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CellExLink improves end-to-end cell-type recognition and Cell Ontology normalization in biomedical text, outperforming existing tools across diverse corpora.

CNVeil infers haplotype-specific copy number and subclonal architecture from single-cell cancer genomes, outperforming existing methods in accuracy and resolution.

This paper presents AmarylOmicBase, a unified transcriptomic database for Amaryllidoideae species, integrating assemblies, annotations, and expression profiles to support gene discovery and pathway analysis.

RETROFIT deconvolves cell-type mixtures in spatial transcriptomics without requiring references, outperforming existing methods and matching reference-based approaches when references are imperfect.

The paper introduces BIP, a pipeline for DNA barcode inference from sequencing data, which outperforms existing tools by accurately distinguishing target and non-target sequences.

The paper introduces spatialproteomics, a Python toolbox for analyzing highly multiplexed fluorescence images, demonstrating its use on lymph node and lymphoma data.

The paper introduces an automated pipeline for whole-genome sequencing analysis of microbial pesticides to improve hazard characterization and risk assessment.

GatorPrism integrates spatial multi-omics data by balancing cross-omics consensus with modality-specific signals, achieving strong performance across clustering metrics and revealing tissue structure organization.

VizR provides an interactive web platform for end-to-end RNA-seq analysis and visualization in plant biology, reducing technical barriers through automation and integration.

The paper designs water-soluble analogs of EBV membrane proteins using QTY residues, showing minimal structural changes and reduced hydrophobicity.

The paper uses deconvolution of bulk RNA-seq to generate cell-type-specific targets for predicting gene expression from personal genome sequences, finding that sequence-derived models outperform genotype-feature baselines.

CHIMIYA-1 is a foundation model for ADMET property prediction that outperforms many public methods on the TDC ADMET benchmark, with strong performance on toxicity and physicochemical endpoints.

PhytoFam automates plant gene family analysis through a Nextflow pipeline, integrating multiple tools for homolog detection, orthology assignment, and phylogenetic reconstruction.

GraTools is a command-line tool for manipulating pangenome variation graphs, enabling efficient subgraph extraction, sequence retrieval, and analysis of genomic diversity.

GeneKnow synthesizes biological evidence from literature with auditability, achieving higher claim support and citation fidelity than existing AI systems.

GenoSim simulates diploid SNP genotypes with population stratification and pedigree constraints, providing outputs compatible with clinical and population genetics formats.

Autocorrelation-aware bivariate Moran's I, bivariate Gaussian process tests and generalized additive models (R package sbivar) test cross-modality colocalisation on disjoint coordinates; many existing permutation tests inflate false positives.

scSAID provides a cross-species single-cell skin atlas to study psoriasis, revealing species-specific molecular signatures and identifying a novel drug target.

cellGeometry deconvolutes bulk RNA-Seq using geometric methods, offering faster and more accurate results than existing approaches.

This study compares transcriptomic profiles of penile and vulvar lichen sclerosus to identify shared deregulated genes and potential biomarkers.