database / resource

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

The paper introduces the C. elegans Connectome Toolbox, a framework for integrating and analyzing multimodal connectomic data, enabling comparison across datasets and modalities.

NBDC Data Tools automate dataset preparation from ABCD and HBCD releases, enabling reproducible and reusable analysis workflows in R and Python.

The paper highlights the lack of standardized genomic metadata in plant and metazoan genome assemblies and proposes making ploidy, cultivar, and subgenome structure mandatory metadata fields.

This paper presents a chromosome-level genome assembly for the wolverine, providing a more complete and sex chromosome-inclusive reference for conservation studies.

The paper introduces a longitudinal neuroimaging dataset of Alzheimer's disease pathology, including multimodal data from patients and controls, to identify and validate novel biomarkers.

The paper presents a curated dataset of 1,413 LNP cytotoxicity measurements to examine structure-activity relationships and develop computational models of lipid nanoparticle cytotoxicity.

The paper generates a multi-tissue RNA-seq atlas of adult medaka under salinity and seasonal contrasts to study gene-expression plasticity and comparative biology.

This study integrates GEDI LiDAR with an existing data assimilation system to improve terrestrial carbon monitoring, reducing woody biomass uncertainty by 63.7% and achieving RMSE reduction of 38.3 kg/m2.

This paper introduces ramped phase randomization to improve cryo-EM map comparison and data augmentation by reducing fine-scale detail while preserving low-frequency content and enhancing machine learning performance.

The paper presents 25 new microsporidian genomes, revealing extreme pangenome diversity and novel tetraploid structures in some species.

The paper describes the development of a harmonized multisite MRI protocol for pediatric brain imaging and validates its cross-site consistency.

This study creates a label-free volumetric atlas of ten fresh mouse organs using D-FFOCT, revealing dynamic tissue features and heterogeneity across organs.

SYMBIO-SCAN identifies high-quality full-length 16S rRNA gene sequences from long reads to discover bacterial symbionts in beetles, revealing novel genera and species.

iGEX provides an interactive platform for exploring transcriptomic and proteomic datasets, enabling comparison of expression patterns across experiments and public resources.

Region-stratified scRNA-seq of 607,370 cells plus 500-gene MERFISH maps adult Danionella cerebrum cell types body-wide, revealing fibroblast Hox and limb-identity programs and telencephalon regeneration dynamics.

The paper introduces the Microbiology Galaxy Lab, a community-driven platform for reproducible and FAIR microbial data analysis, offering tools for various omics data types and use cases.

Arena3D 3.0 is a web server for exploring, analyzing, and sharing multilayered biological networks in 3D with various layouts and visualization tools.

This paper identifies histone modification-associated nucleosome positions in cfDNA that correlate with tumor fraction and cancer state across multiple cancers.

UHPLC-MS/MS lipidomics of maize leaves (149 species, three genotypes, four growth stages, three leaf zones) shows genotype and leaf number explain most lipid variation.

This study identifies genomic adaptations in an endangered California plant to coastal fog, revealing candidate genes and potential impacts of wind farms on gene flow.

Thyra converts Mass Spectrometry Imaging data into the SpatialData format to improve interoperability and enable multi-modal spatial analysis.

Neuroline integrates multimodal neurophysiology data into a standardized format, enabling FAIR data sharing and cross-modal analysis.

The paper integrates ATAC-seq and RNA-seq data from zebrafish osteoblasts to identify chromatin and transcriptomic signatures and mechanisms of entpd5a regulation.

The paper identifies sRNA candidates in B. burgdorferi and maps their regulatory interactions across growth phases, revealing a dynamic RNA-RNA interactome.

SMARTFlexDB links ligand-bound and ligand-free RNA structures to study conformational flexibility and small-molecule recognition, providing a resource for RNA-targeted drug discovery.

This paper develops a culturomics-guided FMT framework that enables stable, antibiotic-independent engraftment by targeting metabolic niches in recipient microbiomes.

The paper creates a comprehensive reference map of the RAS/RAF/MEK/ERK pathway interactomes and their mutation-driven rewiring, revealing new interactions and disease links.

The paper introduces mobileRNA, an R package that efficiently identifies mobile RNA molecules in grafted plants using merged genome alignment and simulated datasets.

The paper introduces the GA4GH Workflow Execution Service API, which standardizes workflow execution across different compute environments and demonstrates its cross-site functionality.