Team

The CDS Lab lab is based in Trieste, but some members are physically located across other institutes and, in that case, co-supervised with other PIs.
2024 Trieste
Front: Giorgia, Elena R, Elena B, Lucrezia, Katzyarina, Sara, VirginiaBack: Alice, Riccardo, Giovanni, Nicola, Azad, Giulio
Missing: Salvatore, Eriseld

Principal Investigator

Prof. Giulio Caravagna, PhD 


Current positions
Training:
  • 2017-20, The Institute of Cancer Research, UK. With Andrea Sottoriva.
  • 2015-17, University of Edinburgh, UK. With Guido Sanguinetti. 
  • 2011-15, University of Milan-Bicocca, Italy. With Giancarlo Mauri and Marco Antoniotti.  
  • 2011, PhD in Computer Science (University of Pisa, Italy). 
  • BSc, MSc in Computer Science (University of Pisa, Italy). 

Postdoctoral scientists

Dr. Riccardo Bergamin, PhD (since 2020)


Training:
  • 2020, PhD in Theoretical Physics (SISSA, Italy). 
  • MSc in Physics (University of Padova, Italy); 
  • BSc in Physics (University of Padova, Italy); 
 Topic: mathematical modelling and inference for evolutionary processes. 
Email

Dr. Nicola Calonaci, PhD (since 2021)


Training:
  • 2021. PhD in Physics and Chemistry of Biological Systems (SISSA, Italy). 
  • MSc in Physics (University of Pisa, Italy); 
  • BSc in Physics (University of Pisa, Italy); 

Topic: Artificial Intelligence for clonal evolution under therapy. 
Email

TBD (see openings)


Training:
  • TBD

Topic: Machine Learning algorithms for single-cell and long-reads sequencing technologies.
Email

PhD students

Dr. Alice Antonello (2022-25)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy).  
Training:
  • MSc in Quantitative and Computational Biology (University of Trento, Italy); 
  •  BSc in Biotechnology (University of Turin, Italy);

Topic: Bayesian models for aneuploidy from whole-genome sequencing. 
Email

Dr. Salvatore Milite (2022-26)


Computational Biology PhD Program (European School of Molecular Medicine, Italy). Co-supervised with Andrea Sottoriva (Human Technopole, Italy). 
Training:
  • MSc in Data Science and Scientific Computing (University of Trieste, Italy); 
  • BSc in Molecular Biology (University of Padua, Italy); 

Topic: statistical methods for longitudinal single cell sequencing. 
Email

Dr. Arianna Tasciotti (2022-25)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy). Sponsored by Plus srl. Co-supervised with Alberto d'Onofrio (University of Trieste, Italy)
Training:
  • MSc in Data Science and Scientific Computing (University of Trieste, Italy); 
  • BSc in Physics (University of Trieste, Italy);

Topic:  inference of latent dynamical systems from time-series data. 
Email

Dr. Elena Buscaroli (2023-26)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy). 
Training:
  • MSc in Data Science and Scientific Computing (University of Trieste, Italy);
  • BSc in Genetics (University of Bologna, Italy);

Topic:  statistical models for high-resolution image demultiplexing.
Email

Dr. Katsiaryna Davydzenka (2023-26)


National PhD program in Artificial Intelligence (hosted at SISSA, Italy). Co-supervised with Guido Sanguinetti (SISSA, Italy).
Training:
  • BSc in Medical ecology (International Sakharov Environmental Institute, Belarus);
  • MSc in Food and Beverage Innovation and Management (Marche Polytechnic University, Italy);
  • Master of II level in Bioinformatics and Data Science (University of Siena, Italy);

Topic:  TBD.
Email

Dr. Giovanni Santacatterina (2023-26)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy). Co-supervised with Leonardo Egidi (University of Trieste, Italy)

Training:
  • MSc in Data Science and Scientific Computing (University of Trieste, Italy); 
  • BSc in Physics (University of Trento, Italy); 

Topic:  model-based statistical methods for single-cell data analysis. 
Email

Dr. Lucrezia Valeriani (2023-26)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy). Co-supervised with Alberto Cazzaniga and Alessio Ansuini (Area Science Park).
Training:
  • MSc in Data Science and Scientific Computing (University of Trieste, Italy);
  • BSc in Genetics (University of Bologna, Italy);

Topic: statistical methods for long-reads sequencing.
Email

Dr. Giorgia Gandolfi (2024-27)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy), sponsored by Hospital San Raffaele, Italy. Co-supervised with Giovanni Tonon (San Raffaele, Italy).
Training:
  • MSc in Bioinformatics (University of Bologna, Italy);
  • BSc in Biology (University of Parma, Italy);

Topic: statistical methods for single-cell sequencing.
Email

Dr. Virginia Gazziero (2024-27)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy), sponsored by Toscana Life Sciences, Italy. Co-supervised with Anna Kabanova (Toscana Life Sciences, Italy).
Training:
  • MSc in Functional Genomics (University of Trieste, Italy);
  • BSc in Biotechnology (University of Insubria, Italy);

Topic: applying machine learning for clonal evolution in chronic lymphocytic leukaemia.
Email

Dr. Eriseld Krasniqi (2024-27)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy), sponsored by Regina Elena National Cancer Institute, Italy.
Training:
  • Degree in Medicine and Surgery (University of Rome II, Italy); 
  • Specialty in Medical Oncology (University of Rome II, Italy)

Topic: applying machine learning for clonal evolution in breast cancer.
Email

Dr. Azad Sadr (2024-27)


Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy).
Training:
  • MSc in Data Science and Scientific Computing (University of Trieste, Italy); 
  • BSc in Biology (University of Parma, Italy);

Topic: TBD
Email

Master and Bachelor students

Lorenzo Taroni  (2023)


Program: MSc Data Science and Scientific Computing.
Topic (MSc thesis): variational autoencoders for single-cell gene-set enrichment analysis
Co-supervised with Lucrezia Valeriani and Salvatore Limite..

Abdula Kalus  (2024)


Program: BSc Artificial Intelligence and Data Analytics.
Topic (BSc thesis): TBD

Elena Rivaroli  (2024)


Program: MSc Data Science and Scientific Computing.
Topic (MSc thesis): TBD

Sara Cocomello (2024)


Program: MSc Data Science and Scientific Computing.
Topic (MSc thesis): Markov kernels for copy number inference.

Visiting PhD students

Over the years, PhD students from other groups visited our group.

Alumni

PhD students

MSc students

BSc students

Pictures

2021 Lab retreat. Passo del Pura.(Riccardo, Salvatore, Alice, Giulio, Nicola) 
2022 Lab lunch. Venice.(Riccardo, Giulio, Nicola) 
2022 Lab dinner. Trieste.(Nic, Alice, Ric, Elena, Giulio, Salvatore
2022 Genomics England Research Summit (Giulio)
2022 Lab meeting epiphany (Giulio)
2023 Off work. Alps (Nicola, Riccardo, Giovanni, Lucrezia, Elena, Clara, Lucrezia, Alice)
2023 Project meeting. Bormio. (Lucrezia, Giulio, Salvatore)