benchmarking

Agentic AI enables cell segmentation-free cell-type inference and cell-type-guided cell segmentation in spatial transcriptomics

This paper introduces SSAF-T, a segmentation-free framework for cell-type inference in spatial transcriptomics that avoids cell segmentation and enables accurate cell-type-guided segmentation.

From Fill to Freeze: Redesigning homeRNA to Enable Robust Sampling and Scalable Downstream Processing Workflows for Remote Blood Transcriptomics

This paper validates the redesigned homeRNA platform's robustness to remote study stresses, showing it maintains RNA quality under varied conditions and storage times.

The biochemical composition of coronavirus Nucleocapsid proteins drives the bicistronic properties of their sub-genomic mRNAs

The paper identifies conserved overlapping accessory ORFs in coronavirus N genes and shows that nucleotide and codon biases drive their formation.

SARDINE unlocks EWAS summary statistics for large-scale epigenetic biomarker analysis

SARDINE uses EWAS summary statistics to estimate epigenetic clock-phenotype associations without individual-level data, revealing heterogeneity in biomarker associations with aging and diseases.

Residual barcode-like sequences and barcode-associated artifacts after Dorado and Barbell preprocessing of metagenomic reads

The paper evaluates Dorado and Barbell preprocessing tools for metagenomic reads, finding Barbell reduces barcode-like sequences more effectively while retaining most reads.

Hybrid RY-mers increase aDNA alignment sensitivity

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

Learning Strand-Equivariant Tokenizations of DNA with MirrorDNA

This paper introduces MirrorDNA, a DNA language model with a strand-equivariant tokenizer that improves prediction consistency across DNA strands.

Hub labeling makes exact distance calculation practical for large human pangenome graphs

The paper introduces a hub labeling method to reduce the space required for distance indexing in large pangenome graphs, improving query support and reducing storage needs.

A biomimetic deep encoder for auditory restoration by cortical stimulation

This paper introduces Braincodec, a deep encoder that improves sound transmission via cortical stimulation, achieving high-fidelity sound reconstruction and matching non-implanted mice in sound discrimination.

pLM-bVAE: protein language model-enhanced binary representation improves quantum annealing-based protein sequence design

This paper introduces pLM-bVAE, a binary variational autoencoder enhanced with protein language model representations, showing improved sequence reconstruction and design performance in quantum annealing-based protein sequence design.

scCircaSim: A Circadian Simulator for Single-Cell and Spatial Transcriptomics

scCircaSim generates circadian single-cell and spatial transcriptomic data with known ground truth to evaluate analysis methods.

Contrastive Learning Improves Generalization on M2OR Olfactory Binding Dataset

The paper evaluates contrastive learning on VOC-OR binding datasets, showing improved generalization and reduced performance inflation from identity leakage.

Theoretical prediction of assembly contiguity

The paper derives a formula (Z-value) to predict contig length from read length, coverage, and genome properties, showing high accuracy and practical applications for assembler choice and experimental design.

Plate design confounds donor variation and model evaluation in single-cell perturbation screens

The paper shows that plate design confounds donor variation in single-cell perturbation screens and demonstrates how improved analysis methods can change interpretations of recent studies.

Stoichiometric Encoding of Amplification Kinetics Enables High-Level Multiplexing in Single-Channel TaqMan Real-Time PCR

This paper introduces a method to increase multiplexing in TaqMan qPCR by encoding target-specific information into amplification curves and decoding them with a transformer model, achieving 8-plex detection with high accuracy.

High reproducibility demonstrated in a direct-to-consumer microbiome testing workflow under real-world conditions using fecal reference material

This study demonstrates high reproducibility in a DTC microbiome testing workflow using NIST fecal reference material across multiple processing steps and real-world conditions.

Protify: A Benchmarking Platform Revealing Task Dependence and Homology Leakage in Protein Language Model Evaluation

Protify benchmarks protein language models across tasks and evaluation settings, revealing task dependence and homology leakage in model performance.

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.