benchmark study

Which pLM to choose?

This study benchmarks fourteen protein-language models (pLMs) to determine which best captures biological properties, finding that mid-scale models often outperform larger ones for general tasks.

Development of self-phenotyping tools to empower patients and improve diagnostics

The paper evaluates two self-phenotyping tools, showing that GenomeConnect provides more accurate phenotype profiles while Phenotypr offers greater precision and user preference for its autocomplete format.

Assessment of Nucleic Acid Structure Prediction in CASP16

Across 42 CASP16 nucleic acid targets, accuracy stayed tied to template availability; human experts (Vfold first) led servers and AlphaFold 3, though servers now improve on templates on average.

Orchestrating Microbiome Analysis with Bioconductor

The paper introduces an open-source ecosystem for microbiome data science using Bioconductor, supporting modular workflows for analyzing complex, multi-modal datasets.

3D Structure-based Generative Small Molecule Drug Design: Are We There Yet?

This paper introduces two metrics to evaluate the chemical plausibility of molecules generated by structure-based generative algorithms and compares them to virtual screening hits for three protein targets.

A structured evaluation and benchmarking of Boolean logical modelling tools

This paper evaluates 20 Boolean modelling tools for signal transduction and gene regulatory networks using FAIR4RS and usability criteria, finding significant variation in functionality and simulation capabilities.

Benchmarking large-scale single-cell RNA-seq analysis

This paper benchmarks five scRNA-seq analysis frameworks on scalability, efficiency, and accuracy using large and small datasets, finding GPU acceleration and optimized algorithms improve performance.

Benchmarking Cell Type and Gene Set Annotation by Large Language Models with AnnDictionary

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

An integrative review of the impact of ungulates on wetland carbon storage and greenhouse gas emissions

This study reviews how ungulates affect wetland carbon storage and greenhouse gas emissions, finding reduced carbon stocks and higher emissions with ungulate presence.

Synergies and trade-offs between maintaining climate niche variability and preserving climate stability

This study identifies spatial priorities for protecting climatic niche variability and stability in European vertebrates, finding overlaps and trade-offs between conservation strategies.

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

High-throughput plasma proteomic platforms: Insights from a multi-ethnic Asian cohort

The paper compares three proteomic platforms in a multi-ethnic Asian cohort, finding limited overlap, platform-specific performance metrics, and ethnicity-related protein differences.

Uncovering novel therapeutics for schizophrenia: a multitarget approach using the CANDO platform

This paper uses the CANDO platform to identify repurposable drugs for schizophrenia, finding 25 high-corroboration candidates with validated targets and biological relevance.

A database of biological thermal performances

The paper constructs a database of thermal performance curves for species across multiple domains, enabling ecological predictions and integration with environmental data.

Comparative Performance of Scribe and Database Search Engines in Metaproteomic Profiling of a Ground-Truth Microbiome Dataset

This study compares Scribe and database search engines in metaproteomic analysis of a ground-truth microbiome dataset, finding Scribe detects more proteins and quantifies microbial composition more accurately.

GWASHub: An Automated Cloud-Based Platform for Genome-Wide Association Study Meta-Analysis

GWASHub is a cloud-based platform for GWAS meta-analysis that automates data handling, QC, and analysis workflows to improve reproducibility and reduce researcher burden.

An optimized variant prioritization process for rare disease diagnostics: recommendations for Exomiser and Genomiser

This paper optimizes variant prioritization parameters for Exomiser and Genomiser to improve diagnostic yield in rare disease cases using WES and WGS data.

The human neuroblastoma SH-SY5Y cell line as a model to assess β-amyloid neurotoxicity: A systematic review and meta-analysis

This paper reviews and analyzes 359 studies on β-amyloid toxicity in SH-SY5Y cells, finding that toxicity depends on Aβ concentration, exposure time, and aggregation state, not cell differentiation.

Advancing Protein Ensemble Predictions Across the Order-Disorder Continuum

The paper introduces a benchmark for evaluating protein ensemble generators across ordered and disordered proteins and presents a new model that improves performance on disordered regions.

Systematic review of biodiversity monitoring shows gradual rise of scaleable and automated methods and inherent spatial and taxonomic biases

This paper reviews biodiversity monitoring methods over 22 years, finding increasing use of scalable techniques but persistent spatial and taxonomic biases.

Recommendations for Bioinformatics in Clinical Practice

This paper provides consensus recommendations for standardizing bioinformatics practices in clinical whole genome sequencing to ensure accuracy, reproducibility, and comparability of results.

Cell-Type-Specific Transcriptomic Signatures in Prefrontal Cortex Reveal lncRNA-mediated Gene Silencing and Enhancer Activities Contributing to the Pathophysiology of Major Depressive Disorder

The paper identifies cell-type-specific lncRNA-mediated gene silencing and enhancer activities in MDD, linking them to disrupted neuron-glia interactions and Hippo signaling.

TranslAGE: A Comprehensive Platform for Systematic Validation of Epigenetic Aging Biomarkers

TranslAGE provides a standardized framework for benchmarking epigenetic aging biomarkers by harmonizing datasets and precomputing scores across multiple performance domains.

LabOS: The AI-XR Co-Scientist That Sees and Works With Humans

LabOS is an AI co-scientist that integrates computational reasoning with physical experimentation through multimodal perception and human-AI collaboration, enhancing scientific discovery in biomedical and materials science.

The Taiwan Precision Medicine Initiative: A Cohort for Large-Scale Studies

The Taiwan Precision Medicine Initiative (TPMI) recruits a large cohort for genetic and electronic medical record studies to advance precision medicine.

Single-cell exploration of ovarian aging across mammalian models

This study analyzes ovarian aging across species using single-cell RNA-seq data to identify conserved and species-specific features and suggests drug repurposing candidates.

AniMarkerDB: a comprehensive database for exploring cell types and marker genes in livestock and poultry at single-cell resolution

AniMarkerDB provides a curated database of marker genes and immune epitopes for livestock and poultry, enabling cross-species analysis and applications in immunology and disease research.

Systematic Review of Over A Century of Global Bioscience Research

This study reviews over a century of bioscience research trends using bibliometric analysis, finding exponential growth since 2007 and dominance by high-income countries.

Assessing scoring metrics for AlphaFold2 and AlphaFold3 protein complex predictions

This study evaluates scoring metrics for AlphaFold2 and AlphaFold3 protein complex predictions, finding that interface-specific scores like ipTM and model confidence are most reliable, and introduces a new combined score, C2Qscore, to improve assessment.

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.