software / tool

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.

Bioprocess Modeling Made Easy With Hybrax

Hybrax simplifies hybrid bioprocess modeling by providing a framework that automates model setup and data handling, enabling reproducible and reusable models.

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.

Optimiser Repairs for Living-Cell Self-Driving Laboratories: Performance and Redundancy under Experimental Constraints

This paper evaluates optimiser repairs in living-cell self-driving labs, showing when they improve performance and when constraints make them redundant.

Steering Before Selection: Energy-Limited Developmental Control as a Phenotypic Capacitor, a Pre-Specified Simulation Study

This paper uses simulations to show that developmental control conceals genetic variation from selection, acting as an energy-dependent phenotypic capacitor that can be beneficial if harmful mutations are reversed.

A validation approach for RNA structures based on deep-learning 3D-structure predictions

This paper extends a protein structure validation method to RNA, showing it can detect errors in low-resolution structures where map-based methods fail.

FastaGuard: FASTA preflight QC for modern bioinformatics pipelines

FastaGuard is a FASTA preflight QC tool that detects structural issues in assemblies and stops pipelines before expensive analysis, with high accuracy in identifying faults.

ConfUSIus: an accessible and scalable toolkit for functional ultrasound imaging analysis

ConfUSIus provides an open-source toolkit for analyzing functional ultrasound imaging data, unifying processing steps and improving accessibility and reproducibility.

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.

scRM: A single-cell foundation model trained on scRNA-seq reads

scRM is a single-cell foundation model trained on raw scRNA-seq reads, showing that raw data pretraining is feasible and cost-effective compared to count-based models.

MaCADEMIA: a software toolbox for single-molecule fluorescence image quantification

MaCADEMIA is a MATLAB toolbox for single-molecule fluorescence image analysis, providing accurate quantification of molecular properties in living cells.

Pycea: a scverse toolkit for single-cell lineage tracing analysis

Pycea provides a toolkit for analyzing single-cell lineage tracing data, integrating with Scanpy and offering visualization and statistical methods for lineage trees.

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.

Single-cell perturbation prediction near experimental reproducibility with GENESIS

GENESIS predicts single-cell perturbation responses from experimental conditions, outperforming existing models and approaching experimental reproducibility.

FiberBrowser: a unified framework for single-molecule genomics

FiberBrowser converts diverse single-molecule footprinting datasets into a unified representation for analyzing chromatin structure and function across assays.

Estimating glioblastoma migration-to-proliferation ratio from single time-point MRI data via radial density distribution

A reaction-diffusion model fitted to shell-averaged tumor density from one pre-treatment MRI estimates glioblastoma migration/proliferation ratio (D/k); in BraTS 2017, higher D/k went with shorter overall survival.

AI-driven discovery and engineering of human endogenous nanocage proteins for mRNA delivery

The paper develops DeepDelivery, an AI platform that identifies human proteins for mRNA delivery, validating 80% of top candidates for efficient, non-inflammatory delivery.

SiSaNA: A Python-based command line interface for Single-Sample Network Analysis

SiSaNA provides a command line interface for single-sample regulatory network analysis without requiring programming experience.

PHENOMS: Open-Source Software for Rust-Accelerated Hydrogen-Bond Analysis in Molecular Dynamics Simulations

PHENOMS analyzes hydrogen-bond networks in molecular dynamics simulations using Rust-accelerated code, achieving significant speedup over Python-based tools and demonstrating its utility with HDX-MS data.

Agentic cryo-EM structure determination with CryoPilot

CryoPilot uses two language model agents to automate cryo-EM structure determination, improving resolution and model accuracy through adaptive decision-making.

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.

Citizen science gamers enable automated flow cytometry gating through machine learning

The paper develops flowMagic, a machine learning tool for automated flow cytometry gating trained on expert data and citizen science gaming annotations, achieving high accuracy in cell population identification.

OocystMeter, a machine-learning algorithm to count and measure Plasmodium oocysts, reveals clustering patterns in the Anopheles midgut

OocystMeter automates oocyst counting and sizing in mosquito midguts, revealing clustered spatial patterns in malaria infections.

PrEditR: A protein-centric platform for CRISPR-mediated base editor sgRNA design

PrEditR is a tool for designing sgRNAs for CRISPR-based base editors, allowing users to target specific amino acids and annotate resulting mutations.

Open Blink: Low-cost TIRF microscopy for super-resolutionimaging via μManager

Open Blink provides a low-cost, open-source TIRF microscope for quantitative multi-color super-resolution imaging with high localization precision and axial stability.

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.