bioRxiv Subject Collection: Genomics Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics"
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Global tree encoding of atlas-scale single-cell genomics
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https://www.biorxiv.org/content/10.64898/2026.08.31.747971v1?rss=1
2026-09-04doi:10.64898/2026.08.31.747971Cold Spring Harbor Laboratory2026-09-04
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Visualizing and integrating linear and graph pangenomes at the Maize Genetics and Genomics Database
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https://www.biorxiv.org/content/10.64898/2026.08.31.748368v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748368Cold Spring Harbor Laboratory2026-09-04
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siProGenA: Generative siRNA Candidate Construction via Position Proposal and Guide Generation
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https://www.biorxiv.org/content/10.64898/2026.08.31.748303v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748303Cold Spring Harbor Laboratory2026-09-04
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BROOQS: Spectral Methods Resolve Level-1 Hybridization Cycles without Tests of Symmetry
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https://www.biorxiv.org/content/10.64898/2026.08.31.748319v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748319Cold Spring Harbor Laboratory2026-09-04
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LEAPING A CONSERVATION GENETICS GAP: COMBINING POPULATION GENETICS AND SOCIAL NETWORK ANALYSIS FOR LUPINUS PERENNIS RESTORATION
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https://www.biorxiv.org/content/10.64898/2026.08.31.748316v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748316Cold Spring Harbor Laboratory2026-09-04
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Poly Pipeline: A Polyvalent Spatial Transcriptomics Workflow Validated Across Polyploid and Diploid Organisms
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https://www.biorxiv.org/content/10.64898/2026.08.31.748304v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748304Cold Spring Harbor Laboratory2026-09-04
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AltraFlowSOM: A Semi-Supervised Framework for Imaging Mass Cytometry Phenotyping
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https://www.biorxiv.org/content/10.64898/2026.08.31.748226v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748226Cold Spring Harbor Laboratory2026-09-04
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QuickSeg: A fast, versatile and accurate algorithm for genomic copy number segmentation using dynamic programming
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https://www.biorxiv.org/content/10.64898/2026.08.31.747916v1?rss=1
2026-09-04doi:10.64898/2026.08.31.747916Cold Spring Harbor Laboratory2026-09-04
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Modelling interpretable patient-level representationsfrom structured and simple multimodal data
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https://www.biorxiv.org/content/10.64898/2026.08.31.748244v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748244Cold Spring Harbor Laboratory2026-09-04
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Gene function prediction from bulk coexpression is bounded by cell-type-level signal
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https://www.biorxiv.org/content/10.64898/2026.08.31.748380v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748380Cold Spring Harbor Laboratory2026-09-04
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On doubting image quality assessment metrics for microscopy virtual staining
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https://www.biorxiv.org/content/10.64898/2026.08.31.748410v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748410Cold Spring Harbor Laboratory2026-09-04
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Creating DNAm Algorithms Using the Illumina Methylation Screening Array (MSA)
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https://www.biorxiv.org/content/10.64898/2026.08.31.748429v1?rss=1
0.6). This stable feature space supported two modelling streams. First, we trained 134 epigenetic biomarker proxies (EBPs) natively on MSA, with and without kernel principal component analysis (kPCA) for sample-level harmonisation. All 134 reached same-beadchip ICC(2,1) >= 0.80 (median 0.97) and 96.3% reached different-beadchip ICC(2,1) >= 0.60 (median 0.81), with a median Spearman correlation of 0.48 against observed values. Among the 72 kPCA-selected models with a comparable stable-probe baseline, 70 (97%) showed higher cross-beadchip ICC (median improvement +0.18). Second, we transferred three established clocks using model-specific strategies: OMICmAge and SystemsAge were retrained to estimate their EPICv1-derived values (held-out test-set rho = 0.944 and 0.912-0.949), whereas DunedinPACE required stable-probe normalisation and robust linear calibration, which raised cross-array ICC(2,1) from 0.784-0.810 to 0.891-0.925 and reduced MAE from 0.085-0.089 to 0.041-0.050 across three sample sets. Reduced probe content does not preclude reproducible DNAm biomarker measurement, and transfer strategy must be matched to model architecture.
