Here I keep an updated track of my Publications, grouped by type and date. Need a PDF which is not available? Shoot me an email

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Journal Publications

1. [2011 - Accepted for Publication, article]
   D. Nordsletten, B. Yankama, R. Umeton, S. Ayyadurai, and C. F. Dewey, "Multi-scale Mathematical Modeling to Support Drug Development," IEEE Transactions on Biomedical Engineering, p. i, 2011 – Accepted for Publication.
   @ARTICLE{ umeton2011ieee-tbme,
  AUTHOR = {David Nordsletten and Beracah Yankama and Renato Umeton and Shiva Ayyadurai and {Dewey},
  {C.F}},
  TITLE = {Multi-scale Mathematical Modeling to Support Drug Development},
  JOURNAL = {IEEE Transactions on Biomedical Engineering},
  PUBLISHER = {IEEE},
  YEAR = {2011 - Accepted for Publication},
  PAGES = {Accepted for Publication},
  URL = {http://dx.doi.org/10.1109/TBME.2011.2173245}
}
2. [2011 - Accepted for Publication, article]
   R. Umeton, G. Nicosia, and C. F. Dewey, "OREMPdb: a Semantic Dictionary of Computational Pathway Models," BMC Bioinformatics, p. i, 2011 – Accepted for Publication.
   @ARTICLE{ umeton2011bmcbioinformatics,
  AUTHOR = {Umeton, Renato and Nicosia, Giuseppe and {{Dewey}},
  {C.F}},
  TITLE = {OREMPdb: a Semantic Dictionary of Computational Pathway Models},
  JOURNAL = {BMC Bioinformatics},
  YEAR = {2011 - Accepted for Publication},
  PAGES = {Accepted for Publication},
  URL = {http://www.umeton.com/papers/Umeton-BMC-Bioinf2011.pdf}
}
3. [2011, article]
   R. Calabrese, M. Zampieri, R. Mechelli, V. Annibali, T. Guastafierro, F. Ciccarone, G. Coarelli, R. Umeton, M. Salvetti, and P. Caiafa, "Methylation-dependent PAD2 upregulation in multiple sclerosis peripheral blood," Multiple Sclerosis Journal, p. I, 2011.
   @ARTICLE{ salvetti-umeton2011ms,
  AUTHOR = {Roberta Calabrese and Michele Zampieri and Rosella Mechelli and Viviana Annibali and Tiziana Guastafierro and Fabio Ciccarone and Giulia Coarelli and Renato Umeton and Marco Salvetti and Paola Caiafa},
  TITLE = {Methylation-dependent {PAD2} upregulation in multiple sclerosis peripheral blood},
  JOURNAL = {Multiple Sclerosis Journal},
  PUBLISHER = {SAGE},
  YEAR = {2011},
  PAGES = {In Press},
  URL = {http://dx.doi.org/10.1177/1352458511421055},
  ABSTRACT = {Background: Peptidylarginine deiminase 2 (PAD2) and peptidylarginine deiminase 4 (PAD4) are two members of PAD family which are over-expressed in the multiple sclerosis (MS) brain. Through its enzymatic activity PAD2 converts myelin basic protein (MBP) arginines into citrullines - an event that may favour autoimmunity - while peptidylarginine deiminase 4 (PAD4) is involved in chromatin remodelling. Objectives: Our aim was to verify whether an altered epigenetic control of PAD2, as already shown in the MS brain, can be observed in peripheral blood mononuclear cells (PBMCs) of patients with MS since some of these cells also synthesize MBP. Methods: The expression of most suitable reference genes and of PAD2 and PAD4 was assessed by qPCR. Analysis of DNA methylation was performed by bisulfite method. Results: The comparison of PAD2 expression level in PBMCs from patients with MS vs. healthy donors showed that, as well as in the white matter of MS patients, the enzyme is significantly upregulated in affected subjects. Methylation pattern analysis of a CpG island located in the PAD2 promoter showed that over-expression is associated with promoter demethylation. Conclusion: Defective regulation of PAD2 in the periphery, without the immunological shelter of the blood-brain barrier, may contribute to the development of the autoimmune responses in MS.}
}
4. [2010, article]
   A. Papini, G. Nicosia, G. Stracquadanio, P. Liò, and R. Umeton, "Key enzymes for the optimization of CO2 uptake rate and nitrogen concentration in the C3 photosynthetic Carbon metabolism," Journal of Biotechnology, vol. 150, iss. Supplement 1, pp. 525-526, 2010.
