Meet Our Team
Faculty Members
Postdocs and PhD Students
Carlo Cipriani
@San Raffaele Telethon Institute for Gene TherapyPhD Candidate – XXXVIII cycle
Information Technology,
Politecnico di Milano
Francesco Gazzo
@San Raffaele Telethon Institute for Gene TherapyPhD Candidate – XXXVIII cycle
Information Technology,
Politecnico di Milano
Andrea Vergani
@Human TechnopolePhD Candidate – XXXVIII cycle
Information Technology,
Politecnico di Milano
Simone Tomè
@Istituto Neurologico Carlo BestaPhD Candidate – XXXIX cycle
Information Technology,
Politecnico di Milano
Linda Maldera
@Istituto Neurologico Carlo BestaPhD Candidate – XL cycle
Information Technology,
Politecnico di Milano
Riccardo Pizzichemi
@San Raffaele Telethon Institute for Gene TherapyPhD Candidate – XLI cycle
Data Analytics and Decision Sciences,
Politecnico di Milano
Isaia Belardinelli: Master Thesis in Computer Science and Engineering (CSE), ‘Metabarcoding and machine learning analysis of wather ecosystems for identification, classification and annotation of tassonomic profiles’ in collaboration with BMR Genomics srl
Daniele Bottazzi: Master Thesis in Computer Science and Engineering (CSE), ‘Biologically-informed machine learning via differentiable convex optimization’, in collaboration with the Saez-Rodriguez group, EMBL-EBI Hinxton, UK
Simone Callegarin: Master Thesis in Computer Science and Engineering (CSE), ‘Nerve fiber density quantification through deep learning strategies’, in collaboration with the MIND lab – Neurological Institute ‘Carlo Besta’
Alessandro Del Fatti: Master Thesis in Computer Science and Engineering (CSE), ‘Deep learning for microscopy fluorescence bioimages’, in collaboration with the MIND lab – Neurological Institute ‘Carlo Besta’
Laura Guerra: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Cell segmentation algorithms for imaging-based spatial transcriptomics‘, in collaboration with Dynamics of Immune Responses – San Raffaele Hospital
Alipoor Mehrshad: Master Thesis in Computer Science and Engineering (CSE), ‘Large Language Models for transcriptomics data analysis and patient stratification’
Denisa Sufaj: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Next-Generation Sequencing data analysis of prostate cancer‘, in collaboration with Institute of Oncology Research, Swizerland
2024 – 2025, Tommaso Alfonsi: Data integration and knowledge discovery in viral genomics
2016 – 2020, Arif Canakoglu: Heterogeneous biomolecular and clinical knowledge data integration for biomedical inference
Ruba Al Khalaf: “Knowledge modeling and data analysis methods for understanding the viral genome evolution”, XXXVI cycle, PhD in Information Technology, Politecnico di Milano
Tommaso Alfonsi: “Methods and tools for data integration and knowledge discovery in viral genomics”, XXXVI cycle, PhD in Information Technology, Politecnico di Milano
Silvia Cascianelli: “Machine Learning in Oncogenomics: a key to dissecting cancer inner heterogeneity”, XXXVI cycle, PhD in Information Technology, Politecnico di Milano
Aldo Sergi: “Computational methods for studying potential biomarkers for early diagnosis and treatment of ovarian cancer”, XXXV cycle, PhD in Information Technology, Politecnico di Milano
Carolina Testa: “Integration of Genomic Computing and the Nichoid 3D culture system for repurposing and testing Synthetic Lethality-based antimetastatic drugs”, XXXV cycle, PhD in Information Technology, Politecnico di Milano
Andrea Gulino: “Distributed processing and optimization methods for querying big genomic datasets”, XXXIII cycle, PhD in Information Technology, Politecnico di Milano
Michele Leone: “Genomic metadata integration and data processing methods for the analysis of chromatin behaviour in different biological conditions”, XXXIII cycle, PhD in Information Technology, Politecnico di Milano
Luca Nanni: “Computational inference of DNA folding principles: from data management to machine learning”, XXXIII cycle, PhD in Information Technology, Politecnico di Milano
Anna Bernasconi: “Model, integrate, search… repeat: a sound approach to building integrated repositories of genomic data”, XXXII cycle, PhD in Information Technology, Politecnico di Milano
Gaia Ceddia: “Computational methods for data-driven predictions and understanding of biological interactions”, XXXII cycle, PhD in Information Technology, Politecnico di Milano
Olha Horlova: “Exploiting the array data model for genomic data management”, XXXII cycle, PhD in Information Technology, Politecnico di Milano;
