Claudio Angione



Journal papers

9.   M. Taffi, N. Paoletti, C. Angione, S. Pucciarelli, M. Marini and P. Lió, "Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis", Frontiers in Genetics - Systems Biology, 2014 (to appear)
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8.   C. Angione, A. Occhipinti, and G. Nicosia, "Satisfiability by Maxwell-Boltzmann and Bose-Einstein Statistical Distributions", ACM Journal of Experimental Algorithmics, 2014 (to appear)

7.   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Design and strain selection criteria for bacterial communication networks", Nano Communication Networks, 4(4), 155-163, 2013

6.   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Pareto Optimality in Organelle Energy Metabolism Analysis", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(4), 1032-1044 2013

5.   C. Angione, J. Costanza, G. Carapezza, P. Lió, and G. Nicosia, "A Design Automation Framework for Computational Bioenergetics in Biological Networks", Molecular BioSystems, 9(10), 2554-2564, 2013

4.   C. Angione, A. Occhipinti, G. Stracquadanio, and G. Nicosia, "Bose-Einstein Condensation in Satisfiability Problems", European Journal of Operational Research, 227(1), 44-54, 2013 - Featured in Le Scienze - Scientific American

3.   G. Carapezza, R. Umeton, J. Costanza, C. Angione, G. Stracquadanio, A. Papini, P. Lió, G. Nicosia, "Efficient Behavior of Photosynthetic Organelles via Pareto Optimality, Identifiability and Sensitivity Analysis", ACS Synthetic Biology Journal, 2(5), 274-288, 2013

2.   C. Angione, P. Lió, and G. Nicosia, "How to Compute with Metabolism in Bacteria?", ERCIM News, 12, 2012

1.   J. Costanza, G. Carapezza, C. Angione, P. Lió, and G. Nicosia, "Robust Design of Microbial Strains", Bioinformatics, 28(23), 3097-3104, 2012


Refereed conference papers with proceedings

14.   C. Angione, P. Lió, "Discovering the Escherichia coli nutritional phase space from a compendium of environmental conditions", in Proceedings of NETTAB 2014 – 14th International Workshop on Network Tools and Applications in Biology, Turin, Italy, October 15-17, 2014

13.   C. Angione, E. Bartocci, L. Bortolussi, P. Lió, A. Occhipinti and G. Sanguinetti, "Bayesian Design for Whole Cell Synthetic Biology Models", in Proceedings of HSB 2014 - the Third International Workshop on Hybrid Systems Biology, Vienna, Austria, July 23-24, 2014

12.   C. Angione, N. Pratanwanich, and P. Lió, "A hybrid of multi-omics FBA and Bayesian factor modeling to identify pathway crosstalks", in Proceedings of the 6th International Workshop on Bio-Design Automation (IWBDA), Boston, MA, June 11-12, 2014

11.   C. Angione, J. Costanza, G. Carapezza, P. Lió, and G. Nicosia, "Identifiability Analysis to Characterize Mitochondrial Diseases", in Proceedings of the 5th International Workshop on Bio-Design Automation (IWBDA) at Imperial College, London, UK, July 12-13, 2013

10.   J. Costanza, C. Angione, G. Carapezza, P. Lió, and G. Nicosia, "Multi-objective Optimisation of Escherichia coli for Direct Production of 1,4-butanediol", in Proceedings of the 5th International Workshop on Bio-Design Automation (IWBDA) at Imperial College, London, UK, July 12-13, 2013

9.   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Multi-objective design for bacterial communication networks", in Proceedings of IEEE ICC'13 - Workshop MoNaCom - The 3rd IEEE International Workshop on Molecular and Nanoscale Communications. Budapest, Hungary, June 9-13, 2013

8.   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Pareto epsilon-Dominance and Identifiable Solutions for BioCAD Modeling", in Proceedings of DAC 2013 - The 50th ACM/EDAC/IEEE Design Automation Conference. Austin, Texas, USA, June 2-6, 2013

7.   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "Rational Design of Organelle Compartments in Cells", in Proceedings of NETTAB 2012 - Twelth International Workshop on Network Tools and Applications in Biology - Workshop focused on Integrated Bio-Search, Como, Italy, November 14-16, 2012, EMBnet Journal

6.   J. Costanza, G. Carapezza, C. Angione, P. Lió, and G. Nicosia, "Multi-objective Optimisation, Sensitivity and Robustness Analysis in FBA modeling", in Proceedings of CMSB 2012 - The 10th Conference on Computational Methods in Systems Biology. The Royal Society, London, UK. October 3-5, 2012, Springer LNCS

