database / resource

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

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

Residual barcode-like sequences and barcode-associated artifacts after Dorado and Barbell preprocessing of metagenomic reads

The paper evaluates Dorado and Barbell preprocessing tools for metagenomic reads, finding Barbell reduces barcode-like sequences more effectively while retaining most reads.

Hybrid RY-mers increase aDNA alignment sensitivity

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

CauloBrowser 2.0: an AI powered update

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

The C. elegans Connectome Toolbox: an open, extensible framework for multimodal connectomic data integration and analysis

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

TIGRdisco: a tool for the discovery of TIGR arrays and TIGR-associated Tas proteins from nucleotide sequences

TIGRdisco identifies TIGR arrays and Tas proteins from nucleotide sequences, recovering most array units and uncovering unannotated loci across datasets.

NORMA 3.0: aesthetic and group-aware visualization and analysis of annotated biological networks

NORMA 3.0 provides enhanced visualization and analysis of annotated biological networks with improved group representation and layout algorithms.

PLATE: a global atlas of food metaplasmidomes

PLATE provides a global resource of food metaplasmidomes, offering curated catalogs and annotations for studying plasmid diversity and function in food ecosystems.

Generalizable virtual staining from histopathology to spatial proteomics across biological scales

This study introduces QUEST, a model that uses H&E histology to predict spatial protein expression, enabling virtual staining and analysis across biological scales.

Stable large-scale network architecture and structured individual variability in the awake mouse brain

The paper introduces the Awake Mouse Connectome Project (AMCP), a dataset of 212 awake mice, and presents functional network atlases and analysis tools for studying brain connectivity and variability.

QC-espresso: Brewing quality in proteomics

QC-espresso provides an automated quality-control workflow for DIA proteomics data, generating structured reports to assess acquisition quality and quantitative reliability.

Ancient environmental DNA reveals the distinct fingerprints of whaling and climate change on Antarctic marine biodiversity

This study uses ancient environmental DNA to show how whaling and climate change impacted Antarctic marine biodiversity over two centuries.

Consensus methods for trees of blobs and level-1 phylogenetic networks

This paper introduces a consensus framework for phylogenetic networks, demonstrating its effectiveness on simulated and real datasets.

The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression

The paper presents the Almond Expression Atlas, a comprehensive transcriptomic resource integrating RNA-seq data to identify tissue-specific genes and improve gene expression analysis in almond.

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.

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.

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.

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.

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.