Eirini Stamoulakatou: “Impact of mutational processes on regulatory elements in human cancer”, XXXII cycle, PhD in Information Technology, Politecnico di Milano
Stefano Perna: “Data-driven techniques for knowledge discovery in regulomics”, XXXI cycle, PhD in Information Technology, Politecnico di Milano
Abdulrahman Kaitoua: “Scalable data management and processing for genomic computing”, XXIX cycle, PhD in Information Technology, Politecnico di Milano
Arif Canakoglu: “Modular schema based data warehousing of evolving, redundant and incomplete data: Application to biomolecular knowledge data integration and inference”, XXVIII cycle, PhD in Information Technology, Politecnico di Milano
Vahid Jalili: “Efficient data structures for cross-sample inferences on genomic data”, XXVIII cycle, PhD in Information Technology, Politecnico di Milano
Fernando Paluzzi: “Novel genome-scale data models and algorithms for molecular medicine and biomedical research”, XXVIII cycle, PhD in Information Technology, Politecnico di Milano
Pietro Pinoli: “Modeling and querying genomic data”, XXVIII cycle, PhD in Information Technology, Politecnico di Milano
Francesco Venco: “Modeling and querying genomic data”, XXVIII cycle, PhD in Information Technology, Politecnico di Milano
Davide Chicco: “Computational Prediction of Gene Functions through Machine Learning methods and Multiple Validation Procedures”, XXVI cycle, PhD in Information Technology, Politecnico di Milano
2025 – Simone Airaghi: Master Thesis in Computer Science and Engineering (CSE), ‘Interactome-driven subtyping of colorectal cancer via epithelium–stroma interactions’, in collaboration with the Oncogenomics lab – Candiolo Cancer Institute
2025 – Alex Amati: Master Thesis in Computer Science and Engineering (CSE), ‘Machine learning strategies for multi-omics investigation of RAS-associated mutations in colorectal cancer’
2025 – Elisa Bonomi: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘CHIM-CAT: a bioinformatic framework to dissect viral-host interactions’, in collaboration with the Telethon Institute for Gene Therapy – San Raffaele Hospital
2025 – Daniele Bottazzi: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Evaluating the impact of prior knowledge and inductive biases in predicting combinatorial gene perturbations with GEARS’, in collaboration with the Saez-Rodriguez group, EMBL-EBI – Hinxton, UK
2025 – Alessandro Cacciatore: Master Thesis in Computer Science and Engineering (CSE), ‘An integrative bioinformatics and machine learning approach for non-coding RNA-based signatures in Amyotrophic Lateral Sclerosis’, in collaboration with the MIND lab – Neurological Institute ‘Carlo Besta’
2025 – Francesca Conti: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Transcriptomic analysis to improve diagnosis and patient stratification in primary mitochondrial myopathies’, in collaboration with the MIND lab – Neurological Institute ‘Carlo Besta’
2025 – Francesco De Sio: Master Thesis in Computer Science and Engineering (CSE) ‘Computational framework for identifying actionable mutations through genomic and transcriptomics data integration’
2025 – Sara Resta: Master Thesis in Computer Science and Engineering (CSE), ‘Convolutional neural networks for [18F]FDG PET imaging-based prediction of clinical relapse in patients with Takayasu Arteritis’, in collaboration with the Nuclear Medicine Unit – San Raffaele Hospital
2025 – Luca Zanotto: Master Thesis in Computer Science and Engineering (CSE), ‘Deep learning approaches for alpha-synucleinopathies classification using skin biopsy images’, in collaboration with the MIND lab – Neurological Institute ‘Carlo Besta’
2024 – Cristina Iudica: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Exploring mutational profile in triple-negative breast cancer with statistical and machine learning methods’
2024 – Alessia Lorenzi: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Rare variants and genetic predictors in Covid-19 outcome in the ORIGIN cohort’, in collaboration with the Center of Human Genetics – Pharmacological Research Institute ‘Mario Negri’
2024 – Valentina Margiotta: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Data modelling and machine learning approaches for quantitative analysis of Seed Amplification Assay kinetic curves: advancing the understanding of α-synucleinopathies from biological samples’, in collaboration with the MIND lab – Neurological Institute ‘Carlo Besta’
