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ORCIDJournal of Computational Biology, Volume 32
Volume 32, Number 1, 2025
- Acknowledgment of Reviewers 2024. 1-2
- Tandy J. Warnow
, Yasamin Tabatabaee, Steven N. Evans:
Advances in Estimating Level-1 Phylogenetic Networks from Unrooted SNPs. 3-27 - Célia Biane, Greg Hampikian, Sergey Kirgizov, Khaydar Nurligareev:
Endhered Patterns in Matchings and RNA. 28-46 - Rong Zhu, Yong Wang, Ling-Yun Dai:
CLHGNNMDA: Hypergraph Neural Network Model Enhanced by Contrastive Learning for miRNA-Disease Association Prediction. 47-63 - Lidan Bai, Jun Sun, Vasile Palade, Chao Li, Hengyang Lu, Cong Gao:
Optimizing Metabolite Production with Neighborhood-Based Binary Quantum-Behaved Particle Swarm Optimization and Flux Balance Analysis. 64-88 - Elias Devoe, Honey V. Reddi, Bradley W. Taylor, Samantha Stachowiak, Jennifer L. Geurts, Ben George, Reza Shaker, Raul Urrutia, Michael T. Zimmermann:
An Analytical Approach that Combines Knowledge from Germline and Somatic Mutations Enhances Tumor Genomic Reanalyses in Precision Oncology. 89-103 - Juan Felipe Sánchez Gutierrez, Salah Ramtani, Abdelkader Boucetta, Marco Antonio Velasco, Juan Jairo Vaca-González, Carlos A. Duque-Daza, Diego Alexander Garzón-Alvarado:
Is Tumor Growth Influenced by the Bone Remodeling Process? 104-124
Volume 32, Number 2, 2025
- Murray Patterson:
Special Issue, Part 2 19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023). 125-126 - Letu Qingge, Kushal Badal, Richard Annan, Jordan Sturtz, Xiaowen Liu, Binhai Zhu:
Generative AI Models for the Protein Scaffold Filling Problem. 127-142 - Wanyi Yang, Qingsong Du, Xunyu Zhou, Chuanfang Wu, Jinku Bao:
PDFll: Predictors of Disorder and Function of Proteins from the Language of Life. 143-155 - Yan Zhang, Xin Liu, Panrui Tang, Zuping Zhang:
AFMDD: Analyzing Functional Connectivity Feature of Major Depressive Disorder by Graph Neural Network-Based Model. 156-163 - Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Pathway Realizability in Chemical Networks. 164-187 - Filipp Rondel, Hafsa Farooq, Roya Hosseini, Akshay Juyal, Sergey Knyazev, Serghei Mangul, Artem S. Rogovskyy, Alexander Zelikovsky:
Estimating Enzyme Expression and Metabolic Pathway Activity in Borreliella-Infected and Uninfected Mice. 188-197 - Guishen Wang, Hui Feng, Chen Cao:
BiRNN-DDI: A Drug-Drug Interaction Event Type Prediction Model Based on Bidirectional Recurrent Neural Network and Graph2Seq Representation. 198-211 - Ya Lv, Jin Liu, Xu Tian, Pei Yang, Yi Pan:
CFINet: Cross-Modality MRI Feature Interaction Network for Pseudoprogression Prediction of Glioblastoma. 212-224 - Jovial Niyogisubizo, Keliang Zhao, Jintao Meng, Yi Pan, Didi Rosiyadi, Yanjie Wei:
Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-Based Cell Segmentation in Microscopy Images. 225-237
Volume 32, Number 3, 2025
- Ziqian Wu, Jiyoon Park, Paul R. Steiner, Bo Zhu, John X. J. Zhang:
A Graph-Based Machine-Learning Approach Combined with Optical Measurements to Understand Beating Dynamics of Cardiomyocytes. 239-252 - Xiang Chen, Yibing Ma, Yongle Shi, Bai Zhang, Hanwen Wu, Jie Gao:
Fuzzy-Based Identification of Transition Cells to Infer Cell Trajectory for Single-Cell Transcriptomics. 253-273 - Fengqian Pang, Chunyue Lei, Hongfei Zhao, Zhiqiang Xing:
