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IEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 21
Volume 21, Number 1, January - February 2024
- Yamane El-Zein
, Mathieu Lemay
PrivaTree: Collaborative Privacy-Preserving Training of Decision Trees on Biomedical Data. 1-13 - Chao Tu
Deep Multi-Dictionary Learning for Survival Prediction With Multi-Zoom Histopathological Whole Slide Images. 14-25 - Jordan Morris
An Event-Driven Approach to Genotype Imputation on a Custom RISC-V Cluster. 26-35 - Souradipto Choudhuri
CodonU: A Python Package for Codon Usage Analysis. 36-44 - Shengpeng Yu
A Multi-Relational Graph Encoder Network for Fine-Grained Prediction of MiRNA-Disease Associations. 45-56 - Rui Guo
Graph-Based Fusion of Imaging, Genetic and Clinical Data for Degenerative Disease Diagnosis. 57-68 - Jonas Kristiansen Nøland
The Exact Stochastic Process of the Haploid Multi-Allelic Wright-Fisher Mutation Model. 69-83 - Wenliang Tang
MVDINET: A Novel Multi-Level Enzyme Function Predictor With Multi-View Deep Interactive Learning. 84-94 - Shujie Dong
scCAN: Clustering With Adaptive Neighbor-Based Imputation Method for Single-Cell RNA-Seq Data. 95-105 - Nicolò Rossi
Inferring Markov Chains to Describe Convergent Tumor Evolution With CIMICE. 106-119 - Dandan Li
Prediction of Drug-Disease Associations Based on Multi-Kernel Deep Learning Method in Heterogeneous Graph Embedding. 120-128 - Changyong Yu
MiniDBG: A Novel and Minimal De Bruijn Graph for Read Mapping. 129-142 - Wei Wang
SMGCN: Multiple Similarity and Multiple Kernel Fusion Based Graph Convolutional Neural Network for Drug-Target Interactions Prediction. 143-154 - Rituparna Sinha
ENLIGHTENMENT: A Scalable Annotated Database of Genomics and NGS-Based Nucleotide Level Profiles. 155-168 - Eric J. Barnett
Genomic Machine Learning Meta-regression: Insights on Associations of Study Features With Reported Model Performance. 169-177 - Yuerui Liu
A Novel Multi-Scale Graph Neural Network for Metabolic Pathway Prediction. 178-187 - Junchang Xin
BIC-LP: A Hybrid Higher-Order Dynamic Bayesian Network Score Function for Gene Regulatory Network Reconstruction. 188-199 - Pengcheng Zeng
scICML: Information-Theoretic Co-Clustering-Based Multi-View Learning for the Integrative Analysis of Single-Cell Multi-Omics Data. 200-207 - Bindi M. Nagda
promSEMBLE: Hard Pattern Mining and Ensemble Learning for Detecting DNA Promoter Sequences. 208-214
Volume 21, Number 2, March - April 2024
- Fernando Cruz
BioISO: An Objective-Oriented Application for Assisting the Curation of Genome-Scale Metabolic Models. 215-226 - Hao Zhang
GERWR: Identifying the Key Pathogenicity- Associated sRNAs of Magnaporthe Oryzae Infection in Rice Based on Graph Embedding and Random Walk With Restart. 227-239 - Daniel Manu
GraphGANFed: A Federated Generative Framework for Graph-Structured Molecules Towards Efficient Drug Discovery. 240-253 - Zhao-Qi Hu
NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition. 254-264 - Sichen Jin
SADR: Self-Supervised Graph Learning With Adaptive Denoising for Drug Repositioning. 265-277 - Alina F. Leuchtenberger
Learning From an Artificial Neural Network in Phylogenetics. 278-288 - Wenjing Wang
LMGATCDA: Graph Neural Network With Labeling Trick for Predicting circRNA-Disease Associations. 289-300 - Tiantian Li
Flanked Block-Interchange Distance on Strings. 301-311
Volume 21, Number 3, May - June 2024
- João Paulo Pereira Zanetti
Counting Sorting Scenarios and Intermediate Genomes for the Rank Distance. 316-327 - Nan Sheng
A Survey of Deep Learning for Detecting miRNA- Disease Associations: Databases, Computational Methods, Challenges, and Future Directions. 328-347 - Tara Newman
DinoKnot: Duplex Interaction of Nucleic Acids With PseudoKnots. 348-359 - Juan Wang
A Clustering Method for Single-Cell RNA-Seq Data Based on Automatic Weighting Penalty and Low-Rank Representation. 360-371 - Xiaohui Yang
SLPA-Net: A Real-Time Recognition Network for Intelligent Stomata Localization and Phenotypic Analysis. 372-382 - Shan Zhang
Functional Neural Networks for High-Dimensional Genetic Data Analysis. 383-393 - Cheng Yan
PMDAGS: Predicting miRNA-Disease Associations With Graph Nonlinear Diffusion Convolution Network and Similarities. 394-404 - Sheena K. S.
