Simone Ciccolella

I am a Ph.D. student in Computer Science at University of Study Milano-Bicocca (DISCo), from November 2018.
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:

  • Cancer phylogenies
  • Graph theory
  • Data structures

Publications:

  • S. Ciccolella, M. Gomez, M.Patterson, G. Della Vedova, I. Hajirasouliha and P. Bonizzoni.
    gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data
    Invited to BMC Bioinformatics, 2018.
  • P. Bonizzoni, S. Ciccolella, G. Della Vedova, and M. Soto.
    Does relaxing the infinite site assumption give better tumor phylogenies? An ILP-based comparative approach.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics.
  • P. Bonizzoni, S. Ciccolella, G. Della Vedova, and M. Soto.
    Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP.
    ACM-BCB ’17 Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics, 2017.

Talks:

  • 2018 IEEE 8th International Conference on Computational Advances in Bio and medical Sciences (ICCABS), 2018. Las Vegas, NV, USA.
  • SCANGEN: Single-cell cancer genomics, special session of ISMB, 2018. Chicago, IL, USA.
  • RECOMB-Computational Cancer Biology (CCB), 2018. Paris, France.
  • 8th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), 2017. Boston, MA, USA.

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.

Preprints:

  • S. Malikic, S. Ciccolella, F. Mehrabadi, C. Ricketts, Md. Khaledur Rahman, E. Haghshenas, D. Seidman, F. Hach, I. Hajirasouliha, S. Cenk Sahinalp.
    PhISCS – A Combinatorial Approach for Sub-perfect Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data
    BioRxiv, doi: https://doi.org/10.1101/376996, 2018
  • 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.
    BioRxiv, doi: https://doi.org/10.1101/268243, 2018

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: s [dot] ciccolella [atsymbol] campus [dot] 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