Simone Ciccolella

I am a PostDoc in the BIAS Lab in the Computer Science Department at University of Study Milano-Bicocca (DISCo).

I obtained my Ph.D. student in Computer Science at University of Study Milano-Bicocca (DISCo), in February 2022.
During my M.Sc. I visited Iman Hajirasouliha at IH Lab in Weill Cornell Medicine in New York and we established an active collaboration between the two research groups.
My main research interests range from the definition of methods and algorithms for graph theory to the development of algorithms for the reconstruction of cancer progression from sequencing data.

Research interests:

  • Evolutionary phylogenies
  • Graph theory
  • Machine Learning

Publications:

  • Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola & Marco Previtali. MALVIRUS: an integrated application for viral variant analysis. BMC Bioinformatics. https://doi.org/10.1186/s12859-022-04668-0
  • Sarwan Ali, Simone Ciccolella, Lorenzo Lucarella, Gianluca Della Vedova, and Murray Patterson. Simpler and Faster Development of Tumor Phylogeny Pipelines. Journal of Computational Biology, https://doi.org/10.1089/cmb.2021.0271
  • Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova. Inferring Cancer Progression from Single Cell Sequencing while allowing loss of mutations. Bioinformatics, , btaa722, https://doi.org/10.1093/bioinformatics/btaa722
  • Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova, Triplet-based similarity score for fully multilabeled trees with poly-occurring labels, Bioinformatics, , btaa676, https://doi.org/10.1093/bioinformatics/btaa676
  • Malikic S, Mehrabadi FR, Ciccolella S, Rahman MK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC. PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. Genome Res. 2019 Nov;29(11):1860-1877. doi: 10.1101/gr.234435.118. Epub 2019 Oct 18. PMID: 31628256; PMCID: PMC6836735.
  • Bonizzoni P, Ciccolella S, Vedova GD, Soto M. Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. IEEE/ACM Trans Comput Biol Bioinform. 2019 Sep-Oct;16(5):1410-1423. doi: 10.1109/TCBB.2018.2865729. PMID: 31603766.
  • P. Bonizzoni, S. Ciccolella, G. Della Vedova, and M. Soto. Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. ACM-BCB 2017.

Talks:

  • 19th European Conference on Computational Biology, 2020, Barcelona, Spain (Virtual)
  • 24th Annual International Conference RECOMB, 2020. Verona, Italy (Virtual)
  • RECOMB-Computational Cancer Biology (CCB), 2020. Verona, Italy (Virtual). Presenting author.
  • SCANGEN: Single-cell cancer genomics, special session of ISMB (the main Conference in BioInformatics), 2018. Chicago, IL, USA. Presenting author.
  • Cancer Development And Complexity, 2018. Como, Italy. Presenting author.
  • 22nd Annual International Conference RECOMB, 2018. Paris, France.
  • RECOMB-Computational Cancer Biology (CCB), 2018. Paris, France. Presenting author.
  • 8th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), 2017. Boston, MA, USA. Presenting author.
  • 17th Workshop on Algorithms in Bioinformatics (WABI), 2017. Boston , MA, USA.
  • Cancer Development And Complexity, 2017. Como, Italy.
  • Workshop on Graph Assembly Algorithms for omics data, 2016. Milano, Italy.

Posters:

  • S. Ciccolella, M. Gomez, M.Patterson, G. Della Vedova, I. Hajirasouliha and P. Bonizzoni.
    Inferring Cancer Progression from Single Cell Sequencing while allowing loss of mutations.
    Poster accepted at RECOMB-CCB 2018 and SCANGEN at ISMB 2018 Conferences.

Education:

  • 2016-2018: M.Sc. in Computer Science, University of Study Milano-Bicocca.
    Master’s Thesis: Inferring cancer progression from Single Cell Sequencing data while allowing loss of mutations
    Supervisor: Prof. Gianluca Della Vedova, University of Study Milano-Bicocca.
    Co-supervisor: Dr. Iman Hajirasouliha, Weill Cornell Medicine, New York.
  • 2013-2016: B.Sc. in Computer Science, University of Study Milano-Bicocca.
    Bachelor’s Thesis: A linear Programming Approach to reconstruct cancer phylogenies from multi-sample sequencing data
    Supervisor: Prof. Gianluca Della Vedova, University of Study Milano-Bicocca.
    Co-supervisor: Prof. Paola Bonizzioni, University of Study Milano-Bicocca.

Contacts:

Email: simone [dot] ciccolella [atsymbol] unimib [dot] it

Address: Stanza 1001, c/o Edificio U14, Dip. di Informatica Sistemistica e Comunicazione, Viale Sarca, 336, I-20126 Milano (Italy)

Phone Number: +39 02 6448 7917