September 21, 2017, Thursday

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Chiara Damiani

Contents

Position

Post-doc research associate at the Department of Informatics, Systems and Communication
Affiliated with Sysbio Center of Systems Biology 

Research Area

Complex systems and systems biology.


My research interests cover:

- deterministic, stochastic and constraint-based modelling of biochemical systems

- methods for sensitivity analysis of biochemical models

- inference of biochemical networks

- emergente behaviors in boolean models of gene regulatory networks

- stem cells differentiation models

- aggregate behavior of catalytic reaction networks and origin of life


Short Bio

I am currently a post-doc researcher at the of Department of Informatics, Systems and Communication at University of Milan Bicocca and I am affiliated to the SYSBIO center for Systems Biology, which is an Italian “open access” Research Infrastructure (RI), directed by Prof. Lilia Alberghina, distributed throughout different locations, focused on Systems Biology, that integrates molecular analysis with math modeling and simulations.

I am currently working on a project that aims at understanding the links between metabolism and cancer via computational models. I adopt constrained-based modeling which, by relying on a steady state assumption, does not require any knowledge about the kinetic parameters of the enzymatic reactions and this is an invaluable advantage when dealing with genome-wide metabolic networks.  

I work in a tight connection with experimental biologists. My principal research interest is indeed to find computational solutions that can help biologists to answer to important questions.

I am characterized by the multidisciplinary approach typical of complex systems science, which I mainly learnt from Stuart Kauffman who was a pioneer in biocomplexity research. During my PhD, I had the opportunity to closely collaborate with him during six months where I pursued my research interest of investigating the influence of cell communication on the dynamics of gene regulatory networks, focusing the attention on the information storage, processing and transfer capabilities of gene regulatory networks by means of measures borrowed from information theory.

The mobility and heterogeneity of my work experience pushed forward my multidisciplinary approach: between my PhD and my current position I spent two years at the The Microsoft Research - University of Trento Centre for Computational and Systems Biology where I was in charge of developing new methods for computational biology. There I conceived and published:
- a novel sensitivity analysis methodology for stochastic models
- a novel causal approach to infer networks from metabolic concentration time series
I was also testing the potentialities of a new programming language with the definition and simulation of complex molecular mechanistic models for drug discovery.
I collaborated with two prestigious Italian institutions: with the San Raffaele Scientific Institute on transcriptome data analysis and with the European Institute of Oncology on a stochastic model of cancer stem cells differentiation.


Publications

JOURNALS

  1. M. Villani, A. Filisetti, A. Graudenzi, C. Damiani, T. Carletti and R. Serra. Growth and Division in a Dynamic Protocell Model. Life, 4(4): 837-864, 2014. DOI: 10.3390/life4040837
  2. P. Cazzaniga, C. Damiani, D. Besozzi, R. Colombo, M.S. Nobile, D. Gaglio and M. Vanoni. Computational Strategies for a System-Level Understanding of Metabolism. Metabolites, 4(4):1034-1087, 2014. DOI: 10.3390/metabo4041034
  3. R. Serra, A. Filisetti, M, Villani, A. Graudenzi, C. Damiani and T. Panini. A stochastic model of catalytic reaction networks in protocells. Natural Computing, 13(3): 367-377, 2014. DOI: 10.1007/s11047-014-9445-6
  4. C. Damiani, D. Pescini, R. Colombo, S. Molinari, L. Alberghina, M. Vanoni, and G. Mauri. An ensemble evolutionary constraint-based approach to understand the emergence of metabolic phenotypes. Natural Computing, 13(3): 321-331, 2014. DOI: 10.1007/s11047-014-9439-4
  5. Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, and Paola Lecca. Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks. Comput. Biol. Chem., 42:5–17, February 2013. ISSN 1476-9271. doi: 10.1016/j.compbiolchem.2012.10.007. URL http://dx.doi.org/10.1016/ j.compbiolchem.2012.10.007.
  6. C. Damiani, R. Serra, M. Villani, S.A. Kauffman, and A. Colacci. Cell-cell interaction and diversity of emergent behaviours. Systems Biology, IET, 5(2):137–144, 2011. ISSN 1751-8849. doi: 10.1049/iet-syb.2010.0039.
  7. A. Graudenzi, R. Serra, M. Villani, C. Damiani, A. Colacci, and S. A. Kauff- man. Dynamical properties of a Boolean model of gene regulatory network with memory. Journal of Computational Biology, 18(10):1291–303, 2011.
  8. R. Serra, M. Villani, C. Damiani, A. Graudenzi, and A. Colacci. Comunicazione cellulare, livelli e strutture ordinate. Sistemi Intelligenti, 2(209-220), 2008. ISSN 1120-9550. doi: 10.1422/27403.