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A pan-cohort transcriptional landscape of breast cancer maps subtype and microenvironmental programs
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https://www.biorxiv.org/content/10.64898/2026.08.31.748296v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748296Cold Spring Harbor Laboratory2026-09-04
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A Compendium of 49 Experimental SBS Signatures for Decoding Human Cancer Mutational Processes
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https://www.biorxiv.org/content/10.64898/2026.08.31.748400v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748400Cold Spring Harbor Laboratory2026-09-04
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Mitotic chromosomes are mechanically connected by chromatin-based interchromosome linkers
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https://www.biorxiv.org/content/10.64898/2026.08.31.748267v1?rss=1
2026-09-04doi:10.64898/2026.08.31.748267Cold Spring Harbor Laboratory2026-09-04
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Experimental and In Silico Analysis of the Structural Dynamics of Dengue NS2B-NS3 Protease
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https://www.biorxiv.org/content/10.64898/2026.09.02.748787v1?rss=1
2026-09-04doi:10.64898/2026.09.02.748787Cold Spring Harbor Laboratory2026-09-04
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GLORB: Robust Bayesian inference for differential expression underglobal expression shifts
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https://www.biorxiv.org/content/10.64898/2026.08.28.747928v1?rss=1
2026-09-03doi:10.64898/2026.08.28.747928Cold Spring Harbor Laboratory2026-09-03
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ContrasTED: contrastive domain embeddings for scalable remote homology classification
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https://www.biorxiv.org/content/10.64898/2026.08.28.747864v1?rss=1
2026-09-03doi:10.64898/2026.08.28.747864Cold Spring Harbor Laboratory2026-09-03
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HiC-LEGO: Biologically Guided High-Resolution 3D Genome Reconstruction Preserves Chromatin Organization at Kilobase Resolution
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https://www.biorxiv.org/content/10.64898/2026.08.30.748130v1?rss=1
2026-09-03doi:10.64898/2026.08.30.748130Cold Spring Harbor Laboratory2026-09-03
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Retrieval of binding sites across the AlphaFold human proteome using protein language model representations
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https://www.biorxiv.org/content/10.64898/2026.08.30.748136v1?rss=1
2026-09-03doi:10.64898/2026.08.30.748136Cold Spring Harbor Laboratory2026-09-03
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Bio-Babel: autonomous cross-language reconstruction of agent-ready computational biology ecosystems
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https://www.biorxiv.org/content/10.64898/2026.08.30.743167v1?rss=1
2026-09-03doi:10.64898/2026.08.30.743167Cold Spring Harbor Laboratory2026-09-03
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The human metabolite - protein interactome reveals a global layer of cellular coordination
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https://www.biorxiv.org/content/10.64898/2026.08.28.747909v1?rss=1
2026-09-03doi:10.64898/2026.08.28.747909Cold Spring Harbor Laboratory2026-09-03
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Comprehensive Evaluation of Protein Language Model Embeddings for Drug-Target Affinity Prediction
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https://www.biorxiv.org/content/10.64898/2026.08.31.748056v1?rss=1
2026-09-03doi:10.64898/2026.08.31.748056Cold Spring Harbor Laboratory2026-09-03
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Hi-cGAN: Prediction of Hi-C interaction matrices with conditional generative adversarial networks
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https://www.biorxiv.org/content/10.64898/2026.08.30.748103v1?rss=1
2026-09-03doi:10.64898/2026.08.30.748103Cold Spring Harbor Laboratory2026-09-03
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ClassifyITS: An R Package for assigning taxonomy to fungal ITS sequences using taxon-specific cutoff values
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https://www.biorxiv.org/content/10.64898/2026.08.31.748297v1?rss=1
2026-09-03doi:10.64898/2026.08.31.748297Cold Spring Harbor Laboratory2026-09-03
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scRep: A Latent-Space Self-Distilled Foundation Model for Single-Cell Representation Learning
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https://www.biorxiv.org/content/10.64898/2026.08.31.747784v1?rss=1
2026-09-03doi:10.64898/2026.08.31.747784Cold Spring Harbor Laboratory2026-09-03
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An annotation-overlap-flagged rare-disease gene-prioritisation benchmark and PMC index recipe
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https://www.biorxiv.org/content/10.64898/2026.08.30.748028v1?rss=1
2026-09-03doi:10.64898/2026.08.30.748028Cold Spring Harbor Laboratory2026-09-03
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Ageas enables time-agnostic cell fate inference from single-cell and spatial multi-omics data
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https://www.biorxiv.org/content/10.64898/2026.08.30.748098v1?rss=1
2026-09-03doi:10.64898/2026.08.30.748098Cold Spring Harbor Laboratory2026-09-03
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Kintsugi maps nucleus-poor RNA compartments in subcellular spatial transcriptomics
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https://www.biorxiv.org/content/10.64898/2026.08.30.748061v1?rss=1
2026-09-03doi:10.64898/2026.08.30.748061Cold Spring Harbor Laboratory2026-09-03
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Multiparental RNA-seq driven eQTL screening identifies loci underlying host plant fitness in a generalist herbivore
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https://www.biorxiv.org/content/10.64898/2026.08.30.748081v1?rss=1
2026-09-03doi:10.64898/2026.08.30.748081Cold Spring Harbor Laboratory2026-09-03