Simone Ciccolella

PostDoc at Bias Lab
May 2025

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Publications

Journal

  1. Ciccolella S, Denti L, Avila Cartes J, Della Vedova G, Pirola Y, Rizzi R, Bonizzoni P Differential analysis of alternative splicing events in gene regions using residual neural networks. Neural Computing and Applications. (2025) DOI
  2. Ciccolella S, Cozzi D, Della Vedova G, Kuria SN, Bonizzoni P, Denti L Differential quantification of alternative splicing events on spliced pangenome graphs. PLOS Computational Biology. (2024) DOI
  3. Cartes JA, Bonizzoni P, Ciccolella S, Vedova GD, Denti L PangeBlocks: customized construction of pangenome graphs via maximal blocks. BMC Bioinformtics. (2024) DOI
  4. Avila Cartes J, Bonizzoni P, Ciccolella S, Della Vedova G, Denti L, Didelot X, Monti DC, Pirola Y RecGraph: recombination-aware alignment of sequences to variation graphs. Bioinformatics. (2024) DOI
  5. Ciccolella S, Vedova GD, Filipovic V, Gomez MS Three Metaheuristic Approaches for Tumor Phylogeny Inference: An Experimental Comparison. Algorithms. (2023) DOI
  6. Chourasia P, Ali S, Ciccolella S, Vedova GD, Patterson M Reads2Vec: Efficient Embedding of Raw High-Throughput Sequencing Reads Data. Journal of Computational Biology. (2023) DOI
  7. Cartes JA, Anand S, Ciccolella S, Bonizzoni P, Vedova GD Accurate and fast clade assignment via deep learning and frequency chaos game representation. GigaScience. (2022) DOI
  8. Ali S, Ciccolella S, Lucarella L, Vedova GD, Patterson M Simpler and Faster Development of Tumor Phylogeny Pipelines. Journal of Computational Biology. (2021) DOI
  9. Ciccolella S, Bernardini G, Denti L, Bonizzoni P, Previtali M, Vedova GD Triplet-based similarity score for fully multilabeled trees with poly-occurring labels. Bioinformatics. (2021) DOI
  10. Ciccolella S, Denti L, Bonizzoni P, Vedova GD, Pirola Y, Previtali M MALVIRUS: an integrated application for viral variant analysis. BMC Bioinformatics. (2021) DOI
  11. Ciccolella S, Patterson M, Bonizzoni P, Vedova GD Effective Clustering for Single Cell Sequencing Cancer Data. IEEE Journal of Biomedical and Health Informatics. (2021) DOI
  12. Ciccolella S, Ricketts C, Gomez MS, Patterson M, Silverbush D, Bonizzoni P, Hajirasouliha I, Vedova GD Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. Bioinformatics. https://doi. (2021) DOI
  13. Ciccolella S, Gomez MS, Patterson MD, Vedova GD, Hajirasouliha I, Bonizzoni P gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. BMC Bioinformatics. (2020) DOI
  14. Malikic S, Mehrabadi FR, Ciccolella S, Rahman MdK, Ricketts C, Haghshenas E, Seidman D, Hach F, Hajirasouliha I, Sahinalp SC (2019) PhISCS: a combinatorial approach for subperfect tumor phylogeny reconstruction via integrative use of single-cell and bulk sequencing data. Genome Research. DOI
  15. Bonizzoni P, Ciccolella S, Vedova GD, Gomez MS Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. IEEE ACM Transactions on Computational Biology and Bioinformatics. (2019) DOI

Conference

  1. Juyal A, Tayebi Z, Zelikovsky A, Soto-Gomez M, Ciccolella S, Vedova GD, Patterson M Plastic: An Easy to Use and Modular Tool for Benchmarking Tumor Phylogeny Reconstruction Pipelines. Computational Advances in Bio and Medical Sciences. Springer Nature Switzerland (2025)
  2. Chourasia P, Ali S, Ciccolella S, Vedova GD, Patterson M Clustering SARS-CoV-2 Variants from Raw High-Throughput Sequencing Reads Data. 11th International Conference, ICCABS 2021, Virtual Event, December 16-18, 2021. (2021)
  3. Ciccolella S, Patterson MD, Bonizzoni P, Vedova GD Effective Clustering for Single Cell Sequencing Cancer Data. Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2019, Niagara Falls, NY, USA, September 7-10, 2019. (2019)
  4. Ciccolella S, Gomez MS, Patterson M, Vedova GD, Hajirasouliha I, Bonizzoni P gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. 8th IEEE International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2018, Las Vegas, NV, USA, October 18-20, 2018. (2018)
  5. Bonizzoni P, Ciccolella S, Vedova GD, Gomez MS Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2017, Boston, MA, USA, August 20-23, 2017. (2017)