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

Associate Professor. Department of Mathematics and Geosciences, University of Trieste.
Core Faculty, PhD program in Applied Data Science & Artificial Intelligence, University of Trieste.
Adjoint Faculty, PhD program in Theoretical and Scientific Data Science, SISSA.
Honorary fellow, The Institute of Cancer Research, UK.

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).

Meet me

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.

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.

TBD (see openings)

Training:

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Dr. Azad Sadr (2024-27)

Applied Data Science & Artificial Intelligence PhD program (University of Trieste, Italy).
Training:

MSc in Industrial Engineering (Wayne State University, USA);
BSc in Industrial Engineering (Kar Higher Education Institute, Iran);

Topic: TBD

Sara Cocomello (2024)

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 ....

Topic: TBD

Elena Rivaroli (2024)

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 ....

Topic: TBD

Master and Bachelor students

Silvia De Cleva (2024)

Program: MSc Data Science and Scientific Computing.
Topic (MSc thesis): TBD.
Co-supervised with Nicola Calonaci.

Visiting PhD students

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

Carmen Oroperv, 2024. PhD Student with Søren Besenbacher at the Department of Clinical Medicine, Aarhus University, Denmark.
Nair Varela Ruoco, 2023. PhD Student with David Posada at the Biomedical Research Centre, Vigo University, Spain.

Alumni

PhD students

Lucrezia Patruno (2020-23). Computational strategies for single-cell multi-omics data analysis and integration. Computer Science program at the University of Milan-Bicocca (co-supervised with Marco Antoniotti and Alex Graudenzi), then postdoc at University College London.

MSc students

Sara Cocomello (2024). TBD. Data Science and Scientific Computing at the University of Trieste, then PhD student with us in Trieste.
Elena Rivaroli (2024). TBD. Data Science and Scientific Computing at the University of Trieste, then PhD student with us in Trieste.
Lorenzo Taroni (2024). Variational autoencoders for single-cell gene-set enrichment analysis. Data Science and Scientific Computing at the University of Trieste.
Clara Canavese (2023). A theory and inference model for cancer population epigenetics. Physics at the University of Turin, then PhD student at SISSA - Human Technopole.
Elena Buscaroli (2022). Bayesian multi-lineage inference from gene therapy assays. Data Science and Scientific Computing at the University of Trieste, then PhD student with us in Trieste.
Salvatore Milite (2021). Copy-number variations genotyping from scRNA-seq. Data Science and Scientific Computing at the University of Trieste, then PhD student at the European School for Molecular Medicine, with us.

BSc students

Abdula Khalus (2024). Approximate Bayesian Computation for synthetic tumours. Artificial Intelligence and Data Analytics, at the University of Trieste.
Edoardo Insaghi (2023). Generalised linear models for single cell differential expression. Statistics at the University of Trieste, then MSc student in Data Science in Trieste.

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)

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