu, Daming Zhu:
Flanked Transposition Distance for Two Strings. 2895-2906 - Pengli Lu, Xusheng Liu, Fentang Gao:
Prediction of circRNA-Disease Associations Based on Graph Isomorphism Networks and Graph Sampling Aggregation. 2907-2920 - Wenwen Min, Taosheng Xu, Chris Ding:
Weighted Sparse Partial Least Squares With Joint Sample and Feature Selection for Integrating Multi-Omics Data. 2921-2933 - Clenivaldo Pires da Silva, Mateus F. T. Carvalho, Yandre Maldonado e Gomes da Costa, Franklin César Flores, Julio C. Polonio, Claudete Aparecida Mangolim:
Detection and Analysis of Electrophoresis Gels Using YOLO. 2934-2942 - Shanghui Deng, Xiao Zheng, Chang Tang, Xinwang Liu, Yuanyuan Liu, Shan An:
scSPAF: Cell Similarity Purified Adaptive Fusion Network for Single-Cell Multi-Omics Clustering. 2943-2954 - Ying Zhang, Hong-Jin Yu, Zihao Yan, Tong Pan, Yiwen Zhang, Yan Liu, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu:
Integrating Graph Convolutional Networks for Missing Gene Expression Imputation. 2955-2963 - Weiqi Zhai, Yongjun Deng, Xiaodi Huang, Shaojun Wang, Shanfeng Zhu:
MultiFusion2HPO: A Multimodal Deep Learning Approach for Enhancing Human Protein-Phenotype Association Prediction. 2964-2974 - Kangchen Liu, Jing Xu, Haoran Ma, Fang Liu, Aidi Zhang, Xiujun Zhang:
kmmDE: A Non-Parametric Method for Differential Expression Analysis of Time-Course RNA-Seq Data Using Maximum Mean Discrepancy. 2975-2987 - Minhua Feng, Liping Tang, Juntao Liang, Song Huang, Jianfeng Ma, Zhimin Zheng, Ranran Guo, Wen Shi, Jianing Xi:
Explainable Reasoning Path Inference of Anti-Cancer Drug Sensitivity on Genomic Knowledge Graph via Macro-Micro Agent Collaborative Reinforcement Learning. 2988-2999 - Xintong Chang, Jiemin Xie, Hongyu Duan, Keyi Li, Xuemei Liu, Yunhui Xiong, Xiangqi Bai, Kaida Ning, Li C. Xia:
A Unified Genetic and Epigenetic Model to Predict Breast Cancer Intrinsic Subtypes Using Large DNA-Level Multi-Omics Data and Hierarchical Learning. 3000-3016 - Weijian Huang, Cheng Li, Yousuf Babiker M. Osman, Shanshan Wang:
A Lightweight Network With Uncertainty-Guided Latent Space Refinement for Multi-Modal Brain Tissue and Tumor Extraction. 3017-3028 - Pengcheng Shu, Qichang Zhao, Jie Zhou, Jianxin Wang:
MGRFN: Integrating Multiple Molecular Graph Representations for Molecular Property Prediction. 3029-3040 - Meng Xiao, Weiliang Zhang, Xiaohan Huang, Hengshu Zhu, Min Wu, Xiaoli Li, Yuanchun Zhou:
Knowledge-Guided Gene Panel Selection for Label-Free Single-Cell RNA-Seq Data: A Reinforcement Learning Perspective. 3041-3054 - Cheng Chen, Stephen K. Grady, Levente Dojcsak, Sally R. Ellingson, Michael A. Langston:
Link Prediction in Multipartite Graphs With Application to Drug Repositioning Studies. 3055-3064 - Hai Yang, Zhenbei Yang, Lei Zhang, Yijing Yang, Dan Zhou, Dongdong Li, Jing Zhang, Zhe Wang:
Trans-Driver: A Deep Learning Approach for Cancer Driver Gene Discovery With Multi-Omics Data. 3065-3076 - Bin Hu, Dongxu Zhang, Shiqi Liu, Xiao-Liang Xie, Xiao-Hu Zhou, Hong-Jia Li, Qing-Bing Zheng, Fa Zhang, Zeng-Guang Hou, Ning-Shao Xia:
Particle Restoration: A Novel Image Processing Framework for Improving Real Cryo-EM Image Quality in Single Particle Analysis. 3077-3089 - Lei Wang, Wei Liu, Deheng Cai, Linong Ji, Dawei Shi, Ke Yao, Qian Yang:
Heterogeneous Covariates-Aware Pseudo Supervised Meta-Learning for Few-Shot Diabetes Classification. 3090-3100 - Yichao Zhao, Ruiqing Zheng, Li Tang, Pengzhen Jia, Min Li:
DISHIC: An Effective Method for Identifying Differential Interaction in Single-Cell Hi-C. 3101-3111 - David Núñez-Nepomuceno, José A. Sáez, Pedro Carmona-Saez:
