A review of papers proposing novel GNN methods with application to brain connectivity published in 2017-2020.

Microbial marker identification from cross-cohort datasets

The Ontology for Nutritional Studies (ONS) has been developed as part of the ENPADASI European project (http://www.enpadasi.eu/) with the aim to define a common language and building ontologies for nutritional studies.

A poster showing TIGS project at BioForum2019, ShanghaiTech University

Batch-harmonized ML framework for cross-cohort RNA biomarker discovery in pancreatic adenocarcinoma — bioRxiv 2025 (doi:10.1101/2025.11.14.688421)

My Solution for PrecisionFDA Brain Cancer Predictive Modeling and Biomarker Discovery Challenge

"Identification of Biomarkers for Early-Stage Hepatocellular Carcinoma (HCC)" aims to address the critical global challenge of late-stage cancer diagnosis, which significantly lowers patient survival rates. It explores microarray gene expression datasets from GEO to identify potential early-stage biomarkers for improved patient outcomes.

A package for biomarker selection based on multiset multicover and the cross-entropy-method.

Disease-agnostic biomarker discovery platform — BPF validation across Oncology, Alzheimer's, and Parkinson's disease

BPF Parkinson's disease validation — PPMI expression, genotype, and prodromal detection (AUC 0.766)

ENDORSE model

GeneLit is a literature review tool made with Streamlit that allows researchers to input gene sets and query the latest biomedical literature filtered by specific cancer types and tissue synonyms. Designed to aid biomarker discovery and validation.

🔬 R/biotmle: A package for biomarker discovery combining targeted minimum loss-based estimation with empirical Bayes moderation

Biomarker Database (RDF, reporting, and other utilities)

I extracted the tumor features according to the data annotation of all four stages of 3D MRI data. And I deployed Graph Neural Networks based on important features such as First Order Statistics, Shape-based (3D), Shape-based (2D), GLCM, GLRLM, GLSZN, NGTDM, and GLDM.

Python script for enzyme sequence clustering and metabolic pathway comparison.

Official BSP website — documentation, specification, guides & community hub for the Biological Sovereignty Protocol

DDR biomarker and PARP/ATR inhibitor response pipeline. Full GDSC v17 mutations + CNV + MSI + tissue context. POC: Talazoparib HRD Spearman ρ=+0.12 (p=3e-4, n=912); per-drug CV AUC 0.68–0.77.

Official CLI for the Biological Sovereignty Protocol — manage BEOs, IEOs, consent, and health data from the terminal

lpl package