bioRxiv Subject Collection: Genomics Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics"
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PERREO: An integrated pipeline for repetitive elements analysis enables the repeatome expression profiling in cancer
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https://www.biorxiv.org/content/10.64898/2026.04.08.714730v1?rss=1
2026-04-10doi:10.64898/2026.04.08.714730Cold Spring Harbor Laboratory2026-04-10
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BrightEyes-FFS: an open-source platform for comprehensive analysis of fluorescence fluctuation spectroscopy experiments with small detector arrays
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https://www.biorxiv.org/content/10.64898/2026.04.08.717207v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717207Cold Spring Harbor Laboratory2026-04-10
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Statistical Principles Define an Open-Source Differential Analysis Workflow for Mass Spectrometry Imaging Experiments with Complex Designs
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https://www.biorxiv.org/content/10.64898/2026.04.08.717212v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717212Cold Spring Harbor Laboratory2026-04-10
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Deep learning enables direct HLA typing from immunopeptidomics data
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https://www.biorxiv.org/content/10.64898/2026.04.08.717021v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717021Cold Spring Harbor Laboratory2026-04-10
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A computational model for quantifying instability of tandem repeats across the genome
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https://www.biorxiv.org/content/10.64898/2026.04.08.717199v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717199Cold Spring Harbor Laboratory2026-04-10
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Eco-physiological and transcriptomic plasticity of Dianthus inoxianus in response to drought
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https://www.biorxiv.org/content/10.64898/2026.04.08.702570v1?rss=1
2026-04-10doi:10.64898/2026.04.08.702570Cold Spring Harbor Laboratory2026-04-10
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Structure-aware geometric graph learning for modeling protease-substrate specificity at scale
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https://www.biorxiv.org/content/10.64898/2026.04.08.717168v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717168Cold Spring Harbor Laboratory2026-04-10
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MTB-KB: A Curated Knowledgebase of Mycobacterium tuberculosis Related Studies
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https://www.biorxiv.org/content/10.64898/2026.04.07.716833v1?rss=1
2026-04-10doi:10.64898/2026.04.07.716833Cold Spring Harbor Laboratory2026-04-10
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Genomic epidemiology of the 2017-2023 outbreak of Mycoplasma bovis sequence type ST21 in New Zealand
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https://www.biorxiv.org/content/10.64898/2026.04.07.717125v1?rss=1
2026-04-10doi:10.64898/2026.04.07.717125Cold Spring Harbor Laboratory2026-04-10
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TCMCard: A High-Confidence Digital Infrastructure for Traditional Chinese Medicine Quantified by Multi-Dimensional Evidence Integration
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https://www.biorxiv.org/content/10.64898/2026.04.07.716940v1?rss=1
2026-04-10doi:10.64898/2026.04.07.716940Cold Spring Harbor Laboratory2026-04-10
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Generating, curating, and evaluating trnL reference sequence databases: Benchmarking OBITools3/ecoPCR, RESCRIPt, and MetaCurator
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https://www.biorxiv.org/content/10.64898/2026.04.07.717010v1?rss=1
2026-04-10doi:10.64898/2026.04.07.717010Cold Spring Harbor Laboratory2026-04-10
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Synolog: A Scalable Synteny-Based Framework for Genome Architecture Characterization
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https://www.biorxiv.org/content/10.64898/2026.04.07.717040v1?rss=1
2026-04-10doi:10.64898/2026.04.07.717040Cold Spring Harbor Laboratory2026-04-10
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Impact of Regularization Methods and Outlier Removal on Unsupervised Sample Classification
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https://www.biorxiv.org/content/10.64898/2026.04.07.716815v1?rss=1
2026-04-10doi:10.64898/2026.04.07.716815Cold Spring Harbor Laboratory2026-04-10
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MHCXGraph: A Graph-Based approach to detecting T cell receptor cross-reactivity
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https://www.biorxiv.org/content/10.64898/2026.04.07.717034v1?rss=1
2026-04-10doi:10.64898/2026.04.07.717034Cold Spring Harbor Laboratory2026-04-10
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Benchmarking ambient RNA removal across droplet and well-plate platforms reveals artificial count generation as a critical failure mode of scAR and CellClear
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https://www.biorxiv.org/content/10.64898/2026.04.08.717130v1?rss=1
93% of counts with values derived from matrix factorization, while scAR generates spurious cell types absent from uncorrected data, including three spurious coarse cell types in the BD Rhapsody dataset and up to eight novel cell types in the prefrontal cortex. CellBender and SoupX exhibit reliable contamination removal with minimal count distortion. DecontX and scCDC are the only tools operable on non-droplet platforms without raw count matrix access. Runtime benchmarking at atlas scale (up to 172,000 nuclei) further demonstrates that CellClear fails to scale. Conclusions: Count matrix integrity, not removal sensitivity alone, must be a primary criterion when selecting ambient RNA correction tools. We provide platform-specific recommendations and a decision framework to guide tool selection across experimental contexts.