GenCoder: A Novel Convolutional Neural Network Based Autoencoder for Genomic Sequence Data Compression. 405-415 - Wei Wang
MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling. 416-427 - Sunyong Yoo
Interpretable Prediction of SARS-CoV-2 Epitope-Specific TCR Recognition Using a Pre-Trained Protein Language Model. 428-438 - Pallavi M. Shanthappa
Computational Prediction of Potential Vaccine Candidates From tRNA Encoded peptides (tREP) Using a Bioinformatic Workflow and Molecular Dynamics Validations. 439-449 - Arnav Solanki
Evasive Spike Variants Elucidate the Preservation of T Cell Immune Response to the SARS-CoV-2 Omicron Variant. 450-460 - Yuhang Jia
Accurate Annotation for Differentiating and Imbalanced Cell Types in Single-Cell Chromatin Accessibility Data. 461-471 - Minglie Li
TSVM: Transfer Support Vector Machine for Predicting MPRA Validated Regulatory Variants. 472-479 - Ke Ma
PPRTGI: A Personalized PageRank Graph Neural Network for TF-Target Gene Interaction Detection. 480-491 - Weiling Li
ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data. 492-500 - Gabriel Cardona
Comparison of Orchard Networks Using Their Extended $\mu$μ-Representation. 501-507 - Alejandro Valdés-Jiménez
Parallel Algorithm for Discovering and Comparing Three-Dimensional Proteins Patterns. 508-515
Volume 21, Number 5, September - October 2024
- Zhipeng Cai, Alexander Zelikovsky:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 1141-1142 - Junwen Duan, Shuyue Liu, Xincheng Liao, Feng Gong, Hailin Yue, Jianxin Wang:
Chinese EMR Named Entity Recognition Using Fused Label Relations Based on Machine Reading Comprehension Framework. 1143-1153 - Zeqian Li, Yi-Jia Zhang, Peixuan Zhou:
Temporal Protein Complex Identification Based on Dynamic Heterogeneous Protein Information Network Representation Learning. 1154-1164 - Da Yan, Catia Pesquita, Carsten Görg, Jake Y. Chen:
Guest Editorial Selected Papers From BIOKDD 2022. 1165-1167 - Farhan Tanvir, Khaled Mohammed Saifuddin, Muhammad Ifte Khairul Islam, Esra Akbas:
DDI Prediction With Heterogeneous Information Network - Meta-Path Based Approach. 1168-1179 - Shaina Raza, Chen (Cherie) Ding:
Improving Clinical Decision Making With a Two-Stage Recommender System. 1180-1190 - Cunmei Ji, Ning Yu, Yu-Tian Wang, Jiancheng Ni, Chun-Hou Zheng:
SGLMDA: A Subgraph Learning-Based Method for miRNA-Disease Association Prediction. 1191-1201 - Junwen Duan, Huai Guo, Han Jiang, Fei Guo, Jian-xin Wang:
Boundary-Aware Dual Biaffine Model for Sequential Sentence Classification in Biomedical Documents. 1202-1210 - Yen-Che Hsiao, Abhishek Dutta:
Network Modeling and Control of Dynamic Disease Pathways, Review and Perspectives. 1211-1230 - Qingsong Wang, Ruiquan Ge, Changmiao Wang, Ahmed Elazab, Qiming Fang, Renfeng Zhang:
TDFFM: Transformer and Deep Forest Fusion Model for Predicting Coronavirus 3C-Like Protease Cleavage Sites. 1231-1241 - Ana León Palacio, Alberto García S., José Fabián Reyes Román, Mireia Costa, Oscar Pastor:
The Delfos Platform: A Conceptual Model-Based Solution for the Enhancement of Precision Medicine. 1242-1253 - Changfeng Cai, Jianghui Li, Yuanling Xia, Weihua Li:
FluPMT: Prediction of Predominant Strains of Influenza A Viruses via Multi-Task Learning. 1254-1263 - Sumona Biswas, Shovan Barma:
Feature Fusion GAN Based Virtual Staining on Plant Microscopy Images. 1264-1273 - Wenya Yang, Sai Zou, Hongfeng Gao, Lei Wang, Wei Ni:
A Novel Method for Targeted Identification of Essential Proteins by Integrating Chemical Reaction Optimization and Naive Bayes Model. 1274-1286 - Sen Yang, Peng Cheng, Yang Liu, Dawei Feng, Shengqi Wang:
Exploring the Knowledge of an Outstanding Protein to Protein Interaction Transformer. 1287-1298 - Xiaoya Chong, Howard Leung, Qing Li, Jianhua Yao, Niyun Zhou:
Deep Spatio-Temporal Network for Low-SNR Cryo-EM Movie Frame Enhancement. 1299-1310 - Yin Guo, Yanni Xiao, Limin Li:
