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ORCIDJournal of Computational Biology, Volume 33
Volume 33, Number 1, 2026
- Mona Singh:
Preface. 1 - Leah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir
:
Pharming: Joint Clonal Tree Reconstruction of Single-Nucleotide Variant and Copy Number Aberration Evolution from Single-Cell DNA Sequencing of Tumors. 2-18 - Nina Corvelo Benz, Lucas Miranda, Dexiong Chen, Janko Sattler, Karsten M. Borgwardt:
Conformal Prediction with Knowledge Graphs for Reliable Antimicrobial Resistance Detection with MALDI-TOF Mass Spectra. 19-35 - Christy Lee, Dongyuan Song, Siqi Chen, Jingyi Jessica Li:
ClusterDE : A Statistical Software Package for Removing Double-Dipping Bias in Post-Clustering Differential Expression Analysis. 36-42 - Pan Liu, Jingyi Jessica Li:
mcRigor : A Statistical Software Package for Evaluating and Optimizing Metacell Partitioning in Single-Cell Data Analysis. 43-47 - Junyan Dai, Erin K. Molloy:
StarCDP: Dynamic Programming Algorithms for Fast and Accurate Cell Lineage Tree Reconstruction from CRISPR-Based Lineage Tracing Data. 48-66 - Pramesh Shakya, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang:
An Efficient Dynamic Data Structure for Haplotype Matching and Compression on Biobank-Scale Data. 67-89 - Jiahan Li, Shitong Luo, Congyue Deng, Chaoran Cheng, Jiaqi Guan, Leonidas J. Guibas, Jian Peng, Jianzhu Ma:
Learning Protein Structure Representation with Orientation-Aware Networks. 90-106 - Adam Park, David Koslicki:
Elucidating Transitions of k -mer-Based Objects Across k -mer Sizes. 107-133 - Tianshuo Zhou, Apoorv Malik, Wei Yu Tang, David H. Mathews, Liang Huang:
Theory, Algorithms, and Applications for Identification of Undesignable RNA Secondary Structures and Motifs. 134-167 - Nathaniel K. Brown, Vikram Shivakumar, Ben Langmead:
Col-BWT: Pangenomic Seed Chaining with Maximal Matches Improves Read Classification. 168-183 - Zexin Xue, Michael Bailey, Abhinav Gupta, Ruijiang Li, Alejandro Corrochano-Navarro, Sizhen Li, Lorenzo Kogler-Anele, Qui Yu, Heidi Rommelaere, Wander Van Breedam, Norbert Furtmann, Joseph Batchelor, Ziv Bar-Joseph, Sven Jager:
Deep Batch Active Learning for Protein Structure Modeling. 184-200 - Acknowledgment of Reviewers 2025. 201-202
Volume 33, Number 2, 2026
- Yao-ban Chan, Céline Scornavacca, Michael A. Charleston:
A Probabilistic Algorithm for Gene-Species Reconciliation with Segmental Duplications. 203-218 - Xiao Liang, Lenwood S. Heath:
Reflections on the Presence of Human Cancer Genes in Primate Genomes. 219-235 - Vy Q. Ong, Bich N. Choi, Devin P. Lundy, Yingnan Zhang, Yin Wan, Hongyan Xu, Santu Ghosh, Hui Jiang, Yang Shi:
MCMC-CE: A Novel and Efficient Algorithm for Estimating Small Right-Tail Probabilities of Quadratic Forms with Applications in Genomics. 236-254 - Xiang Shi, Jiayi Kang, Nan Sun, Xin Zhao, Stephen S.-T. Yau:
Multi-Perspective Natural Vector: A Novel Method for Viral Sequence Feature Extraction. 255-266 - Donghui Son, Jaejik Kim:
Bayesian Validation of Dynamic Systems for Biological Networks. 267-279
Volume 33, Number 3, 2026
- Inass Soukarieh, Gerhard Hessler, Hervé Minoux, Marcel Mohr, K. Friedemann Schmidt, Jan Wenzel, Pierre Barbillon, Hugo Gangloff, Pierre Gloaguen:
HyperSBINN: A Hypernetwork-Enhanced Systems Biology-Informed Neural Network for Efficient Drug Cardiosafety Assessment. 281-300 - Chayan Maitra, Dibyendu Bikash Seal, Vivek Das, Rajat K. De:
NeuroMDAVIS: Visualization of Single-Cell Multi-Omics Data under Deep Learning Framework. 301-317 - Thi-Xuan Tran, Nguyen-Quoc-Khanh Le, Duc-Hau Le, Van-Nui Nguyen:
DP-OTG: A Feature-Free Deep Learning Model for Accurate Prediction of Human O-Linked Threonine Glycosylation Sites. 318-335 - Heewon Park, Satoru Miyano:
Gene Network Enrichment Analysis and Its Application to Explore Enriched Immune Disease Pathways for Gene Network of Acute Myeloid Leukemia Cell Lines. 336-354 - Yanyan Du, Zong Wang:
