software / tool

reactifpTM: an accessible reimplementation of actifpTM

reactifpTM reimplements actifpTM to calculate interface quality scores using standard outputs from model prediction software, showing strong correlation with actifpTM on a PDB dataset.

Low-latency multicamera 3D tracking of insects with Braid

This paper introduces Braid, an open-source software for low-latency 3D tracking of insects using multiple cameras, achieving sub-millimeter accuracy in a controlled environment.

Self-blinking dye restores efficient use of nanobodies in single-molecule localization microscopy.

This paper demonstrates that self-blinking dye JF635b improves nanobody performance in single-molecule localization microscopy, enabling reliable imaging across multiple modalities with high precision.

MyoAssist 1.0: An Open-Source Framework for Neuromechanical Simulation of Physical Human-Device Interaction

MyoAssist 1.0 provides an open-source framework for simulating human-device interaction in assistive technologies, offering modular models and controller frameworks for research and development.

KSTITCH links cellular morphology and gene expression in spatial transcriptomics

STITCH pairs size-independent tangent-PCA contour shape modes with expression factors by canonical correlation, recovering keratinocyte, fibroblast and melanoma shape-expression links in Xenium and CosMx data.

Spectral Unmixing: A modular and reproducible Python package for directed and blind spectral unmixing in multidimensional microscopy stacks

The paper introduces a Python package for reproducible spectral unmixing in microscopy data, demonstrating improvements in bleed-through correction across different unmixing methods.

Enrichment-free glycoproteomics harnessing real-time mass defect-driven glycopeptide classification reveals sex differences in murine fucosylation

The paper develops an enrichment-free glycoproteomics method using mass defect-driven glycopeptide classification to identify sex differences in murine plasma fucosylation.

PINN-ing the Balloon: A Physically Informed Neural Network Modelling the Nonlinear Haemodynamic Response Function in MRI

This paper introduces a physics-informed neural network to model the haemodynamic response function in MRI, achieving high accuracy in estimating neurovascular state variables and BOLD signals.

OMIO: A policy-driven Python library for reproducible microscopy image I/O

OMIO provides a policy-driven Python library to standardize microscopy image I/O, ensuring reproducible and interoperable data handling across formats and workflows.

AFIDs-Validator: An Open-Access AI-Guided Platform for Learning Anatomical Landmark Placement

Open browser platform embeds a language-model neuroanatomy tutor in an MRI viewer and scores landmark placements against 21 expert-annotated templates using trained-rater error distributions.

CodonMamba: a foundation model for programmable mRNA coding sequence design

CodonMamba is a foundation model for mRNA coding sequence design that achieves state-of-the-art performance and enables programmable codon optimization through inference-time steering.

Click-Prep: An Interactive Data Preparation Tool for Click-qPCR

Click-Prep simplifies creating Click-qPCR input files by automating data formatting, quality control, and mean Cq calculation from qPCR instrument outputs.

Kiosc: an integrated platform for managing bioinformatics data analysis containers

Kiosc simplifies managing containerized web apps for bioinformatics analysis, enabling interactive result visualization and sharing across projects and institutions.

RapidMACS: MACS3-identical peak calling, 50x faster

RapidMACS provides a faster narrow peak caller for ATAC-seq and related data, achieving 3.5 to 51x speed improvements over MACS3 while producing identical output.

ResiRuler: A Toolkit for Visualizing Residue-Residue Distances and Structural Changes in Biomolecular Models

ResiRuler quantifies and visualizes residue-residue distances and structural changes across protein ensembles to identify conformational differences.

LifeSciBench: Evaluating Language Models on Realistic, Expert-Level Tasks in the Life Sciences

LifeSciBench evaluates language models on 750 expert-authored tasks across seven life science domains and workflows, revealing significant gaps in model performance.

Searching the Druggable Genome using Large Language Models

The paper develops a server enabling large language models to access drug-gene interaction data through natural language queries.

De novo Design of Macrocyclic Molecular Glues

This paper introduces EvoBind-multimer, a deep learning framework for designing molecular glues from protein sequences, demonstrating its ability to recruit E3 ligases to oncoproteins and showing context-dependent functionality.

VIProDesign: Viral Protein Panel Design for Highly Variable Viruses to Evaluate Immune Responses and Identify Broadly Neutralizing Antibodies

VIProDesign is a computational tool that designs viral protein panels to balance diversity and size, enabling better evaluation of immune responses and identification of broadly neutralizing antibodies.

AlphaVaR: an R framework for the statistical interpretation of AlphaGenome variant-effect predictions

AlphaVaR structures AlphaGenome's per-track variant scores in R and adds multiple-testing-corrected enrichment and shift tests, a tissue-specificity index and transparent ranking; on rs1427407 it recovers BCL11A erythroid-enhancer biology.

SVlog: a logic programming framework for understanding structural variation in genomic disease

SVlog provides a logic programming framework for analyzing structural variants in genomic disease by applying deterministic rules to genomic data and annotations.

Celldega: Integrated Toolkit for Visualization and Analysis of Spatial Data

Celldega provides an open-source toolkit for scalable, interactive visualization and analysis of spatial-omics data, supporting the entire analysis lifecycle from quality control to public sharing.

ResLit: A Large-Scale Automated Literature Mining Database for Antimicrobial Resistance

ResLit couples BioMistral-7B screening with two-pass Qwen3-30B extraction to build an antimicrobial-resistance database of 3,120 genes and 13,593 mutations, evidence-tiered against CARD, ResFinder, and NCBI RGC.

An open multimodal spatial resource integrating same-tissue transcriptomics, proteomics, and histology

The paper presents a workflow and dataset integrating spatial transcriptomics, proteomics, and histology on the same tissue section, along with an open-source tool for multimodal data analysis.

A multi-agent molecular optimization framework leads to a rapid-recovery intravenous anesthetic candidate with an improved safety margin

The paper introduces MASCOT, a multi-agent framework for molecular optimization, which improves anesthetic candidates with better safety and recovery properties.

An interoperable research agent network for scientific discovery

This paper introduces GUIA, an interoperable research-agent network that enables collaboration between scientific agents across domains, demonstrating its utility in therapeutic target discovery, drug discovery, and spatial proteomics analysis.

A single-antigen, multi-epitope subunit vaccine candidate against lumpy skin disease virus designed by conservation-guided reverse vaccinology

Cell-Hub: a graphical interface for end-to-end single-cell RNA sequencing analysis

Cell-Hub provides a user-friendly interface for single-cell RNA sequencing analysis, integrating multiple tools to support all essential analysis steps without requiring programming expertise.

A survey of multi-targeting and off-targeting sgRNAs across five genome-wide CRISPR-Cas9 knockout sgRNA libraries with GuideRefine

The paper develops GuideRefine to identify and remove multi-targeting and off-targeting sgRNAs from CRISPR-KO libraries, improving the accuracy of gene hit lists.

A generalizable normalization framework to decouple protocol and instrument effects: Application to high-sensitivity proteomics multicentric study (PME13)

This paper introduces a normalization framework to decouple protocol and instrument effects in multicenter proteomics studies, demonstrating its application to the PME13 dataset.