bioRxiv Subject Collection: Genomics Bioinformatics Genetics Molecular Biology Developmental Biology
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This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics Genetics Molecular Biology Developmental Biology"
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MCD Stitcher: An open-source tool for whole-slide stitching and conversion of Imaging Mass Cytometry data
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https://www.biorxiv.org/content/10.64898/2026.06.26.732348v1?rss=1
2026-07-01doi:10.64898/2026.06.26.732348Cold Spring Harbor Laboratory2026-07-01
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Direct probabilistic quantification of mosaic loss of chromosome Y from sequencing data
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https://www.biorxiv.org/content/10.64898/2026.06.26.734767v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734767Cold Spring Harbor Laboratory2026-07-01
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Pericystic brain transcriptomics reveals molecular signatures of immune activation and neurovascular remodelling in viable and post-treatment porcine neurocysticercosis
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https://www.biorxiv.org/content/10.64898/2026.06.26.734379v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734379Cold Spring Harbor Laboratory2026-07-01
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MintCNA: A Unified Framework for Integrative Copy Number Profiling with Single-Cell Multi-Omics Data
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https://www.biorxiv.org/content/10.64898/2026.06.26.734559v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734559Cold Spring Harbor Laboratory2026-07-01
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An axiomatic approach to cultivar ranking in multi-environment trials
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https://www.biorxiv.org/content/10.64898/2026.06.27.734959v1?rss=1
2026-07-01doi:10.64898/2026.06.27.734959Cold Spring Harbor Laboratory2026-07-01
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AI-guided discovery for low-resource peptide engineering using evolutionary scale modeling
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https://www.biorxiv.org/content/10.64898/2026.06.25.734678v1?rss=1
2026-07-01doi:10.64898/2026.06.25.734678Cold Spring Harbor Laboratory2026-07-01
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Fly Viral Atlas: A single-nucleus transcriptomic atlas of RNA viruses and transposable elements (TEs) in Drosophila melanogaster
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https://www.biorxiv.org/content/10.64898/2026.06.28.735102v1?rss=1
2026-07-01doi:10.64898/2026.06.28.735102Cold Spring Harbor Laboratory2026-07-01
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Revising the genetic and epigenetic architecture of in vitro regeneration capacity in natural Arabidopsis thaliana populations
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https://www.biorxiv.org/content/10.64898/2026.06.26.734650v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734650Cold Spring Harbor Laboratory2026-07-01
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mirCCC: Repression-aware graph learning for miRNA-mediated cell-cell communication inference
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https://www.biorxiv.org/content/10.64898/2026.06.26.734694v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734694Cold Spring Harbor Laboratory2026-07-01
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Evolutionary Stratification of Codon Usage Bias In Plants Arises from GC3 Composition and Translational Optimization
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https://www.biorxiv.org/content/10.64898/2026.06.26.734692v1?rss=1
11 million coding sequences. Relative synonymous codon usage, codon adaptation index, codon-anticodon mapping, effective number of codon (ENC)-GC3, GC1,2-GC3, parity rule 2 (PR2-bias), molecular economy, and machine learning approaches were used for the study. It was found that codon usage bias was strongly non-random and exhibited a clear phylogenetic structuring. The higher plants favoured A/T-ending, whereas early-diverging lineages were enriched in G/C-ending codons. Analysis of RSCU, codon adaptation index, and codon-anticodon pairing indicated that translational selection is mediated by tRNA availability, contributing sustainability to these molecular patterns. Machine-learning approaches identified a small subset of codons having outsized influence on genome-wide codon usage landscapes. Further studies revealed the presence of robust inverse relationships between the effective number of codons and GC content at synonymous third positions. Neutrality analysis revealed approximately 61% of variation was driven by mutational pressure, tempered by selective constraints. Phylogenetic reconstruction showed a progressive relaxation of codon bias from algae to angiosperms while maintaining a conserved molecular economy cost of ~ 30 ATP per codon across the lineages. The study revealed codon usage bias is lineage-specific evolutionary conserved trait governed by mutation, selection, and translational optimization.
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Pathogenic impact of ABCA4 missense variants in the structurally uncharacterized ECD1 region: implications for Stargardt disease.
