bioRxiv Subject Collection: Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Bioinformatics"
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LIVIA: a browser-based tool for assessing and visualizing predicted protein interactions
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https://www.biorxiv.org/content/10.64898/2026.05.01.721633v1?rss=1
2026-05-10doi:10.64898/2026.05.01.721633Cold Spring Harbor Laboratory2026-05-10
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Deciphering the Molecular Structure of the Type III Secretion System in Chlamydia trachomatis for Structure-Based Therapeutic Targeting
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https://www.biorxiv.org/content/10.64898/2026.05.06.723290v1?rss=1
2026-05-09doi:10.64898/2026.05.06.723290Cold Spring Harbor Laboratory2026-05-09
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Know Your Alphabet: Conformational Noise, Latent-Space Encodings, and the Future of Structural Phylogenetics
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https://www.biorxiv.org/content/10.64898/2026.05.06.722973v1?rss=1
2026-05-09doi:10.64898/2026.05.06.722973Cold Spring Harbor Laboratory2026-05-09
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A structural grammar of truncation across the human homodimer landscape
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https://www.biorxiv.org/content/10.64898/2026.05.06.723091v1?rss=1
2026-05-09doi:10.64898/2026.05.06.723091Cold Spring Harbor Laboratory2026-05-09
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Building an open ecosystem for molecular neuroimaging: standards and tools from the OpenNeuroPET initiative
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https://www.biorxiv.org/content/10.64898/2026.05.06.722876v1?rss=1
2026-05-09doi:10.64898/2026.05.06.722876Cold Spring Harbor Laboratory2026-05-09
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A Fractal-Dimension Framework for Quantifying Self-Similarity in Chromatin Folding
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https://www.biorxiv.org/content/10.64898/2026.05.06.723123v1?rss=1
2026-05-09doi:10.64898/2026.05.06.723123Cold Spring Harbor Laboratory2026-05-09
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Machine learning cross-platform proteomic imputation enables protein quality scoring and replication of epidemiological associations
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https://www.biorxiv.org/content/10.64898/2026.05.05.723059v1?rss=1
2026-05-09doi:10.64898/2026.05.05.723059Cold Spring Harbor Laboratory2026-05-09
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Cross Dataset Transcriptomic Analysis Identifies Oxidative Stress Inflammation Gene Networks Modulated by Nutrigenomic Interventions in Parkinson Disease
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https://www.biorxiv.org/content/10.64898/2026.05.05.723100v1?rss=1
2026-05-09doi:10.64898/2026.05.05.723100Cold Spring Harbor Laboratory2026-05-09
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PromptBio-Bench: Benchmarking LLM-based Bioinformatics Agents for End-to-End Data Analysis
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https://www.biorxiv.org/content/10.64898/2026.05.05.723092v1?rss=1
2026-05-08doi:10.64898/2026.05.05.723092Cold Spring Harbor Laboratory2026-05-08
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Structural bias in machine learning-guided peptide design
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https://www.biorxiv.org/content/10.64898/2026.05.06.721805v1?rss=1
2026-05-08doi:10.64898/2026.05.06.721805Cold Spring Harbor Laboratory2026-05-08
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Open-Rosalind: Tool-First Biomedical LLM Agents with Process-Aware Benchmarking
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https://www.biorxiv.org/content/10.64898/2026.05.06.722404v1?rss=1
2026-05-08doi:10.64898/2026.05.06.722404Cold Spring Harbor Laboratory2026-05-08
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vartracker: an end-to-end tool for pathogen longitudinal variant analysis and visualisation
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https://www.biorxiv.org/content/10.64898/2026.05.06.723370v1?rss=1
2026-05-08doi:10.64898/2026.05.06.723370Cold Spring Harbor Laboratory2026-05-08
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BART-spatial unravels biologically significant transcriptional regulators from spatial omics data
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https://www.biorxiv.org/content/10.64898/2026.05.05.723027v1?rss=1
2026-05-08doi:10.64898/2026.05.05.723027Cold Spring Harbor Laboratory2026-05-08
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RAPID: an interactive R/Shiny platform for end-to-end 16S rRNA and ITS amplicon sequence analysis using DADA2
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https://www.biorxiv.org/content/10.64898/2026.05.05.723040v1?rss=1
2026-05-08doi:10.64898/2026.05.05.723040Cold Spring Harbor Laboratory2026-05-08
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TopoFuseNet: Hierarchical Graph Representation Learning with Multi-Scale Topological Features for Accurate Drug Synergy Prediction
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https://www.biorxiv.org/content/10.64898/2026.05.05.722940v1?rss=1
2026-05-08doi:10.64898/2026.05.05.722940Cold Spring Harbor Laboratory2026-05-08
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A Differentiable dFBA Simulator for Scalable Bayesian Inference over Microbial Metabolic Models
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https://www.biorxiv.org/content/10.64898/2026.05.05.722888v1?rss=1
2026-05-08doi:10.64898/2026.05.05.722888Cold Spring Harbor Laboratory2026-05-08
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SaVanache: indexing and visualizing pangenome variation graphs
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https://www.biorxiv.org/content/10.64898/2026.05.05.722901v1?rss=1
2026-05-08doi:10.64898/2026.05.05.722901Cold Spring Harbor Laboratory2026-05-08
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Efficient Stochastic Trace Generation for Transcription
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https://www.biorxiv.org/content/10.64898/2026.05.05.722871v1?rss=1
2026-05-08doi:10.64898/2026.05.05.722871Cold Spring Harbor Laboratory2026-05-08
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LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing
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https://www.biorxiv.org/content/10.64898/2026.05.05.722992v1?rss=1
2026-05-08doi:10.64898/2026.05.05.722992Cold Spring Harbor Laboratory2026-05-08
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Allosteric Protein Chemical Shift Perturbations are Ubiquitous
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https://www.biorxiv.org/content/10.64898/2026.05.04.722792v1?rss=1
8%) of CSPs distant from the binding site. This analysis across a large number of protein structures demonstrates and documents that structural plasticity is a ubiquitous and fundamental property of proteins.
