bioRxiv Subject Collection: Genomics Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics"
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Scalable genotyping in fixed transcriptomes resolves clonal heterogeneity via single-cell sequencing
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https://www.biorxiv.org/content/10.64898/2026.04.11.717967v1?rss=1
99% genotyping accuracy and flexible capture of hundreds of mutations per cell, including in FFPE (Formalin-Fixed Paraffin-Embedded) tissue, enabling clonal lineage tracing in heterogeneous settings. We demonstrate the unique scalability of GIFT by profiling >700,000 cells from 35 donors with myeloproliferative neoplasms (MPN), revealing mutation-dependent hematopoietic responses to systemic inflammation associated with the characteristic JAK2V617 mutation, including an allelic dose gradient of interferon-associated transcriptional programs and transcriptional priming of hematopoietic stem cells that develop into divergent disease states. Together, the unique technical advantages of GIFT enable direct resolution of genotype-to-phenotype relationships via clonal lineage tracing with comprehensive cell state measurements at single-cell resolution.
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Metabolomic Fingerprinting from Dried Blood Spots Enables Individual Identification Across 1,257 Participants at 94% User-Level Accuracy
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https://www.biorxiv.org/content/10.64898/2026.04.08.717286v1?rss=1
2026-04-11doi:10.64898/2026.04.08.717286Cold Spring Harbor Laboratory2026-04-11
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Evaluation of somatic variant calling methods on high coverage tumour-only amplicon sequencing data in a clinical environment
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https://www.biorxiv.org/content/10.64898/2026.04.08.717310v1?rss=1
2026-04-11doi:10.64898/2026.04.08.717310Cold Spring Harbor Laboratory2026-04-11
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TFBindFormer:A Cross-Attention Transformer for Transcription Factor--DNA Binding Prediction
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https://www.biorxiv.org/content/10.64898/2026.04.09.717563v1?rss=1
2026-04-11doi:10.64898/2026.04.09.717563Cold Spring Harbor Laboratory2026-04-11
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FM-GPT: Bayesian fine mapping for phenome-wide transcriptome-wide association studies
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https://www.biorxiv.org/content/10.64898/2026.04.07.717122v1?rss=1
2026-04-11doi:10.64898/2026.04.07.717122Cold Spring Harbor Laboratory2026-04-11
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A Large Yield Model for Crop Production and Design in Western Canada
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https://www.biorxiv.org/content/10.64898/2026.04.08.717277v1?rss=1
2026-04-11doi:10.64898/2026.04.08.717277Cold Spring Harbor Laboratory2026-04-11
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RNA Folding Nearest Neighbor Parameters Including the Modification 1-Methyl-Pseudouridine
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https://www.biorxiv.org/content/10.64898/2026.04.09.717343v1?rss=1
2026-04-11doi:10.64898/2026.04.09.717343Cold Spring Harbor Laboratory2026-04-11
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Generative design of intrinsically disordered protein regions with IDiom
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https://www.biorxiv.org/content/10.64898/2026.04.10.717777v1?rss=1
2026-04-11doi:10.64898/2026.04.10.717777Cold Spring Harbor Laboratory2026-04-11
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A unified spatial transcriptome profiling of ten mouse organs
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https://www.biorxiv.org/content/10.64898/2026.04.08.715765v1?rss=1
2026-04-11doi:10.64898/2026.04.08.715765Cold Spring Harbor Laboratory2026-04-11
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Living by the sea: chromosome-scale genome assembly and salt gland transcriptomes provide insights into ion regulatory mechanisms in the saline-tolerant mosquito Aedes togoi
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https://www.biorxiv.org/content/10.64898/2026.04.09.717544v1?rss=1
2026-04-11doi:10.64898/2026.04.09.717544Cold Spring Harbor Laboratory2026-04-11
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A segmental duplication-mediated deletion leads to neocentromere formation in orangutans
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https://www.biorxiv.org/content/10.64898/2026.04.09.717302v1?rss=1
2026-04-11doi:10.64898/2026.04.09.717302Cold Spring Harbor Laboratory2026-04-11
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EVEE: Interpretable variant effect prediction from genomic foundation model embeddings
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https://www.biorxiv.org/content/10.64898/2026.04.10.717844v1?rss=1
2026-04-11doi:10.64898/2026.04.10.717844Cold Spring Harbor Laboratory2026-04-11
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Genomic insights into bacterial isolates dominating honeypot ant crop microbiomes reveal metabolically distinct Fructilactobacillus sp.
