benchmarking

41% of Gram-negative bacteria encode a Type Six Secretion System

The paper quantifies T6SS prevalence in Gram-negative bacteria using genome analysis and finds it is present in 41% of well-sampled genera.

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.

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.

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.

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.

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.

NTAD: A longitudinal neuroimaging dataset of Alzheimer's disease pathology

The paper introduces a longitudinal neuroimaging dataset of Alzheimer's disease pathology, including multimodal data from patients and controls, to identify and validate novel biomarkers.

A cytotoxicity dataset for data-driven design of ionizable lipid nanoparticles

The paper presents a curated dataset of 1,413 LNP cytotoxicity measurements to examine structure-activity relationships and develop computational models of lipid nanoparticle cytotoxicity.

FedEpitope: Parameter-Efficient Federated Protein Language Models for Linear B-Cell Epitope Prediction

FedEpitope uses federated learning with LoRA to predict linear B-cell epitopes without centralizing data, achieving good performance across multiple clients.

Improving real-time search through deep learning-enhanced fragment ion indexing

The paper develops a deep learning-enhanced fragment ion indexing method to reduce memory usage in tandem mass spectrometry searches while maintaining search accuracy and speed.

QC-espresso: Brewing quality in proteomics

QC-espresso provides an automated quality-control workflow for DIA proteomics data, generating structured reports to assess acquisition quality and quantitative reliability.

Consensus methods for trees of blobs and level-1 phylogenetic networks

This paper introduces a consensus framework for phylogenetic networks, demonstrating its effectiveness on simulated and real datasets.

Harmonizing Repeated Multi-Platform Optical and LiDAR Observations for Continental-Scale Terrestrial Carbon Cycle Data Assimilation.

This study integrates GEDI LiDAR with an existing data assimilation system to improve terrestrial carbon monitoring, reducing woody biomass uncertainty by 63.7% and achieving RMSE reduction of 38.3 kg/m2.

Low-pass filtering revisited: ramped phase randomization for cryo-EM map comparison and data augmentation

This paper introduces ramped phase randomization to improve cryo-EM map comparison and data augmentation by reducing fine-scale detail while preserving low-frequency content and enhancing machine learning performance.

Cross-modal transfer enables zero-shot prediction of drug responses across cell types

GRAFT predicts drug responses across cell types without direct measurements by transferring genetic perturbation data to chemical perturbations.

Batch Effect Correction to Enhance Utility of a Publicly Available ALS Proteomics Dataset

The paper corrects batch effects in the Answer ALS proteomics dataset using BDCs and ComBat, improving data utility while preserving biological variability.

A genomic baseline for long-term monitoring of economically important aquatic species in the Netherlands

The paper establishes a genomic baseline for six aquatic species in the Netherlands using SNP data to assess population structure, diversity, and conservation priorities.

SMFnet reveals principles of combinatorial transcription factor assembly

The paper introduces SMFNet and PRISM to analyze how transcription factor assemblies influence chromatin accessibility and identifies sequence-encoded principles of combinatorial TF assembly.

Aneuploidy profiling among different types of brain metastases reveals a colon cancer-specific chromosomal signature

This study identifies a unique aneuploidy profile in colorectal cancer brain metastases compared to other cancer types and metastatic sites.

ARG-PASS v2.0 expands global resistome surveillance to reveal previously unrecognized antibiotic resistance genes reaching the human gut

ARG-PASS v2.0 identifies previously unrecognized antibiotic resistance genes in environmental samples and links them to human gut microbiomes through dietary exposure.

GLESKit: an MCP-based system for gene-level biomedical investigation and evidence synthesis

GLESKit is a gene-centered system that synthesizes biomedical evidence by integrating multiple data types, achieving high report quality and performance in benchmark tasks.

iGEX: an interactive Gene EXpression exploration platform for the analysis of transcriptomic and proteomic datasets

iGEX provides an interactive platform for exploring transcriptomic and proteomic datasets, enabling comparison of expression patterns across experiments and public resources.

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

The paper introduces the Microbiology Galaxy Lab, a community-driven platform for reproducible and FAIR microbial data analysis, offering tools for various omics data types and use cases.

Arena3D 3.0: a web server for exploring, analyzing, annotating and sharing multilayered networks in 3D

Arena3D 3.0 is a web server for exploring, analyzing, and sharing multilayered biological networks in 3D with various layouts and visualization tools.

The B-value calculator: expected diversity with background selection

The paper introduces Bvalcalc, a tool to calculate B-values, which quantify the effect of background selection on genetic diversity, and validates it using simulations and public data.

Survey of the human proteostasis network: the ubiquitin-proteasome system

The paper provides a comprehensive survey of the ubiquitin-proteasome system (UPS) and estimates its size and scope within the human proteostasis network.

Histone modifications define distinct nucleosome positions in cell-free DNA

This paper identifies histone modification-associated nucleosome positions in cfDNA that correlate with tumor fraction and cancer state across multiple cancers.

Salmonid science on the move: Twenty years of research through the lens of early career researchers

This review analyzes 20 years of salmonid research through early-career researchers' contributions, identifying trends, gaps, and future directions in the field.

Integrating sequence-to-omics predictions and personal multi-omics for rare variant prioritization

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.