A Survey of Preprocessing Techniques for Flow Cytometry Data in Classification Tasks. 3112-3130 - Domonkos Pogány, Péter Antal:
Hyperbolic Nature of Differential Expression Signatures. 3131-3142 - Xiang Zhang, Mingjie Yang, Xunhang Yin, Yining Qian, Fei Sun:
DeepGene: An Efficient Foundation Model for Genomics Based on Pan-Genome Graph Transformer. 3143-3152 - Gihyeon Kim, Geonhui Jo, Minjeong Kim, Soo Young Cho, Jang Hwan Choi:
SeqDA-HLA: Language Model and Dual Attention-Based Network to Predict Peptide-HLA Class I Binding. 3153-3163 - Mustafa Coskun, Mehmet Koyutürk:
Multiplex Embedding of Biological Networks Using Cross-Network Node Similarities. 3164-3174 - Zeyuan Zeng, Jingxian Zeng, Defu Li, Qinke Peng, Haozhou Li, Ruimeng Li, Wentong Sun, Qingbo Zhang, Jinzhi Wang:
Dynamic Graph Attention Meets Pretrained Language Models: Adaptive K-Mer Decomposition for LncRNA-Protein Interaction Prediction. 3175-3187 - Zhen Zhao, Xinyu Li:
A Novel Low-Resource Graph Convolutional Neural Network Approach for Entity Recognition. 3188-3201 - Liwei Liu, Qi Zhang, Yuxiao Wei:
MTF-hERG: A Multi-Type Features Fusion-Based Framework for Predicting hERG Cardiotoxicity of Compounds. 3202-3212 - Pingjing Li, Jiuxin Feng, Jun Guo, Jian Liu:
HiADN: Lightweight Resolution Enhancement of Hi-C Data Using High Information Attention Distillation Network. 3213-3223 - Siyu Tao, Yang Yang, Xin Liu, Yimiao Feng, Jie Zheng:
Learning Universal Knowledge Graph Embedding for Predicting Biomedical Pairwise Interactions. 3224-3235 - Quynh My Khanh Le, Bao Mau Gia Nguyen, Le Van Trinh, Thanh Le:
Enhancing Multi-Label Protein Interaction Prediction via Hypergraph Modeling of Higher-Order Patterns. 3236-3247 - Naga Raju Gudhe, Jaana M. Hartikainen, Maria Tengström, Katri Pylkäs, Robert Winqvist, Veli-Matti Kosma, Hamid Behravan, Arto Mannermaa:
GenoGraph: An Interpretable Graph Contrastive Learning Approach for Identifying Breast Cancer Risk Variants. 3248-3259 - Yu Song, Tatsuaki Goh, Yinhao Li, Jiahua Dong, Shunsuke Miyashima, Yutaro Iwamoto, Yohei Kondo, Keiji Nakajima, Yenwei Chen:
Accurate Tracking of Arabidopsis Root Cortex Cell Nuclei in 3D Time-Lapse Microscopy Images Based on Genetic Algorithm. 3260-3272 - Zi-Yi Zeng, Xi-Yue Cao, Yue-Chao Li, Hai-Ru You, Zhu-Hong You, Yu-An Huang:
scTECTA: Asymmetric Deep Transfer Learning for Cross-Patient Tumor Microenvironment Single-Cell Annotation. 3273-3284 - Xiaojun Ge, Shaojie Cheng, Kang Liu, Kun Xie, Yang Guo:
LMADCNV: A CNV Detection Method Based on Local Features and MAD for NGS Data. 3285-3293 - Xuliang Guo, Xiangfei Zou, Huilian Xu, Jinsong Gu:
M 2 BA-MDA: A Multi-Modal Multi-View Bidirectional Attention Network for Microbe-Disease Association Prediction. 3294-3304 - Zhipeng Hu, Xiaoyan Kui, Canwei Liu, Shen Jiang, Min Zhang, Ziwei Zou, Beiji Zou:
Predicting Driver Genes From Multi-Omics Data Using Hierarchical Multi-Feature Synergy Model. 3305-3316 - Xiang Du, Xinliang Sun, Min Zeng, Wei Tan, Min Li:
A Hypergraph Convolutional Network With Explicit High-Order Interaction Information Extraction for Drug Repositioning. 3317-3329 - Xingyi Li, Gaoyuan Du, Zhelin Zhao, Junming Li, Ju Xiang, Jialu Hu, Xuequn Shang:
DualMarker: A Multi-Source Fusion Identification Method for Prognostic Biomarkers of Breast Cancer Based on Dual-Layer Heterogeneous Network. 3330-3339 - Enqiang Zhu, Xianhang Luo, Chanjuan Liu, Xiaolong Shi, Jin Xu:
A DNA Strand Displacement-Based Computing Model for Solving Intractable Graph Problems. 3340-3349 - Dongliang Chen, Chunxu Xu, Ping Xuan, Mengxia Wang, Tiangang Zhang:
Fourier Transform and Kolmogorov-Arnold Network Enhanced Relation-Aware Generative and Adversarial Network for miRNA-Disease Association Prediction. 3350-3362 - Junran Zhao, Yueyi Cai, Shunfang Wang:
