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Evgenios Kladis

PhD Student

University of Zurich

About Me

I am a PhD Student in Clinical Immunology at the Department of Quantitative Biomedicine of the University of Zürich. My project focuses on the study of immunological dysregulation in Systemic Lupus Erythematosus patients (SLE). Primary goal is to explain the heterogeniety of the disease by finding markers linked to the phenotype, severity and flares of the disease and proceed to the evaluation of potential diagnostic targets in a clinical setting. Using my strong computational and biology background, through my PhD, I would like to contribute fully to the project by, 1) doing patient selection based on design of experiments methods, 2) following a data-driven biofluid sample profiling strategy, 3) analysing data using state-of-the-art tools. I believe seeing the project from sample aquisition to analysis would give me a practical understanding of the nuances of biological data production, aiding in a more complete research endeavor.

Education & Work

Education

University of Zurich – PhD in Clinical Immunology (2023 – now)

Onassis Foundation Scholarship for PhD studies

ETH Zürich, UZH, Unibasel – MSc in Computational Biology and Bioinformatics (2021 - 2023)

ETH D-BSSE department conference representative for the Computational Biology and Bioinformatics MSc

ETH Teaching comission member for the Computational Biology and Bioinformatics MSc

Onassis Foundation Scholarship for MSc studies

Kapodistrian University of Athens – BSc in Informatics (2016 - 2020)

Best student award from the Greek State Scholarship Foundation (IKY)

Work Experience

Bioinformatics Research Intern - Roche Basel, PMDA team, pRED (09/2022 – 03/2023)

Collaborating Researcher - Complex Event Recognition Group, NCSR "Demorkitos" (09/2020 – 06/2021)

Skills

Data Analysis

Single-cell data, Transcriptomic, Proteomic, Epigenomic, BCR-TCR
Time-series, (Temporal) Clinical data, Flow cytometry

Programming

Python, R, C/C++, Java, HTML, CSS

Tools & Libraries

Hugginface, Snakemake, Tensorflow, Git, Docker, Seurat (R), FlowSOM (R)

Projects

Click on a project to view more details & Publications.

B Cell evolution using Protein Language Models

Studying of B cell evolution, phylogeny, in-silico affinity maturation using various Foundational and Antibody-specific protein language models with inhouse BCR data.

CRISPR-Cas9 single-cell transcriptome analysis workflow development

Development of a single-cell transcriptomics analysis pipeline of CRISPR-Cas9 experiments, including preprocessing, Quality Control and Analysis workflows

Early Time-Series Classification

Forecasting outcomes using time-series data mainly from Biological and Maritime data by implementing/applying NLP methods