bioRxiv: Bioinformatics Preprints · Scour

zFISHer: Automated 3D Registration, Detection, and Colocalization with Interactive Curation for Sequential Multiplexed FISH

Spectral Prompting: Unsupervised Recovery of Human Hair Follicle Cell-Type and Multiscale Systems Architecture from Bulk and Single-Cell RNA-Seq Datasets via Si...

Multimodal single-cell analysis uncovers transcription factor networks underlying T-cell aging

Multi-layer transcriptomic characterization of age-related immune dynamics

geneML: Gene annotation across diverse fungal species using deep learning

MirMachine 2: a scalable, evolutionarily informed pipeline for microRNA annotation and comparative genomics across thousands of animal genomes

Structural Pockets and Interacting RNA-Associated Ligands (SPIRAL): A DSSR-enabled Meta-Analysis of RNA-Small Molecule Recognition

ParaDISM: Precise mapping of short reads to genes with highly homologous regions

A phylogeny-guided framework for decoding mechanisms of human endogenous retrovirus regulation in health and disease

MolCodon: A Codon-Based Molecular Language for InterpretableStructural Representation and Similarity Search

A community machine learning challenge to predict the effects of gene perturbations on T cell differentiation for cancer immunotherapy

Benchmarking full-length ITS metabarcoding across Illumina 2x500, PacBio, and Oxford Nanopore sequencing using mock and soil communities

Min-frame transformation enables more sensitive viral genome alignment

AbSolution: interactive exploration of sequence-derived features in AIRR-seq repertoires

RANKOR: Direct Drug Prioritization from Bulk and Single-Cell Transcriptomic Signatures

Predicting and Elucidating Peptide Retention Mechanisms with Graph Attention Networks

ToxCastLite: A portable semantic evidence graph linking in vitro bioactivity, in vivo toxicity, and exposure-use context

Early terminated transcripts and missing proteins reflect artifacts in bacterial proteomes

Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation

NANOTAXI: A Shiny-Based GUI for Real-Time Classification and Analysis of 16S rRNA Nanopore Reads

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