SELECTED PEER-REVIEWED PUBLICATIONS


ARCHIVES    : PUBMED  |   DBLP 
PRE-PRINTS : arXiv  |  bioRxiv

Selected peer-reviewed papers, divided by area/type. A full list of drafts, edited volumes, book chapters, posters etc. is available in my CV. 

Data Science

  1. Algorithmic methods to infer the evolutionary trajectories in cancer progressionG.Caravagna, A.Graudenzi, D.Ramazzotti, R.Sanz-Pamplona, L.De Sano, G.Mauri ,V.Moreno, M.Antoniotti, B.Mishra. PNAS 113 (28), E4025–E4034 2016. 
  2. CAPRI: efficient inference of cancer progression models from cross-sectional data. D.Ramazzotti, G.Caravagna, L.Olde Loohuis, A.Graudenzi, I.Korsunsky, G.Mauri, M.Antoniotti, B.Mishra. Bioinformatics 31(18), 3016-3026, 2015.
  3. Inferring tree causal models of cancer progression with a shrinkage estimator and probability raising. L.Olde Loohuis, G.Caravagna, A.Graudenzi, D.Ramazzotti, G.Mauri, M.Antoniotti, B.Mishra. PLoS ONE, 9(10):e108358, 2014.

Modelling

  1. Gene switching rate determines response to extrinsic perturbations in a transcriptional network motifS.de Franciscis, G.Caravagna, A.d'Onofrio. Scientific Reports 6, 26980, 2016.
  2. Investigating the relation between stochastic differentiation, homeostasis and clonal expansion in intestinal crypts via multiscale modelingA.Graudenzi, G.Caravagna, G.De Matteis, M.Antoniotti. PLoS ONE, 9(5):e97272, 2014.
  3. Stochastic Hybrid Automata with non-instantaneous transitions to model biochemical systems with delays. G.Caravagna, A.d'Onofrio, M.Antoniotti, G.Mauri. Information and Computation, 236, 19-34, 2014.    
  4. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks. G.Caravagna, G.Mauri, A.d'Onofrio. PLoS ONE 8(2):e51174, 2013.
  5. Fine-tuning anti-tumor immunotherapies via stochastic simulationsA.d'Onofrio, G.Caravagna, R.Barbuti. BMC Bioinformatics, Volume 13, Supplement 4, 2012.
  6. Bio-PEPAd: a non-Markovian extension of Bio-PEPA. G.Caravagna, J.Hillston. Theoretical Computer Science 419, 26-49, 2012. 
  7. Delay stochastic simulation of biological systems: a purely delayed approach. R.Barbuti, G.Caravagna, A.Maggiolo-Schettini, P.Milazzo.: Transactions on Computational Systems Biology XIII, Lecture Notes in Bioinformatics 6575, 61-84, 2011.
  8. Tumour suppression by immune-system through stochastic oscillations. G.Caravagna, A.d'Onofrio, P.Milazzo, R.Barbuti. Journal of Theoretical Biology, 265 (3), 336-345, 2010. 


Software

  1. TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. L.De Sano, G.Caravagna, D.Ramazzotti, A.Graudenzi, G.Mauri, B.Mishra, M.Antoniotti. Bioinformatics 32, 1911-1913, 2016. 
  2. CABeRNET: a Cytoscape app for Augmented Boolean models of gene Regulatory NETworksA.Paroni, A. Graudenzi, G.Caravagna, C.Damiani, G.Mauri, M. Antoniotti. BMC Bioinformatics 17(64), 1-12, 2016. 
  3. Automatising the analysis of stochastic biochemical time-series. G.Caravagna, L.De Sano and M.Antoniotti. BMC Bioinformatics 16(Suppl 9):S8, 2015.
  4. CoGNaC: a Chaste plugin for the multiscale simulation of gene regulatory networks driving the spatial dynamics of tissues and cancer. S.Rubinacci, A.Graudenzi, G.Caravagna, J.Osborne, J.Pitt-Francis, G.Mauri and M.Antoniotti. Cancer Informatics 14 (S4), 53-65, 2015.
  5. GeStoDifferent: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process M.Antoniotti, G.Bader, G.Caravagna, S.Crippa, A.Graudenzi, G.Mauri. Bioinformatics 29(4), 513-514, 2013.


Conference proceedings 

  1. Matching models across abstraction levels with Gaussian Processes. G.Caravagna, L.Bortolussi, G.Sanguinetti. Computational Methods in Systems Biology (CMSB 2016), LNCS 9859, 49-66,  2016. 
  2. NoisySIM: exact simulation of stochastic chemically reacting systems with extrinsic noises. G.Caravagna, G.Mauri, A.d'Onofrio. Proc. of the Symposium on Theory of Modeling and Simulation (TMS 2013) 12:1-6, Society for Computer Simulation International, San Diego, CA, USA. 
  3. Effects of delayed immune-response in tumor immune-system interplay. G.Caravagna, A.Graudenzi,M.Antoniotti, G.Mauri, A.d'Onofrio. Proc. of 1st. Int. Work. Hybrid Systems and Biology (HSB 2012), Electronic Proceedings in Theoretical Computer Science 92, 106-121, 2012.