benchmarking

MIEN: a deep-learning model for pocket-conditioned glycan pose and conformation discrimination

MIEN improves glycan pose ranking by distinguishing experimentally observed conformations from non-native ones in protein-carbohydrate interactions.

Determinants of cysteine coverage by chemoproteomics

This study identifies factors governing cysteine detection in chemoproteomics using machine learning and statistical filtering, showing that peptide properties and abundance are key determinants.

Identifying and ranking species that need urgent management action to achieve Target 4 of the Global Biodiversity Framework

This paper presents a protocol to identify and rank species needing urgent management action for Target 4 of the Global Biodiversity Framework using IUCN Red List data.

Structural order emerges without mechanical order inside living cells

The paper investigates intracellular mechanical properties and structural organization in RPE1 cells, finding no significant spatial mechanical patterns or correlations between structures and mechanical properties.

Auditing Confidence-Calibrated Benchmarking of Single-Cell Perturbation Models

The paper audits a benchmarking framework for single-cell perturbation models, revealing flaws in metric interpretation and calibration, and identifies a specific calibration failure in split-conformal prediction.

Hemodynamic-Structural Multi-Fidelity Assessment of Endovascular Flow Diversion Strategies for Cerebral Aneurysm Treatment: An Integrated Computational and Experimental Framework

The paper evaluates hemodynamic and structural outcomes of endovascular flow diversion strategies for cerebral aneurysms using computational models and experimental tests.

Predicting Lifespan-Extending Compounds Using Supervised Machine Learning

This study uses supervised machine learning to predict lifespan-extending compounds in C. elegans by comparing different feature representations and models.

CROSS-PLATFORM CONCORDANCE ANALYSIS REVEALS ROBUST AND CLINICALLY RELEVANT GENE SIGNATURES IN BREAST CANCER

The paper identifies robust and clinically relevant gene signatures in breast cancer by integrating two RNA-seq workflows and validating them across multiple datasets and analyses.

A synthetic MALDI-TOF MS atlas for microbial classification across hospitals

The paper creates a synthetic MALDI-TOF MS atlas to improve microbial classification across hospitals by addressing dataset fragmentation and variability.

Understanding genetic and environmental complexity in phenotypic resemblance across relatedness in population-scale data

The paper evaluates non-linearities in phenotypic similarity versus genetic relatedness by analyzing three processes: imperfect tagging, assortative mating, and shared environments, using UK Biobank and All of Us data.

Entering and Exiting Awareness are Asymmetrical: Evidence from tracking Continuous Flash Suppression

This paper introduces a mathematical model to correct for reaction-time-induced overshoot in continuous flash suppression paradigms, revealing asymmetry in thresholds for entering and exiting awareness.

RDEmbed: A Sentence-Embedding Framework for Rare Disease Phenotype Representation and Phenotypic Similarity Analysis

RDEmbed uses sentence embeddings to analyze rare disease phenotypes from clinical text, outperforming ontology-based methods in similarity analysis and clustering.

New whole slide image analysis method for detection and quantification of hepatocellular vacuolization in European flounder (Platichthys flesus) in multipollutant exposure context

The paper develops a new whole slide image analysis method to detect and quantify hepatocellular vacuolization in European flounder exposed to multiple pollutants, showing significant differences between polluted and control sites.

Establishing toxicologically relevant primary alveolar macrophage models to enable a realistic assessment of nanomaterials safety

The paper evaluates six alveolar macrophage models to identify those best representing in vivo AMs for assessing nanomaterial toxicity, finding AMs GTR and BM-AMs most suitable.

Stain Normalisation Does Not Consistently Improve Matched-Location Retrieval with Pathology Foundation Models

This study tests if stain normalization improves retrieval with pathology foundation models, finding no consistent benefit and potential harm from Macenko normalization.

