bioRxiv Subject Collection: Genomics Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics"
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bgnorm: A Generative Statistical Framework for Background Correction, Normalisation, and Quality Control in Multiplex Spatial Proteomics
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https://www.biorxiv.org/content/10.64898/2026.08.05.743141v1?rss=1
2026-08-11doi:10.64898/2026.08.05.743141Cold Spring Harbor Laboratory2026-08-11
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stCNASim: Allele-aware spatial RNA-seq simulator enables systematic benchmarking of copy number inference
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https://www.biorxiv.org/content/10.64898/2026.08.06.743179v1?rss=1
2026-08-11doi:10.64898/2026.08.06.743179Cold Spring Harbor Laboratory2026-08-11
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Most published human disease RNA-seq cannot be uniformly reanalyzed: a population-scale audit of reprocessability in the Gene Expression Omnibus
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https://www.biorxiv.org/content/10.64898/2026.08.05.742891v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742891Cold Spring Harbor Laboratory2026-08-11
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ChlORIS: Chloroplast Orthologs Resource & Identification Suite
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https://www.biorxiv.org/content/10.64898/2026.08.05.743164v1?rss=1
2026-08-11doi:10.64898/2026.08.05.743164Cold Spring Harbor Laboratory2026-08-11
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Community-level diversity of viral counter-defensomes
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https://www.biorxiv.org/content/10.64898/2026.08.10.744029v1?rss=1
2026-08-11doi:10.64898/2026.08.10.744029Cold Spring Harbor Laboratory2026-08-11
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A chromosome-scale genome of Colletotrichum cereale reveals a large, dynamic accessory genome within a deeply structured species
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https://www.biorxiv.org/content/10.64898/2026.08.06.743313v1?rss=1
2026-08-11doi:10.64898/2026.08.06.743313Cold Spring Harbor Laboratory2026-08-11
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siDiff: De Novo siRNA Design via Efficacy-Guided Discrete Masked Diffusion
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https://www.biorxiv.org/content/10.64898/2026.08.11.744092v1?rss=1
2026-08-11doi:10.64898/2026.08.11.744092Cold Spring Harbor Laboratory2026-08-11
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Discovery and Targeting of a Cryptic Human Proteome
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https://www.biorxiv.org/content/10.64898/2026.08.05.743124v1?rss=1
8,000 raw MS data files (~7TB of MS data), derived from 2,229 patient samples), we empirically identified ~80,000 cryptic peptides (~10,000 cancer-associated or cancer-upregulated) at <1% FDR. Altogether, these datasets establish the CypherAtlas, a comprehensive proteogenomic atlas of an unreported proteome comprising thousands of novel proteins, including membrane proteins with targetable extracellular domains, and intracellular proteins accessible through antigen presentation. By linking dark-RNA transcripts, predicted proteins, and patient-level metadata across RyboDyn's proprietary experimental data, CypherAtlas further provides the training substrate for multimodal models such as DarkCypher, which is being developed to prioritize cryptic targets and to forecast their expression in new patient samples. As proof of therapeutic potential, we disclose evidence for a cancer-associated, cryptic protein expressed from the YBX1 locus (cryptic YBX1; cYBX1) and demonstrate selective in vitro tumor cell killing through a cryptic peptide-MHC (pMHC) complex derived from this protein with a TCR-mimic (TCRm) antibody when formatted as antibody-drug conjugates (ADCs). Together, RyboCypher and CypherAtlas establish the dark proteome as a vast and previously inaccessible reservoir of novel targetable biology, laying the foundation for the next generation of first-in-class therapeutics.