Identifying Differentially Expressed Genes in RNA Sequencing Data With Small Labelled Samples. 1311-1321 - Seyed Hamid Hosseini, Mahdi Imani:
Modeling Defensive Response of Cells to Therapies: Equilibrium Interventions for Regulatory Networks. 1322-1334 - Huan Wang, Ziwen Cui, Yinguang Yang, Baijing Wang, Lida Zhu, Wen Zhang:
A Network Enhancement Method to Identify Spurious Drug-Drug Interactions. 1335-1347 - Ying Liang, Xiya You, Ze-Qun Zhang, Shi Qiu, Suhui Li, Lianlian Fu:
MGFmiRNAloc: Predicting miRNA Subcellular Localization Using Molecular Graph Feature and Convolutional Block Attention Module. 1348-1357 - Ruiquan Ge, Yixiao Xia, Minchao Jiang, Gangyong Jia, Xiaoyang Jing, Ye Li, Yunpeng Cai:
HybAVPnet: A Novel Hybrid Network Architecture for Antiviral Peptides Prediction. 1358-1365 - Xubin Wang, Yunhe Wang, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li:
Exhaustive Exploitation of Nature-Inspired Computation for Cancer Screening in an Ensemble Manner. 1366-1379 - Xiaowen Hu, Ying Jiang, Lei Deng:
Exploring ncRNA-Drug Sensitivity Associations via Graph Contrastive Learning. 1380-1389 - Sankar Mondal, Pradipta Maji:
Multi-Task Learning and Sparse Discriminant Canonical Correlation Analysis for Identification of Diagnosis-Specific Genotype-Phenotype Association. 1390-1402 - Dian Liu, Zi Liu, Yunpeng Xia, Zhikang Wang, Jiangning Song, Dong-Jun Yu:
TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning. 1403-1412 - Wei Lan, Chunling Li, Qingfeng Chen, Ning Yu, Yi Pan, Yu Zheng, Yi-Ping Phoebe Chen:
LGCDA: Predicting CircRNA-Disease Association Based on Fusion of Local and Global Features. 1413-1422 - Mingshuai Chen, Quan Zou, Ren Qi, Yijie Ding:
PseU-KeMRF: A Novel Method for Identifying RNA Pseudouridine Sites. 1423-1435 - Razan Alkhanbouli, Amira Al-Aamri, Maher Maalouf, Kamal Taha, Andreas Henschel, Dirar Homouz:
Analysis of Cancer-Associated Mutations of POLB Using Machine Learning and Bioinformatics. 1436-1444 - Pengli Lu, Yuehao Wang:
RDGAN: Prediction of circRNA-Disease Associations via Resistance Distance and Graph Attention Network. 1445-1457 - Lingling Zhao, Yan Zhu, Naifeng Wen, Chunyu Wang, Junjie Wang, Yongfeng Yuan:
Drug-Target Binding Affinity Prediction in a Continuous Latent Space Using Variational Autoencoders. 1458-1467 - Muhao Xu, Zhenfeng Zhu, Yawei Zhao, Kunlun He, Qinghua Huang, Yao Zhao:
RedCDR: Dual Relation Distillation for Cancer Drug Response Prediction. 1468-1479 - Hang Gao, Wenjun Shen, Rui Li, Cheng Liu, Si Wu:
Collaborative Structure-Preserved Missing Data Imputation for Single-Cell RNA-Seq Clustering. 1480-1491 - Zile Wang, Hai-Yun Wang, Jianping Zhao, Junfeng Xia, Chun-Hou Zheng:
scVSC: Deep Variational Subspace Clustering for Single-Cell Transcriptome Data. 1492-1503 - Mohammad Alali, Mahdi Imani:
Bayesian Lookahead Perturbation Policy for Inference of Regulatory Networks. 1504-1517 - Yanan Zhang, Xiangzhi Bai:
Geometry-Augmented Molecular Representation Learning for Property Prediction. 1518-1528 - Jianshen Zhu, Naveed Ahmed Azam, Kazuya Haraguchi, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
Molecular Design Based on Integer Programming and Splitting Data Sets by Hyperplanes. 1529-1541 - Qiang Yu, Yana Hu, Xinnan Hu, Jingfen Lan, Yang Guo:
An Efficient Exact Algorithm for Planted Motif Search on Large DNA Sequence Datasets. 1542-1551 - Huaxin Pang, Shikui Wei, Zhuoran Du, Yufeng Zhao, Shengxing Cai, Yao Zhao:
Graph Representation Learning Based on Specific Subgraphs for Biomedical Interaction Prediction. 1552-1564 - Longxin Zhang, Wenliang Zeng, Jingsheng Chen, Jianguo Chen, Keqin Li:
ParaCPI: A Parallel Graph Convolutional Network for Compound-Protein Interaction Prediction. 1565-1578 - Maotao Liu, Yifan Yang, Qun Liu, Li Liu, Guoyin Wang:
A Knowledge-Driven Self-Supervised Approach for Molecular Generation. 1579-1590 - Xiaoxiao Sun, Paul Sajda:
Circular Clustering With Polar Coordinate Reconstruction. 1591-1600
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