2024 – Cecilia Mongardi: Master Thesis in Biomedical Engineering (BioMed), ‘Characterization and improvement of patient prognosis integrating transcriptomic data and Sarculator nomogram in extremity soft tissue sarcomas’, in collaboration with the Molecular Pharmacology – National Cancer Institute
2024 – Francesca Pia Panaccione: Master Thesis in Computer Science and Engineering (CSE), ‘Generative AI for gene expression: A biologically informed Graph Neural Network approach’
2024 – Clara Pessia: Master Thesis in Biomedical Engineering (BioMed), ‘Deciphering the immune microenvironment in paediatric Acute Myeloid Leukaemia (AML) using single-cell multi-omics’, in collaboration with the Genomics Research Centre – Human Technopole
2024 – Sara Resta: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Role of AI and advanced [18F]FDG PET analysis in the management of patients with Takayasu Arteritis’, in collaboration with the Nuclear Medicine Unit – San Raffaele Hospital
2024 – Manuel Tacca: Master Thesis in Computer Science and Engineering (CSE), ‘Integrating biological prior knowledge into tree-based machine learning models for comprehensive gene expression analysis’
2024 – Raffaele Valota: Master Thesis in Bioinformatics for Computational Genomics (BCG), ‘Effect of Raloxifene on cells treated with SARS-CoV-2 Spike protein, a transcriptomic approach’, in collaboration with the Computational Pharmacology and Toxicology unit – Pharmacological Research Institute ‘Mario Negri’
2023 – Riccardo Campi: Master Thesis in Computer Science and Engineering (CSE), ‘Machine learning-based forecast of helmet-CPAP therapy failure in acute respiratory distress syndrome patients’, in collaboration with the Vimercate Hospital
2023 – Maria Laura Chieruzzi: Master Thesis in Biomedical Engineering (BioMed), ‘Identification of RAS co-occurrent mutations in colorectal cancer patients: workflow assessment and enhancement’
2023 – Alireza Ketabdari: Master Thesis in Computer Science and Engineering (CSE), ‘Reinforcement learning force field’, in collaboration with the Fundació Institut de Recerca Biomèdica – Barcelona, Spain
2023 – Iva Milojkovic: Master Thesis in Biomedical Engineering (BioMed), ‘Machine learning for gene expression-based multi-label classification of cancer subtypes’
2023 – Simone Tomè: Master Thesis in Computer Science and Engineering (CSE), ‘Unraveling tumor-stroma interactions in colorectal cancer through gene co-expression network analysis’, in collaboration with the Oncogenomics lab – Candiolo Cancer Institute
2022 – Michele Bellomo: Master Thesis in Mathematics Engineering (ME), ‘Statistical and machine learning methods for discovering mutational signatures in RAS-mutated colorectal patients’
2022 – Amos Mainetti: Master Thesis in Computer Science and Engineering (CSE), ‘Discovery and identification of a new colorectal cancer subtype through multiple clustering and classification approaches’, in collaboration with the Oncogenomics lab – Candiolo Cancer Institute
2022 – Andrea Vergani: Master Thesis in Computer Science and Engineering (CSE), ‘Shifting from machine learning in genomic prediction to phenomic forecasting for the study of bovine daily milk yield with genotype data’, in collaboration with the Veterinary Medicine and Animal Sciences Department, University of Milan
2021 – Chiara Barbera: Master Thesis in Computer Science and Engineering (CSE), ‘Development of single-sample classifiers for subtyping of Colorectal Cancer’, in collaboration with the Oncogenomics lab – Candiolo Cancer Institute
2021 – Sotoodeh Naeemi Sanatdoost: Master Thesis in Biomedical Engineering (BioMed), ‘Investigation of transcript isoform RNA-seq data and machine learning techniques for breast cancer intrinsic subtyping’
2020 – Tommaso Alfonsi: Master Thesis in Computer Science and Engineering (CSE), ‘Integration of DNA variation data into a GDM repository and API development for identification of genomic populations’
2020 – Elena Danchenko: Master Thesis in Computer Science and Engineering (CSE), ‘Re-engeneering of a tool for drug repositioning with NMTF’
2020 – Luca Guarrera: Master Thesis in Biomedical Engineering (BioMed), ‘Multi-omic computational analysis to develop a new strategy for pharmacological treatment of Cornelia De Lange syndrome’, in collaboration with the Computational Pharmacology and Toxicology unit – Pharmacological Research Institute ‘Mario Negri’
2020 – Federica Ioli: Master Thesis in Biomedical Engineering (BioMed), ‘A novel computational approach in breast cancer transcriptomics to understand tumor evolution’, in collaboration with the Computational Pharmacology and Toxicology unit – Pharmacological Research Institute ‘Mario Negri’
