Hi. I am Xenophon.

About

296 bytes about myself.

Profile Picture

My research aims to make human genomic data more interpretable and actionable, particularly for use in translational and clinical settings. I'm especially interested in cross-genomic regulation, causal inference, and integrating multi-layered biological data into decision-grade systems.

Profile

I'm a statistical geneticist working at the intersection of genomics, AI, and translational medicine. I currently work at Pheiron, where I help develop systems that turn complex biological data into causal evidence to guide drug discovery and clinical translation. My academic training spans machine learning, statistical genetics, and multi-omic integration. My PhD work at Helmholtz Pioneer Campus focused on cross-genomic regulation — specifically how mitochondrial and nuclear genomes interact to shape gene expression across tissues. I later contributed to the Alzheimer’s Disease Atlas by rearchitecting its data integration pipeline using graph-based methods. I'm drawn to projects where systems thinking meets rigorous computation — and where data complexity is an opportunity, not a burden.

General Info

  • Full Name: Xenophon Giannoulis
  • Location: Bavaria, Germany
  • Email: xgiannoulis@proton.me

Technical Depth

I design and implement computational frameworks that support evidence generation from human genomic data. My strengths lie in bridging statistical genetics with system-level thinking — whether it’s developing scalable GWAS and eQTL pipelines, integrating multi-omic datasets, or engineering data layers for causal inference. I work fluently across R (Bioconductor, Rshiny), Python (pandas, Limix), and C/C++ (PLINK, REGENIE, LDAK, GCTA), and have led projects involving Neo4j graph models, SPARQL/RDF integration, and cloud-ready analytics platforms. Beyond tools, I focus on reproducibility, robustness, and aligning computational strategy with scientific objectives.

  • 95%
    Statistical Genetics
  • 90%
    Data Integration & Pipelines
  • 90%
    Machine Learning
  • 85%
    Bioinformatics
  • 85%
    Knowledge Graphs & Neo4j
Resume

My extensive professional background and educational qualifications.

Work Experience

Statistical Geneticist

July 2025 - now

Pheiron

Designing genomic evidence systems that support clinical translation and drug discovery. My work spans integration of the largest human genetic cohorts, development of scalable analytical pipelines, and platform design — combining AI and statistical genetics to extract causal insight from population-scale multi-omic data.

Postdoctoral Researcher

January 2025 - June 2025

Helmholtz Institute of Computational Biology

Joined the Computational Neurobiology Group at Helmholtz Computational Health Center to integrate large-scale omics data into the Alzheimer’s Disease Atlas using the Neo4j database. I develop unified scoring schemas to harmonize multi-omics and phenotypic data, enabling the prioritization of candidate drugs through advanced network-based and AI-driven methodologies.

Doctoral Researcher

June 2020 - December 2024

Helmholtz Pioneer Campus

As a graduate student at the Munich School of Data Science (MUDS) , I joined the Institute of Translational Genetics to research the genetic basis of mental health disorders. I designed architectures, trained models, and conducted statistical analyses on genetic data to understand human health and disease. Additionally, I co-organized two retreats at MUDS, overseeing speaker invitations and agenda management.

Research Fellow

August 2024 - September 2024

Maximilian University of Munich

I was awarded a fellowship from the Data Science for Social Good Foundation (DSSG), during which I collaborated with Munich's Machine Learning Center (MCML), the statistical department of LMU, and Bavaria's state Ministry of the Interior (BMI). Our collaboration aimed to develop a web application for identifying optimal water extraction points for firefighting purposes. The project involved integrating statistical mapping, machine learning techniques, and interactive maps. Additionally, we implemented routing algorithms, containerized the application using Docker, deployed it on AWS, and presented our findings to Germany's federal parliament.

Teaching Assistant

October 2022 - March 2023

Technical University of Munich

I developed and configured educational material for TUM's Medicine department's Human Genetics of Complex Traits course (ME 1660-P). In addition, as part of our team, I served as a tutor in lectures and workshops, where we covered a diverse range of topics including UNIX, quality control, association testing, meta-analysis, and polygenic risk scores. These roles, helped me facilitate a comprehensive learning experience for students, which later inspired me to pursue a professional certificate in Teaching in Higher Education from TUM ProLehre Media & Didactics.

Analytics Intern

October 2019 - April 2020

Helmholtz Munich

Implemented my master thesis at the Institute of Translational Genomics (ITG), where I developed a quality control pipeline to analyze pre-processed data. The pipeline ensured accuracy during merging, corrected for population structure, imputed missing data, and identified biases. Focused on improving the quality of genome-wide association studies (GWAS) data, I processed peripheral whole blood samples collected from 250 patients across four cohorts undergoing total joint replacement surgery. The project involved merging cohorts from different array versions, necessitating specialized handling of genetic data assumptions.

Education

Dr. rer. nat.

June 2020 - December 2024

Technical University of Munich, DE

During my doctoral program in experimental medicine and health sciences, I developed a computational pipeline to analyze mtDNA-nucDNA interactions across 48 tissues, identifying discrepancies related to psychiatric conditions. Leveraging machine learning approaches, we revealed regulatory relationships between mitochondria and the nucleus, pinpointing causal genomic variations, particularly in the central nervous system tissues. This research sheds light on tissue-specific mito-nuclear interactions, crucial for understanding health and disease.