CONFERENCE PROCEEDINGS

  1. A. Graudenzi, C. Damiani, A. Paroni, A. Filisetti, M. Villani, R. Serra and M. Antoniotti. Investigating the role of network topology and dynamical regimes on the dynamics of a cell differentiation model. Proceedings of Wivace 2014, Italian Workshop on Artificial Life and Evolutionary Computation, 2014 May 14-15, Vietri sul Mare, Salerno, Italy. In Advances in Artificial Life and Evolutionary Computation, Communications in Computer and Information Science 445:151-168. Springer International Publishing. DOI: 10.1007/978-3-319-12745-3_13
  2. A. Filisetti, M. Villani, C. Damiani, A. Graudenzi, A. Roli, W. Hordijk, and R: Serra. On RAF sets and autocatalytic cycles in random reaction networks. Proceedings of Wivace 2014, Italian Workshop on Artificial Life and Evolutionary Computation, 2014 May 14-15, Vietri sul Mare, Salerno, Italy. In Advances in Artificial Life and Evolutionary Computation, Communications in Computer and Information Science 445:113-126. Springer International Publishing. DOI: 10.1007/978-3-319-12745-3_10
  3. A. Filisetti, A. Graudenzi, C. Damiani, M. Villani, and R. Serra. The role of backward reactions in a stochastic model of catalytic reaction network. In Li Pietro, Miglino Orazio, Nicosia Giuseppe, Nolfi Stefano, and Pavone Mario, editors, Advances in Artificial Life ECAL 2013 2-6 September 2013, Taormina, Italy Proceedings of the twelfth European Conference on the Synthesis and Simulation of Living Systems, page number 793. MIT press, 2013. URL http: //dx.doi.org/10.7551/978-0-262-31709-2-ch114.
  4. Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani, and Roberto Serra. Recent developments in research on catalytic reaction networks. In Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, and Marco Antoniotti, editors, EPTCS 130 Proceedings of Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation. Milan, Italy, July 1-2, 2013. EPCTS, 2013. doi: 10.4204/EPTCS.130.
  5. Chiara Damiani and Paola Lecca. Model identification using correlation-based inference and transfer entropy estimation. Computer Modeling and Simulation, UKSIM European Symposium on, 0:129–134, 2011. doi: http://doi. ieeecomputersociety.org/10.1109/EMS.2011.58.
  6. C. Damiani, S. A. Kauffman, R. Serra, M. Villani, and A. Colacci. Information transfer among coupled random Boolean networks. In S. Bandini, H.Umeo, S.Manzoni, and G.Vizzari, editors, Cellular Automata, 9th International Conference on Cellular Automata for Research and Industry, (ACRI 2010, Ascoli Piceno, Italy, September 21-24), volume 6350/2010 of Lecture Notes in Computer Science, pages 1–11. Springer-Verlag Berlin Heidelberg, 2010.
  7. A. Graudenzi, R. Serra, M. Villani, C. Damiani, A. Colacci, and S. A. Kauffman. Timing of molecular processes in a synchronous Boolean model of genetic regulatory network. In Proceedings of the European Conference on Complex Systems, ECCS 09, Warwick 21-25 September, 2009, 2009.
  8. C. Damiani, A. Graudenzi, R. Serra, A. Colacci M. Villani, and S. A. Kauffman. On the fate of perturbations in critical random Boolean networks. In Proceedings of the European Conference on Complex Systems, ECCS 09, Warwick 21-25 September, 2009, 2009.
  9. C. Damiani, A. Graudenzi, and M. Villani. How critical random boolean networks may be affected by the interaction with others. In M. Villani R. Serra and I. Poli, editors, Artificial Life and evolutionary computation, proceeding of WIVACE 2008, pages 271–283. World Scientific, 2008. ISBN 978-981-4287-44- 9.
  10. C. Damiani, M. Villani, Ch. Darabos, and M. Tomassini. Dynamics of interconnected Boolean networks with scale-free topology. In M. Villani R. Serra and I. Poli, editors, Artificial Life and evolutionary computation, proceeding of WIVACE 2008, Venice, 8-10 September 2008, pages 271–283. World Scientific, 2008.
  11. R. Serra, M. Villani, C. Damiani, A. Graudenzi, and A. Colacci. The diffusion of perturbations in a model of coupled random Boolean networks. In H. Umeo, S. Morishiga, K. Nishinari, T. Komatsuzaki, and S. Banidini, editors, Cellular Automata (proceedings of 8th International Conference on Cellular Auotomata ACRI 2008, Yokohama, September 2008), ISBN 0302-9743., volume 5191/2008, pages 315– 322, Berlin, 2008. Springer Lecture Notes in Computer Science.
  12. R. Serra, M. Villani, C. Damiani, A. Graudenzi, P. Ingrami, and A. Colacci. In- vestigating cell criticality. In G. Minati and A. Pessa, editors, Towards a general theory of emergence, pages 271–283. World Scientific, 2007.
  13. R. Serra, M. Villani, C. Damiani, A. Graudenzi, A. Colacci, and S. A. Kauffman. Interacting random Boolean networks. In J. Jost and D. Helbing, editors, Proceedings of ECCS07: European Conference on Complex Systems, page paper 35, 2007.


