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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
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