database / resource

Harmonizing Repeated Multi-Platform Optical and LiDAR Observations for Continental-Scale Terrestrial Carbon Cycle Data Assimilation.

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.

Low-pass filtering revisited: ramped phase randomization for cryo-EM map comparison and data augmentation

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.

Gene Embedding Hub: a standardized resource for human gene representations

The paper introduces a standardized resource of human gene embeddings derived from diverse biological data sources, enabling comparison and use across modalities.

Cross-modal transfer enables zero-shot prediction of drug responses across cell types

GRAFT predicts drug responses across cell types without direct measurements by transferring genetic perturbation data to chemical perturbations.

Batch Effect Correction to Enhance Utility of a Publicly Available ALS Proteomics Dataset

The paper corrects batch effects in the Answer ALS proteomics dataset using BDCs and ComBat, improving data utility while preserving biological variability.

Twenty-five new microsporidian genomes: Insights into ploidy, reproduction, and the group's pangenome

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

The Canadian Pediatric Imaging Platform (C-PIP) Reference Sample: Neuroimaging Protocol and Cross-site Validation for Harmonized Multimodal Pediatric Imaging

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

Advancing global DNA-referencing of bushmeat in African tropical forests: a tool for identifying trade hotspots and dynamics in western and central Africa

The paper develops a DNA-typing reference database to trace bushmeat trade in Africa, identifying species and trade hotspots with high accuracy.

Silent travelers: the potential of migratory birds and their ticks to introduce emerging viruses into Switzerland

This study surveys the virome of migratory birds and ticks in Switzerland, detecting novel viruses and highlighting the role of birds in virus and tick dispersal.

A genomic baseline for long-term monitoring of economically important aquatic species in the Netherlands

The paper establishes a genomic baseline for six aquatic species in the Netherlands using SNP data to assess population structure, diversity, and conservation priorities.

SMFnet reveals principles of combinatorial transcription factor assembly

The paper introduces SMFNet and PRISM to analyze how transcription factor assemblies influence chromatin accessibility and identifies sequence-encoded principles of combinatorial TF assembly.

The Braarudosphaera bigelowii genome reveals cellular remodeling around a nitrogen-fixing organelle

This paper presents the genome of Braarudosphaera bigelowii, revealing genomic and metabolic adaptations associated with its symbiotic nitrogen-fixing organelle.

Aneuploidy profiling among different types of brain metastases reveals a colon cancer-specific chromosomal signature

This study identifies a unique aneuploidy profile in colorectal cancer brain metastases compared to other cancer types and metastatic sites.

Assembly of minimally fragmented metagenomic pangenome graphs

The paper introduces PANIMaSTA, a method to construct minimally fragmented metagenomic pangenome graphs for highly diverse viral genomes, improving graph topology for comparative analysis.

GolgiFold: A Structural Predictome of Human Golgi Protein Complexes

The paper develops GolgiFold, a structure-based PPI map of human Golgi proteins, identifying over 1,800 interactions and confirming new protein contacts through experimental validation.

ARG-PASS v2.0 expands global resistome surveillance to reveal previously unrecognized antibiotic resistance genes reaching the human gut

ARG-PASS v2.0 identifies previously unrecognized antibiotic resistance genes in environmental samples and links them to human gut microbiomes through dietary exposure.

ProtoPure: Literature Mining and Analysis of Protein Purification Protocols at Proteome Scale

ProtoPure automates the extraction and analysis of protein purification protocols from literature, revealing trends in recombinant expression practices and diverse downstream purification strategies.

Label-free volumetric dynamic atlas of fresh mouse organs using dynamic full-field optical coherence tomography

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

Digital twins forecast individual immune trajectories

The paper introduces ImmuneTwins, a digital twin framework that personalizes immune response models for individuals, improving prediction accuracy of immune trajectory changes.

GLESKit: an MCP-based system for gene-level biomedical investigation and evidence synthesis

GLESKit is a gene-centered system that synthesizes biomedical evidence by integrating multiple data types, achieving high report quality and performance in benchmark tasks.

SYMBIO-SCAN, a full-length 16S rRNA gene-based workflow optimized for bacterial symbiont detection and discovery from long read sequencing

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: an interactive Gene EXpression exploration platform for the analysis of transcriptomic and proteomic datasets

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

Structural clustering across the tree of life reveals candidate Asgard-eukaryote homologs and a shared expansion of solenoids

The paper identifies candidate eukaryote homologs of Asgard archaea by analyzing structural clusters, revealing shared expansions of solenoid proteins.

Lineage-mixed neurodevelopmental programs in pediatric sarcomas nominate tumor-selective surface antigen pairs.

This paper develops an AI framework to interpret single-cell RNA-seq data from pediatric solid tumors, identifying tumor-specific surface antigen pairs for targeted therapies.

Whole-body single-cell atlas of an adult vertebrate in homeostasis and regeneration

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.

Metabolic landscape of inborn errors of metabolism

This study uses metabolomics to analyze 474 subjects with inborn errors of metabolism, identifying genotype-specific metabolic alterations and providing diagnostic tools and a database of metabolomic features.

CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers

CellMethMarker provides a database of DNA methylation markers specific to human cell and tissue types, improving deconvolution accuracy in single-cell methylomes.

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

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.

Validated backbone assignments for natural-abundance 1H,15N spectra of commercial hen egg white lysozyme and example applications thereof

The paper provides validated 1H,15N backbone assignments for commercial hen egg white lysozyme at natural 15N abundance and demonstrates their utility in various applications.

Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D

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