   @ARTICLE{ umeton2010jbiotech,
  AUTHOR = {Papini, Alessio and Nicosia, Giuseppe and Stracquadanio, Giovanni and Li\`o, Pietro and Umeton, Renato},
  TITLE = {Key enzymes for the optimization of CO2 uptake rate and nitrogen concentration in the C3 photosynthetic Carbon metabolism},
  JOURNAL = {Journal of Biotechnology},
  PUBLISHER = {Elsevier},
  YEAR = {2010},
  PAGES = {525--526},
  VOLUME = {150},
  NUMBER = {Supplement 1},
  MONTH = {November},
  URL = {http://dx.doi.org/10.1016/j.jbiotec.2010.09.846}
}

Refereed Conference Proceedings

1. [2012, inproceedings]
   R. Umeton, G. Stracquadanio, A. Papini, J. Costanza, P. Liò, and G. Nicosia, "Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism," in Advances in Systems Biology, 2012, pp. 441-459.
   @INPROCEEDINGS {umeton2012AdvExpMedBiol,
  AUTHOR = {Umeton, Renato and Stracquadanio, Giovanni and Papini, Alessio and Costanza, Jole and Li{\`o},
  Pietro and Nicosia, Giuseppe},
  affiliation = {Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA},
  title = {Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism},
  booktitle = {Advances in Systems Biology},
  series = {Advances in Experimental Medicine and Biology},
  editor = {Goryanin, Igor I. and Goryachev, Andrew B.},
  publisher = {Springer New York},
  isbn = {978-1-4419-7210-1},
  keyword = {Biomedical and Life Sciences},
  pages = {441-459},
  volume = {736},
  url = {http://dx.doi.org/10.1007/978-1-4419-7210-1_26},
  note = {10.1007/978-1-4419-7210-1_26},
  abstract = {Understanding and optimizing the CO 2 fixation process would allow human beings to address better current energy and biotechnology issues. We focused on modeling the C 3 photosynthetic Carbon metabolism pathway with the aim of identifying the minimal set of enzymes whose biotechnological alteration could allow a functional re-engineering of the pathway. To achieve this result we merged in a single powerful pipe-line Sensitivity Analysis (SA), Single- (SO) and Multi-Objective Optimization (MO), and Robustness Analysis (RA). By using our recently developed multipurpose optimization algorithms (PAO and PMO2) here we extend our work exploring a large combinatorial solution space and most importantly, here we present an important reduction of the problem search space. From the initial number of 23 enzymes we have identified 11 enzymes whose targeting in the C 3 photosynthetic Carbon metabolism would provide about 90% of the overall functional optimization. Both in terms of maximal CO 2 Uptake and minimal Nitrogen consumption, these 11 sensitive enzymes are confirmed to play a key role. Finally we present a RA to confirm our findings.},
  year = {2012}
}
2. [2011, inproceedings]
   R. Umeton, G. Nicosia, and C. F. Dewey, "OREMPdb: a Semantic Dictionary of Runnable Biological Circuits," in Proceedings of the 8th meeting of the Bioinformatics Italian Society (BITS), Pisa, Italy, June 20-22, 2011, pp. 16-18.