An Earth Mover's Distance-Based Self-Supervised Framework for Cellular Dynamic Grading in Live-Cell Imaging. 274-297 - Yingxin Hu, Yanjun Liu, Yuefei Yang:
Adaptive Arithmetic Coding-Based Encoding Method Toward High-Density DNA Storage. 298-315 - Hanieh Abbasi, Amir Lakizadeh:
Drug Repurposing Using Hypergraph Embedding Based on Common Therapeutic Targets of a Drug. 316-329 - Emre Sefer:
DRGAT: Predicting Drug Responses Via Diffusion-Based Graph Attention Network. 330-350
Volume 32, Number 4, 2025
- Daniel Cutting, Frédéric A. Dreyer, David Errington, Constantin Schneider, Charlotte M. Deane:
De Novo Antibody Design with SE(3) Diffusion. 351-361 - Anna Sophie Klingenberg, Dario Ghersi:
VIPER: Virus Inhibition Via Peptide Engineering and Receptor Mimicry. 362-373 - Joosung Min, Olga Vishnyakova, Angela Brooks-Wilson, Lloyd T. Elliott:
A Joint Bayesian Model for Change-Points and Heteroskedasticity Applied to the Canadian Longitudinal Study on Aging. 374-393 - Brenda Ivette Garcia-Maya, Yehtli Morales-Huerta, Raul Salgado-García:
Disease Spread Model in Structurally Complex Spaces: An Open Markov Chain Approach. 394-416 - Devleena Ghosh, Chittaranjan Mandal:
Subject-Specific Dosage Estimation for Primary Hypothyroidism Using Sparse Data. 417-443 - Michael Squires, Peng Qiu:
Recursive Clustering of Cellular Diversity in scRNA-Seq Data. 444-460
Volume 32, Number 5, 2025
- Ida Egendal, Rasmus Froberg Brøndum, Marta Pelizzola, Asger Hobolth, Martin Bøgsted:
On the Relation Between Linear Autoencoders and Non-Negative Matrix Factorization for Mutational Signature Extraction. 461-472 - Rahul Nihalani, Jaroslaw Zola, Srinivas Aluru:
Disambiguating a Soft Metagenomic Clustering. 473-485 - Xin Duan, Xinnan Ding, Yuelin Lu:
Compressed Representation of Extreme Learning Machine with Self-Diffusion Graph Denoising Applied for Dissecting Molecular Heterogeneity. 486-497 - Bunsho Koyano, Tetsuo Shibuya:
Faster and More Accurate Estimation of Protein Hinges Based on Information Criteria. 498-519 - Lingwei Lai, Jing Geng, Haochen Duan, Siyuan Chen, Lvwen Huang, Jiantao Yu:
A New Structure Feature Introduced to Predict Protein-Protein Interaction Sites. 520-536 - Pankaj Singh Rana, Nitin Sharma, Sunil Singh Negi, Haci Mehmet Baskonus:
On the Dynamics of HIV-Tuberculosis Coinfection Model with Temporal Recovery from Tuberculosis: An Analysis. 537-555
Volume 32, Number 6, 2025
- Inci M. Baytas:
The 2nd International Workshop on Pattern Recognition in Healthcare Analytics 2023 Preface. 557 - Egemen Isgüder, Özlem Durmaz Incel:
FedOpenHAR: Federated Multitask Transfer Learning for Sensor-Based Human Activity Recognition. 558-572 - Cassandra Czobit, Reza Samavi:
Generative Adversarial Networks for Neuroimage Translation. 573-583 - Mehmet Yildirim, Savas Sezik, Ayse Basar:
Using Traditional and Deep Machine Learning to Predict Emergency Room Triage Levels. 584-600 - Shunqin Zhang, Wei Kong, Shuaiqun Wang, Kai Wei, Kun Liu, Gen Wen, Yaling Yu:
Effective Integration of Single-Cell Multi-Omics Data Using Improved Network-Based Integrative Clustering with Multigraph Regularization. 601-614 - Paulo Henrique Ribeiro, Jorge Francisco Cutigi, Rodrigo Henrique Ramos, Cynthia de Oliveira Lage Ferreira, Adriane Feijo Evangelista, Adenilso da Silva Simão:
Exploring the Influence of Gene Networks on Driver Gene Classification. 615-625 - Martí Cortada Garcia, Adrià Diéguez Moscardó, Marta Casanellas:
