bioRxiv Subject Collection: Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Bioinformatics"
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Why rescue-based transcript ranking can mislead: normalization displacement and shared-control coupling in perturbation transcriptomics
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https://www.biorxiv.org/content/10.64898/2026.09.27.754762v1?rss=1
2026-10-02doi:10.64898/2026.09.27.754762Cold Spring Harbor Laboratory2026-10-02
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Downstream mRNA Secondary Structure, Not Codon Elongation Supply, Coordinates Co-Translational Protein Folding Across the Human Ribosomal Exit Tunnel
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https://www.biorxiv.org/content/10.64898/2026.09.27.753847v1?rss=1
2026-10-02doi:10.64898/2026.09.27.753847Cold Spring Harbor Laboratory2026-10-02
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Auditing Protein-Protein Interaction Signals with Sparse Autoencoder Fingerprints
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https://www.biorxiv.org/content/10.64898/2026.09.27.754758v1?rss=1
2026-10-02doi:10.64898/2026.09.27.754758Cold Spring Harbor Laboratory2026-10-02
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GGE: General-purpose deep meta-learning for classification of human transcriptomes with limited data
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https://www.biorxiv.org/content/10.64898/2026.09.27.754054v1?rss=1
2026-10-02doi:10.64898/2026.09.27.754054Cold Spring Harbor Laboratory2026-10-02
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GroundAnnot: a closed-vocabulary contract for grounding LLM gene-set annotation in live enrichment backends
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https://www.biorxiv.org/content/10.64898/2026.09.27.754741v1?rss=1
2026-10-02doi:10.64898/2026.09.27.754741Cold Spring Harbor Laboratory2026-10-02
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EnsPlex: Integrative Protein Complex Prediction through Multi-source Complementary Structural Sampling and Topology-Aware Candidate Selection
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https://www.biorxiv.org/content/10.64898/2026.09.26.754739v1?rss=1
2026-10-02doi:10.64898/2026.09.26.754739Cold Spring Harbor Laboratory2026-10-02
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AbRefine: Framework-Conditioned Refinement for Structure-Guided Antibody CDR Design
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https://www.biorxiv.org/content/10.64898/2026.09.27.754743v1?rss=1
2026-10-02doi:10.64898/2026.09.27.754743Cold Spring Harbor Laboratory2026-10-02
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Inference on paths of yeast transcription pre-initiation complex assembly by model-based analysis of altered occupancy profiles
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https://www.biorxiv.org/content/10.64898/2026.09.30.755594v1?rss=1
2026-10-02doi:10.64898/2026.09.30.755594Cold Spring Harbor Laboratory2026-10-02
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SCITRAM: a Single-cell Integrated transcription regulation modeler for predicting master transcription factors
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https://www.biorxiv.org/content/10.64898/2026.09.30.755779v1?rss=1
2026-10-01doi:10.64898/2026.09.30.755779Cold Spring Harbor Laboratory2026-10-01
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A cross-species meta-transcriptomic analysis of viral infection-induced shifts in microbial transcript profiles across insects.
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https://www.biorxiv.org/content/10.64898/2026.09.28.754049v1?rss=1
2026-10-01doi:10.64898/2026.09.28.754049Cold Spring Harbor Laboratory2026-10-01
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Systematic exploration of predicted quaternary structures within pandemic-relevant viral proteomes
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https://www.biorxiv.org/content/10.64898/2026.09.29.755321v1?rss=1
2026-10-01doi:10.64898/2026.09.29.755321Cold Spring Harbor Laboratory2026-10-01
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Widespread 3-Base Periodicity in Complex DNA Mixtures and an Alignment-Free Algorithm to Uncover its Source
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https://www.biorxiv.org/content/10.64898/2026.09.26.754620v1?rss=1
2026-10-01doi:10.64898/2026.09.26.754620Cold Spring Harbor Laboratory2026-10-01
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In-silico Exploration of Drug Leads Targeting Mycobacterial Ag85C
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https://www.biorxiv.org/content/10.64898/2026.09.26.754622v1?rss=1
2026-10-01doi:10.64898/2026.09.26.754622Cold Spring Harbor Laboratory2026-10-01
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QuImputer: an LD-informed QUBO/Ising formulation of genotype imputation with quantum-hardware execution
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https://www.biorxiv.org/content/10.64898/2026.09.26.754587v1?rss=1
2026-10-01doi:10.64898/2026.09.26.754587Cold Spring Harbor Laboratory2026-10-01
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IQC: A Novel Criterion for Assessing Feature Selection Stability in High-Dimensional Analyses
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https://www.biorxiv.org/content/10.64898/2026.09.26.754480v1?rss=1