   @INPROCEEDINGS{ umeton2011bits,
  AUTHOR = {Renato Umeton and Giuseppe Nicosia and {Dewey},
  {C.F}},
  TITLE = {OREMPdb: a Semantic Dictionary of Runnable Biological Circuits},
  booktitle = {Proceedings of the 8th meeting of the Bioinformatics Italian Society (BITS), Pisa, Italy, June 20-22},
  YEAR = {2011},
  PAGES = {16-18},
  URL = {http://www.bits2011.it/parts/download.php?filename=../files/Bits-2011.pdf}
}
3. [2011, inproceedings]
   R. Umeton, G. Stracquadanio, A. Sorathiya, A. Papini, P. Liò, and G. Nicosia, "Design of Robust Metabolic Pathways," in Proceedings of the 48th Design Automation Conference (DAC), San Diego, CA, USA, June 5-9, 2011, pp. 747-752.
   @INPROCEEDINGS{ umeton2011dac,
  AUTHOR = {Renato Umeton and Giovanni Stracquadanio and Anil Sorathiya and Alessio Papini and Pietro Li{\`o} and Giuseppe Nicosia},
  TITLE = {Design of Robust Metabolic Pathways},
  booktitle = {Proceedings of the 48th Design Automation Conference (DAC), San Diego, CA, USA, June 5-9},
  publisher = {ACM},
  year = {2011},
  pages = {747--752},
  isbn = {978-1-4503-0636-2},
  url = {http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5981995},
  abstract = {In this paper we investigate plant photosynthesis and microbial fuel cells. We report the following: 1) we introduce and validate a novel multi-objective optimization algorithm, PMO2; 2) in photosynthesis we increase the yield of 135\%, while in Geobacter sulfurreducens we determine the tradeoff for growth versus redox properties; 3) finally, we discuss Pareto-Front as an estimator of robust metabolic pathways.}
}
4. [2011, inproceedings]
   G. Stracquadanio, R. Umeton, J. Costanza, V. Annibali, R. Mechelli, M. Pavone, L. Zammataro, and G. Nicosia, "Large Scale Agent-Based Modeling of the Humoral and Cellular Immune Response," in Proceedings of the 10th International Conference on Artificial Immune Systems, Cambridge, United Kingdom, July 18-21, 2011, pp. 15-29.
   @INPROCEEDINGS{ umeton2011icaris, title = {Large Scale {Agent-Based} Modeling of the Humoral and Cellular Immune Response},
  volume = {6825},
  isbn = {978-3-642-22370-9},
  url = {http://www.springerlink.com/content/4u442m1g41610474/},
  booktitle = {Proceedings of the 10th International Conference on Artificial Immune Systems, Cambridge, United Kingdom, July 18-21},
  publisher = {Springer Berlin Heidelberg},
  AUTHOR = {Stracquadanio, Giovanni and Umeton, Renato and Costanza, Jole and Annibali, Viviana and Mechelli, Rosella and Pavone, Mario and Zammataro, Luca and Nicosia, Giuseppe},
  editor = {Li\`o, Pietro and Nicosia, Giuseppe and Stibor, Thomas},
  year = {2011},
  pages = {15--29},
  abstract = {The Immune System is, together with Central Nervous System, one of the most important and complex unit of our organism. Despite great advances in recent years that shed light on its understanding and in the unraveling of key mechanisms behind its functions, there are still many areas of the Immune System that remain object of active research. The development of in-silico models, bridged with proper biological considerations, have recently improved the understanding of important complex systems [1,2]. In this paper, after introducing major role players and principal functions of the mammalian Immune System, we present two computational approaches to its modeling; i.e., two in-silico Immune Systems. (i) A large-scale model, with a complexity of representation of 106 − 108 cells (e.g., APC, T, B and Plasma cells) and molecules (e.g., immunocomplexes), is here presented, and its evolution in time is shown to be mimicking an important region of a real immune response. (ii) Additionally, a viral infection model, stochastic and light-weight, is here presented as well: its seamless design from biological considerations, its modularity and its fast simulation times are strength points when compared to (i). Finally we report, with the intent of moving towards the virtual lymph note, a cost-benefits comparison among Immune System models presented in this paper. }
}
5. [2011, inproceedings]
   D. Nordsletten, B. Yankama, R. Umeton, S. Ayyadurai, and C. F. Dewey, "Multi-scale Mathematical Modeling to Support Drug Development," in Proceedings of Biomedical Engineering Society (BMES), Hartford, CT, USA, October 12-15, 2011.
