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<!DOCTYPE html>
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<meta charset="utf-8">
<title>Xenofon Giannoulis | Resume and Presentation</title>
<meta name="description" content="Resume and presentation of Xenofon Giannoulis, a data scientist and statistical genetics researcher.">
<meta name="Keyword" content="Xenofon Giannoulis, machine learning, deep learning, genetics, genomics, bioinformatics, researcher, MUDS, ITG, Data analysis, Statistical analysis, Machine learning algorithms, Predictive modeling, mtDNA, Multi-omics, GWAS, eQTL, Epigenetics" >
<meta name="author" content="Xenofon Giannoulis" >
<meta property="og:title" content="Xenofon Giannoulis | Resume and Presentation">
<meta property="og:description" content="Resume and presentation of Xenofon Giannoulis, a data scientist and statistical genetics researcher.">
<meta property="og:image" content="images/xphoto.jpeg">
<meta property="og:url" content="https://xenophong.github.io/web/">
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<header class="s-header">
<nav class="header-nav-wrap">
<ul class="header-nav">
<li><a class="smoothscroll" href="#home" title="home">Home</a></li>
<li><a class="smoothscroll" href="#about" title="about">About</a></li>
<li><a class="smoothscroll" href="#resume" title="resume">Resume</a></li>
<li><a class="smoothscroll" href="#contributions" title="contributions">Contributions</a></li>
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<section id="intro">
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<h1>Hi, I'm Xenofon Giannoulis.</h1>
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<span>Data Scientist</span>
<span>Statistician</span>
<span>Bioinformatician</span>
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<div class="row button-section">
<a href="Xenofon_Giannoulis_CV.pdf" title="Download CV" class="button button-primary">Download CV</a>
</div>
</div> <!-- /intro-content -->
<ul class="intro-social">
<li><a href="https://github.com/xenophong"><i class="fa fa-github"></i></a></li>
<li><a href="https://twitter.com/Xenofon_G"><i class="fa fa-twitter"></i></a></li>
<li><a href="https://www.linkedin.com/in/xenog/"><i class="fa fa-linkedin"></i></a></li>
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<h5>About</h5>
<h1>2144 bits about myself.</h1>
<div class="intro-info">
<img src="images/xphoto.jpeg" alt="Profile Picture">
<p class="lead">I am a passionate data scientist with experience in statistical genetics, computational biology and bioinformatics.
Possessing a strong analytical mindset, I thrive on solving complex problems to drive meaningful outcomes, deliver effective solutions, and enhance the interpretability of predictive systems.
</p>
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</div>
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<h2>Profile</h2>
<p>After obtaining a bachelor's degree in statistics and actuarial science, I transitioned to the field of computer science and biomedical informatics. For my master's thesis, my focus has been on performing quality control and imputation on genomic data. In my doctoral studies, I specialized in the field of computational biology, where I focused on predicting genes and variants to uncover insights into the regulation of gene expression in mitochondrial-nuclear communication. </p>
<h4>General Info</h4>
<ul class="info-list">
<li>
<strong>Full Name:</strong>
<span>Xenofon Giannoulis</span>
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<li>
<strong>Location:</strong>
<span>Bavaria, Germany</span>
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<strong>Email:</strong>
<span>[email protected]</span>
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<h4>Languages</h4>
<ul class="info-list">
<li>
<strong>Greek:</strong>
<span>Mother Tongue</span>
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<strong>English:</strong>
<span>Fluent</span>
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<strong>German:</strong>
<span>Intermediate</span>
</li>
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<h2>Skills</h2>
<p>I have profound experience in statistical data analysis, data cleaning and machine learning. I take pleasure in determining the best computational method based on the particular problem at hand. I work mostly in <b>R</b> (<b>Bioconductor</b>, <b>EdgeR</b>, <b>dplyr</b> and <b>data.table</b>), <b>Python</b> (<b>Limix</b>, <b>Flask</b>) and <b>C/C++</b> (<b>PLINK</b>, <b>LDAK</b>, <b>GCTA</b>) and have completed projects in <b>MySQL</b>, <b>HTML</b>, <b>Leaflet</b>, <b>RDFs</b>, <b>XML</b> and <b>SPARQL</b>.</p>
<ul class="skill-bars">
<li>
<div class="progress percent95"><span>95%</span></div>
<strong>Statistical Genetics</strong>
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<div class="progress percent90"><span>90%</span></div>
<strong>Data Science</strong>
