bioRxiv Subject Collection: Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Bioinformatics"
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DextraDemixer enables accurate identification of antigen-specific T cells from pMHC multimer experiments
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https://www.biorxiv.org/content/10.64898/2026.06.23.733339v1?rss=1
2026-06-25doi:10.64898/2026.06.23.733339Cold Spring Harbor Laboratory2026-06-25
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ComplexDesign: sequence-hallucination design of protein binders bridging multiple proteins
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https://www.biorxiv.org/content/10.64898/2026.06.21.733655v1?rss=1
2026-06-24doi:10.64898/2026.06.21.733655Cold Spring Harbor Laboratory2026-06-24
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V3Cell: A Vision-Guided Virtual 3D Cell Framework for Phenotypic Modeling and Perturbation Prediction
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https://www.biorxiv.org/content/10.64898/2026.06.23.734130v1?rss=1
2026-06-24doi:10.64898/2026.06.23.734130Cold Spring Harbor Laboratory2026-06-24
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fastQpick: scalable bootstrap and subsampling of FASTQ reads
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https://www.biorxiv.org/content/10.64898/2026.06.23.734068v1?rss=1
2026-06-24doi:10.64898/2026.06.23.734068Cold Spring Harbor Laboratory2026-06-24
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RNabel-A Standalone Software Tool for Annotating Tandem Mass Spectra of Modified Ribonucleic Acids
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https://www.biorxiv.org/content/10.64898/2026.06.22.733900v1?rss=1
2026-06-24doi:10.64898/2026.06.22.733900Cold Spring Harbor Laboratory2026-06-24
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Development of Deep-Learning Models that Predict Quantitative Protein-Ligand Interac-tions in Glycobiology as a part of a Capstone Course
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https://www.biorxiv.org/content/10.64898/2026.06.19.733466v1?rss=1
2026-06-24doi:10.64898/2026.06.19.733466Cold Spring Harbor Laboratory2026-06-24
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A comprehensive analysis of calreticulin mutants reveals distinct biophysicochemical proprieties with a potential for refined targeted therapies
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https://www.biorxiv.org/content/10.64898/2026.06.19.733337v1?rss=1
2026-06-24doi:10.64898/2026.06.19.733337Cold Spring Harbor Laboratory2026-06-24
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InVitroGap: an open-source tool for automated quantification of wound closure in the in vitro scratch assay
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https://www.biorxiv.org/content/10.64898/2026.06.19.733445v1?rss=1
0.05), strong pooled correlations (R square = 0.964 for RWD; R square = 0.983 for wound confluence), and small mean biases (absolute bias [≤] 1.64%). The tool successfully processed crisscross wounds from brightfield image series, and a complete four-timepoint series was analyzed in approximately 10 seconds, with robust performance across distinct cell morphologies and wound geometries. Conclusions: InVitroGap provides a transparent, computationally efficient, and platform-independent alternative for scratch assay analysis, delivering performance comparable to commercial systems while remaining freely accessible at https://invitrogap.vercel.app/.
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Generative Modeling of Mouse Embryogenesis for Fate and Disease Prediction
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https://www.biorxiv.org/content/10.64898/2026.06.18.733286v1?rss=1
2026-06-24doi:10.64898/2026.06.18.733286Cold Spring Harbor Laboratory2026-06-24
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Systematic benchmarking of multi-modal approaches for tumor-naive ctDNA detection and quantification
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https://www.biorxiv.org/content/10.64898/2026.06.19.733293v1?rss=1
2026-06-24doi:10.64898/2026.06.19.733293Cold Spring Harbor Laboratory2026-06-24
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Statistical tests for bivariate spatial association across multi-omics data with disjoint coordinates
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https://www.biorxiv.org/content/10.64898/2026.06.19.732250v1?rss=1
2026-06-24doi:10.64898/2026.06.19.732250Cold Spring Harbor Laboratory2026-06-24
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trAIt: Species-by-Trait Data Retrieval using Large Language Models
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https://www.biorxiv.org/content/10.64898/2026.06.19.732660v1?rss=1
2026-06-24doi:10.64898/2026.06.19.732660Cold Spring Harbor Laboratory2026-06-24
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Beyond statistical significance: ranking transcription factor binding motifs by effect size
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https://www.biorxiv.org/content/10.64898/2026.06.19.732679v1?rss=1
2026-06-24doi:10.64898/2026.06.19.732679Cold Spring Harbor Laboratory2026-06-24
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SEMFA: A General Framework for Inferring Statistical Significance of Mahalanobis Similarity between Multi-Omics Profiled Samples Built on Multiple Factor Analysis
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https://www.biorxiv.org/content/10.64898/2026.06.18.733287v1?rss=1
2026-06-24doi:10.64898/2026.06.18.733287Cold Spring Harbor Laboratory2026-06-24
