Dimitris Papakonstantinou

About Me

My academic and professional interests include Bioinformatics, Statistical Learning, and Information Theory. In February 2025 acquired my PhD in Bioinformatics and Immuno-oncology, and gained an expertise in genetic and transcriptomic analyses accross multiple domains like single-cell and spatial. I'm also experienced in developing models and automatic processing tools for information extraction from Biomedical texts and relate them to biological databases. I have a strong programming and data science background while being competent in data visualisation, DB manipulation. My engineering background in Applied Mathematics and Physics forms a strong interdisciplinary basis giving me the ability to quickly adapt in rapidly changing research directions and environments

Education

2025	PhD: University Paris-Saclay, Doctoral School Cancérologie : biologie - médecine - sante (CBMS)
Thesis Title:	Genetic and Transcriptomic Analysis of Pancreatic Ductal Adenocarcinoma
Notable Features:	DNA mutation analysis, RNA analysis, Spatial Transcriptomics Supervisor: C. Bleriot

2019:	M.Sc., Bioinformatics and Computational Biology, Faculty of Biology, National Kapodistrian University of Athens
Thesis Title:	Machine Learning Techniques and Cell Irradiation
Notable Features:	Ensemble Methods, Decisions Trees, K-neighbors data imputation, Hidden Markov Models, Principal Component Analysis, Post-Hoc Interpretation models Supervisor: A. Georgakilas

2014	Engineering Diploma : Applied Mathematics and Physical Sciences, National Technical University of Athens
Specialisation:	Theoretical and Computational Physics Solid State Physics
Thesis Title:	Philosophy and Physics: The Evolution of the Materialist Interpretation Supervisor: A.Arageorgis

Experience

Title:	Bioinformatician \| Data Scientist
Year:	2021
Location:	Paris, France
Institution:	Gustave Roussy Institute
Responsibilities:	Structurization of clinical data Data extraction and analysis from medical text NLP tasks: text classification, named entity recognition NLP toolkits (nltk, spacy, prodigy) Transformers models Pytorch, Cuda

Title:	Bioinformatician \| Data Scientist
Location:	Athens, Greece
Institution:	Biomedical Research Foundation, Academy of Athens
Responsibilities:	Development of models and automatic tools to extract information from biomedical texts and relate them to proper biological DBs Data extraction and analysis from diverse databases NLP tasks: text classification, named entity recognition, aspect-based sentiment analysis, question answering NLP toolkits (nltk, word2vec) Transformers models Pytorch, Cuda Google Colab notebooks

Skills

Programming:	Python, R, C, C++, JavaScript, PHP, Java, Perl, Haskell
Python Tools:	NumPy, SciPy, Statistics, Anaconda, Jupyter Notebook
ML Libraries:	Scikit‑Learn (Advanced), TensorFlow (Basic), PyTorch (Basic)
Other Scientific Suites:	Octave, Matlab, Mathematica
Web Development & Visualization:	NodeJS, ReactJS, ELM, HTML5, CSS3, JavaScript, WordPress, Drupal, Flask
Databases:	MySQL, Oracle, MongoDB
Natural Languages:	English: full working proficiency, French: limited working proficiency, Greek: native