database / resource

GenDiMug: a generic inclusive multigraph framework to analyze genomic organizations and -omics data at multiple scales

GenDiMug is a multigraph framework for analyzing genomic organization and multi-omics data across scales, revealing gene expression clumping and circadian regulation in a photosynthetic alga.

From APTs to advanced persistent biological threats (APBTs): a taxonomy and large-scale metadata audit of genomic surveillance infrastructure

The paper audits metadata vulnerabilities in genomic repositories, identifying structural weaknesses that could enable malicious metadata poisoning as part of an APBT operation.

Pervasive effect of bottom trawling on benthic biodiversity unravelled by metabarcoding across the Tree of Life

This study uses eDNA metabarcoding to show that bottom trawling affects prokaryotic and Animalia benthic communities, with long-term impacts on Animalia diversity and unexpected effects on community structure.

Ayahuasca plant genomes reveal retrotransposon-derived centromeres and contrasting routes to DMT and β-carbolines

The paper presents the genomes of Ayahuasca source plants, revealing retrotransposon-derived centromeres and distinct biosynthetic pathways for DMT and beta-carbolines.

TurbOmics: a web-based platform for the analysis of metabolomics data using a multi-omics integrative approach

TurbOmics is a web-based platform that enables multi-omics integration of metabolomics, proteomics, and transcriptomics data, addressing limitations in metabolomics annotation and accessibility.

Shedding light on the virome of Caliothrips phaseoli, an emergent pest in peanut

This study uses RNA HTS to analyze the virome of Caliothrips phaseoli, identifying 18 novel viruses across multiple families.

A semi-automated tool for improving Assessments and Lab Tests data annotation in ImmPort

The paper introduces a semi-automated tool to improve data annotation in ImmPort by streamlining template population and ensuring formatting consistency.

Additive in size, synergistic in composition: selection across the eastern oyster larval genome under coastal acidification and sewage effluent

The paper exposes eastern oyster larvae to combined stressors and finds compositional genomic synergy despite additive survival and allele-frequency change.

A pan-eukaryotic analysis of mitochondrial ribosomes uncovers major evolutionary transitions

This study analyzes mitoribosome protein composition across 85 eukaryotes to uncover evolutionary transitions and update nomenclature.

StereoMapper: Clarifying Metabolite Identity Through Stereochemically Aware Relationship Assignment

StereoMapper clarifies metabolite identity by assigning stereochemically aware relationships, achieving high performance in benchmark datasets and improving GEM accuracy.

SCKAnalyzer: A Web Tool for Single-Cycle Kinetics Analysis and Simulation

SCKAnalyzer processes and fits single-cycle kinetics data from biosensors, offering simulation and analysis tools for biomolecular interactions.

Community-level diversity of viral counter-defensomes

The paper analyzes the counter-defensome diversity across 50,595 DNA phage genomes from different environments, revealing variation linked to host range, habitat, and geography.

An endolithic Gloeobacter and other novel cyanobacterial diversity in alpine dolomites of Piora Valley

The paper reports the discovery of a novel Gloeobacter species in alpine dolomites and describes its unique genomic features related to cyanate metabolism.

KRAKEN: A provenance-tracked knowledge graph for multiomic and wellness research

A Biolink-compliant graph (∼15 million nodes, ∼113 million edges) adds RefMet and LIPID MAPS metabolite and lipid classifications, plus polygenic score and clinical data element entities, to Translator content.

Fine-tuning genomic models on rare splicing events identifies a novel biomarker of TDP-43 pathology

A sample-to-identification workflow to monitor animal and plant biodiversity using metabarcoding and real time analysis

The paper presents an eDNA workflow integrating metabarcoding and real-time analysis to improve biodiversity monitoring by overcoming limitations in sensitivity, taxonomic range, and processing time.

Hidden Medicines in Herbarium Collections: Medicinal Plant Diversity and Ethnopharmacological Knowledge from GSUH, Nigeria

The paper analyzes medicinal plant diversity and ethnopharmacological knowledge from herbarium records in Nigeria, finding significant associations between plant parts and therapeutic applications.

Stemflow as a Storm-Driven Pathway for Fungal eDNA Transport

The paper uses ITS2 metabarcoding to analyze fungal eDNA in stemflow from three tree species, finding distinct communities influenced by host species and storm events.

ERGA-BGE genome of Valencia hispanica (Valenciennes, 1826): a critically endangered Iberian toothcarp

The paper presents the chromosome-level genome assembly of Valencia hispanica, a critically endangered fish, to support conservation and ecological studies.

High-throughput in vivo DNA data encoding by multiplexed conjugationand orthogonal base editing

The paper introduces a system for high-throughput in vivo DNA data encoding using bacterial conjugation and base editing, successfully encoding and retrieving binary data with high accuracy.

Large language models unlock the ecology of species interactions

This paper uses large language models to extract species interaction data from citizen science comments, expanding ecological data coverage and enabling new ecological research.

REFinder: Mining new enzymes from metagenomes

REFinder improves enzyme discovery from metagenomes by combining alignment-free annotation with targeted assembly, identifying more novel enzymes at lower cost than traditional methods.

Phylogenetic, genomic, and morphological characterization of Rickettsia senegalensis sp. nov., a novel Rickettsia species detected worldwide

This paper describes the discovery and characterization of a new Rickettsia species, Rickettsia senegalensis, based on genomic, morphological, and epidemiological data.

Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC)

In 174 sedentary adults, resistance exercise changed more muscle molecular features than endurance exercise across omes and time points; network analysis nominates MEF2A and NFIC as regulatory hubs.

CADENCE: Open-source software for signal conditioning, feature extraction, visualization and analysis of cardiac optical mapping data

CADENCE is an open-source MATLAB-based tool for processing cardiac optical mapping data, offering end-to-end analysis with features for denoising, conduction velocity, alternans, and rotor detection across multiple species and tissue types.

Automated Segmentation and Tractography of Brainstem and Subcortical White Matter

The paper develops an automated pipeline for segmenting and parcellating brainstem and subcortical white matter pathways using diffusion MRI data.

A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

A prime-editing recorder in one mouse embryo yields a dated, zygote-rooted lineage tree of 1.28M cells at E13.5, enabling clonal dominance, sibling-fate and cell-type coupling analyses.

Validated Semantic Scoring Improves Filtering of Generic Concepts from Knowledge-Graphs for Drug Repurposing Queries

This paper introduces a semantic precision score to filter generic concepts from biomedical knowledge graphs, outperforming existing methods in drug repurposing queries.

mzQC: a versatile way to communicate quality information for biological mass spectrometry

The paper introduces mzQC, a standard for representing quality control metrics in mass spectrometry, enabling interoperable and machine-readable QC reporting.

Trait-Based Selection of Annual Plant Species for Enhancing Ecosystem Functioning in Extensive Green Roof Systems: A Systematic Review

This review identifies annual plant species suitable for extensive green roofs and highlights functional traits important for their success in rooftop conditions.