Private forest reserves in Brazils agricultural landscapes effectively sustain the occupancy and abundance of multiple threatened large vertebrate

This study evaluates how private forest reserves in Brazil's agricultural landscapes affect the occupancy and abundance of threatened large vertebrates, finding that higher forest cover correlates with increased species presence.

On Motivating the Choice of Link Function in Binomial Regression Through A Latent Abundance Process

This paper introduces a framework for choosing link functions in binomial regression based on latent abundance processes, proposing a new generalized complementary log-log link for overdispersed counts.

Pareto fronts reveal constraints on the evolution of ecological niches

The paper uses Pareto fronts to detect evolutionary constraints on niche-determining traits in phytoplankton, showing that trade-offs persist across scales despite differing evolutionary outcomes.

Modeling Paralinguistic Features for Speech Neuroprostheses: A Systematic Review

This paper reviews research on integrating paralinguistic features into speech neuroprostheses to enhance emotional and expressive communication.

Sample overlap in genome-wide association meta-analysis: practical comparisons across significance thresholds

The paper evaluates the impact of sample overlap in GWAS meta-analysis across different significance thresholds and shows minimal impact when overlap is small.

Latent-Factor Stability Is Not Sufficient: Evaluating SABLE-MO in Simulated and Cancer Multi-Omics Data

The paper evaluates SABLE-MO's performance in identifying shared factors in multi-omics data, finding that stricter retention reduces errors but does not eliminate them.

Distinct activation mechanisms underlie ligand efficacy at a GPCR

This study uses deep mutational pharmacology to show how different residues in the -opioid receptor determine the efficacy of opioids by shaping distinct activation mechanisms.

Metalink: Joint taxonomic and functional profiling of metagenomes and metatranscriptomes across resolution scales

Metalink integrates taxonomic and functional profiling across resolution scales in metagenomes and metatranscriptomes, improving accuracy and enabling mechanistic insights.

Multi-parametric spectral modeling disentangles synaptic kinetics and neural excitability from non-invasive electrophysiological recordings

This paper introduces a multi-parametric spectral analysis to disentangle neural excitability and synaptic kinetics from non-invasive electrophysiological recordings, showing its ability to detect Alzheimer's disease signatures.

Sequence-dependent conformational and mechanical landscapes of double-stranded nucleic acids

This study introduces cgNA+, a model predicting sequence-dependent mechanical properties of dsNAs with high accuracy, revealing hidden regulatory layers in nucleic acid mechanics.

Exposure to childhood adversity and adult alcohol, nicotine, and illicit drug use in Germany: a cross-sectional analysis of the German National Cohort (NAKO)

This study examines the association between childhood adversity and adult substance use in Germany, finding stronger links with opioid and stimulant use and identifying distinct substance use profiles.

Scalable Enzyme Reaction Retrieval Enables Metagenomic Biocatalyst Discovery

EzHit retrieves enzyme-reaction associations efficiently, outperforming baselines and enabling large-scale metagenomic biocatalyst discovery.

Benchmarking the AlphaGenome Variant Impact score against SpliceAI on post-release ClinVar classifications and experimental splicing assays

This paper benchmarks the AlphaGenome Variant Impact score against SpliceAI on post-release ClinVar classifications and experimental splicing assays, finding AVI performs well but not outperforms splicing predictors on AUROC.

Stepwise Proteinase K Digestion Improves Genomic DNA Yield and Purity from Goat Semen: A Comparative Pilot Study of Five Extraction Protocols

This study compares five DNA extraction protocols from goat semen, finding that Modified Protocol 2 provides the highest DNA yield, purity, and PCR success.

Source-Decomposed Multimodal Graph Connectivity: A Temporal Mixture-Manifold Pipeline for Tracking Ischemic Injury and Treatment

This paper introduces a multimodal graph connectivity framework to track ischemic injury and treatment in non-human primates using resting state fMRI and DTI, revealing significant connectivity disruptions and enabling early detection of metabolic collapse.