2026-10-01doi:10.64898/2026.09.26.754480Cold Spring Harbor Laboratory2026-10-01
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LOL: a Python package for leakage-aware phenotype prediction and confounding diagnostics in GEO transcriptomics datasets
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https://www.biorxiv.org/content/10.64898/2026.09.26.754596v1?rss=1
2026-10-01doi:10.64898/2026.09.26.754596Cold Spring Harbor Laboratory2026-10-01
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Ultrafast and Accurate Selection of High-Quality Protein Complex Models from Large-Scale Prediction
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https://www.biorxiv.org/content/10.64898/2026.09.26.754618v1?rss=1
2026-10-01doi:10.64898/2026.09.26.754618Cold Spring Harbor Laboratory2026-10-01
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Quantifying the Provenance-to-Function Gap in Antidiabetic Peptide Prediction: Homology-Aware Evaluation and the ADP-Hybrid Baseline
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https://www.biorxiv.org/content/10.64898/2026.09.25.754557v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754557Cold Spring Harbor Laboratory2026-10-01
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Three-Year Longitudinal Analysis of Splicing Changes in Myotonic Dystrophy Type 1
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https://www.biorxiv.org/content/10.64898/2026.09.25.754454v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754454Cold Spring Harbor Laboratory2026-10-01
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Octave: Scale-resolved Evaluation of Spatial Gene Expression Prediction from Histology
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https://www.biorxiv.org/content/10.64898/2026.09.25.754484v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754484Cold Spring Harbor Laboratory2026-10-01
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Rank-Preserving Alignment Enables Cross-platform Learning and Phenotyping for Single-Cell and Spatial Proteomics
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https://www.biorxiv.org/content/10.64898/2026.09.25.754510v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754510Cold Spring Harbor Laboratory2026-10-01
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Sparse dynamic graphical models for longitudinal non-Gaussian data
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https://www.biorxiv.org/content/10.64898/2026.09.25.754276v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754276Cold Spring Harbor Laboratory2026-10-01
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Evidence Scaling for Zero-Shot Protein Reasoning with Large Language Models
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https://www.biorxiv.org/content/10.64898/2026.09.27.754822v1?rss=1
2026-10-01doi:10.64898/2026.09.27.754822Cold Spring Harbor Laboratory2026-10-01
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Limitations of differential expression for cell-type marker discovery in single-cell RNA sequencing atlases
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https://www.biorxiv.org/content/10.64898/2026.09.25.754486v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754486Cold Spring Harbor Laboratory2026-10-01
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AmyloCore-ML: AI/Machine Learning Enabled Identification of Amyloid Fibril Core Regions Using Protein Language Models
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https://www.biorxiv.org/content/10.64898/2026.09.25.754455v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754455Cold Spring Harbor Laboratory2026-10-01
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The recoverable resolution of cellular perturbation-response prediction
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https://www.biorxiv.org/content/10.64898/2026.09.30.755756v1?rss=1
2026-10-01doi:10.64898/2026.09.30.755756Cold Spring Harbor Laboratory2026-10-01
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SFUMATO: Bayesian probabilistic clustering for uncertainty-aware spatialtranscriptomics analysis and mapping
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https://www.biorxiv.org/content/10.64898/2026.09.25.754409v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754409Cold Spring Harbor Laboratory2026-10-01
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biomes: An R package for reproducible occurrence-to-biome classification using 31 global biome schemes
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https://www.biorxiv.org/content/10.64898/2026.09.25.754345v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754345Cold Spring Harbor Laboratory2026-10-01
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Integrative Multi-Omics Analysis Reveals Molecular Signatures of Age-Related Decline in Vervet Leg Skeletal Muscle
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https://www.biorxiv.org/content/10.64898/2026.09.25.754162v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754162Cold Spring Harbor Laboratory2026-10-01
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Rank-based integration identifies convergent disease mechanisms across omics
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https://www.biorxiv.org/content/10.64898/2026.09.25.754380v1?rss=1
2026-10-01doi:10.64898/2026.09.25.754380Cold Spring Harbor Laboratory2026-10-01