Publications

Conference Oral Presentations

  • Sarto Basso R. Efficient algorithms to discover alterations with complementary functional association in cancer. 22nd International Conference on Research in Computational Molecular Biology (RECOMB) 2018, April 21, 2018, Paris, France.
  • Baruzzo G. SPARSim: taking account of data sparsity in single cell and 16S rRNA gene sequencing. 15th Annual Meeting of the Bioinformatics Italian Society Meeting 2018, June 28, 2018, Turin, Italy.
  • Zorzan I. Capturing Spatiotemporal Patterns in Cell Differentiation by Local Cell-Cell Communication Modeling. 5th International Synthetic & Systems Biology Summer School – Biology meets Engineering & Computer Science, July 27, 2018, Certosa di Pontignano (Siena), Italy.
  • Di Camillo B. A multi-agents based space-temporal model of the interaction between immune system and tumor growth. Invited talk at the 5th International Synthetic & Systems Biology Summer School – Biology meets Engineering & Computer Science, July 27, 2018, Certosa di Pontignano (Siena), Italy.
  • Vandin F. Finding Patterns in Cancer Genomes: Algorithms and Challenges, Workshop on the Future of Algorithms in Biology. Carnegie Mellon University (CMU), USA, 2018.
  • Vandin F. Computational methods to discover significant mutations in cancer genomes. UNIBO-UCSD Cooperation Project Workshop, University of Bologna, 2018.
  • Baruzzo G. SPARSim Single Cell: a count data simulator for single cell RNA-seq data. 3rd Annual MAQC Society Conference, April 9, 2019, Riva del Garda, Italy.
  • Yoo-Ah Kim. Identifying Drug Sensitivity Subnetworks with NETPHLIX. RECOMB-CCC 2019 Meeting. May 3, 2019, Washington D.C., USA.
  • Zorzan I. Localized spatial emergent behaviour in bacterial cells via band-detect network
    motif. 2019 18th European Control Conference (ECC), June 26, 2019, Naples, Italy.
  • Di Camillo B. MAST: A Multi-Agent based Spatio-Temporal Model of the interaction between immune system and tumor growth. 16th Annual Meeting of the Bioinformatics Italian Society Meeting 2019, June 27, 2019, Palermo, Italy.
  • Yoo-Ah Kim. Identifying Drug Sensitivity Subnetworks with NETPHIX. ISMB / ECCB 2019 (NetBio). July 23, 2019, Basel, Switzerland.
  • Di Camillo B. Reverse engineering single cell data: challenges and perspectives. Invited talk at EMBO Workshop: Network inference in biology and disease. 10 – 13 September 2019, Naples, Italy.
  • Baruzzo G. Reliable simulation of count data for single cell RNA sequencing. NETTAB / BBCC 2019 Meeting, November 13, 2019, Fisciano, Italy.

Conference Abstracts/Posters

  • Zorzan I, Del Favero S, Di Camillo B, Schenato L. Capturing Spatio-temporal Patterns in Cell Differentiation by Local Cell-Cell Communication Modeling. Computational Systems Biology School. May 9-11, 2018, Rome, Italy.
  • Patuzzi I, Baruzzo G, Ricci A, Losasso C, Di Camillo B. SPARSim: taking account of data sparsity in single cell and 16S rRNA gene sequencing. 15th Annual Meeting of the Bioinfomatics Italian Society Meeting 2018, June 27-29, 2018, Turin, Italy.
  • Zorzan I, Del Favero S, Di Camillo B, Schenato L. Capturing Spatiotemporal Patterns in Cell Differentiation by Local Cell-Cell Communication Modeling. 5th International Synthetic & Systems Biology Summer School – Biology meets Engineering & Computer Science, July 25-29, 2018, Certosa di Pontignano (Siena), Italy.
  • Baruzzo G, Patuzzi I, Di Camillo B. SPARSim Single Cell: a count data simulator for single cell RNA-seq data. 11th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics, December 8-10, 2018, New York, USA.
  • Baruzzo G, Finco G, Morandini F, Alotto P, Di Camillo B. MAST: A Multi-Agent based Spatio-Temporal Model of the interaction between immune system and tumor growth. 11th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics, December 8-10, 2018, New York, USA.
  • Baruzzo G, Cappellato M, Zorzan I, Del Favero S, Schenato L, Vandin F, Di Camillo B. A
    computational approach to predict scRNA-seq cells spatial position using scRNA-seq and in situ hybridization data. 11th annual RECOMB/ISCB Conference on Regulatory & Systems Genomics, December 8-10, 2018, New York, USA.
  • Baruzzo G, Patuzzi I, Di Camillo B. SPARSim Single Cell: a count data simulator for single cell RNA-seq data. 3rd Annual MAQC Society Conference, April 8-10, 2019, Riva del Garda, Italy.
  • Baruzzo G, Finco G, Morandini F, Alotto P, Di Camillo B. MAST: A Multi-Agent based Spatio-Temporal Model of the interaction between immune system and tumor growth. 16th Annual Meeting of the Bioinformatics Italian Society Meeting 2019, June 26-28, 2019, Palermo, Italy.
  • Baruzzo G, Patuzzi I, Di Camillo B. SPARSim Single Cell: a count data simulator for single cell RNA-seq data. 27th Conference on Intelligent Systems for Molecular Biology and the 18th European Conference on Computational Biology, July 21-25, 2019, Basel, Switzerland.
  • Zorzan I. Biological networks analysis from a control engineering perspective. Delft Mechanical Engineering Talent Event, October 17-18, 2019. Delft, Netherlands.
  • Baruzzo G, Patuzzi I, Di Camillo B.  Reliable simulation of count data for single cell RNA sequencing. NETTAB / BBCC 2019 Meeting, November 12-13, 2019, Fisciano, Italy.

Conference Articles

  • Zorzan I, Schenato L. Localized spatial emergent behaviour in bacterial cells via Band-Detect network motif. 2019 European Control Conference, June 25-29, 2019, Napoli, Italy (in submission, November 2018).

Journal Articles

  • Dal Molin A, Di Camillo B. How to design a single-cell RNA-sequencing experiment: pitfalls, challenges and perspectives. Briefings in Bioinformatics, bby007 (2018).
  • Zorzan I, Del Favero S, Di Camillo B, Schenato L. Analysis of a Minimal Gene Regulatory Network for Cell Differentiation. IEEE Control Systems Letters (2018, accepted for publication).
  • Patuzzi I, Baruzzo G,  Losasso C, Ricci A, Di Camillo B. metaSPARSim: a 16S rRNA gene sequencing count data simulator. BMC Bioinformatics,  20, 416 (2019).
  • Baruzzo G, Patuzzi I, Di Camillo B. SPARSim Single Cell: a count data simulator for single cell RNA-seq data. Bioinformatics, btz52 (2019).
  • Sarto Basso R, Hochbaum DS, Vandin F. Efficient algorithms to discover alterations with
    complementary functional association in cancer. PLOS Computational Biology (2019)
  • Tanevski et al. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Life Science Alliance (2020).
  • Kim, Y. A., Basso, R. S., Wojtowicz, D., Liu, A. S., Hochbaum, D. S., Vandin, F., & Przytycka, T. M. (2020). Identifying Drug Sensitivity Subnetworks with NETPHIX. Iscience, 23(10), 101619 (2020)
  • Kim, Y.A., Wojtowicz, D., Sarto Basso, R., Sason, I., Robinson, W., Hochbaum, D.S., Leiserson, M.D., Sharan, R., Vandin, F. and Przytycka, T.M. Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer. Genome medicine, 12, pp.1-12 (2020).
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