benchmarking

Verifiable Agentic Science on Public Infrastructure

This paper demonstrates agentic science on public infrastructure to ensure reproducibility by making all agent actions and workflows publicly accessible.

Identification of an Endothelial Senotype Predicted by Ion Channel Expression in Aged Murine Perigonadal Adipose Tissue

The paper identifies age-dependent senescent endothelial cells in adipose tissue using snRNA-Seq and finds ion channel genes as predictive biomarkers.

Community needs for FAIR pathogen data: a cross-sectional survey of infectious-disease researchers and educators

This paper surveys infectious-disease stakeholders to identify barriers to FAIR pathogen data and prioritize training and infrastructure needs.

Low-Cost Real-Time Fiber-Optic Distance Sensing for OPM-based Biomagnetic Measurements

This paper evaluates low-cost polymer fiber sensors for real-time distance measurement in OPM-based biomagnetic measurements, finding high accuracy over 0-10 mm with some error beyond.

Neuroscience in Conversation: Tracking Scientific Change Through an Open Seminar Archive

This paper analyzes neuroscience seminar transcripts to track scientific trends and predict future discourse, finding limited predictive power in spoken scientific conversations.

Metric-driven Pre-acquisition Diagnostics for Automated Microscopy Ultraviolet Surface Excitation (MUSE)

The paper introduces a pre-acquisition quality-control framework for MUSE microscopy that uses tile-level metrics to detect and correct imaging errors before data collection.

Intrinsic Goals for Autonomous Agents: Hierarchical Exploration Captures Future Volitional Action in Drosophila

This study uses intrinsic motivation algorithms to create agents that mimic Drosophila exploration behavior and neural representations of future actions.

Scaling genetic discovery through automated post-GWAS interpretation

This paper introduces PGI, a system that automates post-GWAS interpretation, achieving high recovery of findings and enabling cross-study biological evidence accumulation.

Intermediate, rather than Isohydric or Anisohydric, Species were More Resilient to an Extreme Heatwave in a Common Garden in Sydney

The study evaluates resilience of urban tree and shrub species to an extreme heatwave using functional traits, finding that crown dieback better predicts thermal stress than survival.

Regularized logistic regression-based gene selection for functional analysis of heterogeneous scRNA-seq macrophage populations in muscle aging and regeneration.

The paper introduces DisTwiner, a method for subgroup-aware gene selection in scRNA-seq data, showing it captures biologically relevant aging pathways in macrophages.

Characterizing features of Kv channel activation currents by a minimal-state kinetic model

This paper introduces a minimal-state kinetic model to compare Kv channel activation currents by simplifying complex kinetic schemes and capturing essential features with few parameters.

BenchMHC: a reproducible framework for peptide-MHC presentation prediction

BenchMHC reproduces and evaluates pMHC presentation models using public data, showing improvements in prediction accuracy and speed.

The self-sufficient Aspergillus fumigatus Δ9-fatty acid desaturase SdeA requires a fused cytochrome b5 domain and hinge-dependent self-association for virulence

Pervasive short hairpin folding in non-encapsidated RNA viruses

The paper identifies pervasive short hairpin RNA structures in non-encapsidated viruses and shows their association with structural constraints and evolutionary origins.

Disease-associated NK-cell state remodeling reveals transcriptional profiles predictive of clinical phenotypes

The paper establishes the Human NK-cell Atlas and identifies disease-specific NK-cell state remodeling, developing a model to predict clinical phenotypes.

Xenograft supervision and joint methylation-fragment-end encoding define a reusable molecular scoring layer for cell-free tumor DNA

ctDNA-BERT scores individual bisulfite reads for cell-free DNA methylation analysis, achieving high accuracy in cancer staging without cohort-specific retraining.

ProtCell: a foundation model for single-cell proteomics

ProtCell connects fragmented proteomic profiles, extends information beyond measured panels, and guides more informative measurements.

Autonomous sampling and eDNA metabarcoding for offshore biodiversity monitoring: a pilot study around an FPSO in the Southwestern Atlantic

This paper evaluates autonomous eDNA metabarcoding for offshore biodiversity monitoring around an FPSO, finding that repeated sampling is needed to distinguish transient from persistent patterns.

Mixtures of stably coexisting species overyield

In generalized Lotka–Volterra communities, stable coexistence almost always requires overyielding; in four long-term biodiversity experiments, underyielding raised species-loss odds within two observations (pooled odds ratio 2.61).

Benchmarking Large Language Models for Transcriptomic Data Analysis and Visualization: Multi-Model Workflow Evaluation

This study benchmarks large language models for automated transcriptomic data analysis and visualization workflows, finding that prompt specificity improves code quality but performance varies with preprocessing and environment.

Ambient light color does not detectably change the transient, flight-specific DEET response of Aedes aegypti

The study reanalyzes mosquito flight data to show DEET's transient repellent effect is not influenced by ambient light color.

Beyond Delta Masses: MS Andrea Directly Resolves Combinatorial Peptide Modifications in Open Searches

MS Andrea, a tag-filtered open search engine, scores and localizes up to four Unimod modifications per peptide-spectrum match, with identification counts competitive with MSFragger and Sage.

Neuroline: an integrated modular pipeline for FAIR multimodal neurophysiology data processing

Neuroline integrates multimodal neurophysiology data into a standardized format, enabling FAIR data sharing and cross-modal analysis.

Choosing a lipid force field for membrane remodeling: pore formation and membrane mimetics in CHARMM36, AMBER Lipid21 and Slipids

This study compares three lipid force fields for membrane remodeling using molecular dynamics simulations, finding differences in pore formation and stability under enhanced sampling methods.

Fragile streak goals induce pressure responses and an inverted-U performance pattern

This paper induces pressure through a fragile streak goal in a force-control task, showing an inverted-U performance pattern and increased physiological responses, but no consistent group-level signatures of pressure effects.

Simplifying complexity: the reliability of lidar-derived forest structural complexity metrics for conservation management

This study evaluates how resolution choices affect lidar-derived forest structural complexity metrics and their ecological interpretations in conservation management.

CBX3 Deletion Overcomes Ferroptosis Resistance in Colorectal Cancer by Targeting IFNγ/SLC7A11/SLC3A2 Axis

This study shows that CBX3 deletion increases ROS and lipid ROS levels in CRC cells, sensitizing them to ferroptosis by disrupting the IFNγ/SLC7A11/SLC3A2 axis.

A maximum entropy model for m6A prediction: from human transcripts to influenza A viral segments

The paper introduces MEMAR, a Maximum Entropy model for predicting m6A methylation in human transcripts and influenza A viral segments, showing improved performance over existing methods.

RNA-SpecFlow: RNA-Conditioned Spectral Flow for Histology Synthesis

RNA-SpecFlow synthesizes histology images conditioned on RNA data, showing that increased detection counts can coincide with reduced segmentation agreement.

Taxon-in-context reveals ecological individuality in the human gut microbiome

The paper introduces taxon-in-context to capture individualized microbial context in the human gut microbiome, showing that microbes occupy different contexts across individuals and over time, improving recurrence prediction.