benchmarking

Emergent metabolic cooperation in communities of microbes that maximise growth rate by optimal protein expression

This paper develops a mathematical framework to model microbial communities optimizing growth rates through metabolic cooperation and resource allocation.

Citizen science gamers enable automated flow cytometry gating through machine learning

The paper develops flowMagic, a machine learning tool for automated flow cytometry gating trained on expert data and citizen science gaming annotations, achieving high accuracy in cell population identification.

Coordinated Drift of Image Representations in Human EEG

The paper investigates drift in human EEG responses to images across sessions, finding coordinated drift along image identity dimensions and preserved global structure.

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.

OocystMeter, a machine-learning algorithm to count and measure Plasmodium oocysts, reveals clustering patterns in the Anopheles midgut

OocystMeter automates oocyst counting and sizing in mosquito midguts, revealing clustered spatial patterns in malaria infections.

How goals shape naturalistic memories: bias in gaze and narrative recall

This study shows how induced goals shift attention during memory encoding and bias narrative recall in a naturalistic setting.

Stop guessing thinning distances: a data-driven framework for spatial thinning parametrization for ecological modelling

This paper introduces a data-driven framework for spatial thinning parameterization in ecological modelling, showing that optimal thinning parameters vary with species range size and that uniform approaches can lead to information loss or reduced spatial clustering.

Out-of-the-box bioinformatics capabilities of large language models (LLMs)

This study evaluates the performance of three large language models on basic bioinformatics tasks compared to human performance, finding LLMs match human accuracy in some areas but struggle with complex tasks like sequence alignment.

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.

Ground-truth evaluation of sparse autoencoder features on spatial, single-cell and language-model embeddings

The paper evaluates sparse autoencoder features on various embeddings, finding that reproducibility does not guarantee meaningfulness, and proposes reporting features with concept coverage and purity.

Transcriptomic similarity guides source selection beyond tissue lineage

The paper shows that transcriptomic similarity can rank candidate sources for response prediction better than random, but does not resolve aggregation or transfer uncertainty.

The B-value calculator: expected diversity with background selection

The paper introduces Bvalcalc, a tool to calculate B-values, which quantify the effect of background selection on genetic diversity, and validates it using simulations and public data.

Optimisation and Validation of a UHPLC-MS/MS Assay Using Timed Post-Column Ammonium Fluoride Infusion for Sensitive Serum Steroids Quantitation

The paper develops and validates a UHPLC-MS/MS assay for quantifying 18 steroids in serum, showing improved sensitivity and applied it to healthy individuals.

Closing the phenotyping gap: non-invasive electromagnetic induction enables high-throughput screening of crop root function in the field

This study uses electromagnetic induction to measure crop root function in the field, showing it can accurately predict water use and root traits across different genotypes and row spacings.

MutQA: A Cross-Validated Q&A Dataset for Genetic Mutations

The paper introduces MutQA, a cross-validated Q&A dataset linking genetic mutations to their functional consequences, and demonstrates its utility in improving LLM performance.

Multi-resolution humanness scoring of antibodies via a region-isolated language model

The paper introduces IgScope, a language model for antibody humanness scoring at multiple resolutions, showing improved accuracy over existing methods and revealing issues with generative models.

Preserving Information and Integrity in Cryo-EM: A Fourier-Space Deposition Approach

The paper identifies limitations in current cryo-EM data deposition practices and proposes an alternative approach to better preserve information and support validation.

Survey of the human proteostasis network: the ubiquitin-proteasome system

The paper provides a comprehensive survey of the ubiquitin-proteasome system (UPS) and estimates its size and scope within the human proteostasis network.

From deployment to functioning ecosystems: assessing taxonomic richness and community composition on modular shellfish reefs using environmental DNA metabarcoding

The paper assesses biodiversity recovery on modular shellfish reefs using eDNA metabarcoding, showing rapid taxonomic richness gains but ongoing compositional shifts over time.

Inferring the multi-host fitness landscape of endive necrotic mosaic virus from cross-inoculation experiments

The paper infers a multi-host fitness landscape of endive necrotic mosaic virus using cross-inoculation experiments and a Bayesian model linked to Fisher's geometrical model.

Histone modifications define distinct nucleosome positions in cell-free DNA

This paper identifies histone modification-associated nucleosome positions in cfDNA that correlate with tumor fraction and cancer state across multiple cancers.

PepPr: De Novo peptide sequencing with peptide priors

PepPr improves peptide sequencing by integrating peptide priors, enhancing reference and variant peptide identification while maintaining discovery flexibility.

Fixing the Measurement Model Before the Selection Heuristics: Optimiser Repairs for Living-Cell Self-Driving Laboratories

This paper compares measurement-aware models and selection-level repairs in Bayesian optimisation for living-cell experiments, finding that measurement-aware models reduce regret and improve coverage under data contamination.

Non-destructive tree volume estimation using mobile laser scanning: Impact of the tree shape on measurement error.

This study evaluates the accuracy of mobile laser scanning for tree volume estimation, finding that tree shape has a limited impact on measurement error compared to scanning conditions and forest structure.

Salmonid science on the move: Twenty years of research through the lens of early career researchers

This review analyzes 20 years of salmonid research through early-career researchers' contributions, identifying trends, gaps, and future directions in the field.

Circulating hematopoietic stem and progenitor cells in myeloproliferative neoplasms

This study profiles circulating hematopoietic stem and progenitor cells in MPN patients, identifying transcriptional signatures and quantitative readouts to distinguish MF from other MPNs and predict progression.

Creator 1.0: Phylogeny-Guided Stagewise Pretraining for Plant Genome Foundation Models across 1,000 Species

Creator 1.0 is a plant genome foundation model pretrained on 1,000 species using phylogeny-guided stagewise pretraining, achieving strong performance on plant-related tasks.

Integrating sequence-to-omics predictions and personal multi-omics for rare variant prioritization

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

Preprint solicitation as a natural experiment in scholarly publishing

This study compares acceptance rates and outcomes of solicited preprints versus traditional submissions in Proceedings B, finding higher acceptance rates and visibility for solicited preprints.

Maps of historical forests in France and their temporal continuity since the first half of the 19th century

This paper digitizes and vectorizes 19th-century French forest maps to analyze historical land-use changes and their impact on current forest cover and conservation strategies.