M.Sc.

October 2018 - April 2020

Thessaly University, GR

Joined the department of computer science and biomedical informatics, where I took focused courses on applied machine learning, ontology engineering, biosensors and digital imaging. My master's thesis centered around identifying biased individuals and SNPs, statistical imputation and concatenating cohorts from different Illumina genotyping arrays.

B.Sc. (Hons)

October 2012 - April 2018

Piraeus University, GR

During my 4-year degree in statistics and actuarial mathematics, I gained a solid educational background in probability theory, linear algebra, bayesian statistics, biostatistics, risk management and stochastic processes. In my bachelor thesis, I explored the application of fitting probability distributions to empirical data, where I analyzed various techniques to optimize model selection and enhance the accuracy of predictive systems.

Contributions

A list of my academic contributions.

Interplay between mitochondrial and nuclear DNA in gene expression regulation.

By using linear mixed models (LMMs) to conduct expression quantitative trait locus (eQTL) mapping, we explored the crosstalk between mitochondria and the cell nucleus across 48 different tissues. Through the integration of our identified eQTLs with various molecular data, we applied a series of analyses, including statistical colocalization, causal inference, graph neural networks, and over-representation analysis. These methods helped us identify disease genes, variants, and ontological pathways. Our study shows potential for unveiling new therapeutic approaches aimed at a wide range of diseases, from metabolic disorders to neurodegenerative conditions.

Mito-Nuclear Interactions, Mediation, colocalization, Mendelian Randomization, Graph Neural Networks, Interpretable Machine Learning

Tissue Specific Regulation of Mitochondria Encoding Genes.

During the conference, I showcased my poster on the interaction between mitochondrial and nuclear communication in regulating tissue-specific gene expression. In addition to receiving excellent feedback, I had the privilege of meeting numerous outstanding scientists and fostering valuable discussions.

Mito-Nuclear Interactions, Causal Inference, Graph Neural Networks

HydroXplorer: A Fire Hydrant Range Finder Application.

This project aims to develop a web application to help firefighters determine the areas covered with existing and planned hydrants. The application identifies accessible zones utilizing hydrant location or natural water sources, pinpoints nearby water sources for firefighting purposes, and calculates elevation disparities between the fire location and surrounding water sources.

Data Science for Social Good, DSSGxMunich, MCML, Machine Learning, BERD, BYTE, Bavarian Ministry for Digital Affairs

Human Genetics of Complex Traits.

I have been involved in the curation of a workshop at TUM that covers key subjects in human genetics and genomics. The course included various topics such as tools for genome-wide association studies (GWAS), UNIX command line, association testing, meta-analysis methods, rare genetic variations, molecular QTL mapping, bioinformatics databases, and polygenic scores. Moreover, I led the creation of interactive Jupyter lab exercises during the workshop's hands-on sessions, allowing participants to apply their knowledge of the course content to real-world data.

GWAS, UNIX, Complex Traits, Meta-analysis, Bioinformatics, TUM, VSS, JupyterLab

Tissue-specific apparent mtDNA heteroplasmy and its relationship with ageing and mtDNA gene expression.

In this study, we comprehensively characterize the landscape of common mtDNA heteroplasmy and mtRNA modifications across 49 human tissues assayed with bulk RNAseq in GTEx v8. As mtDNA heteroplasmy and mtRNA modifications are tissue-specific, we aim to establish a robust framework for identifying and testing both types of variations from tissue-specific RNAseq data. our study provides the first comprehensive and tissue-specific description of the apparent mtDNA heteroplasmy, their relationship with donor age, and their regulatory effects on mitochondrial gene expression.

Mito-Nuclear Interactions, Interpretable Machine Learning, Gene Expression Regulation, Heteroplasmy

Tissue-specific apparent mtDNA heteroplasmy and its relationship with ageing and mtDNA gene expression.

We presented research findings related to mitochondrial DNA (mtDNA) heteroplasmy and its association with ageing and gene expression patterns, shedding light on the potential functional consequences of mtDNA variation within different tissues.

mitochondria, Heteroplasmy, Aging, Molecular Genetics, Gene Regulation, Bioinformatics

Quality Control and Imputation of Genotype data from different Illumina arrays

This thesis explores the crucial importance of quality control (QC) procedures in genome-wide association studies (GWAS), which are vital for ensuring the trustworthiness of genetic associations. It focuses on integrating cohorts from different array versions, tackling the computational hurdles and genetic assumptions present in Illumina genotyping data. By employing thorough QC filtering and imputation methods, the thesis introduces a strong framework for detecting outlier individuals and SNPs, ultimately generating a top-notch dataset suitable for precise association testing.

QC, GWAS, Osteoarthritis, Imputation, Genomic Variation, Bioinformatics, Statistical Genetics, PCA

Science Game Design

STARS GAME is a project that is transforming the way science education is approached for 10-13-year-olds. As part of the game's design team, we secured and executed an EU commission-funded initiative. Through design thinking, we developed an educational escape room, integrating science into school curricula across 30 institutions in four European countries. Our main objective was to connect theoretical knowledge with practical application, utilizing game-based learning to nurture curiosity and improve critical thinking abilities.

Science education, Design Thinking, Digital Escape Room, Game-based learning, Erasmus, EU