Alexander L. R. Lubbock

Microbench: Automated metadata management for systems biology benchmarking and reproducibility in Python

Microbench automates metadata capture for reproducibility in computational systems biology by recording execution details and environment information.

Programmatic modeling for biological systems

The paper introduces a programmatic modeling approach for biological systems using Python, enhancing reproducibility and collaboration through software engineering practices.

Functionally Coherent Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

The paper introduces NetNC, a tool to identify functionally coherent TF targets, showing it effectively finds neutral binding and reveals new gene functions in EMT processes.

ACDC: Automated Cell Detection and Counting for Time-lapse Fluorescence Microscopy

ACDC automates cell detection and counting in time-lapse microscopy images, achieving high accuracy without large annotated datasets.

A computational framework to explore cellular response mechanisms from multi-omics datasets

The paper introduces MAGINE, a framework for analyzing multi-omics time-course data to build mechanistic hypotheses of cellular responses to perturbations.

Accelerated Simulations of Chemical Reaction Systems using the Stochastic Simulation Algorithm on GPUs

The paper presents GPU-SSA, a GPU-accelerated implementation of the Stochastic Simulation Algorithm, showing significant speedup over CPU implementations for chemical reaction simulations.