Multi-Omics Correlation Reconstruction of Complete Graph Forms Based on the Self-Expressive Learning Network for Cancer Subtype Prediction. 3363-3374 - Qiu Xiao, Yan Zhang, Wanwan Shi, Li Wang, Ying Zuo, Fei Guo, Jiawei Luo:
scMID: A Deep Multi-Omics Integration Framework for Comprehensive Single-Cell Data Analysis. 3375-3385 - Junkai Cheng, Yi-Jia Zhang, Hengyi Zhang, Yifan Peng, Mingyu Lu:
An Interpretable Complex Knowledge Multi-Hop Reasoning Model for Predicting Synthetic Lethality in Human Cancers. 3386-3398 - Sagnik De, Anurag Singh, Ashish Kumar Bhandari:
A Novel Vision Transformer Based Multimodal Fusion Approach for Clinical MDD Diagnosis Using EEG and Audio Signals. 3399-3409 - Sivan Leviyang:
Resolution Tradeoffs in Modularity Clustering of Single Cell RNA-Seq Datasets. 3410-3418 - Zhiwei Li, Guoqiang Zhou, Haoran Li, Jiacong Mi, Jiahua Shi, Jun Shen:
Deep Learning-Driven Protein-Ligand Binding Affinity Prediction: Data, Architecture, Training and Evaluation. 3419-3437 - Shuang Ge, Yiming Ren, Huan Xu, Qiang Shawn Cheng, Shuqing Sun, Zhixiang Ren:
Few-Shot Generalization to Novel Compounds in Single-Cell Drug Response via Graph-Infused Meta-Pretraining. 3438-3449 - Jianrui Chen, Jiamin Li, Zhihui Wang, Peijie Wang:
A Dynamics-GCN Hybrid Framework for Feature Learning in Disease-Related Association Prediction. 3450-3462 - Jihwan Ha:
Transfer Learning With BioBERT Embeddings for lncRNA-Disease Association Prediction. 3463-3475 - Jun Liu, Guang-Xing He, Kai-Long Zhao, Xiao-Gen Zhou, Gui-Jun Zhang:
De Novo Protein Structure Prediction by Model Quality Assessment Dynamic Feedback Mechanism Using Deep Learning. 3476-3485 - Jinyu Tu, Ruiling Li, Xiang Gao, Li Ma:
A Novel GAER-GMM Framework for Overlapping Protein Complex Detection in Protein Interaction Networks. 3486-3499 - Yu Wang, Wei Ma, Yaxiong Ma, Wei Zhao, Xiaoke Ma:
Identifying Spatial Domains From Spatial Multi-Omics Data With Graph Mutual Information and Deep Subspace Learning. 3500-3512 - Yuchen Shi, Jian Wan, Xin Zhang, Yuyu Yin:
scGCRC: Graph and Contrastive-Based Representation Learning for Single-Cell RNA-Seq Data Clustering. 3513-3523 - Seyed Hamid Hosseini, Mahdi Imani:
Decentralized Reinforcement Learning for Asymmetric Gene Network Interventions. 3524-3537 - Songyeon Lee, Hojung Nam:
KG-SLomics: Synthetic Lethality Prediction Using Knowledge Graph and Cancer Type-Specific Multiomics Integrated Graph Neural Network. 3538-3549 - Venkat Suprabath Bitra, Reddy Rani Vangimalla, Jaya Sreevalsan-Nair:
Network-Based Diseasome Construction From Multi-Omics Data and RadTrix Visualization. 3550-3556 - Dongxu Li, Zhenfeng Li, Bowei Zhao, Xiao-Rui Su, Guodong Li, Lun Hu:
DeepHIV: A Sequence-Based Deep Learning Model for Predicting HIV-1 Protease Cleavage Sites. 3557-3563 - Liyuan Gao, Linpeng Sun, Victor S. Sheng:
Enhancing Transcription Factor Prediction via Domain Knowledge Integration With Logic Tensor Networks. 3564-3570 - Cédric Chauve, Louxin Zhang:
On the Size of the Neighborhoods of a Word. 3571-3575 - Manisha Ganguly, Hriddhi Maitra, Amlan Roychowdhury, Ditipriya Hazra:
Drug Designing against PfHT1 Coupled With Molecular Dynamics in Plasma Membrane Environment Reveals, Ligand-Induced Conformational Change From Open to Closed State. 3576-3583 - Hao Feng, Sakshar Chakravarty, Stefano Lonardi:
Prediction of DNA Methylation With Long-Range State-Space Models. 3584-3590 - Xing Cai, Tong Zhang, Yide Qiu, Zhen Cui:
Fragment-Driven Progressive Alternating Diffusion for De Novo Molecular Design. 2650-2660
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