Repositories list

• Shape2Force

  Public
  A deep learning model to predict cell force from microscopy bright field images of single-cell or spheroid

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 19, 2026Jun 19, 2026

• FateFormer

  Public
  Code and documents for predicting lineage outcomes in direct reprogramming by integrating transcriptomic, epigenomic, and metabolic signals at the single cell l…

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 12, 2026Apr 12, 2026

• SpatialMST

  Public
  Spatial Multimodal Self-supervised Transformer

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 4, 2026Apr 4, 2026

• XTREAM-WP2-metabolic-modelling

  Public
  Metabolic models and code for WP2 of project XTREAM - xtream-project.eu/

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 23, 2026Mar 23, 2026

• Bioprocess-optimisation-via-joint-machine-learning-and-metabolic-modelling

  Public
  MATLAB

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• TAP_TU_SyntheticModelGenerator

  Public
  Generate Synthetic models used in KTP Paper

  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 5, 2026Mar 5, 2026

• Predicting-gut-microbial-behavior-in-human-diseases-via-community-metabolic-modeling-and-ML

  Public
  Combining Pairwise Modelling and Machine Learning

  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 3, 2026Mar 3, 2026

• Mitochondrial-G-actin-metabolic-rewiring

  Public
  Mitochondrial G-actin activates a transcriptional and metabolic rewiring program that affects tumor-associated-macrophages

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 4, 2026Jan 4, 2026

• Fusing-imaging-and-metabolic-modelling-via-deep-learning

  Public
  Integrated framework for fusing radiogenomics and metabolic modelling via deep learning in ovarian cancer

  Jupyter Notebook

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 23, 2025Dec 23, 2025

• NSCLC-Survival-Prediction-models

  Public
  Python

  •11 fork•66 stars•00 issues•00 pull requests•Updated Nov 30, 2025Nov 30, 2025

• bulk-to-single-cell-spatial-data-for-metabolic-disruptions

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 20, 2025Nov 20, 2025

• Multimodal_breast_cancer_subtype_analysis

  Public
  Profiling intratumoural heterogeneity of breast cancer subtypes through integrated transcriptomic and metabolic analysis at single-cell and spatial resolution

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 6, 2025Oct 6, 2025

• Benchmarking_ML_and_Cox_for_lung_cancer

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 27, 2025Feb 27, 2025

• NK-A-17E-233I-DHODH-Inhibitor-for-the-Treatment-of-Colorectal-Cancer

  Public
  NK-A 17E-233I, a Natural Small Molecule Human Dihydroorotate Dehydrogenase (DHODH) Inhibitor for the Treatment of Colorectal Cancer

  MATLAB

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 8, 2025Feb 8, 2025

• Halomonas-elongata-Metabolic-Modelling

  Public
  Genome-scale metabolic modelling derived flux analysis in Halomonas elongata 153B explains polyhydroxyalkanoates and ectoine biosynthesis

  00 forks•33 stars•00 issues•00 pull requests•Updated Apr 11, 2024Apr 11, 2024

• Benchmarking-ML-and-Cox-for-lung-cancer

  Public
  Benchmarking machine learning and Cox regression approaches for lung cancer on combined RNA-seq and metabolic modelling

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 17, 2023Nov 17, 2023

• Synechococcus7002-metabolic-modelling

  Public
  Bi-level regularized flux balance analysis of Synechococcus spp. PCC 7002

  machine-learningmultiobjective-optimizationmetabolic-network+ 3

  machine-learningmultiobjective-optimizationmetabolic-networkflux-balance-analysiscyanobacteriamultiomics

  MATLAB

  •22 forks•44 stars•11 issue•00 pull requests•Updated Nov 10, 2023Nov 10, 2023

• Hepatoblastoma-Children-Classification

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 12, 2023Mar 12, 2023

• GEM-Chromohalobacter-canadensis-85B

  Public
  Genome-scale metabolic model of Chromohalobacter canadensis 85B

  00 forks•00 stars•00 issues•00 pull requests•Updated Sep 25, 2022Sep 25, 2022

• survival_analysis_tutorial

  Public
  Jupyter Notebook

  •00 forks•22 stars•00 issues•00 pull requests•Updated Sep 4, 2022Sep 4, 2022

• 12-machine-learning-models-for-text-classification

  Public
  Jupyter Notebook

  •33 forks•55 stars•00 issues•00 pull requests•Updated Jul 20, 2022Jul 20, 2022

• Tools-for-GEM-reconstruction-and-analysis-

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 5, 2022Jun 5, 2022

• Tutorials_Combining_ML_and_GSMM

  Public
  MATLAB

  •44 forks•66 stars•00 issues•00 pull requests•Updated May 28, 2022May 28, 2022

• Metabolic-modelling-of-SARS-CoV-2-in-cancer-cells

  Public
  Genome-scale metabolic modelling of SARS-CoV-2 infection in cancer cells

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 2, 2021Aug 2, 2021

• Multi-objective-optimization-of-gut-community-metabolic-model

  Public
  MATLAB

  •00 forks•11 star•00 issues•00 pull requests•Updated Jan 27, 2021Jan 27, 2021

• HybridGroupIPFLasso_pc2Lasso

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 5, 2021Jan 5, 2021

• metabolic_modelling_website

  Public
  Rich Text Format

  •33 forks•00 stars•00 issues•00 pull requests•Updated May 21, 2020May 21, 2020

• multiOmicMechanismAwareML

  Public
  Jupyter Notebook

  •

  GNU Affero General Public License v3.0

  •77 forks•11 star•00 issues•00 pull requests•Updated May 14, 2020May 14, 2020

• Emulating-ABMs-with-ML

  Public
  Mathematica notebooks and results for our paper on emulating agent-based models with ML

  Mathematica

  •

  MIT License

  •66 forks•00 stars•00 issues•00 pull requests•Updated Mar 19, 2020Mar 19, 2020

• PGA_and_C-EDGE

  Public
  Code for the paper: "Discovering code Essential Multiple Gene Effects through Large Scale Optimization: an Application to Human Cancer Metabolism"

  MATLAB

  •22 forks•00 stars•00 issues•00 pull requests•Updated Dec 31, 2019Dec 31, 2019