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Denoised MDS-UPDRS Part-III Scores Yield New Patterns of Progression Heterogeneity in Early Stage Parkinson's Disease
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https://www.biorxiv.org/content/10.64898/2026.05.04.722810v1?rss=1
2026-05-08doi:10.64898/2026.05.04.722810Cold Spring Harbor Laboratory2026-05-08
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QuadStack: Specialized convolutional blocks enable in vivo BG4-binding motif prediction and highlight discrepancies with in vitro G-quadruplexes.
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https://www.biorxiv.org/content/10.64898/2026.05.06.723235v1?rss=1
2026-05-08doi:10.64898/2026.05.06.723235Cold Spring Harbor Laboratory2026-05-08
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MUSE enables cross-species multi-omics integration that incorporates transcriptional regulatory modules
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https://www.biorxiv.org/content/10.64898/2026.05.04.722812v1?rss=1
2026-05-07doi:10.64898/2026.05.04.722812Cold Spring Harbor Laboratory2026-05-07
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PHYFUM: Phylogenetic Reconstruction of Normal and Pre-malignant Tissue Evolution Using Fluctuating Methylation
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https://www.biorxiv.org/content/10.64898/2026.05.05.722981v1?rss=1
2026-05-07doi:10.64898/2026.05.05.722981Cold Spring Harbor Laboratory2026-05-07
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Beyond Pathway Boundaries: A Degree-Aware Network Clustering Test for Gene Sets
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https://www.biorxiv.org/content/10.64898/2026.05.04.722765v1?rss=1
2026-05-07doi:10.64898/2026.05.04.722765Cold Spring Harbor Laboratory2026-05-07
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Image-Conditioned Diffusion for Privacy-Preserving Synthetic Medical Images
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https://www.biorxiv.org/content/10.64898/2026.05.04.722524v1?rss=1
2026-05-07doi:10.64898/2026.05.04.722524Cold Spring Harbor Laboratory2026-05-07
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ORBIT: Orthogonal Rotation for Biological Inter-species Transfer
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https://www.biorxiv.org/content/10.64898/2026.05.04.722193v1?rss=1
2026-05-07doi:10.64898/2026.05.04.722193Cold Spring Harbor Laboratory2026-05-07
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Bridging genomes and peptidomes: hybrid sequencing reveals conserved bioactive peptides in crustaceans
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https://www.biorxiv.org/content/10.64898/2026.05.04.721987v1?rss=1
2026-05-07doi:10.64898/2026.05.04.721987Cold Spring Harbor Laboratory2026-05-07
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A lightweight codon-based DNA Transformer for Regulatory Region Identification in the Genome
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https://www.biorxiv.org/content/10.64898/2026.05.04.722647v1?rss=1
2026-05-07doi:10.64898/2026.05.04.722647Cold Spring Harbor Laboratory2026-05-07
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scLASER: a robust framework for simulating and detecting time-dependent single-cell dynamics in longitudinal studies
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https://www.biorxiv.org/content/10.64898/2026.05.04.722712v1?rss=1
0.92), while analysis of COVID-19 data (188,181 cells, 84 patients) identifies three distinct axes of T cell activity (cytotoxic effector, NK immunoreceptor signaling, and interferon-stimulated gene programs) over disease progression. scLASER enables robust longitudinal single-cell analysis and optimization of study design.
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