benchmark study

Network Analysis of Rare Single-Nucleotide Polymorphisms Suggests a Central Role for Type 17 Immune Responses in Trauma-induced, Genotypically Associated Hypo-Inflammation and Critical Illness

The paper identifies rare SNPs associated with hypo-inflammation and adverse outcomes in trauma patients, highlighting type 17 immune responses as central to critical illness.

Benchmarking and Experimental Validation of Machine Learning Strategies for Enzyme Engineering

This study benchmarks machine learning models for enzyme engineering using a curated dataset, finding zero-shot predictors are most generalizable but still modestly correlated with activity, with consensus models improving precision.

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.

A Systematic Review of the Impacts of El Nino-Driven Drought, Fire, and Smoke on Non-Human Primates in Southeast Asia

This paper reviews the impacts of El Nino-driven drought, fire, and smoke on non-human primates in Southeast Asia, finding habitat loss and smoke exposure affect primate behavior and health, with some recovery observed after forest regeneration.

Systematic mapping shows monitoring, evaluation, and engagement are needed to build an evidence base for rewilding

This paper systematically maps monitoring and evaluation practices in rewilding case studies, identifying challenges in data standardization and collaboration to improve evidence-based rewilding.

vardictcpp: A C++ reimplementation of VarDict variant caller

An AI-assisted C++17 port of VarDictJava gives byte-identical calls on five exome samples while running 3.7-4.8 times faster on one core and needing 8-17 times less memory.

Large scale prospective evaluation of co-folding across hundreds of Mac1-ligand complexes and three virtual screens

On 489 evaluable new Mac1 complexes, AlphaFold3, Chai-1 and Boltz-2 placed over half of ligands within 2 Å, but on docking hit-lists AF3 and Boltz-2 added little over docking.

AlphaFold3 and Intrinsically Disordered Proteins: Reliable Monomer Prediction, Unpredictable Multimer Performance

AlphaFold3 pLDDT matches AlphaFold2 at calling disordered residues (Matthews correlation 0.693 vs 0.701); on disorder-containing complexes mean DockQ is similar, but interface features explain less variance (42% vs 58%).

TurbOmics: a web-based platform for the analysis of metabolomics data using a multi-omics integrative approach

TurbOmics is a web-based platform that enables multi-omics integration of metabolomics, proteomics, and transcriptomics data, addressing limitations in metabolomics annotation and accessibility.

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.

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.

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.

Profiling peripheral immune cells in Parkinsons disease: A Scoping Review

This review synthesizes findings on peripheral immune cell changes in Parkinson's disease, identifying common immune signatures and methodological inconsistencies across studies.

Characterizing and Mitigating Protocol-Dependent Gene Expression Bias in 3' and 5' Single-Cell RNA Sequencing

This study identifies and mitigates protocol-dependent gene expression bias between 3' and 5' scRNA-seq by focusing on a small set of biased genes rather than applying broad normalization.

Registered Report: Replication and Extension of Nozaradan, Peretz, Missal and Mouraux (2011)

This study replicates Nozaradan et al.'s 2011 findings on neural activity during imagined beat perception, finding smaller effect sizes and no reliable replication of main effects.

When to Trust Epigenetic Clocks: Avoiding False Positives in Aging Interventions.

This study evaluates epigenetic clocks for aging interventions, finding newer clocks trained on mortality or aging rates are more reliable than those based on chronological age.

The ambiguity of "hybrid swarm": inconsistent definitions and applications in existing research

This paper reviews the inconsistent use of the term 'hybrid swarm' in hybridization studies and advocates for clearer terminology.

Inferring binding specificities of human transcription factors with the wisdom of crowds

The paper benchmarks methods for inferring transcription factor binding specificities using a large community challenge and finds deep learning models outperform traditional methods, though positional weight matrices are competitive.

Misleading inference of schistosome epidemiology from ribosomal internal transcribed spacer (ITS) and mitochondrial DNA

Whole-genome SNVs from Nigerian schistosomes show cox1/ITS genotyping wrongly flags human-derived parasites as recent hybrids or zoonotic infections; they are S. haematobium with low livestock introgression.

GROMTools: scalable individual-level GReX imputation for mega-biobank-scale cohorts

GROMTools, a sparse-weight C++/R engine streaming PLINK2 genotypes, reproduces PrediXcan and PLINK2 GReX imputations with about 100-fold less CPU time and 33-fold less peak memory.

PEtab Select: specification standard and supporting software for automated model selection

PEtab Select provides a standardized format and software for automated model selection in systems biology, supporting diverse modeling frameworks and enabling efficient evaluation of large model spaces.

Serval: A modular framework for decoding imaging based spatial transcriptomics data

Serval is a modular framework for decoding spatial transcriptomics data that introduces Cosine, a method improving transcript recovery and correlation with expression references.

Open-access template and database approaches for pseudo-CT generation in brain PET/MRI attenuation correction

The paper presents an open-access framework for PET attenuation correction using pseudo-CT methods with a database of MRI-CT scans, showing that UCL achieves the lowest quantification error.

BenchHub enables an inclusive and transparent ecosystem for community-focused benchmarking in computational biology

BenchHub provides a modular ecosystem for community-focused benchmarking in computational biology by linking datasets, metrics, and ground truth to improve reproducibility and sustainability.

A Systematic Comparison of Single-Cell Perturbation Response Prediction Models

The paper benchmarks 13 models for predicting single-cell perturbation responses across 25 datasets, finding performance varies with perturbation effect size and evaluation metric.

Building an open infrastructure for molecular neuroimaging: standards and tools from the OpenNeuroPET initiative

The paper describes the OpenNeuroPET initiative, which develops standards and open-source tools to standardize and share PET neuroimaging data, enhancing reproducibility and collaboration.

A metadata managed FAIR end-to-end workflow for microbial community Omics data analysis

The paper presents a metadata-managed FAIR end-to-end workflow for microbial community Omics data analysis, demonstrating its reliability and reproducibility through mock datasets.

The effect of psychedelics on associative learning: a systematic review

This systematic review examines the effects of psychedelics on associative learning in humans and animals, finding enhanced learning in animals but inconsistent results and methodological heterogeneity.

Stoichiometry-dependent specificity in biotin enrichment: a benchmarking framework for proximity labeling proteomics

The paper benchmarks biotin enrichment in proximity labeling proteomics, showing that higher biotinylation improves specificity while lower levels increase background noise.

Exploring the feasibility, acceptability and impact of genomic newborn screening for rare diseases in England: A study protocol for the Generation Study - Process and Impact Evaluation