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https://www.biorxiv.org/content/10.64898/2026.04.09.717501v1?rss=1
2026-04-11doi:10.64898/2026.04.09.717501Cold Spring Harbor Laboratory2026-04-11
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Palaeogenomics-informed inferences of European dog admixture enables scalable dingo conservation
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https://www.biorxiv.org/content/10.64898/2026.04.08.717357v1?rss=1
2026-04-11doi:10.64898/2026.04.08.717357Cold Spring Harbor Laboratory2026-04-11
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Flanking DNA sequences determine DNA methylation maintenance in proliferation, cancer and aging
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https://www.biorxiv.org/content/10.64898/2026.04.09.717557v1?rss=1
2026-04-11doi:10.64898/2026.04.09.717557Cold Spring Harbor Laboratory2026-04-11
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Suppression of upstream ORF translation is not a widespread mechanism of translational stimulation by yeast helicase Ded1
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https://www.biorxiv.org/content/10.64898/2026.04.10.717766v1?rss=1
2026-04-11doi:10.64898/2026.04.10.717766Cold Spring Harbor Laboratory2026-04-11
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scMultiPreDICT: A single-cell predictive framework with transcriptomic and epigenetic signatures
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https://www.biorxiv.org/content/10.64898/2026.04.08.717080v1?rss=1
2026-04-11doi:10.64898/2026.04.08.717080Cold Spring Harbor Laboratory2026-04-11
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A Joint Promoterome-Proteome Atlas Highlights the Molecular Diversity of Human Skeletal Muscles
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https://www.biorxiv.org/content/10.64898/2026.04.08.717200v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717200Cold Spring Harbor Laboratory2026-04-10
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DIANA: Deep Learning Identification and Assessment of Ancient DNA
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https://www.biorxiv.org/content/10.64898/2026.04.09.717429v1?rss=1
2026-04-10doi:10.64898/2026.04.09.717429Cold Spring Harbor Laboratory2026-04-10
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Divergent landscapes of positive and negative selection signatures across residue-resolved human-virus protein-protein interaction interfaces
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https://www.biorxiv.org/content/10.64898/2026.04.10.717550v1?rss=1
2026-04-10doi:10.64898/2026.04.10.717550Cold Spring Harbor Laboratory2026-04-10
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Genomic insights into polyketide toxin synthesis and algal symbiosis using high-quality genome sequences of the early divergent hexacorallian genus Palythoa (Cnidaria, Zoantharia)
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https://www.biorxiv.org/content/10.64898/2026.04.08.717340v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717340Cold Spring Harbor Laboratory2026-04-10
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Aimea gen. nov. defines a novel plant-associated yeast genus in Microbotryomycetes with three novel species
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https://www.biorxiv.org/content/10.64898/2026.04.08.717246v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717246Cold Spring Harbor Laboratory2026-04-10
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The Rayleigh Quotient and Contrastive Principal Component Analysis II
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https://www.biorxiv.org/content/10.64898/2026.04.08.717236v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717236Cold Spring Harbor Laboratory2026-04-10
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TopicVI: A Knowledge-guided deep interpretable model for resolving context-specific gene programs
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https://www.biorxiv.org/content/10.64898/2026.04.08.717220v1?rss=1
2026-04-10doi:10.64898/2026.04.08.717220Cold Spring Harbor Laboratory2026-04-10
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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