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<div class="progress percent90"><span>90%</span></div>
<strong>Bioinformatics </strong>
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<div class="progress percent80"><span>80%</span></div>
<strong>Machine Learning<strong>
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<div class="progress percent80"><span>80%</span></div>
<strong>Network Analysis</strong>
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<div class="progress percent80"><span>80%</span></div>
<strong>Epidemiology </strong>
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<a href="/docs/Xenofon_Giannoulis_CV.pdf" title="Download CV" class="button button-primary">Download CV</a>
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<h5>Resume</h5>
<h1>My extensive professional background and educational qualifications.</h1>
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<h2>Education</h2>
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<h3>PhD Candidate</h3>
<p>June 2020 - September 2024</p>
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<h4>Technical University of Munich, DE</h4>
<p>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.</p>
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<h3>Master of Science</h3>
<p>October 2018 - April 2020</p>
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<h4>Thessaly University, GR </h4>
<p>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.</p>
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<h3 style="white-space: nowrap;">Bachelor of Science (Hons)</span></h3>
<p>October 2012 - April 2018</p>
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<h4>Piraeus University, GR </h4>
<p>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.<p>
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<h2>Work Experience</h2>
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<h3>Research Scientist</h3>
<p>June 2020 - September 2024</p>
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<h4> <a href="https://www.helmholtz-munich.de/helmholtz-pioneer-campus" target="_blank" > Helmholtz Pioneer Campus </a></h4>
<p>
As a graduate student at the Munich School of Data Science <a href="https://www.mu-ds.de/" target="_blank" > (MUDS) </a>, I joined the <a href="https://www.pioneercampus.org/themenmenue-links/about-us0/principal-investigators/na-cai/index.html" target="_blank">Institute of Translational Genetics</a> to research the genetic basis of mental health disorders.
I design architectures, train models, and conduct 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.
</p>
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<i class="fa fa-briefcase"></i>
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<h3>Research Fellow</h3>
<p style="white-space: nowrap;">August 2024 - September 2024</p>
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<div class="timeline-content">
<h4><a href="https://www.lmu.de/en/" target="_blank">Maximilian University of Munich</a></h4>
I was awarded a fellowship from the Data Science for Social Good Foundation<a href="https://www.datascienceforsocialgood.org/" target="_blank"> (DSSG)</a>, during which I collaborated with Munich's Machine Learning Center <a href="https://mcml.ai/" target="_blank"> (MCML)</a>, the statistical department of <a href="https://www.en.statistik.uni-muenchen.de/index.html" target="_blank">LMU</a>, and Bavaria's state Ministry of the Interior <a href="https://www.bmi.bund.de/EN/topics/civil-protection/civil-protection-node.html" target="_blank">(BMI)</a>.
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.
</p>
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<i class="fa fa-briefcase"></i>
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<h3>Teaching Assistant</h3>
<p>October 2022 - March 2023</p>
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<h4>Technical University of Munich</h4>
<p>
I developed and configured educational material for TUM's Medicine department's Human Genetics of Complex Traits course <a href="https://campus.tum.de/tumonline/ee/ui/ca2/app/desktop/#/slc.tm.cp/student/courses/950609499?$ctx=lang=de&$scrollTo=toc_overview" target="_blank">(ME 1660-P).</a>
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 <a href="https://www.prolehre.tum.de/en/prolehre/programs-services/courses-certification/" target="_blank">TUM ProLehre Media & Didactics</a>.
</p>
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<i class="fa fa-briefcase"></i>
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<h3>Analytics Intern</h3>
<p>October 2019 - April 2020</p>
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<h4>Helmholtz Munich</h4>
<p>Implemented my master thesis at the Institute of Translational Genomics <a href="https://www.helmholtz-munich.de/en/itg" target="_blank">(ITG)</a>, 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.
