benchmarking

MetagenomicsBench: A Verifiable Benchmark for Agentic Metagenomics Analysis

MetagenomicsBench evaluates AI agents' ability to analyze metagenomic data through 100 verifiable tasks, finding that performance varies across domains and that technical plausibility does not guarantee correct biological interpretation.

Analysis of Naturally Arising Simple Deletions in Single Human Colon Crypts with Age

The paper analyzes simple deletions in single human colon crypts across age, finding most are due to strand slippage and NHEJ, with age-related accumulation and radiation effects.

Machine Learning Identification of Functional Trait Syndromes Associated with Responsiveness to Arbuscular Mycorrhizal Fungi

The paper develops a machine learning framework to predict plant responsiveness to arbuscular mycorrhizal fungi using functional traits and environmental variables, finding that specific leaf and root traits are key predictors.

Spiders as natural DNA samplers recover arthropod community diversity and biotic interactions across space and time

This study shows spiders can effectively sample arthropod DNA from their gut contents, revealing community diversity and biotic interactions comparable to traditional methods and preserving historical data up to 20 years.

Mapping scientific cosmopolitanism: scientists with publication records substantially split across multiple countries

The paper maps scientific cosmopolitanism by analyzing Scopus data, finding 20.4% of top-cited scientists have substantial publication records in multiple countries.

Fluffy nests and bloody parasites: feather lining does not mitigate bird blow flies infestations

The study investigates whether feather lining in bird nests reduces blow fly infestations but finds no evidence of an anti-parasitic effect.

Root Age Structure Governs Long-Term Architecture and Hydraulic Function in Perennial Plants: a Modelling Framework

The paper develops a modelling framework that incorporates root age structure to simulate perennial root system development and hydraulic function over decades.

CardamomOT: a mechanistic optimal transport-based framework for gene regulatory network inference, trajectory reconstruction and generative modeling

CardamomOT improves gene regulatory network inference and trajectory reconstruction by integrating mechanistic models with optimal transport, using exact time labels and reducing hyperparameters.

RI-SINDy: Regulation-Informed Sparse Model Discovery in Biological Gene Networks

RI-SINDy improves sparse regression for gene network modeling by addressing multicollinearity in regulatory nonlinearities, achieving better coefficient recovery and trajectory accuracy in both experimental and synthetic data.

Desync and connect: noninvasive MEG evidence of long-range coupling between locally desynchronized regions

This paper shows that long-range phase coupling can occur between desynchronized brain regions using MEG, and demonstrates a method to detect this coupling while accounting for spatial leakage.

Inadequate antibody validation places substantial numbers of animal and human tissue samples at risk of waste

Of 760 papers using 35 antibodies that failed knockout-controlled testing in every application, 15.8% showed validation; the other 640 used at least 8,064 animal and 4,424 human tissue samples.

Circular Data Analysis for Spatial Omics

The paper provides guidance on analyzing circular data in spatial omics, using case studies to illustrate key considerations and methods.

ASTRA enables zero-shot super-resolution of spatial transcriptomics across capture geometries

ASTRA enables zero-shot super-resolution of spatial transcriptomics across different capture geometries, improving accuracy and efficiency compared to existing methods.

Large Language Models Predict Human Social Behavior via Interpretable Mechanisms

This study evaluates LLMs' ability to predict human social behavior through interpretable cognitive models in socioeconomic games.

Carnivores in a metropolitan forest island: first spatial capture-recapture estimates reveal high densities of leopards and striped hyenas in Jaipur, India

The paper estimates leopard and striped hyena densities in an urban protected area using camera-traps and spatial capture-recapture models, finding high densities and significant temporal overlap.

Transporting Causal Effects in Ecology: Concepts and Tools

The paper introduces causal effect transportability for ecological research, enabling the transfer of causal findings between domains using structural causal models and R software.

Iterative computational bioprospecting of hydroxymethylfurfural oxidases combining molecular simulation and machine learning

The paper identifies improved hydroxymethylfurfural oxidases through iterative computational methods combining molecular simulation and machine learning.

pre-miRBench: a multispecies benchmark and reference model for animal precursor microRNA prediction

The paper introduces pre-miRBench, a multispecies benchmark for pre-miRNA prediction, showing its model outperforms existing predictors in cross-species and cross-family tests.

Scale matters: the arbuscular mycorrhiza - root hair trade-off from individual plants to communities

This study examines the trade-off between arbuscular mycorrhiza and root hair traits across multiple scales in grassland plants, finding consistent patterns at community and interspecific levels but not at intraspecific or intra-individual levels.

PREpiBind: Protein Representation-integrated Epitope-MHC Class II Binding Prediction

PREpiBind evaluates ten protein representations for pMHC-II binding prediction across multiple datasets, showing varying performance depending on the task and evaluation method.

Development and Analytical Validation of a Smartphone-Based Quantitative Lateral Flow Immunoassay for Serum Cystatin-C

This paper develops and validates a smartphone-based lateral flow immunoassay for serum Cystatin-C, showing high accuracy and reliability in clinical samples.

Forensic likelihood ratios for shotgun sequencing data from DNA mixtures

The paper develops likelihood ratios for forensic DNA mixtures from shotgun sequencing data, showing they can be unreliable and proposing a combined evidence score to improve accuracy.

Intraindividual longitudinal changes of the proteome reveal dynamic markers of biological aging

The paper develops a proteomic aging clock using longitudinal plasma proteomics data to show that biological aging is dynamically influenced by modifiable risk factors.

Coordinated microRNA-mRNA regulatory remodelling across the compressed maturation of the African killifish (Nothobranchius furzeri)

The paper integrates miRNA and mRNA expression across developmental stages in African killifish to identify coordinated regulatory changes during rapid maturation.

HiFIseek: gene-specific enrichment of high-impact mutations in associated genomic regions

HiFIseek identifies gene-specific enrichment of high-impact mutations in genomic regions associated with cancer and breast cancer risk SNPs, showing limited agreement across CRR-score combinations.

SELECTIVE SURVIVAL OF AVIAN ECTOPARASITES IN AGROINTENSIVE HABITATS AND SUBSEQUENT EFFECTS ON HOST SELECTION BY PARASITOIDS

The paper examines how agrointensive habitats affect puparial size and parasitoidism risk in Protocalliphora sialia, finding selective mortality shapes trait distributions in agricultural landscapes.

BettaAI: a machine-learning object detection model for the quantification of aggressive displays in the Siamese fighting fish Betta splendens

BettaAI is a deep learning model that accurately detects and quantifies aggressive displays in Siamese fighting fish using video analysis.

digestome: a licence-clean marker-gene panel for functional profiling of anaerobic digestion microbiomes

The paper introduces digestome, a marker-gene panel for functional profiling of anaerobic digestion microbiomes, and benchmarks it against metagenome-assembled genomes and species representatives.

Mechanistic classification of the AAA superfamily with protein language models

This paper uses a protein language model to classify AAA family proteins by their mechanistic function, showing that sequence context can predict biochemical mechanisms.

A sampling-theory framework for richness-uniqueness relationships

The paper develops a sampling-theory framework to analyze richness-uniqueness relationships, showing that negative slopes can arise from neutral processes rather than ecological uniqueness.