benchmarking

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 mast cell receptor is associated with fibrosis and itch in systemic sclerosis

This study identifies Mrgprb2 as a mast cell receptor involved in fibrosis and itch in systemic sclerosis using a mouse model and human tissue analysis.

Systematic benchmark of demultiplexing workflows for direct RNA sequencing

This study benchmarks two demultiplexing tools for direct RNA sequencing using IVT spike-ins and species identity, showing their performance differences and the need for calibration.

Winnow-tax: sensitive and precise taxonomic profiling of low-coverage organisms in shotgun metagenomes

Winnow-tax improves taxonomic profiling of low-coverage shotgun metagenomes by combining sensitive read-level classification with genome-level confirmation, achieving better precision-sensitivity balance than existing methods.

The CAHRA Challenge: A Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms

The paper introduces the CAHRA Challenge, a community-wide assessment of cryo-EM heterogeneous reconstruction algorithms using three benchmark datasets.

Fecal Contributors to an Urbanized Estuary Identified by a Multi-Species qPCR Approach

This study uses multi-species qPCR to identify human and animal fecal sources in Mobile Bay, finding human waste as a major contributor.

onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation

The paper introduces onsite, a framework for estimating false localization rates in phosphoproteomics, showing pyLucXor achieves high accuracy and localization count.

Autofocusing molecular simulations for integrative structural biology of broad conformational ensembles

This paper introduces autofocusing, a method that improves molecular simulations by integrating experimental data, demonstrating its effectiveness for phospholipid bilayers.

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.

Single-molecule reaction chambers reveal intramolecular protein kinase activation

The paper demonstrates that protein kinases can undergo intramolecular autophosphorylation using single-molecule reaction chambers, challenging the conventional view of intermolecular activation.

Performance comparison of probe-capture enrichment sequencing of viruses in wastewater influent and settled solids from the California Central Valley

The paper compares two viral sequencing pipelines from wastewater influent and solids, finding that solids capture more DNA viruses while influent captures more RNA viruses, with probe-capture enrichment providing comparable results across fractions.

Soil invertebrate biomass estimation from image-derived body area and contour length

This paper develops a framework to estimate soil invertebrate biomass using image-derived body area and contour length, showing good predictive performance across taxa and community scales.

Cheese adaptation beyond Penicillium: contrasting genomic trajectories in the distantly related Nectriaceae molds

This study compares genomic adaptations of cheese-associated Nectriaceae fungi, revealing contrasting evolutionary paths involving gene family expansions, reductions, and horizontal gene transfer.

GRASS-MIL: graph-based representation and discovery of phenotype-associated spatial structures with multiple instance learning

GRASS-MIL predicts phenotypes from spatial single-cell data and decomposes predictions into specific cellular neighborhoods, showing improved performance over composition-based methods.

Certified Design Regions under Parametric Plant Uncertainty with Application to Antithetic Integral Feedback

The paper develops a method to compute certified design regions for robust controller tuning under parametric plant uncertainty, demonstrating improved certification rates using tensor-product Bernstein enclosures.

How does explicit reliability guide choices? Effect of trustworthiness on choice and metacognition

The paper investigates how people use explicit reliability markers in decision-making and find they overestimate source reliability and are influenced by unreliable sources.

Systematic evaluation of integration methods and parameters on single-cell RNA-sequencing biological insights: a case study on cattle embryos.

The paper evaluates integration methods and parameters on cattle embryos to assess their impact on biological insights, finding that parameter choices affect cell type classification and functional interpretation.

Scalable localization of clustering instability for spatial transcriptomics

InSTability identifies seed-sensitive clustering regions in spatial transcriptomics data, revealing instability patterns and their impact on downstream analyses.

JEPA-SORT: World-Model Embeddings Improve Deep-Sea Multi-Object Tracking on Visually Homogeneous Fauna

JEPA-SORT improves deep-sea multi-object tracking by using world-model embeddings to maintain stable identities on visually homogeneous fauna, outperforming standard MOT algorithms in IDF1, MOTA, and BDU.

Probing Genomic Foundation Models with Splice-Variant Perturbations

This paper evaluates genomic foundation models using splice-variant perturbations, finding they match task-specific networks and generalize across mutation types.

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.

sRQA: AN INTEGRATIVE PIPELINE FOR SYMBOLIC RECURRENCE QUANTIFICATION ANALYSIS

The paper introduces sRQA, a software package for symbolic recurrence quantification analysis, validated on simulated and real-world data across multiple domains.

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.

Cerberus: bidirectional state space blocks improve accuracy and efficiency of regulatory sequence models

The paper introduces Cerberus, an improved regulatory sequence model using bidirectional state space blocks, achieving higher accuracy and efficiency than existing models like Borzoi.

Assessing fish biodiversity and community structure in the Ganjiang River using eDNA metabarcoding

This study uses eDNA metabarcoding to assess fish biodiversity and community structure in the Ganjiang River, revealing seasonal and spatial variations influenced by hydropower dams.

Inferring seagrass meadow resilience from self-organized spatial patterns

The paper uses synthetic data generated from a mechanistic model to train deep learning networks that classify seagrass meadow resilience from spatial patterns, showing effective generalization to real-world data.

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

Frustration Quenching and Network Topology of the Energy Landscape as Primary Determinants of Protein-Ligand Binding Pose Prediction by Deep Learning Models

This paper shows that deep learning models' performance in predicting protein-ligand binding poses depends on the energy landscape's frustration quenching and network topology, not algorithmic flaws.

User-friendly software for high-throughput processing of chlorophyll fluorescence images to assess plant stress responses: fvfmPy and fvfmR packages

The paper introduces fvfmPy and fvfmR, user-friendly tools for automated analysis of chlorophyll fluorescence images to assess plant stress responses, significantly reducing processing time compared to manual methods.

Comparative performance of reference-based metagenomic tools to identify species-level taxa among families of bacteria: benchmarking Mycobacteriaceae and Neisseriaceae

This study benchmarks reference-based metagenomic tools for species-level detection in closely related bacterial families, finding metapresence and sylph perform best.