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SimpleFold-Turbo: Adaptive Inference Caching Yields 14-fold Acceleration of Flow-Matching Protein Structure Prediction
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https://www.biorxiv.org/content/10.64898/2026.04.07.714835v1?rss=1
2026-04-10doi:10.64898/2026.04.07.714835Cold Spring Harbor Laboratory2026-04-10
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Structure-Based and Stability-Validated Prioritization of BACE1 Inhibitors Integrating Meta-Ensemble QSAR and Molecular Dynamics
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https://www.biorxiv.org/content/10.64898/2026.04.07.716920v1?rss=1
2026-04-10doi:10.64898/2026.04.07.716920Cold Spring Harbor Laboratory2026-04-10
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Conditional genome-wide associations reveal novel genes
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https://www.biorxiv.org/content/10.64898/2026.04.08.717258v1?rss=1
2026-04-09doi:10.64898/2026.04.08.717258Cold Spring Harbor Laboratory2026-04-09
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LOCOM2: Robust Differential Abundance Analysis for Microbiome Data
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https://www.biorxiv.org/content/10.64898/2026.04.07.716976v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716976Cold Spring Harbor Laboratory2026-04-09
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ARACRA: Automated RNA-seq Analysis for Chemical Risk Assessment
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https://www.biorxiv.org/content/10.64898/2026.04.07.716912v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716912Cold Spring Harbor Laboratory2026-04-09
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ViralMap: Predicting Features in Viral Proteins from Primary Sequence
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https://www.biorxiv.org/content/10.64898/2026.04.07.716565v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716565Cold Spring Harbor Laboratory2026-04-09
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An introgressed galectin-like protein is a candidate driver of the human tropism in the intestinal parasite Cryptosporidium
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https://www.biorxiv.org/content/10.64898/2026.04.07.716958v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716958Cold Spring Harbor Laboratory2026-04-09
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Benchmarking SNP-Calling Accuracy Against Known Citrus Pedigrees Reveals Pangenome Advantages Over Linear References
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https://www.biorxiv.org/content/10.64898/2026.04.07.716967v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716967Cold Spring Harbor Laboratory2026-04-09
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Over-representation of sperm-associated deleterious mutations across wild and ex situ cheetah (Acinonyx jubatus) populations
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https://www.biorxiv.org/content/10.64898/2026.04.07.716683v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716683Cold Spring Harbor Laboratory2026-04-09
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Systemic mutagen exposures reported by normal kidney cell genomes
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https://www.biorxiv.org/content/10.64898/2026.04.07.716715v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716715Cold Spring Harbor Laboratory2026-04-09
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A Grid-Search Framework for Dataset-Specific Calibration of Actigraphy Sleep Detection Algorithms
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https://www.biorxiv.org/content/10.64898/2026.04.07.706161v1?rss=1
2026-04-09doi:10.64898/2026.04.07.706161Cold Spring Harbor Laboratory2026-04-09
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gbdraw: a genome diagram generator for microbes and organelles
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https://www.biorxiv.org/content/10.64898/2026.04.07.716863v1?rss=1
2026-04-09doi:10.64898/2026.04.07.716863Cold Spring Harbor Laboratory2026-04-09
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GMIP-PLSR: A Nextflow Pipeline for GWAS and Multi-Omics Integration in Gene Prioritization Using PLSR
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https://www.biorxiv.org/content/10.64898/2026.04.06.716845v1?rss=1
2026-04-09doi:10.64898/2026.04.06.716845Cold Spring Harbor Laboratory2026-04-09
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Spectral Graph Features for Reference-free RNA 3D Quality Assessment
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https://www.biorxiv.org/content/10.64898/2026.04.06.716854v1?rss=1
200~nt), where SpecRNA-QA provides the strongest available quality signal (rho = 0.72 vs. DFIRE 0.52), revealing clear complementarity between global-topological and local-energy scoring. A training-free heuristic using only three spectral statistics enables quality estimation without any labeled data.
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Quantifying Scientific Consensus in Biomedical Hypotheses via LLM-Assisted Literature Screening
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https://www.biorxiv.org/content/10.64898/2026.04.06.716861v1?rss=1
2026-04-09doi:10.64898/2026.04.06.716861Cold Spring Harbor Laboratory2026-04-09