]]>2026-08-11doi:10.64898/2026.08.05.743124Cold Spring Harbor Laboratory2026-08-11
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Genome-Wide Selection Signatures in Nili-Ravi Buffalo (Bubalus bubalis) Reveal a T-Cell Costimulatory and Cytokine-Signaling Gene Network Distinct from Classical Bovine Tuberculosis Candidate Genes
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https://www.biorxiv.org/content/10.64898/2026.08.10.743898v1?rss=1
2026-08-11doi:10.64898/2026.08.10.743898Cold Spring Harbor Laboratory2026-08-11
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Gene model for the ortholog of DENR in Drosophila pseudoobscura
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https://www.biorxiv.org/content/10.64898/2026.08.11.744233v1?rss=1
2026-08-11doi:10.64898/2026.08.11.744233Cold Spring Harbor Laboratory2026-08-11
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MSGPCA: Multi-Slice Graph PCA for replicate-aware Spatial Omics analysis
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https://www.biorxiv.org/content/10.64898/2026.08.05.743056v1?rss=1
2026-08-11doi:10.64898/2026.08.05.743056Cold Spring Harbor Laboratory2026-08-11
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Chromosome assembly for the Black bean aphid Aphis fabae
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https://www.biorxiv.org/content/10.64898/2026.08.05.743085v1?rss=1
2026-08-11doi:10.64898/2026.08.05.743085Cold Spring Harbor Laboratory2026-08-11
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AbPACER: parent-aware, affinity-label-blind prioritization of affinity-matured scFv clones from phage-display NGS
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https://www.biorxiv.org/content/10.64898/2026.08.05.742956v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742956Cold Spring Harbor Laboratory2026-08-11
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Convergent biology, divergent drivers: a cross-species comparison of human and canine invasive urothelial carcinoma
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https://www.biorxiv.org/content/10.64898/2026.08.05.742970v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742970Cold Spring Harbor Laboratory2026-08-11
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AnchorR: A QuPath and R interface for collaborative exploration of spatial transcriptomics and histology
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https://www.biorxiv.org/content/10.64898/2026.08.05.742985v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742985Cold Spring Harbor Laboratory2026-08-11
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ASPIRE: the Amplicon Sequencing Profiler for Investigating Respiratory Ecosystems
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https://www.biorxiv.org/content/10.64898/2026.08.05.743000v1?rss=1
2026-08-11doi:10.64898/2026.08.05.743000Cold Spring Harbor Laboratory2026-08-11
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Data-Centric Evaluation of Protein Function Prediction Pipelines
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https://www.biorxiv.org/content/10.64898/2026.08.05.742971v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742971Cold Spring Harbor Laboratory2026-08-11
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Systematic assessment of the biological impact of cellular deconvolution on downstream analyses of disease transcriptomes
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https://www.biorxiv.org/content/10.64898/2026.08.05.742993v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742993Cold Spring Harbor Laboratory2026-08-11
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Learning Shared Residue Backgrounds and Modification-Specific Offsets for PTM Site Prediction
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https://www.biorxiv.org/content/10.64898/2026.08.05.743079v1?rss=1
2026-08-11doi:10.64898/2026.08.05.743079Cold Spring Harbor Laboratory2026-08-11
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Fast retrieval of structurally similar antibodies from large sequence databases with AbSLang
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https://www.biorxiv.org/content/10.64898/2026.08.05.742817v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742817Cold Spring Harbor Laboratory2026-08-11
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Moirai: single-cell trajectory inference grounded in gene-level expression dynamics
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https://www.biorxiv.org/content/10.64898/2026.08.05.742709v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742709Cold Spring Harbor Laboratory2026-08-11
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A Practice on Antibody Hydrophobic Interaction Chromatography Retention Time Prediction using Pre-Trained Large Language Model Fine-Tuning
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https://www.biorxiv.org/content/10.64898/2026.08.05.742939v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742939Cold Spring Harbor Laboratory2026-08-11
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Near-infrared phenomic and genomic prediction for seed protein in winter legume white lupin (Lupinus albus L.): A utility comparison
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https://www.biorxiv.org/content/10.64898/2026.08.05.743001v1?rss=1
2026-08-11doi:10.64898/2026.08.05.743001Cold Spring Harbor Laboratory2026-08-11
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Enhanced Detection of Age-related Macular Degeneration in Low-quality Retinal Images via Noise-Augmented YOLO and Adaptive Attention Mechanisms
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https://www.biorxiv.org/content/10.64898/2026.08.04.742925v1?rss=1
2026-08-11doi:10.64898/2026.08.04.742925Cold Spring Harbor Laboratory2026-08-11
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KiMA: Kinematic Motion Analysis for Spinal Cord Injury Research
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https://www.biorxiv.org/content/10.64898/2026.08.05.742960v1?rss=1
2026-08-11doi:10.64898/2026.08.05.742960Cold Spring Harbor Laboratory2026-08-11
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Virtual-cell verification enables self-auditing AI discovery for immune rejuvenation
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https://www.biorxiv.org/content/10.64898/2026.08.04.742916v1?rss=1
2026-08-11doi:10.64898/2026.08.04.742916Cold Spring Harbor Laboratory2026-08-11
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A genome-wide CRISPR activation map of surface protein expression in human CD4 T cells
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https://www.biorxiv.org/content/10.64898/2026.08.08.743670v1?rss=1
2026-08-11doi:10.64898/2026.08.08.743670Cold Spring Harbor Laboratory2026-08-11
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orthoSynAssign: refine orthogroups using synteny information
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https://www.biorxiv.org/content/10.64898/2026.08.10.744007v1?rss=1
2026-08-11doi:10.64898/2026.08.10.744007Cold Spring Harbor Laboratory2026-08-11
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Inference of nodavirus zoonotic transmission networks from publicly available sequencing data
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https://www.biorxiv.org/content/10.64898/2026.08.09.743288v1?rss=1
2026-08-11doi:10.64898/2026.08.09.743288Cold Spring Harbor Laboratory2026-08-11
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Phylogenomics and comparative genomics of the genus Erwinia reveal taxonomic inconsistencies and evolutionary diversification
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https://www.biorxiv.org/content/10.64898/2026.08.06.743344v1?rss=1
2026-08-11doi:10.64898/2026.08.06.743344Cold Spring Harbor Laboratory2026-08-11