bioRxiv Subject Collection: Genomics Bioinformatics
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This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics"
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EcoMorph: Universal morphological trait quantification from natural language prompts for ecological research
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https://www.biorxiv.org/content/10.64898/2026.07.10.737871v1?rss=1
2026-07-12doi:10.64898/2026.07.10.737871Cold Spring Harbor Laboratory2026-07-12
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TEscape: Defining the human transposable element transcriptome using multiplatform long-read sequencing
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https://www.biorxiv.org/content/10.64898/2026.07.08.737305v1?rss=1
83,000 previously unannotated isoforms, the vast majority (84%) originating from a complex combination of multi-TEs. We also identified solo TEs, which are predominantly from LINE1 (14%). We confirmed that TE-transcripts are able to be exemplified by signatures detected in Liver Hepatocellular Carcinoma (LICH). Together, MAS-ISO-seq and TEscape establish the first long-read-based, high-resolution atlas of transcribed human TEs, providing a foundational resource for integrative transcriptome analyses and for investigating TE expression and regulation in health and disease.
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A geometric atlas of how ESM3 organizes modalities across depth
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https://www.biorxiv.org/content/10.64898/2026.07.08.737319v1?rss=1
2026-07-12doi:10.64898/2026.07.08.737319Cold Spring Harbor Laboratory2026-07-12
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Genomic Annotation Infrastructure (GAIn): Pipelines and Resource Repositories for Annotating Variants, Positions, and Regions
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https://www.biorxiv.org/content/10.64898/2026.07.08.737273v1?rss=1
2026-07-12doi:10.64898/2026.07.08.737273Cold Spring Harbor Laboratory2026-07-12
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OCellus: A Language-Model Framework for Single-Cell, Spatial, and Perturbation Biology with Natural-Language Reasoning
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https://www.biorxiv.org/content/10.64898/2026.07.08.737248v1?rss=1
2026-07-12doi:10.64898/2026.07.08.737248Cold Spring Harbor Laboratory2026-07-12
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ProtBLIP2-SST: Protein Function Prediction via BLIP2 with Sequence, Structure, and Text
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https://www.biorxiv.org/content/10.64898/2026.07.10.737551v1?rss=1
2026-07-12doi:10.64898/2026.07.10.737551Cold Spring Harbor Laboratory2026-07-12
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High resolution Streptococcus pyogenes core genome MLST and LIN coding scheme for outbreak detection
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https://www.biorxiv.org/content/10.64898/2026.07.10.737715v1?rss=1
2026-07-11doi:10.64898/2026.07.10.737715Cold Spring Harbor Laboratory2026-07-11
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ArthroVerse: mapping protein family diversity across arthropod-associated microbiomes
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https://www.biorxiv.org/content/10.64898/2026.07.11.737898v1?rss=1
2026-07-11doi:10.64898/2026.07.11.737898Cold Spring Harbor Laboratory2026-07-11
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onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation
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https://www.biorxiv.org/content/10.64898/2026.07.08.737157v1?rss=1
2026-07-11doi:10.64898/2026.07.08.737157Cold Spring Harbor Laboratory2026-07-11
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M6AFormer Prioritizes Unannotated Functional m6A Candidate Sites in the Human m6A Epitranscriptome
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https://www.biorxiv.org/content/10.64898/2026.07.10.737679v1?rss=1
2026-07-11doi:10.64898/2026.07.10.737679Cold Spring Harbor Laboratory2026-07-11
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Panomap: Unbiased Nanopore Signal Mapping with Pangenome Variation Graphs
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https://www.biorxiv.org/content/10.64898/2026.07.10.737796v1?rss=1
2026-07-11doi:10.64898/2026.07.10.737796Cold Spring Harbor Laboratory2026-07-11
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Comparative Analysis of Transposable Elements in Hermetia illucens
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https://www.biorxiv.org/content/10.64898/2026.07.10.737754v1?rss=1
2026-07-11doi:10.64898/2026.07.10.737754Cold Spring Harbor Laboratory2026-07-11
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Characterizing the Small Non-Coding RNA Pathways in the Invasive Zebra Mussel (Dreissena polymorpha)
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https://www.biorxiv.org/content/10.64898/2026.07.10.737777v1?rss=1
2026-07-11doi:10.64898/2026.07.10.737777Cold Spring Harbor Laboratory2026-07-11
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PKProbDesign: RNA inverse folding including pseudoknots by optimizing thermodynamic folding probability
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https://www.biorxiv.org/content/10.64898/2026.07.09.736945v1?rss=1
2026-07-11doi:10.64898/2026.07.09.736945Cold Spring Harbor Laboratory2026-07-11
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ProtPen combines sequence- and structure-based approaches to facilitate protein function predictions on a proteome-wide scale
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https://www.biorxiv.org/content/10.64898/2026.07.11.737882v1?rss=1
90%, and highlighted the complementarity of sequence- and structure-based methods. Further evaluation of ProtPen included its application to biologically relevant datasets, comprising proteins of unknown function that exhibited significant differential abundances in a proteomics dataset of P. aeruginosa, and uncharacterized glycoproteins from Haloferax volcanii. ProtPen is readily extensible to incorporate additional protein function prediction tools. In summary, this pipeline facilitates the systemwide annotation of proteins of unknown function from proteomic datasets and whole proteomes.