PhD THESIS

Chiara Damiani. Dynamics of Interacting Genetic Networks. PhD Thesis


BOOK CHAPTERS

Chiara Damiani. Modeling the influence of cell signaling on the dynamics of gene regulatory networks. In Paola Lecca, editor, Biomechanics of Cells and Tissues, volume 9 of Lecture Notes in Computational Vision and Biomechanics, pages 103–130. Springer Netherlands, 2013. ISBN 978-94-007-5889- 6. doi: 10.1007/978-94-007-5890-2 5. URL http://dx.doi.org/10.1007/ 978-94-007-5890-2_5.


ABSTRACTS

  1. C. Damiani, R. Colombo, S. Molinari, D. Pescini, D. Gaglio, M. Vanoni, L. Alberghina, and G. Mauri. An ensemble approach to the study of the emergence of metabolic and proliferative disorders via flux balance analysis (abstract). In Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, and Marco Antoniotti, editors, EPTCS 130 Proceedings of Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation. Milan, Italy, July 1-2, 2013, 2013. doi: 10.4204/EPTCS.130.
  2. R. Serra, A. Filisetti, A. Graudenzi, C. Damiani, and M. Villani. A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks. In Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, and Marco Antoniotti, editors, EPTCS 130 Proceedings of Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation. Milan, Italy, July 1-2, 2013, 2013. doi: 10.4204/EPTCS.130.
  3. M. Fedeli, T. A. Renzi, D. Morpurgo, T-P. Nguyen, C. Damiani, G. Rossetti, M. Pagani, S. Abrignani, P. Dellabona, and G. Casorati. miRNA control of the gene expression program controlling INKT cell development (abstract). In Atti del 6th International Symposium on CD1 and NKT Cells, September 23 -27, 2011, Gleacher Center, Chicago, IL USA, 2011.


POSTERS

  1. R. Serra, A. Filisetti, M. Villani, A. Graudenzi and C. Damiani, Stochastic dynamics of chemical reaction networks in a stylized protocell model. Poster presentation at ECCS'14, European Conference on Complex systems, September 22-26, 2014, Lucca, Italy.
  2. C. Damiani, D. Pescini, R. Colombo, S. Molinari, M. Vanoni, L. Alberghina, G. Mauri, Ensemble evolutionary flux balance analysis for metabolic network modeling. Poster presentation at BITS2014, Eleventh Annual Meeting of the Bioinformatics Italian Society February 26-28, 2014, Rome, Italy.
  3. R. Colombo, C. Damiani, D. Gaglio, D. Pescini, G. Mauri, E. Sacco, S. Molinari, L. Alberghina, and M. Vanoni. Flux balance analysis approaches towards the definition of cancer-specific metabolic rewiring (poster). Poster presentation at ICSB2013 - 14th International Conference on Systems Biology., 2013.
  4. R. Serra, A. Filisetti, A. Graudenzi, C. Damiani, and M. Villani. The influence of the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks. Poster presentation at ECCS 2013, European Conference on Complex Systems., 2013.
  5. M. Fedeli, V. Milli, T. A. Renzi, D. Morpurgo, T-P. Nguyen, C. Damiani, G. Ros- setti, M. Pagani, S. Abrignani, P. Dellabona, and G. Casorati. miRNA regulation of INKT cell development (poster). Poster presentation at Milan meets immunology 2: 4-23-12, IFOM-IEO campus, Milano, 2012.
  6. M. Fedeli, T. A. Renzi, D. Morpurgo, T-P. Nguyen, C. Damiani, G. Rossetti, M. Pagani, S. Abrignani, P. Dellabona, G. Casorati. miRNA regulation of the gene expression program controlling INKT cell development. Poster presentation at Milan meets immunology 1 : 9-20-11, San Raffaele Scientific Institute, Milano , 2011.


Contacts

Chiara Damiani, Ph.D.
Department of Informatics, Systems and Communication
University of Milan Bicocca
Building U14 - Room 1002 - Viale Sarca 336I-20126 - Milan (MI) -
phone: +39 02 64487918
mail: chiara.damiani@unimib.it