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Pharmacological Stratification of Public Bioactivity Databases: A Reusable, OECD-Anchored Curation and Benchmarking Framework Demonstrated for Opioid Receptors
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https://www.biorxiv.org/content/10.64898/2026.06.18.732083v1?rss=1
2026-06-24doi:10.64898/2026.06.18.732083Cold Spring Harbor Laboratory2026-06-24
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An atlas-scale generative model for unified representation learning of bulk RNA-seq data
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https://www.biorxiv.org/content/10.64898/2026.06.18.733198v1?rss=1
2026-06-24doi:10.64898/2026.06.18.733198Cold Spring Harbor Laboratory2026-06-24
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BATTLE-AMP: Benchmarking Antimicrobial Peptide Predictors
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https://www.biorxiv.org/content/10.64898/2026.06.19.733349v1?rss=1
2026-06-24doi:10.64898/2026.06.19.733349Cold Spring Harbor Laboratory2026-06-24
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EnrichViz: An Interactive R Shiny Application for Visualization of Pathway Enrichment Results from Omics Data
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https://www.biorxiv.org/content/10.64898/2026.06.19.733398v1?rss=1
2026-06-23doi:10.64898/2026.06.19.733398Cold Spring Harbor Laboratory2026-06-23
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FateLimit quantifies the prediction horizon of cell fate
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https://www.biorxiv.org/content/10.64898/2026.06.22.733672v1?rss=1
2026-06-23doi:10.64898/2026.06.22.733672Cold Spring Harbor Laboratory2026-06-23
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Multi-Scale Machine Learning for Antibody-Antigen Binding Affinity Prediction Using Deep Mutational Scanning and Structural Features
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https://www.biorxiv.org/content/10.64898/2026.06.09.730151v1?rss=1
2026-06-23doi:10.64898/2026.06.09.730151Cold Spring Harbor Laboratory2026-06-23
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Comorbidity structure as an inductive bias: Comparing output-head designs for multi-label prediction of diabetes and myocardial infarction complications
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https://www.biorxiv.org/content/10.64898/2026.06.18.733068v1?rss=1
2026-06-23doi:10.64898/2026.06.18.733068Cold Spring Harbor Laboratory2026-06-23
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Learning interpretable structural similarity from tandem mass spectra for small molecule analog discovery
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https://www.biorxiv.org/content/10.64898/2026.06.17.733050v1?rss=1
2026-06-23doi:10.64898/2026.06.17.733050Cold Spring Harbor Laboratory2026-06-23
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VCBench: A Multi-Dimensional Benchmark for Single-Cell Foundation Models
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https://www.biorxiv.org/content/10.64898/2026.06.18.733146v1?rss=1
2026-06-23doi:10.64898/2026.06.18.733146Cold Spring Harbor Laboratory2026-06-23
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Measuring peptide-MHC generalization to unseen alleles across both HLA classes
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https://www.biorxiv.org/content/10.64898/2026.06.18.733075v1?rss=1
2026-06-23doi:10.64898/2026.06.18.733075Cold Spring Harbor Laboratory2026-06-23
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Automated Segmentation of Prostatic Gold Fiducial Markers for MR-Only Radiotherapy Planning Using Multi-Modal Consensus Deep Learning
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https://www.biorxiv.org/content/10.64898/2026.06.18.733061v1?rss=1
2026-06-23doi:10.64898/2026.06.18.733061Cold Spring Harbor Laboratory2026-06-23
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Model-based inference of gene expression noise from single-cell RNA-sequencing data
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https://www.biorxiv.org/content/10.64898/2026.06.18.733122v1?rss=1
2026-06-23doi:10.64898/2026.06.18.733122Cold Spring Harbor Laboratory2026-06-23
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Early Tracheal and Salivary miRNAs in Extremely Preterm Infants Predict BPD-related Pulmonary Hypertension
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https://www.biorxiv.org/content/10.64898/2026.06.17.732493v1?rss=1
2026-06-23doi:10.64898/2026.06.17.732493Cold Spring Harbor Laboratory2026-06-23
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CellOS: Learning a World Model of Cellular State through Joint Embedding Prediction
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https://www.biorxiv.org/content/10.64898/2026.06.18.733163v1?rss=1
2026-06-23doi:10.64898/2026.06.18.733163Cold Spring Harbor Laboratory2026-06-23
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Systematic benchmarking of zero-shot utility and robustness in single-cell transcriptomic foundation models
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https://www.biorxiv.org/content/10.64898/2026.06.18.733285v1?rss=1
2026-06-23doi:10.64898/2026.06.18.733285Cold Spring Harbor Laboratory2026-06-23
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biomeStat: Using Agentic AI for Scalable Genomic Epidemiology Demonstrated Through End-to-End Analysis of 1,000 Asian Dengue Virus Genomes
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https://www.biorxiv.org/content/10.64898/2026.06.10.731380v1?rss=1
2026-06-23doi:10.64898/2026.06.10.731380Cold Spring Harbor Laboratory2026-06-23