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GBZ-base and GAF-base: Indexed pangenome file formats
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https://www.biorxiv.org/content/10.64898/2026.07.10.737775v1?rss=1
2026-07-11doi:10.64898/2026.07.10.737775Cold Spring Harbor Laboratory2026-07-11
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ProtAug: An Empirical Investigation of pLM-Guided Data Augmentation for Protein Sequence Prediction Tasks
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https://www.biorxiv.org/content/10.64898/2026.07.10.737545v1?rss=1
2026-07-11doi:10.64898/2026.07.10.737545Cold Spring Harbor Laboratory2026-07-11
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AptViralDB: A Repository of Experimentally Validated Antiviral Aptamers
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https://www.biorxiv.org/content/10.64898/2026.07.08.737144v1?rss=1
2026-07-11doi:10.64898/2026.07.08.737144Cold Spring Harbor Laboratory2026-07-11
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First-Trimester Non-Invasive Prediction of Preterm Birth Using Cell-Free DNA Fragmentomics
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https://www.biorxiv.org/content/10.64898/2026.07.07.736241v1?rss=1
90%, the model achieved a sensitivity of 94% (95% CI, 78 to 100%). Conclusion. These findings demonstrate that cfDNA EM signatures derived from routine first trimester NIPT can accurately identify pregnancies at risk of spontaneous preterm birth, without additional blood collection or sequencing, thereby extending the clinical utility of existing prenatal screening infrastructure.
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Interactome Specialization Predicts Genome-Wide Binding-Site Degeneracy in Drosophila melanogaster Transcription Factors
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https://www.biorxiv.org/content/10.64898/2026.07.08.737203v1?rss=1
2026-07-11doi:10.64898/2026.07.08.737203Cold Spring Harbor Laboratory2026-07-11
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SPARC: A Graph-based Optimization Framework for Directional Trajectory Reconstruction Across Ordered Single-Cell Conditions
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https://www.biorxiv.org/content/10.64898/2026.07.07.736532v1?rss=1
2026-07-11doi:10.64898/2026.07.07.736532Cold Spring Harbor Laboratory2026-07-11
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Single-cell RNA-seq reveals conserved and divergent cellular states across wound types and species
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https://www.biorxiv.org/content/10.64898/2026.07.07.737032v1?rss=1
2026-07-11doi:10.64898/2026.07.07.737032Cold Spring Harbor Laboratory2026-07-11
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Multiscale harmonization and semantic integration of biomedical data enable biological insights through immersive exploration
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https://www.biorxiv.org/content/10.64898/2026.07.07.737090v1?rss=1
2026-07-11doi:10.64898/2026.07.07.737090Cold Spring Harbor Laboratory2026-07-11
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Locus-Level Transposable Element Profiling Resolves Division-Coupled Transcriptional Dynamics During Human Endoderm Specification
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https://www.biorxiv.org/content/10.64898/2026.07.07.737093v1?rss=1
2026-07-11doi:10.64898/2026.07.07.737093Cold Spring Harbor Laboratory2026-07-11
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Gene model for the ortholog of raptor in Drosophila grimshawi
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https://www.biorxiv.org/content/10.64898/2026.07.07.737051v1?rss=1
2026-07-11doi:10.64898/2026.07.07.737051Cold Spring Harbor Laboratory2026-07-11
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Structure-guided computational design and mechanistic understanding of the p95HER2-targeting NAZ-mAb antibody and its variants
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https://www.biorxiv.org/content/10.64898/2026.07.07.736817v1?rss=1
2026-07-11doi:10.64898/2026.07.07.736817Cold Spring Harbor Laboratory2026-07-11
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AGPI: An AI-Powered Genomic Pathogen Intelligence Platform for Integrated Classification, Visualization, and Therapeutic Targeting
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https://www.biorxiv.org/content/10.64898/2026.07.07.737037v1?rss=1
2026-07-11doi:10.64898/2026.07.07.737037Cold Spring Harbor Laboratory2026-07-11
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Somatic mutation inference from single-cell transcriptomics: A survey in the esophagus
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https://www.biorxiv.org/content/10.64898/2026.07.07.737010v1?rss=1
2026-07-11doi:10.64898/2026.07.07.737010Cold Spring Harbor Laboratory2026-07-11
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Metagenomic contextualization of proteins with state space models
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https://www.biorxiv.org/content/10.64898/2026.07.07.736993v1?rss=1
2026-07-11doi:10.64898/2026.07.07.736993Cold Spring Harbor Laboratory2026-07-11
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AtlasLens: Metadata-centric exploration and analysis of single-cell atlases
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https://www.biorxiv.org/content/10.64898/2026.07.10.735823v1?rss=1
2026-07-10doi:10.64898/2026.07.10.735823Cold Spring Harbor Laboratory2026-07-10