Simone Zaccaria
Simone Zaccaria
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Group Leader
Group Leader
I completed my PhD in 2017 in Computer Science at the university of Milano Bicocca (Milan, Italy) under the supervision of Prof. Paola Bonizzoni, after being a visiting research scholar at the University of Bielefeld (Germany) with Prof. Jens Stoye and a visiting graduate student at Brown University (RI, USA) in 2016 with Prof. Ben Raphael. I then trained for five years as a postdoctoral associate in cancer computational biology at Princeton University (USA) with Prof. Ben Raphael. In 2020, I have started the Computational Cancer Genomics research group at the UCL Cancer Institute. The group is currently supported by a CRUK Career Development Fellowship that I was awarded to in 2022. I am also part of the CRUK Lung Cancer Center and I help leading the TRACERx study and the PEACE autopsy study, led by Profs. Charles Swanton, Mariam Jamal-Hanjani, and Nicholas McGranahan. Lastly, I am an academic editor of the PLOS Computational Biology journal.
My research focuses on the design and development of computational methods to analyse tumour sequencing data (including multi-region/site, liquid biopsies, and single-cell sequencing) and to study the cancer evolutionary process. My background is in Computer Science and my early education included the study of combinatorial optimization, computational complexity, and the design of exact and parameterized algorithms, approximations, and heuristics. One of the goals of my research is to show that rigorous mathematical formulations and formal computational methodologies are crucial to obtain meaningful and impactful results for biological and clinically-related applications.
Positions
06/2022 – Present | Group Leader, Cancer Research UK Career Development Fellow, UCL Cancer Institute, London, UK
09/2020 – 06/2022 | Group Leader, University College London (UCL) Cancer Institute, London, UK
04/2017 – 09/2020 | Postdoctoral Research Associate, Princeton University, Princeton, NJ, USA. Advisor: Prof. Ben Raphael
10/2018 – 06/2019 | Visiting Scientist, New York Genome Center, New York, NY, USA.
01/2017 – 03/2017 | Research Scholar, University of Milano-Bicocca, Milan, Italy. Advisor: Prof. Paola Bonizzoni
09/2016 – 12/2016 | Research Scholar, Princeton University, Princeton, NJ, USA. Advisor: Prof. Ben Raphael.
11/2015 –07/2016 | Visiting PhD Graduate Student, Brown University, Providence, RI, USA. Advisor: Prof. Ben Raphael.
02/2013 – 07/2013 | Research Scholar, University of Bielefeld, Bielefeld, Germany. Advisor: Prof. Jens Stoye.
Roles
2024 – Present | Academic Editor in the Omics Section of PLOS Computational Biology journal.
10/2020 – Present | Deputy Lead of the Informatics Core, CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK.
10/2020 – Present | Visiting Scientist, The Francis Crick Institute, London, UK.
2022 – 2023 | Guest Editor of PLOS Computational Biology journal, editing 3 publications in total.
10/2018 – 06/2019 | Visiting Scientist, New York Genome Center, New York, NY, USA.
Fellowships
06/2022 | CRUK Career Development Fellowship, Cancer Research UK (CRUK), ~£1.6M to support related research.
03/2022 | Sir Henry Dale Fellowship, Wellcome Trust, ~£1.2M to support related research, declined by myself in favour of the CRUK Fellowship.
09/2020 | Rosetrees Trust starting grant, Rosetrees Trust UK Charity, £300k to support establishing independent research group.
10/2019 | GALLO award for outstanding cancer research, Rutgers Cancer Institute of New Jersey, NJ, USA.
Honors and Awards
05/2019 | GALLO award for outstanding cancer research, Rutgers Cancer Institute of New Jersey.
05/2017 | RECOMB 2017 travel fellowship for presenting author, International Society for Computational Biology (ISCB), Hong Kong.
05/2013 | Franco Belli Journalist's Memory Grant, University of Milano-Bicocca.
05/2012 | Exchange program, University of Milano-Bicocca.
03/2012 | EXTRA Plus Program, University of Milano-Bicocca and Cariplo foundation.
Scientific Community Work
05/2023 | Conference Chair of the CRUK Lung Cancer Centre of Excellence Training Workshop, York, UK, May 24 – 26, 2023.
05/2022 | Conference Chair of the RECOMB Satellite Workshop on Computational Cancer Biology 2022, La Jolla, USA, May 20 – 21, 2022.
2022 – Present | Expert Trainer at the EMBL-EBI course on cancer genomics and transcriptomics, Cambridge, UK.
01/2021 – Present | Program Committee member of the yearly international RECOMB Satellite Workshop on Computational Cancer Biology.
01/2020 – Present | Program Committee member of the yearly international Intelligent Systems For Molecular Biology (ISMB) conference.
01/2019 – Present | Program Committee member of the International Workshop on Algorithms in Bioinformatics (WABI).
Education
01/2014 – 01/2017 | PhD in Computer Science, cum laude, University of Milano-Bicocca, Milan, Italy.
Thesis title: Inferring Genomic Variants and their Evolution
Advisor: Prof. Paola Bonizzoni11/2011 – 07/2013 | Masters Degree (M.Sc.) in Computer Science, 110/110 summa cum laude, University of Milano-Bicocca, Milan, Italy.
Advisors: Prof. Paola Bonizzoni and Prof. Jens Stoye (University of Bielefeld, Germany).10/2008 – 09/2011 | Bachelors degree (B.Sc.) in Computer Science, 110/110 summa cum laude, University of Milano-Bicocca, Milan, Italy.
Advisor: Prof. Paola Bonizzoni.
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