benchmarking

Integrating Metabolic Networks into Hybrid Bioprocess Models

This paper introduces FBA-Hyb, a hybrid model integrating metabolic networks into bioprocess modeling, achieving higher predictive accuracy and stoichiometric consistency.

A NEST-based framework unlocks massively parallel simulation of networks of multicompartment neurons with customizable subcellular dynamics.

The paper introduces a framework for simulating multicompartment neurons with customizable subcellular dynamics using NEST and NESTML, enabling efficient and scalable network simulations.

Using SpliceAI to triage splice-altering variants in 7,220 individuals with rare conditions highlights limitations of the precomputed scores

The paper evaluates precomputed SpliceAI scores for splice-altering variant prioritization in NDD cohorts, finding inaccuracies and providing a tool to improve variant triage.

VenusGenome: Genome-Aware Masked Autoencoding for Microbial Genome Representation Learning

VenusGenome improves microbial genome representation learning by using a genome-aware masked autoencoder, achieving high performance in phenotype prediction and gene-level tasks.

Sound Advice: A calibration framework for defining detection space in Passive Acoustic Monitoring

This study quantifies how environmental factors and frequency affect signal detection in Passive Acoustic Monitoring using playback experiments in a tropical agroecosystem.

Mitigating Bias in Spatial Transcriptomic Pipelines via Human Feedback

The paper introduces CSDE, a method that improves differential expression analysis in spatial transcriptomics by incorporating expert feedback to mitigate preprocessing biases.

golgi: an open-source graphical platform for image-to-recruitment modeling of peripheral nerve stimulation

golgi provides an open-source platform for modeling peripheral nerve stimulation, enabling image-to-recruitment analysis with a graphical interface and reproducible results.

Quantifying epigenetic reprogramming and cellular plasticity in preneoplastic lesions reveals dedifferentiation as a key precancer hallmark

PLASTIC quantifies cellular plasticity and epigenetic reprogramming in preneoplastic lesions, revealing dedifferentiation as a key factor in cancer risk.

3D Histology Validates 2D Histology for Axon Radius Distributions and Conduction Velocities

The paper validates 2D histology for representing axon radius distributions and conduction velocities using 3D reconstructions of rat axons and applies this to human data.

Uneven research attention to biodiversity loss revealed by large language models

This paper uses large language models to analyze 2.4 million bibliographic records and identifies gaps in research attention to biodiversity loss across different ecological contexts.

Building virtual cell dynamics that evolve with biological measurements

CellCompass, an agentic AI system, models cell dynamics from single-cell measurements and improves predictions by integrating new biological constraints and experimental data.

Lost and found: beer belly is a novel, ancient regulator of animal development

The paper identifies a novel gene, beer belly, as a regulator of segmentation in spiders using single-cell RNA sequencing and shows its evolutionary loss in mammals and holometabolous insects.

Evaluation design shapes estimates of cross-donor generalization in single-cell classification of cell-type

The paper evaluates how different evaluation designs affect cross-donor generalization in single-cell cell-type classification and finds that random cell-level splitting overestimates performance compared to donor-held-out evaluation.

Asking the Data: Conversational Interrogation of LC-MS/MS Proteomics Data Sets with an LLM Agent

The paper introduces a conversational framework using an LLM agent to interrogate proteomics data sets, identifying issues in four LC-MS/MS datasets and demonstrating its feasibility in reanalyzing data.

How well does electrical source imaging reconstruct neural time series? Evidence from simultaneous scalp and intracranial EEG recordings

This study evaluates how well electrical source imaging reconstructs neural time series using simultaneous scalp and intracranial EEG recordings, finding limited temporal reconstruction and spatial leakage.

Best Practices for Pre-Processing Large-Scale ATAC-Seq Data: Why Epidemiological Studies Demand Greater Stringency

The paper introduces PIPPA, a pipeline for processing large-scale ATAC-seq data, showing that peak calling performance varies by dataset and recommending parameters for high-confidence chromatin accessibility profiles.

Extending Musculoskeletal Modelling Validation Beyond Gait: Knee Loading and Kinematics During Daily Activities

This study validates musculoskeletal models across daily activities, finding good agreement in knee forces but discrepancies in kinematics and EMG during stair descent.

Scalable hardware and software for high-density, multi-regional electrophysiology in non-human primates

The paper introduces MIND and UnitAssay for scalable, high-density, multi-regional electrophysiology in non-human primates, enabling stable recordings and reliable single-unit identification.

Variant effect predictors are shaping the ClinVar classifications used to train and evaluate them

The paper shows that variant effect predictors influence ClinVar classifications, creating circularity in variant classification and prediction.

BaSiCPy: Scalable and Robust Shading Correction for Optical Microscopy Images

BaSiCPy improves illumination correction in microscopy images by addressing foreground correlations and enabling automated processing.

Mimic: A Unified Neural Network Architecture for Modelling Genomic Sequences and Module-level Comparison

This paper introduces Mimic, a unified neural network architecture for genomic sequence modeling, showing it outperforms existing models in protein-DNA interactions and enhancer activity.

Computational Design and Evaluation of De Novo Protein Minibinders Targeting Specific Sites of STAT3

The paper designs and evaluates de novo protein minibinders targeting specific STAT3 sites using AI and AlphaFold3, identifying high-confidence binders with novel sequences.

Robustness of the inference of the distribution of fitness effects to selective sweeps

This study evaluates how selective sweeps affect DFE inference using fitdadi, finding that performance declines at low recombination rates and with unfolded SFS, but remains largely unbiased with a flexible demographic model.

Scaling a context-aware genomic model for condition-specific edit design in plants

CROP-1 predicts gene activity based on DNA sequence and regulatory state, enabling context-specific edit design in plants with higher accuracy than sequence-only models.

Characterization of heterogeneous bioinformatics training needs in the AI era

The paper introduces a network-based clustering method to identify distinct learner profiles from training-needs surveys, revealing heterogeneous bioinformatics training needs in the AI era.

Cornealia: automated collective order analysis reveals density-dependent reorganization of donor corneal endothelium

Cornealia analyzes collective order in donor corneal endothelium, revealing density-dependent reorganization and mechanical responses not captured by traditional metrics.

Open-Source, High-Speed and High-Resolution Data Acquisition Platform for Biopotential Recordings and Neural EIT applications

This paper develops an open-source biopotential recording system with performance comparable to high-end devices, validated through in-vivo and benchtop experiments.

Whole-brain normative modeling across multiple functional connectivity metrics in MEG

This paper introduces M/EEG-FUNCOIN, a normative modeling approach for whole-brain functional connectivity in MEG data, showing improved characterization of age and sex-related patterns and detection of connectivity deviations linked to cognitive ability.

Historical and Contemporary Management of Genetic Diversity in French Local Horse Breeds: Insights from Genomic Data

This study uses genomic data to analyze the genetic diversity and management history of French local horse breeds, showing distinct patterns of kinship and inbreeding linked to different management practices.

Quantification method affects replicability of eQTL analysis, colocalization, and TWAS

The paper shows that RNA-seq quantification methods and reference annotations significantly impact eQTL analysis, colocalization, and TWAS results across multiple tissues and phenotypes.