bioRxiv Subject Collection: Genomics Bioinformatics https://biorxiv.org This feed contains articles for bioRxiv Subject Collection "Genomics Bioinformatics" bioRxiv bioRxiv https://www.biorxiv.org/sites/default/files/bioRxiv_article.jpg https://www.biorxiv.org <![CDATA[ RADF: Reference-Anchored Dynamic Flow for Spatial Perturbation Profile Completion ]]> https://www.biorxiv.org/content/10.64898/2026.08.20.745474v1?rss=1 2026-08-24 doi:10.64898/2026.08.20.745474 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Trust-Aware Sequence-to-Function Modelling in Regulatory Genomics ]]> https://www.biorxiv.org/content/10.64898/2026.08.20.745945v1?rss=1 2026-08-24 doi:10.64898/2026.08.20.745945 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Kiosc: an integrated platform for managing bioinformatics data analysis containers ]]> https://www.biorxiv.org/content/10.64898/2026.08.20.745983v1?rss=1 2026-08-24 doi:10.64898/2026.08.20.745983 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Benchmarking antibody-antigen co-folding on human monomeric antigens ]]> https://www.biorxiv.org/content/10.64898/2026.08.20.745880v1?rss=1 2026-08-24 doi:10.64898/2026.08.20.745880 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Haplotype-resolved chromosome-level genome assembly of four European white oak species ]]> https://www.biorxiv.org/content/10.64898/2026.08.20.745905v1?rss=1 2026-08-24 doi:10.64898/2026.08.20.745905 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Four-species Aspergillus pan-GWAS reveals rare genome expansion in pathogenicity and contraction in domestication ]]> https://www.biorxiv.org/content/10.64898/2026.08.20.745736v1?rss=1 2026-08-24 doi:10.64898/2026.08.20.745736 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Model Validation Protocols for Machine Learning in Small Molecule Drug Discovery ]]> https://www.biorxiv.org/content/10.64898/2026.08.19.745868v1?rss=1 2026-08-24 doi:10.64898/2026.08.19.745868 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Click-Prep: An Interactive Data Preparation Tool for Click-qPCR ]]> https://www.biorxiv.org/content/10.64898/2026.08.20.745930v1?rss=1 2026-08-24 doi:10.64898/2026.08.20.745930 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Coupled transcriptomic divergence establishes a human-specific synaptic glial precursor state ]]> https://www.biorxiv.org/content/10.64898/2026.08.19.745872v1?rss=1 2026-08-24 doi:10.64898/2026.08.19.745872 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Erosion of regenerative regulation: age-associated shifts in the skeletal muscle fiber epigenome and transcriptome ]]> https://www.biorxiv.org/content/10.64898/2026.08.19.744884v1?rss=1 2026-08-24 doi:10.64898/2026.08.19.744884 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Multidimensional telomere diversity and inheritance at individual and population scales ]]> https://www.biorxiv.org/content/10.64898/2026.08.19.745664v1?rss=1 2026-08-24 doi:10.64898/2026.08.19.745664 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ Point-in-time evidence and cross-area clinical precedent anticipate clinical entry across 100 focal areas: retrospective validation of the Intangia triage layer ]]> https://www.biorxiv.org/content/10.64898/2026.08.19.745722v1?rss=1 2026-08-24 doi:10.64898/2026.08.19.745722 Cold Spring Harbor Laboratory 2026-08-24 <![CDATA[ FuncSeek: Multi-PLM contrastive learning for protein functional similarity search ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.738656v1?rss=1 2026-08-14 doi:10.64898/2026.08.07.738656 Cold Spring Harbor Laboratory 2026-08-14 <![CDATA[ Leveraging Targeted Gene Sets and Neural Networks for Zebrafish Transcriptome Extrapolation in High-Throughput Toxicogenomics ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743325v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743325 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ MG2Act: A Mechanism-Inspired Sequential Attention Framework for Molecular Glue Degradation Prediction ]]> https://www.biorxiv.org/content/10.64898/2026.08.08.739980v1?rss=1 2026-08-17 doi:10.64898/2026.08.08.739980 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ Reinforcement Learning via Brain Feedback for real-time fMRI-based adaptive stimulus generation ]]> https://www.biorxiv.org/content/10.64898/2026.08.08.743648v1?rss=1 2026-08-17 doi:10.64898/2026.08.08.743648 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ PARNET: A CLIP-SEQ-BASED FOUNDATION MODEL FOR RNA SEQUENCE REPRESENTATION LEARNING ]]> https://www.biorxiv.org/content/10.64898/2026.08.08.743506v1?rss=1 2026-08-17 doi:10.64898/2026.08.08.743506 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ Exploratory profiling of defense system signatures in Klebsiella pneumoniae clonal populations ]]> https://www.biorxiv.org/content/10.64898/2026.08.13.739500v1?rss=1 2026-08-17 doi:10.64898/2026.08.13.739500 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ CellConsensus: An agent-curated atlas for automatic cell typing ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743503v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743503 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ Peptide-HLA II interaction prediction for post-translationally modified peptides ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743493v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743493 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ IsoMobil: Resolving Molecular Ambiguity in Mass Spectrometry-based Spatial Omics Through Ion Mobility ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743457v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743457 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ Principal Genes: A PCA-based approach to highly variable genes selection for scRNA-Seq analysis ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743504v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743504 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ pastForward: a Snakemake pipeline for ancient and historical DNA with eukaryote-wide taxonomic screening and tracking of copy-number variation ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743613v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743613 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ Exploring vulnerable proteins in the progression of head and neck squamous cell carcinoma ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743269v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743269 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ scDIVA: semi-supervised integration and fine-grained annotation of tumor-immune single-cell atlases ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743520v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743520 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ LactoTypeDB: a regenerable, type-anchored 16S rRNA gene reference for species-level identification of the Lactobacillaceae in foods ]]> https://www.biorxiv.org/content/10.64898/2026.08.12.744342v1?rss=1 2026-08-17 doi:10.64898/2026.08.12.744342 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ Learning from human and chemical languages to predict biological function ]]> https://www.biorxiv.org/content/10.64898/2026.08.09.743788v1?rss=1 2026-08-17 doi:10.64898/2026.08.09.743788 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ ZEISS arivis Cloud: a cloud-based platform for deep learning model training and scalable bioimage analysis ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743540v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743540 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ Longitudinal whole transcriptomic profiling of live cells through domain adaptation ]]> https://www.biorxiv.org/content/10.64898/2026.08.07.743564v1?rss=1 2026-08-17 doi:10.64898/2026.08.07.743564 Cold Spring Harbor Laboratory 2026-08-17 <![CDATA[ MERIT: Mechanism driven model predicts drug outcomes and nominates indications for failed drugs ]]> https://www.biorxiv.org/content/10.64898/2026.08.09.743088v1?rss=1 2026-08-17 doi:10.64898/2026.08.09.743088 Cold Spring Harbor Laboratory 2026-08-17