bioRxiv Subject Collection: Genomics Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics"
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Machine learning classifies subcellular Golgi morphology from imaging flow cytometry during inflammatory activation: an exploratory study
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https://www.biorxiv.org/content/10.64898/2026.10.01.756023v1?rss=1
2026-10-08doi:10.64898/2026.10.01.756023Cold Spring Harbor Laboratory2026-10-08
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Sketching the SRA: experiment-wide similarity search across 4.8 million metagenomes
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https://www.biorxiv.org/content/10.64898/2026.10.07.757297v1?rss=1
2026-10-08doi:10.64898/2026.10.07.757297Cold Spring Harbor Laboratory2026-10-08
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Co-occurrence network multicollinearity artefacts using centered log-ratio transformation
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https://www.biorxiv.org/content/10.64898/2026.10.01.756072v1?rss=1
2026-10-08doi:10.64898/2026.10.01.756072Cold Spring Harbor Laboratory2026-10-08
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8-Oxoguanine transcriptional miscoding can transiently reproduce PAH-associated premature-stop transcripts
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https://www.biorxiv.org/content/10.64898/2026.10.01.756055v1?rss=1
A error in the nascent transcript. We asked whether this chemistry could generate premature-stop transcripts in dosage-sensitive PAH genes. Across 17,880 C>A-accessible coding positions in pulmonary vascular genes, 1,192 could generate premature termination codons, including 883 predicted to engage nonsense-mediated decay (NMD). Restricting these sites to expressed autosomal-dominant PAH genes with definitive ClinGen validity and established haploinsufficiency identified 116 NMD-prone positions in BMPR2, KDR, SMAD9, and TBX4. Eight exactly reproduce ClinVar pathogenic or likely pathogenic stop variants, including five in BMPR2. At BMPR2 c.1424, template-strand 8-oxoG and the expert-panel-reviewed genomic c.1424C>A allele is predicted to generate the same UAA-containing transcript. Published oxidized-guanine maps detect signal at seven of the eight coordinates, providing coordinate-level support for oxidative modification at these sites. These findings define a sequence-resolved route through which repairable oxidative DNA damage could transiently reproduce loss-of-function transcripts encoded by pathogenic PAH alleles without permanent genomic mutation.
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REFinder: Mining new enzymes from metagenomes
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https://www.biorxiv.org/content/10.64898/2026.10.01.756075v1?rss=1
2026-10-08doi:10.64898/2026.10.01.756075Cold Spring Harbor Laboratory2026-10-08
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KENT: Fast Pathogen Screening with NVIDIA Jetson Cluster in Resource-Constrained Areas
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https://www.biorxiv.org/content/10.64898/2026.09.28.754999v1?rss=1
2026-10-08doi:10.64898/2026.09.28.754999Cold Spring Harbor Laboratory2026-10-08
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FilAdh: degradation-aware analysis of focal adhesions and actin stress fibers
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https://www.biorxiv.org/content/10.64898/2026.09.28.755011v1?rss=1
2026-10-08doi:10.64898/2026.09.28.755011Cold Spring Harbor Laboratory2026-10-08
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CryoCodex: learning discrete structural representations for cryo-EM map post-processing
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https://www.biorxiv.org/content/10.64898/2026.09.30.755675v1?rss=1
2026-10-08doi:10.64898/2026.09.30.755675Cold Spring Harbor Laboratory2026-10-08
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FlyAnatoView: Visualization of Drosophila Single-cell RNA-seq Datasets on Anatomographs
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https://www.biorxiv.org/content/10.64898/2026.09.28.755010v1?rss=1
2026-10-08doi:10.64898/2026.09.28.755010Cold Spring Harbor Laboratory2026-10-08
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VINTER: a generative vision-language model for annotating and interrogating spatial tissues
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https://www.biorxiv.org/content/10.64898/2026.10.01.752251v1?rss=1
2026-10-08doi:10.64898/2026.10.01.752251Cold Spring Harbor Laboratory2026-10-08
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Synthesis-aware generative design in trillion-scale chemical spaces for automated drug discovery
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https://www.biorxiv.org/content/10.64898/2026.10.01.755933v1?rss=1
2026-10-08doi:10.64898/2026.10.01.755933Cold Spring Harbor Laboratory2026-10-08
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NomadFlow: unindexed multi-motif scaffolding with independently mobile rigid groups
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https://www.biorxiv.org/content/10.64898/2026.10.01.754115v1?rss=1
2026-10-08doi:10.64898/2026.10.01.754115Cold Spring Harbor Laboratory2026-10-08
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Additive-input encoding fails operator-level target-held-out prediction on current Perturb-seq screens
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https://www.biorxiv.org/content/10.64898/2026.09.30.755776v1?rss=1
2026-10-08doi:10.64898/2026.09.30.755776Cold Spring Harbor Laboratory2026-10-08
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Evaluating Autonomous LLM Agents Across Molecular Prediction and Optimization Benchmarks