Generating Heterogeneous Data on Gene Trees. 626-630
Volume 32, Number 7, 2025
- Anna M. Ritz:
CNB-MAC 2023 Special Issue. 631 - Yang Wang, Zanyu Shi, Pathum Weerawarna, Kun Huang, Timothy Richardson, Yijie Wang:
Building Explainable Graph Neural Network by Sparse Learning for the Drug-Protein Binding Prediction. 632-645 - Shorya Consul, John Robertson, Haris Vikalo:
XVir: A Transformer-Based Architecture for Identifying Viral Reads from Cancer Samples. 646-658 - Peiran Jiang, Jose Lugo-Martinez:
Combined Topological Data Analysis and Geometric Deep Learning Reveal Niches by the Quantification of Protein Binding Pockets. 659-674 - Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa López-Marrero, Shinjae Yoo, Shantenu Jha:
Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge. 675-695 - Natalie Wang, Casey Overby Taylor:
DrIVeNN: Drug Interaction Vectors Neural Network. 696-706 - Pablo M. Redondo, Reza Mousapour, Wayne B. Hayes:
A Novel Graphlet-Based Community Detection Algorithm. 707-720
Volume 32, Number 8, 2025
- Mukul S. Bansal, Wei Chen, Yury Khudyakov, Ion I. Mandoiu, Marmar Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Sharma V. Thankachan, Alex Zelikovsky:
Special Section: 12th International Computational Advances in Bio and Medical Sciences (ICCABS 2023). 721-722 - Nishat Anjum Bristy, Xuecong Fu, Russell Schwartz:
Sc-TUSV-Ext: Single-Cell Clonal Lineage Inference from Single Nucleotide Variants, Copy Number Alterations, and Structural Variants. 723-737 - Alexandra Gavryushkina, Holly R. Pinkney, Sarah D. Diermeier, Alex Gavryushkin:
Filtering for Highly Variable Genes and High-Quality Spots Improves Phylogenetic Analysis of Cancer Spatial Transcriptomics Visium Data. 738-752 - Sing-Hoi Sze:
An Exact Matching Method for 16S rRNA Taxonomy Classification. 753-760 - Aaron Hong, Christina Boucher:
Enhancing Data Compression: Recent Innovations in LZ77 Algorithms. 761-780 - Yuyang Tao, Shufei Ge:
A Mapper Algorithm with Implicit Intervals and Its Optimization. 781-796 - Petr Rysavý, Filip Zelezný:
An Algorithm to Calculate the p-Value of the Monge-Elkan Distance. 797-812 - Jurate Saltyte Benth, Fred Espen Benth, Espen Rostrup Nakstad:
Rebuttal to Flaws in the Paper 'Nearly Instantaneous Time-Varying Reproduction Number for Contagious Diseases - a Direct Approach Based on Nonlinear Regression'. 819-823
Volume 32, Number 9, 2025
- Junlai Qiu, Qingfeng Chen, Wei Lan, Junyue Cao:
Multichannel Contribution Aware Network for Prostate Cancer Grading in Histopathology Images. 826-837 - Xue Pan, Chunping Ouyang, Linlin Zhang, Yongbin Liu, Ying Yu:
Counterfactual Debiased Co-Embedding Model for Enhanced Drug-Drug Interaction Prediction. 838-849 - Xinyuan Shi, Fangfang Zhu, Wenwen Min:
VTrans: A VAE-Based Pre-Trained Transformer Method for Microbiome Data Analysis. 850-864 - Lilu Guo:
Effloc: An Efficient Locating Algorithm for Mass-Occurrence Biological Patterns with FM-Index. 865-878 - Xia Chen, Hao Nie, Quanwei Chen, Xiang Zhang, Zixing He, Xiuxiu Chao, Weihao Ou, Xiangzheng Fu, Haowen Chen:
A Innovative Strategy for Identifying Subtypes Through the Analysis of Multi-Omics Data with Adversarial Autoencoders. 879-895 - Leyi Hu, Xuan Liu, Xiangyu Qu, Chenyan Wang, Bingmeng Hu, Jieyao Wei:
Biogeography-Based Multi-Objective Discrete Optimization with Constraints. 896-910
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