2020 – Simone Lanzillotta: Master Thesis in Computer Science and Engineering (CSE), ‘Learning text embeddings on virus sequences for candidate drug discovery’
2020 – Lorenzo Perino: Master Thesis in Biomedical Engineering (BioMed), ‘Hybrid gene selection framework for predicting breast cancer relapse’
2020 – Nicholas Ravasio: Master Thesis in Biomedical Engineering (BioMed), ‘A computational drug repositioning approach towards new pharmacological strategies for trabectedin treatment’, in collaboration with the Pharmacological Research Institute ‘Mario Negri’
2019 – Francesco Guzzo: Master Thesis in Computer Science and Engineering (CSE), ‘Imputation of biochemical activity associated with functional elements of the genome produced by epigenomic experiments’
2019 – Sara Pidò: Master Thesis in Computer Science and Engineering (CSE), ‘Network integration algorithms for the analysis of biological data’
2019 – Piervincenzo Ventrella: Master Thesis in Computer Science and Engineering (CSE), ‘Forecast of renal failure for patients affected by chronic kidney disease with machine learning techniques on hospital data’, in collaboration with the Vimercate Hospital
2018 – Luana Brancato: Master Thesis in Computer Science and Engineering (CSE), ‘Development of a visual tool suite to integratively use the GenoMetric Query Language within the Galaxy framework for computational genomics’
2018 – Silvia Cascianelli: Master Thesis in Computer Science and Engineering (CSE), ‘RNA sequencing-based computational subtyping of Breast Cancer for clinical outcome prediction’, in collaboration with the Oncogenomics lab – Candiolo Cancer Institute
2018 – Alessandra Castagna: Master Thesis in Biomedical Engineering (BioMed), ‘Studio della componente immunologica del tumore: dall’analisi di pathway ai metodi di deconvoluzione di dati di espressione genica provenienti da campioni eterogenei’, in collaboration with the Computational Pharmacology and Toxicology unit – Pharmacological Research Institute ‘Mario Negri’
2018 – Fabrizio Frasca: Master Thesis in Computer Science and Engineering (CSE), ‘Data-driven modeling of epigenetic transcriptional regulation’, in collaboration with the Institute of Molecular Oncology of the Italian Association for Cancer Research
2018 – Antonella Lancieri: Master Thesis in Biomedical Engineering (BioMed), ‘Individuazione, implementazione e validazione di criteri clinici per supportare il processo di “presa in carico” nell’ASST di Vimercate’, in collaboration with the Vimercate Hospital
2018 – Riccardo Mologni: Master Thesis in Computer Science and Engineering (CSE), ‘RoadmapImporter modules for GMQL-Importer: integration of Roadmap Epigenomics Project data and metadata into a GDM repository’
2018 – Chiara Regondi: Master Thesis in Computer Science and Engineering (CSE), ‘Predictive modeling of gene expression regulation in ovarian cancer’, in collaboration with the Computational Pharmacology and Toxicology unit – Pharmacological Research Institute ‘Mario Negri’
2017 – Andrea Corneo: Master Thesis in Computer Science and Engineering (CSE), ‘Motif discovery in the Next-Generation Sequencing era’, in collaboration with the Biosciences Department, University of Milan
2017 – Alberto Marchesi: Master Thesis in Biomedical Engineering (BioMed), ‘Identificazione di zone di DNA ricche di fattori di trascrizione: sviluppo di nuovi strumenti di calcolo e analisi in diverse linee cellulari’, in collaboration with the Institute of Molecular Oncology of the Italian Association for Cancer Research
2017 – Simone Pallotta: Master Thesis in Computer Science and Engineering (CSE), ‘Extension of R/Bioconductor environment with support for GenoMetric Query Language for genomic big data processing’
2017 – Jorge Ignacio Vera Pena: Master Thesis in Computer Science and Engineering (CSE), ‘Automation of retrieval, transformation and uploading of genomic data and their metadata for their integration into a GDM repository’
2016 – Marta Falabretti: Master Thesis in Biomedical Engineering (BioMed), ‘Integrazione e analisi dati dell’offerta sanitaria ambulatoriale in Lombardia e proposta di riorganizzazione nell’ospedale di Vimercate’ in collaboration with the Vimercate Hospital
2016 – Liuba Nausicaa Martino: Master Thesis in Mathematics Engineering (ME), ‘Identicazione di associazioni tra fattori di trascrizione e di loro complessi regolatori della trascrizione nel DNA’