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https://www.biorxiv.org/content/10.64898/2026.10.01.755314v1?rss=1
2026-10-08doi:10.64898/2026.10.01.755314Cold Spring Harbor Laboratory2026-10-08
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Evaluation of synthetic data generation for longitudinal 6-year follow-up subclinical cardiovascular disease data using GAN models
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https://www.biorxiv.org/content/10.64898/2026.10.01.755916v1?rss=1
2026-10-08doi:10.64898/2026.10.01.755916Cold Spring Harbor Laboratory2026-10-08
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RiboWin: A computational framework to identify non-canonical open reading frames
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https://www.biorxiv.org/content/10.64898/2026.10.01.752299v1?rss=1
2026-10-08doi:10.64898/2026.10.01.752299Cold Spring Harbor Laboratory2026-10-08
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Robust ORF Deconvolution from Multiple Ribo-seq Datasets with Group LASSO Penalty
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https://www.biorxiv.org/content/10.64898/2026.10.01.755973v1?rss=1
2026-10-08doi:10.64898/2026.10.01.755973Cold Spring Harbor Laboratory2026-10-08
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The impact of sex and ancestry on the molecular landscape of pancreatic adenocarcinoma
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https://www.biorxiv.org/content/10.64898/2026.10.06.757201v1?rss=1
2026-10-08doi:10.64898/2026.10.06.757201Cold Spring Harbor Laboratory2026-10-08
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A strategy for ionic current analysis of nanopore protein readouts
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https://www.biorxiv.org/content/10.64898/2026.09.28.755023v1?rss=1
2026-10-08doi:10.64898/2026.09.28.755023Cold Spring Harbor Laboratory2026-10-08
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HapSolo2: GPU-accelerated optimization for removing secondary haplotigs from diploid genome assemblies
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https://www.biorxiv.org/content/10.64898/2026.10.02.756147v1?rss=1
2026-10-08doi:10.64898/2026.10.02.756147Cold Spring Harbor Laboratory2026-10-08
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Sex-dependent DNA methylation in amyotrophic lateral sclerosis
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https://www.biorxiv.org/content/10.64898/2026.09.30.755680v1?rss=1
2026-10-08doi:10.64898/2026.09.30.755680Cold Spring Harbor Laboratory2026-10-08
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Heterochromatin protein 1α acts as an essential stabilizer of chromatin packing domains
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https://www.biorxiv.org/content/10.64898/2026.10.05.753292v1?rss=1
2026-10-08doi:10.64898/2026.10.05.753292Cold Spring Harbor Laboratory2026-10-08
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A gene-centric analysis of copy number variation reveals tumour suppressor modulation of cancer risk and novel associations with common diseases
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https://www.biorxiv.org/content/10.64898/2026.10.06.757170v1?rss=1
2026-10-08doi:10.64898/2026.10.06.757170Cold Spring Harbor Laboratory2026-10-08
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Quantifying performance inflation from hidden sample dependence in biomedical image classification benchmarks
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https://www.biorxiv.org/content/10.64898/2026.10.01.755883v1?rss=1
2026-10-08doi:10.64898/2026.10.01.755883Cold Spring Harbor Laboratory2026-10-08
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D-plus: Beyond the D-statistic -- Accurate Detection and Characterization of Introgression Despite Among-Lineage Rate Variation
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https://www.biorxiv.org/content/10.64898/2026.10.01.755911v1?rss=1
2026-10-08doi:10.64898/2026.10.01.755911Cold Spring Harbor Laboratory2026-10-08
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scStable: assessing scRNA-seq analysis stability under bulk-derived between-sample variation
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https://www.biorxiv.org/content/10.64898/2026.10.01.755876v1?rss=1
2026-10-08doi:10.64898/2026.10.01.755876Cold Spring Harbor Laboratory2026-10-08
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msengine: Adaptive Open-Source Signal Extraction for HDX MS
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https://www.biorxiv.org/content/10.64898/2026.09.30.755802v1?rss=1
2026-10-08doi:10.64898/2026.09.30.755802Cold Spring Harbor Laboratory2026-10-08
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HyperCom: a hypergraph-based method to infer cell-resolved cell-cell communication
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https://www.biorxiv.org/content/10.64898/2026.09.30.755742v1?rss=1
2026-10-08doi:10.64898/2026.09.30.755742Cold Spring Harbor Laboratory2026-10-08
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Transfer Matrix and Tensor Approaches to Nucleic Acid Secondary Structure Thermodynamics
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https://www.biorxiv.org/content/10.64898/2026.09.30.755805v1?rss=1
2026-10-08doi:10.64898/2026.09.30.755805Cold Spring Harbor Laboratory2026-10-08
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PaleoRigor: a bounded research agent with a reproducible evidence trail for paleomicrobiome data processing
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https://www.biorxiv.org/content/10.64898/2026.09.30.755547v1?rss=1
2026-10-08doi:10.64898/2026.09.30.755547Cold Spring Harbor Laboratory2026-10-08