Stability Analysis of Age-Structured Stochastic Delayed Population-Toxicant Model with Lévy Noise. 355-378 - Jan Pawel Jastrzebski, Monika Gawronska, Wiktor Babis, Miriana Quaranta, Damian Czopek:
PMScanR: An R Package for the Large-Scale Identification, Analysis, and Visualization of Protein Motifs. 379-384
Volume 33, Number 4, 2026
- Giltae Song:
Special Issue: RECOMB Satellite Conference on Comparative Genomics (RECOMB-CG 2025). 385 - Hao Yu, Michael Fuchs, Guan-Ru Yu, Louxin Zhang:
Exact and Asymptotic Counts of Binary Phylogenetic Networks with a Few Reticulation Events. 386-400 - Muyao Huang, Martin C. Frith:
Probability-Based Sequence Comparison Finds Pre-Eutherian Nuclear Mitochondrial DNA Segments in Mammalian Genomes. 401-419 - Martin C. Frith, Patrick Boppert, Patrick Styll, Milot Mirdita:
Simple and Thorough Detection of Related Sequences with Position-Varying Probabilities of Substitutions, Insertions, and Deletions. 420-438 - Triveni Shelke, Vanika Gupta, Ishaan Gupta:
A Cross-Order Comparative Genomics Analysis of Insect Innate Immunity Suggests Niche-Specific Adaptation. 439-455 - Reza Kalhor, Manuel Lafond, Céline Scornavacca:
Beyond Synteny: A Scalable Phylogenomics Method for Whole-Genome Duplication Detection. 456-481 - Meijun Gao, Kevin J. Liu:
A REsampling and Visual EvALuation Method to Detect and Map Local Model Violations During Biomolecular Sequence Analysis. 482-498 - Songdi Hu, Vladimir Reinharz, Olivier Tremblay-Savard:
Reconstructing Ancestral Non-Coding RNAs of Multiple Families Using Sequence and Structural Information with Tree Decomposition. 499-517 - Kaari Landry, Olivier Tremblay-Savard:
CherryRed: A Software Implementation of Cherry Distance with a New Optimization and Heuristic. 518-534 - Alitzel López Sánchez, Guillaume E. Scholz, Peter F. Stadler, Manuel Lafond:
From Small Parsimony to Horizontal Gene Transfer: Inferring Horizontal Transfer and Gene Loss for Single-Origin Characters. 535-557 - Yue Zhang, David Sankoff:
Branching-Process Modeling of Homology Distribution in Salmonid Genomes. 558-572
Volume 33, Numbers 5-6, 2026
- Mohammed Alser, Mukul S. Bansal, Yury Khudyakov, Serghei Mangul, Ion I. Mandoiu, Marmar R. Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Shibu Yooseph, Alexander Zelikovsky:
Special Issue: 13th International Conference on Computational Advances in Bio and Medical Sciences. 573-574 - Enrico Rossignolo, Matteo Comin:
USTAR-CR: Efficient and Compact Compression of k -Mer Sets Through Colored de Bruijn Graphs. 575-592 - Leonardo Gemin, Cinzia Pizzi, Matteo Comin:
Fast Hashing of Spaced Seeds with DuoHash. 593-610 - Ashwag Altayyar, Li Liao:
FDS-CAP: Modeling Fragmented Disease Subgraphs with Component-Level Attention for Comorbidity Prediction. 611-623 - Ivan Makohon, Mohamad Najafi, Jian Wu, Mathias Brochhausen, Yaohang Li:
Enhancing Clinical Note Generation with ICD-10, Clinical Ontology Knowledge Graphs, and Chain-of-Thought Prompting Using GPT-4. 624-642 - Arpit Mehta, Vitalii Stebliankin, Kalai Mathee, Giri Narasimhan:
ME ditome : Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes. 643-659 - Mohamed Abdelnaby, Marmar R. Moussa:
Random Projection Methods Outperform Principal Component Analysis for Dimensionality Reduction in Single Cell RNA-Seq. 660-679 - Taslim Murad, Prakash Chourasia, Sarwan Ali, Imdad Ullah Khan, Murray Patterson:
DANCE: Deep Learning-Assisted Analysis of ProteiN Sequences Using Chaos Enhanced Kaleidoscopic Images. 680-691 - Ayotomiwa Ezekiel Adeniyi, Akshay Juyal, Pavel Skums, Murray Patterson, Alex Zelikovsky:
Uncovering Epistatic Interactions in SARS-CoV-2 Evolution Through Hidden Markov Models. 692-704 - Seth Sims, Yury Khudyakov, Alexander Zelikovsky:
Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing. 705-715
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