benchmarking

Benchmarking Statistical Methods for Differential Composition Analysis in Population-Scale Single-Cell Data

This study benchmarks 12 methods for differential composition analysis in scRNA-seq data, finding LOCOM performs best in controlling false discovery rate and maintaining power.

OncoSpot enables benchmarking of cancer spatial transcriptomics methods across tumor evolutionary modes

OncoSpot benchmarks cancer spatial transcriptomics methods across tumor evolutionary modes by simulating realistic cancer data with known subclonal and copy-number features.

European LD proxies lose tagging for 43% of GWAS leads in the African panel: a chromosome 22 analysis with SwiftLD, an 826-fold faster, byte-identical vcftools LD

SwiftLD, a faster alternative to vcftools for computing LD, shows European LD proxies poorly tag 43% of GWAS leads in African populations.

Dated public evidence and known genes for retrospective evaluation of gene prioritization

The paper provides per-gene evidence tables from public resources for retrospective gene prioritization, including dates and leakage risk grades for four disease areas.

Transportability of mouse gene knockout models to human complex phenotypes

The paper assesses the transportability of mouse gene knockout models to human complex phenotypes using GPAT framework, finding evidence for 12 phenotypes but limited for others.

TIGRdisco: a tool for the discovery of TIGR arrays and TIGR-associated Tas proteins from nucleotide sequences

TIGRdisco identifies TIGR arrays and Tas proteins from nucleotide sequences, recovering most array units and uncovering unannotated loci across datasets.

Age-specific pediatric templates improve EEG source-reconstructed biomarkers in children

This study compares age-specific pediatric EEG templates to adult templates and finds they better match individual MRI-based biomarkers in children up to 12 years old.

Polymerase and primer biases in eukaryote ultra-long-read metabarcoding

This study evaluates polymerase and primer biases in ultra-long-read metabarcoding for soil eukaryotes, finding that certain polymerases and primer pairs improve data quality and biodiversity recovery.

GPBench: A benchmark framework for genomic prediction

GPBench provides a standardized benchmark framework for genomic prediction, evaluating 21 models across 16 species and offering tools for analysis and comparison.

NBDC Data Tools: Building Analysis-ready Datasets From ABCD and HBCD Releases in R and Python

NBDC Data Tools automate dataset preparation from ABCD and HBCD releases, enabling reproducible and reusable analysis workflows in R and Python.

AlphaFold 3 Prediction Accuracy and Reliability across RNA Structures and Protein-RNA Interfaces

This study evaluates AlphaFold 3's accuracy and reliability in predicting RNA structures and protein-RNA interfaces, finding that confidence scores do not always correlate with correct predictions.

Auditing Biomedical Literature with Blinded AI Peer Review: Where Peer Review Works, Where It Fails, and How to Strengthen It

This paper evaluates the effectiveness of a blinded AI peer review system (BARS) in auditing biomedical literature, finding it improves consistency and detects flaws while highlighting issues with megajournals and template studies.

Hazard Structure and Repair Kinetics: A 2x2 Classification that Resolves the Stochastic-Death / Individual-Tolerance Dilemma

The paper classifies hazard structures in toxicology models and identifies peak-based hazard as the appropriate default for certain toxicants.

Decision benchmarking of cryo-EM re-refinement

The paper benchmarks cryo-EM re-refinement selection methods against no operation using a fixed cohort and scoring tools, finding increased disagreement with higher-resolution references.

TensorPLS: an R package for exploring molecular and temporal patterns in longitudinal omics data using PLS-DA

TensorPLS is an R package for analyzing longitudinal omics data using PLS-DA, handling missing data and providing temporal insights through VIP scores and cross-validation.

An end-to-end in silico framework for truth-based validation and regression testing of clinical genome sequencing pipelines, from simulated reads to reportable findings

This paper introduces an end-to-end in silico framework to validate and test clinical genome sequencing pipelines from simulated reads to reportable findings using a fixed truth set.

Optimiser Repairs for Living-Cell Self-Driving Laboratories: Performance and Redundancy under Experimental Constraints

This paper evaluates optimiser repairs in living-cell self-driving labs, showing when they improve performance and when constraints make them redundant.

SPaRTA: Spatial Reasoning in Text-to-SQL for Omics Analysis

SPaRTA enables non-experts to query spatial-omics data via natural language, achieving 63-77% accuracy with fine-tuning on cancer tissue datasets.

Error-Controlled Discovery of Protein Interactions via Conformal Calibration

PPI-Caliper controls false discovery rate in protein interaction prediction using conformal calibration without retraining models.

Atmospheric pollution contributed to destabilizing a small mammal community amid four decades of environmental changes

The paper uses Empirical Dynamic Modelling to show atmospheric pollution destabilized a small mammal community over 39 years in the Black Triangle of Europe.

Autonomous generalizability auditing of scientific foundation models

This paper introduces AutoSPECTRA, a protocol for auditing generalizability of scientific foundation models across biological domains.

Steering Before Selection: Energy-Limited Developmental Control as a Phenotypic Capacitor, a Pre-Specified Simulation Study

This paper uses simulations to show that developmental control conceals genetic variation from selection, acting as an energy-dependent phenotypic capacitor that can be beneficial if harmful mutations are reversed.

Model-Agnostic Decomposition of the Difference in Mean Response Between Two Groups via Game-Theoretic Attribution with Minimum-Switching-Distortion Coupling

This paper introduces a model-agnostic decomposition method to analyze differences in mean response between groups, using game-theoretic attribution and optimal transport coupling.

Contributions of Site Heterogeneity in Multi-site Brain-Phenotype Predictions

This paper evaluates how site heterogeneity affects brain-phenotype predictions in multi-site data, finding that larger sample sizes improve accuracy more than multi-site composition.

Peptorama: Structure creation and exploratory data analysis for non-ribosomal peptides

Peptorama provides tools for creating and analyzing non-ribosomal peptide structures, enabling efficient comparison of known and predicted peptides to aid in biodiscovery.

Rho: A Purpose-Driven Workspace for Human-AI Collaborative Analysis

Rho is a collaborative analysis environment that organizes materials by scientific purpose to support human-AI judgment in bioinformatics.

HiFiTaxa: a reproducible analysis pipeline for full length 16S rRNA gene and ITS amplicon sequencing from PacBio reads

HiFiTaxa is a Nextflow pipeline for analyzing PacBio HiFi reads of 16S rRNA and ITS amplicons, offering multiple classifiers and benchmarking their performance on mock communities and holdouts.

Facilitating the identification of cryo-EM hit matter in drug discovery with Astex-Faro

Astex-Faro improves cryo-EM hit identification by detecting structural deviations and enhancing weak features across diverse datasets.

The Test Used to Choose Between Pesticide Survival Models Tracks Lesion Persistence, Not Hazard Structure

The paper evaluates pesticide survival models by analyzing lesion persistence, showing that post-exposure death rates better reflect hazard structure than peak-based assumptions.

BioTrajX: evaluating biological plausibility in single-cell trajectory inference

BioTrajX evaluates biological plausibility of single-cell trajectories using three metrics to compare different trajectory inference results.