benchmark study

Systematic Survey of Public Datasets for Behavioral Research in Invertebrate Models: Toward FAIR and Standardized Data Sharing

The paper surveys public behavioral datasets for invertebrate models, evaluates their FAIR compliance, and provides guidance for standardized data sharing and AI benchmarking.

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

This study benchmarks six duplex sequencing technologies to evaluate their performance in detecting somatic mutations across different genomic contexts and tissue types.

DNA metabarcoding and environmental DNA across Brazilian biomes: trends, challenges, and conservation applications

This paper reviews DNA metabarcoding and eDNA applications in Brazilian biomes, highlighting trends, challenges, and the need for investment in infrastructure and collaboration.

Evaluation of the Ultima Genomics UG 100™ sequencing platform for clinical services

This paper evaluates the Ultima Genomics UG 100 sequencing platform's ability to identify short variants, particularly in long homopolymer regions, compared to Illumina NovaSeq 6000 for clinical use.

SEAL: Spatially-resolved Embedding Analysis with Linked Imaging Data

SEAL integrates spatial imaging context with dimensionality reduction embeddings to improve interpretation of complex datasets through interactive visualization and feature importance analysis.

A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing

The paper evaluates 47 highly variable gene selection methods for scRNA-seq across 19 datasets and finds hybrid methods outperform individual methods, proposing a new approach called mixHVG.

Evaluating the practical aspects and performance of commercial single-cell RNA sequencing technologies

This study compares commercial single-cell RNA sequencing platforms based on performance metrics and practical considerations.

TO BE OR NOT TO BE A PI: ADVICE FOR TRAINEES IN THE BIOMEDICAL/BASIC SCIENCES

The paper surveys PIs to provide insights into the PI career path, revealing mixed attitudes and the importance of luck alongside scientific skills.

Comparison of Interventional Causal Structure Learning Algorithms for Gene Regulatory Network Inference

This paper benchmarks causal structure learning algorithms for gene regulatory network inference using synthetic and CRISPR perturbation data, finding reliable performance on synthetic data but limitations on real data due to noise and scalability.

When Task-Specific Learning Outperforms Transfer Learning: A Benchmark of Gene and Expression Encoding Strategies

The paper benchmarks gene and expression encoding strategies in single-cell models, finding task-specific learning outperforms transfer learning from large protein models.

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Phold pairs ProstT5-predicted 3Di tokens with Foldseek searches against 1,363,704 curated phage structures, annotating 49.4% of CDS in 1,419 INPHARED genomes versus 34.7% for Pharokka MMseqs2.

FungiGutDB: Curated database for taxonomic assignment of the gut mycobiome by whole genome sequencing

FungiGutDB is a curated database for accurate gut mycobiome taxonomic assignment using whole genome sequencing, showing improved performance over standard databases in characterizing fungal communities in human microbiome studies.

starbase: A Database and Toolkit for Exploration of Extremely Large Mobile Elements in Fungi

The paper introduces starbase, a database and toolkit for exploring Starship mobile genetic elements in fungi, providing curated annotations and tools for classification and comparative analysis.

Large-scale quantitative benchmark reveals accuracy limits of proteomics

The paper benchmarks proteomics accuracy using a large-scale dataset, identifying systematic errors and providing a resource for method optimization and software evaluation.

Genetic Architecture of Circulating Metabolic Biomarkers Across Ancestral Populations

This study identifies genetic associations with metabolic biomarkers across ancestries and shows their predictive value for disease risk.

Trump Administration Impacts on Early Career Scientists and How To Fight Back

This paper surveys early career researchers impacted by Trump administration policies, finding funding cuts threaten their careers and lead to consideration of leaving science.

Shared and distinct microRNA profiles between HT22, N2A and SH-SY5Y cell lines and primary mouse hippocampal neurons

The paper compares miRNA profiles across HT22, N2A, SH-SY5Y cell lines and primary mouse hippocampal neurons to assess their similarity to primary neurons.

Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention

This study integrates large-scale omics and electronic health records to identify risk proteins and drugs for cancer prevention, finding 101 novel proteins and three drugs associated with reduced colorectal cancer risk.

Nucleotide context models outperform protein language models for predicting antibody affinity maturation

This study compares nucleotide context models and protein language models for predicting antibody affinity maturation, finding nucleotide-based models perform better.

Benchmark for simple and complex genome inversions

The paper presents a benchmark for detecting simple and complex genome inversions using Strand-seq and long-read assemblies, revealing method strengths and limitations across sequencing platforms.

A benchmark of DNA methylation deconvolution methods for tumoral fraction estimation using DecoNFlow

This study benchmarks DNA methylation deconvolution methods for tumoral fraction estimation in cfDNA, finding CelFiE most accurate and introducing DecoNFlow as a comprehensive pipeline.

Field-validation of multiple species distribution models shows variation in performance for predicting Aedes albopictus distributions at the invasion edge

The paper evaluates multiple species distribution models for predicting Aedes albopictus distributions at its invasion edge using field-validation and finds variation in model performance across validation methods and invasion stages.

Clinical Implications of SRPK1 Expression in Human Tumours: A Comprehensive Pan-Cancer Analysis Based on Multi-Omics Databases

This study investigates SRPK1 expression across multiple cancer types using multi-omics data, finding its association with poor survival and chemoresistance.

Dissecting the genetic and proteomic risk factors for delirium

This study identifies genetic and proteomic risk factors for delirium, highlighting APOE as a key gene and novel biomarkers, and suggests potential drug targets.

LEAP-InovAND a multiscale resource to explore genetics, brain imaging and clinical data in autism

The paper introduces a multiscale resource integrating genetics, brain imaging, and clinical data from autistic individuals and their relatives to explore genetic and neurobiological patterns in autism.

Robustness of Ancestral Recombination Graph Inference Tools to Phasing Errors

This study evaluates how well four ARG inference tools perform with phasing errors, finding they remain robust despite inaccuracies in haplotype phasing.

VSPGx: A High-Accuracy Pharmacogenomics Interpretation Software Solution with Automated CPIC Guideline Integration

VSPGx is a pharmacogenomics software that accurately identifies diplotypes and annotates them with CPIC guidelines, outperforming existing tools in synthetic and clinical benchmarks.

NLRP1 Shapes Immune and Inflammatory Signatures in Human Melanoma but Not in Mouse Models

This study shows NLRP1 improves prognosis in human melanoma but not in mouse models, and highlights its potential as a prognostic biomarker and therapeutic target.

Analysis of the economic viability and environmental impacts of a conceptual process for the recovery of lactic acid from spent media in cultivated meat production

This study evaluates the economic and environmental impacts of recovering lactic acid from spent media in cultivated meat production, finding it economically viable and environmentally beneficial.

Identifying compounds to treat opiate use disorder by leveraging multi-omic data integration and multiple drug repurposing databases.

The paper identifies FDA-approved drugs targeting genes associated with opioid use disorder by integrating multi-omic data and drug databases.