5.   C. Angione, G. Carapezza, J. Costanza, P. Lió, and G. Nicosia, "The Role of the Genome in the Evolution of the Computational Complexity of Metabolic Machines", in Proceedings of the European Conference in Complex Systems - ECCS'12, Brussels, September 3-7, 2012, Springer Complexity

4.   C. Angione, G. Carapezza , J. Costanza, P. Lió, and G. Nicosia, "Computing with Metabolic Machines", in Proceedings of Turing100: The Alan Turing Centenary Conference. University of Manchester, UK. June 22-26, 2012, pp. 1-15. Best paper award presented by Sir Roger Penrose [photo] [photo] [photo] [photo]

3.   J. Costanza, C. Angione, P. Lió, and G. Nicosia, "Are Bacteria Unconventional Computing Architectures?", in Proceedings of CiE 2012: Turing Centenary Conference. University of Cambridge, UK. June 18-23, 2012

2.   J. Costanza, G. Carapezza, C. Angione, R. Umeton, P. Lió, and G. Nicosia, "MetaDesign: Bacterial Strain Design Automation Software", in Proceedings of the 4th International Workshop on Bio-Design Automation (IWBDA) at Design Automation Conference (DAC 2012), San Francisco, CA, USA, June 3-4, 2012, pp. 18-19

1.   C. Angione, G. Nicosia, G. Stracquadanio, "Characteristic Phase Transitions and Complex Networks in Random Satisfiability Problems", From Self-Organisation in Living Systems to Sensor and Wireless Networks, 2nd Workshop on Bio-Inspired Design of Networks, BIOWIRE 2009. Pietro Lio', Eiko Yoneki, Jon Crowcroft, Dinesh C. Verma (Eds.). Cambridge, UK, June 11-12, 2009


Extended abstracts

1.   M. Taffi, N. Paoletti, C. Angione, E. Merelli, M. Marini, and P. Lió, "Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis", Frontiers in Genetics, 2013


Refereed conference papers

6.   M. Taffi, S. Pucciarelli, N. Paoletti, C. Angione, M. Marini, and P. Lió "Bioengineering metabolic pathways of PCBs degrading bacteria for the optimisation of ecological functions", in 10th European Symposium on Biochemical Engineering Sciences and 6th International Forum on Industrial Bioprocesses in collaboration with ACS. Lille, France. September 7-10, 2014

5.   C. Angione, J. Costanza, G. Carapezza, P. Lió, and G. Nicosia, "Pareto Front and Identifiability Analysis to Characterize Mitochondrial Diseases", in Mitochondrial Disease: Translating biology into new treatments, Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, October 2-4, 2013

4.   J. Costanza, C. Angione, G. Carapezza, P. Lió, and G. Nicosia, "Pareto-based Gene and Pathway Sieve for Biofuel Production", in Proceedings of the 5th International Workshop on Bio-Design Automation (IWBDA) at Imperial College, London, UK, July 12-13, 2013

3.   J. Costanza, G. Carapezza, C. Angione, P. Lió, G. Nicosia. “Reducing atmospheric CO2 by optimizing the consumption from synthetic organisms”, in SB 6.0 Biobricks at Imperial College - London, UK. July 9-11, 2013

2.   C. Angione, A. Occhipinti, G. Nicosia. "Bose-Einstein Condensation in Satisfiability Networks", in NetSci 2012: The International School and Conference on Complex Networks. Northwestern University - Evanston, Illinois. June 18-22, 2012.

1.   J. Costanza, G. Carapezza, C. Angione, P. Lió, G. Nicosia. "Pareto Front Sensitivity in Large Scale Biological Networks", in NetSci 2012: The International School and Conference on Complex Networks. Northwestern University - Evanston, Illinois. June 18-22, 2012.


Technical reports

3.   C. Angione, E. Camilo, J. Harvey, P. Beltrao, "Post-translational modifications: a call to arms for computational biologists". Department of Applied Mathematics and Theoretical Physics, University of Cambridge, 2013

2.   C. Angione, G. Nicosia, G. Stracquadanio, "Characteristic Phase Transitions and Bose-Einstein Condensation in Networks of Random Satisfiability Problems". University of Catania, 2009

1.   C. Angione, G. Nicosia, G. Stracquadanio, "Chaotic Quicksort: One-dimensional Chaotic Maps to Improve the Performances of Quicksort Algorithms". University of Catania, 2008