database / resource

An evidence-governed agent harness for spatial transcriptomics prioritizes ICAM-1 as a target in lung fibrosis

DeepMAST, an AI system for spatial transcriptomics, identifies ICAM-1 as a therapeutic target in lung fibrosis through evidence-based analysis and validation.

Systematic genome analysis enables long-overdue taxonomic reorganization of genus Orthoflavivirus; potential assignment of over 50 new species

The paper proposes a genetic divergence threshold for demarcating orthoflavivirus species, identifying 25 new Euflavivirus and 33 new Fusivirus species.

SMARTFlexDB: a paired apo-holo RNA structure database and analysis platform for RNA conformational flexibility and small-molecule recognition

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.

Culturomics-Guided Precision FMT Enables Stable Antibiotic-Independent Engraftment via Metabolic Niche Targeting

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

RAStoERK: a reference interaction atlas for insights into signaling and disease

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 global β-lactam resistome revealed by comprehensive sequence analysis

The paper maps the global distribution of β-lactamases across environments and microbes, revealing their abundance and potential origins in plant and wastewater ecosystems.

SAbDab2: The structural antibody database in the age of machine learning

SAbDab2 provides updated antibody structures with machine learning-ready data and standardized splits for research.

In-silico Tandem Mass Spectral Libraries for the Blood Exposome and Metabolomics Workbench Databases: Application of Gemini Large Language Model

The paper generates in-silico mass spectral libraries for human metabolomics using the Gemini large language model, achieving 55% accuracy compared to NIST 23.

An integrative cardio-informatics approach identifies positionally conserved ancestors of human lncRNA genes transcribed across vertebrate hearts

The paper identifies conserved genomic positions of human heart-related lncRNA genes across vertebrates using integrative analysis and a neural network tool.

mobileRNA: a tool for efficient analysis of mobile RNA molecules in multiple genomes.

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

Differential k-mer distributions enable identification of tetrapod subterminal heterochromatin

The paper identifies subterminal heterochromatin in tetrapods using k-mer distributions, revealing ancient subgenome-specific repeats in Xenopus laevis.

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

The GA4GH Workflow Execution Service: A Standard API for Workflow Execution and Management in Genomics

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

corrdeconv corrects deconvolution's misreading of disease cell states as abundance, overturning benchmarks and outperforming every published deconvolution method

corrdeconv corrects deconvolution errors by addressing misread disease cell states as abundance, outperforming existing methods and reducing refuted effects.

A clinically annotated proteomic and histological resource of 1,000 colorectal cancers

Deep proteomics of 997 treatment-naïve colorectal cancers defines six subgroups, splitting chromosomally unstable tumors into three and revealing a rare adverse subgroup, with H&E slide benchmarks.

The yEvo Mutation Browser: Enhancing student understanding of experimental evolution and genomics through interactive data visualization

The yEvo Mutation Browser helps students and researchers visualize and interpret genome sequencing data from experimental evolution studies of yeast.

An integrated semantic publishing workflow for taxonomy: a review of the Afrotropical dung beetle genus Amietina (Coleoptera: Scarabaeinae)

The paper introduces a semantic publishing workflow for taxonomic studies, applying it to describe four new species of dung beetles and update taxonomic data.

Cuticulome.org: a centralized database of proteins in arthropod cuticles

Cuticulome.org provides a curated database of arthropod cuticle proteins with standardized nomenclature and tools for sequence analysis and dataset customization.

Robust and accessible in situ sequencing with an open-source automated sequencer

The paper introduces Seq-o-Matic, an open-source automated in situ sequencer that reduces hands-on time and improves sequencing consistency across tissue sections.

Data mining of global sequence datasets markedly expands known diversity within the Tobamovirus genus

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

Elucidating changes in gene expression driving nuclear dynamics across a foraminiferal life cycle with Pheno2Seq

The paper develops Pheno2Seq to study gene expression changes in foraminifera life cycle transitions, identifying genes involved in nuclear dynamics and genome stability.

Description of two novel Corynebacterium species isolated from human nasal passages and skin

This paper describes two novel Corynebacterium species isolated from human nasal passages and skin, along with characteristics of two strains of a recently named species.

A pilot computer-vision model trained to identify slide-mounted scale insect pests from the family Rhizoecidae

The paper trains a computer-vision model to identify 16 species of root mealybugs using high-resolution images from museum specimens, achieving 79% F1 score.

The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics

The paper updates the ModelSEED Biochemistry Database with expanded compounds and reactions, integrating multi-source thermodynamic data and grading reaction reliability.

NuFold RNA Structure Database: Large-Scale RNA Tertiary Structure Prediction with Confidence Metrics

The paper introduces NuFold, a tool for large-scale RNA tertiary structure prediction, and provides a database with precomputed structures and confidence metrics.

LiverHomo: An Integrated and Interactive Human Liver Single-Cell Atlas with Protein Interaction and Cell-Cell Communication Networks

LiverHomo integrates human liver scRNA-seq data with PPI and cell-cell communication networks to provide an interactive resource for exploring liver health and disease.

SpacePath enables pathway and molecular-family analysis beyond annotation ambiguity in spatial metabolomics and lipidomics

SpacePath improves spatial metabolomics analysis by handling molecular ambiguity and identifying novel lipid families in spatial datasets.

DREM: integrating resistance and domain probabilities to prioritize plant immune receptors

DREM is a deep learning model that improves the identification of plant immune receptors by learning from sequence data, outperforming existing methods and identifying novel resistance proteins.

DNA sequence sets the destination of spontaneous epimutations in plants

The paper shows DNA sequence determines the destination of spontaneous epimutations in plants, using a deep-learning model trained on one methylome to predict methylation set points across species.

TRUEDA overturns replicated, decontaminated low-biomass disease-microbe associations and clinical decisions, recovers true pathogens and outperforms every decontamination method

TRUEDA identifies true pathogens in low-biomass disease-microbe associations by accounting for contamination, outperforming existing decontamination methods and correcting false associations.