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https://www.biorxiv.org/content/10.64898/2026.06.25.734683v1?rss=1
2026-07-01doi:10.64898/2026.06.25.734683Cold Spring Harbor Laboratory2026-07-01
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A conserved architectural domain shapes centromere evolution in Drosophila
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https://www.biorxiv.org/content/10.64898/2026.06.30.735607v1?rss=1
2026-07-01doi:10.64898/2026.06.30.735607Cold Spring Harbor Laboratory2026-07-01
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Single molecule footprinting measures low nucleosome occupancy in mature spermatozoa of mice and men
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https://www.biorxiv.org/content/10.64898/2026.06.30.735528v1?rss=1
2026-07-01doi:10.64898/2026.06.30.735528Cold Spring Harbor Laboratory2026-07-01
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Genome architecture shapes the evolutionary origins of redundant enhancers in fly and mouse
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https://www.biorxiv.org/content/10.64898/2026.06.26.734851v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734851Cold Spring Harbor Laboratory2026-07-01
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BOSE: A Bayesian Order Statistics-Based Estimator for Recovering the Sample Mean and Standard Deviation
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https://www.biorxiv.org/content/10.64898/2026.06.26.734829v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734829Cold Spring Harbor Laboratory2026-07-01
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Penumbria: Advanced 3D cell segmentation for biomedical imaging
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https://www.biorxiv.org/content/10.64898/2026.06.30.735527v1?rss=1
2026-07-01doi:10.64898/2026.06.30.735527Cold Spring Harbor Laboratory2026-07-01
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Gene model for the ortholog of tgo in Drosophila busckii
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https://www.biorxiv.org/content/10.64898/2026.06.26.734908v1?rss=1
2026-07-01doi:10.64898/2026.06.26.734908Cold Spring Harbor Laboratory2026-07-01
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A refined Saccharomyces cerevisiae reference transcriptome from Direct RNA Sequencing, with a reusable pipeline for UTR annotation updates
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https://www.biorxiv.org/content/10.64898/2026.06.30.735557v1?rss=1
2026-06-30doi:10.64898/2026.06.30.735557Cold Spring Harbor Laboratory2026-06-30
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Near-complete genomes for nine haplochromine cichlid fishes reveal a novel centromeric satellite structure organised around a pair of inverted elements
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https://www.biorxiv.org/content/10.64898/2026.06.30.735501v1?rss=1
2026-06-30doi:10.64898/2026.06.30.735501Cold Spring Harbor Laboratory2026-06-30
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CyStainer: A transformer-based variational autoencoder for robust marker imputation in high-parameter cytometry
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https://www.biorxiv.org/content/10.64898/2026.06.30.735235v1?rss=1
2026-06-30doi:10.64898/2026.06.30.735235Cold Spring Harbor Laboratory2026-06-30
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Spike-in-normalised single-cell RNA-seq reveals cell-type-specific transcriptional repression during ageing
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https://www.biorxiv.org/content/10.64898/2026.06.25.733584v1?rss=1
2026-06-30doi:10.64898/2026.06.25.733584Cold Spring Harbor Laboratory2026-06-30
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Sequencing, Chromosome-scale Assembly, and Annotation of the Genome of the Halophilic Nanoflagellate Halocafeteria seosinensis
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https://www.biorxiv.org/content/10.64898/2026.06.25.734631v1?rss=1
2026-06-30doi:10.64898/2026.06.25.734631Cold Spring Harbor Laboratory2026-06-30
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A robot model of compass cue calibration in the insect brain
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https://www.biorxiv.org/content/10.64898/2026.06.25.734539v1?rss=1
2026-06-30doi:10.64898/2026.06.25.734539Cold Spring Harbor Laboratory2026-06-30
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Real-World Progression-Free Survival with Erlotinib versus Osimertinib in EGFR L858R+T790M Compound Mutation Non-Small Cell Lung Cancer: An Exploratory Analysis of the MSK-CHORD Dataset
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https://www.biorxiv.org/content/10.64898/2026.06.25.734551v1?rss=1
2026-06-30doi:10.64898/2026.06.25.734551Cold Spring Harbor Laboratory2026-06-30
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A High-Quality Acetylation Dataset Reveals Modest Data Requirements for Transfer Learning to Identify Little Studied Post-Translational Modifications
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https://www.biorxiv.org/content/10.64898/2026.06.25.733353v1?rss=1
2026-06-30doi:10.64898/2026.06.25.733353Cold Spring Harbor Laboratory2026-06-30
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Abundance, diversity and activity of endogenous retroviruses in the slow loris.
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https://www.biorxiv.org/content/10.64898/2026.06.25.734490v1?rss=1
2026-06-30doi:10.64898/2026.06.25.734490Cold Spring Harbor Laboratory2026-06-30
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Integrating Semantic Retrieval, LLM-based Refinement, and Structured Expert Curation for Scalable AOP Gene Mapping
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https://www.biorxiv.org/content/10.64898/2026.06.25.734475v1?rss=1
2026-06-30doi:10.64898/2026.06.25.734475Cold Spring Harbor Laboratory2026-06-30
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A pan-cancer benchmark of integrated ferroptosis, cuproptosis and disulfidptosis prognostic signatures
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https://www.biorxiv.org/content/10.64898/2026.06.25.734481v1?rss=1
2026-06-30doi:10.64898/2026.06.25.734481Cold Spring Harbor Laboratory2026-06-30
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A gapless Landrace pig genome resolves centromeres and telomeres and highlights telomere repeat structures in different pig breeds
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https://www.biorxiv.org/content/10.64898/2026.06.25.734473v1?rss=1
2026-06-30doi:10.64898/2026.06.25.734473Cold Spring Harbor Laboratory2026-06-30
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Epigenetic signatures of infection within and across generations in the endangered Loggerhead sea turtle
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https://www.biorxiv.org/content/10.64898/2026.06.25.734236v1?rss=1
2026-06-30doi:10.64898/2026.06.25.734236Cold Spring Harbor Laboratory2026-06-30