</p>
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<section id="contributions" class="s-blog target-section">
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<h5>Contributions</h5>
<h1>A list of my academic contributions.</h1>
</div>
<div class="row ab"<img src="favicon.png" alt="">
<div class="col-six tab-full">
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<div class="blog-date">
<a href="https://meetings.cshl.edu/abstracts.aspx?meet=GENOME&year=24">Scientific Poster, Biology of Genomes (CSHL), Cold Spring Harbor Laboratory, May 2024</a>
</div>
<h4 class="h02"><a href="">Tissue Specific Regulation of Mitochondria Encoding Genes.</a></h4>
</p> 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.<p>
<div class="blog-cat">
<p>Mito-Nuclear Interactions, Causal Inference, Graph Neural Networks</p>
</div>
</article>
</div>
<div class="blog-list block-1-2 block-tab-full">
<article class="col-block">
<div class="blog-date">
<a href="">Manuscript in preparation, 2024</a>
</div>
<h4 class="h02"><a href="">Tissue Specific Regulation of Mitochondria Encoding Genes.</a></h4>
</p>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. </p>
<div class="blog-cat">
<p>Mito-Nuclear Interactions, Mediation, colocalization, Mendelian Randomization, Graph Neural Networks, Interpretable Machine Learning</p>
</div>
</article>
</div>
<div class="blog-list block-1-2 block-tab-full">
<article class="col-block">
<div class="blog-date">
<a href="https://adsaannualmeeting2023.sched.com/event/1QUhu/">Scientific Poster, American Dairy Science Association (ADSA), University of Texas, USA 2023</a>
</div>
<h4 class="h02"><a href="https://github.com/DSSGxMunich/hydroxplorer-web-app">HydroXplorer: A Fire Hydrant Range Finder Application.</a></h4>
<p>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.</p>
<div class="blog-cat">
<p>Data Science for Social Good, DSSGxMunich, MCML, Machine Learning, BERD, BYTE, Bavarian Ministry for Digital Affairs </p>
</div>
</article>
</div>
<div class="blog-list block-1-2 block-tab-full">
<article class="col-block">
<div class="blog-date">
<a href="https://github.com/hmgu-itg/HumanMolecularGenetics_TUM">Lecture Notes 2022</a>
</div>
<h4 class="h02"><a href="https://github.com/hmgu-itg/HumanMolecularGenetics_TUM">Human Genetics of Complex Traits.</a></h4>
<p>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.</p>
<div class="blog-cat">
<p>GWAS, UNIX, Complex Traits, Meta-analysis, Bioinformatics, TUM, VSS, JupyterLab</p>
</div>
</article>
</div>
</div>
</div>
<div class="col-six tab-full">
<div class="row blog-content">
<div class="blog-list block-1-2 block-tab-full">
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<div class="blog-date">
<a href="https://2024.eshg.org/">Scientific Poster, European Human Genetics Conference (ESHG), Berlin, June 2024</a>
</div>
<h4 class="h02"><a href="">Tissue Specific Regulation of Mitochondria Encoding Genes.</a></h4>
</p> During the conference, I showcased my poster on the interaction between mitochondrial and nuclear communication in regulating tissue-specific gene expression.<p>
<div class="blog-cat">
<p>Mito-Nuclear Interactions, Causal Inference, Graph Neural Networks</p>
</div>
</article>
</div>
<div class="blog-list block-1-2 block-tab-full">
<article class="col-block">
<div class="blog-date">
<a href="http://recomb2023.bilkent.edu.tr/posters.html">Scientific Poster, Computational Molecular Biology (RECOMB) 2023</a>
</div>
<h4 class="h02"><a href=""> Tissue-specific apparent mtDNA heteroplasmy and its relationship with ageing and mtDNA gene expression.</a></h4>
<p>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.</p>
<div class="blog-cat">
<p>mitochondria, Heteroplasmy, Aging, Molecular Genetics, Gene Regulation, Bioinformatics</p>
</div>
</article>
</div>
<div class="blog-list block-1-2 block-tab-full">
<article class="col-block">
<div class="blog-date">
<a href=""> Scientific Poster, International Genetic Epidemiology Society (IGES) 2021</a>
</div>
<h4 class="h02"><a href="">Tissue-Specific Expression Patterns of Mitochondrial DNA Genes.</a></h4>
<p>Presented up to date research, received valuable feedback, and had meaningful discussions on genetic epidemiology implications.</p>
<div class="blog-cat">
<p>IGES, Epidemiology, mtDNA, Gene Regulation</p>
</div>
</article>
</div>
<div class="blog-list block-1-2 block-tab-full">
<article class="col-block">
<div class="blog-date">
<a href="masterthesis.pdf">Master Thesis, Thessaly University 2020</a>
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<h4 class="h02"><a href="">Quality Control and Imputation of Genotype data from different Illumina arrays</a></h4>
<p>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.</p>
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<p>QC, GWAS, Osteoarthritis, Imputation, Genomic Variation, Bioinformatics, Statistical Genetics, PCA</p>
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<div class="blog-date">
<a href="https://project.starsgame.eu/the-project/">ERASMUS+ project ”STARS GAME” 2021</a>
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<h4 class="h02"><a href="">Science Game Design</a></h4>
<p>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.</p>
<div class="blog-cat">
<p>Science education, Design Thinking, Digital Escape Room, Game-based learning, Erasmus, EU </p>
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