   @INPROCEEDINGS{nordsletten_bmes_2011, TITLE = {Multi-scale Mathematical Modeling to Support Drug Development},
  BOOKTITLE = {Proceedings of Biomedical Engineering Society (BMES), Hartford, CT, USA, October 12-15},
  AUTHOR = {David Nordsletten and Beracah Yankama and Renato Umeton and Shiva Ayyadurai and {Dewey},
  {C.F}},
  YEAR = {2011},
  URL = {http://www.umeton.com/papers/Nordsletten-BMES11.pdf}
}
6. [2010, inproceedings]
   R. Umeton, B. Yankama, G. Nicosia, and C. F. Dewey, "A Cross-format Framework for Consistent Information Integration among Molecular Pathways and Ontologies," in Proceedings of 6th World Congress on Biomechanics (WCB), Singapore, August 1-6, Singapore, 2010, pp. 1595-1598.
   @INPROCEEDINGS{ umeton2010wcb,
  AUTHOR = {Umeton, Renato and Yankama, Beracah and Nicosia, Giuseppe and {Dewey},
  {C.F}},
  TITLE = {A Cross-format Framework for Consistent Information Integration among Molecular Pathways and Ontologies},
  BOOKTITLE = {Proceedings of 6th World Congress on Biomechanics (WCB), Singapore, August 1-6},
  ADDRESS = {Singapore},
  SERIES = {IFMBE Proceedings},
  EDITOR = {Lim, C. T. and Goh, J. C. H.},
  YEAR = {2010},
  PAGES = {1595--1598},
  VOLUME = {31},
  ISSN = {1680-0737},
  URL = {http://dx.doi.org/10.1007/978-3-642-14515-5_406},
  PUBLISHER = {Springer Berlin Heidelberg},
  ABSTRACT = {The information coming from biomedical ontologies and runnable pathways is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedicated resources published on the web. Having different objectives and different abstraction levels, most of these resources “speak” different languages. Employing an extensible collection of interpreters, we propose a system that abstracts the information from different resources and combines them together into a common meta-format. Preserving the resource independence, we provide an alignment service that can be used for multiple pur- poses. Two recent examples are: 1) The new web application Cytosolve uses an embedded version of this system to provide congruous parallel simulation of multiple models; 2) Using the BioModels.net database, a searchable dictionary of equivalent molecular reaction paths was built. Finally, the enriched knowledge can be exported in OWL and queried by semantically-enabled tools such as Prot\'eg\'e. In this approach, we see a valuable tool to integrate and test information originating from different sources, while preserving the independence of the model curation process.}
}
7. [2010, inproceedings]
   B. Yankama, R. Umeton, S. Ayyadurai, and C. F. Dewey, "Editing and Aligning Complex Molecular Pathways Using 3D Models," in Proceedings of Biomedical Engineering Society (BMES), Austin, TX, USA, October 6-9, 2010.
   @INPROCEEDINGS{yankama_bmes_2010, TITLE = {Editing and Aligning Complex Molecular Pathways Using {3D} Models},
  BOOKTITLE = {Proceedings of Biomedical Engineering Society (BMES), Austin, TX, USA, October 6-9},
  AUTHOR = {Yankama, Beracah and Umeton, Renato and Ayyadurai, Shiva and {Dewey},
  {C.F}},
  YEAR = {2010},
  URL = {http://www.umeton.com/papers/Yankama-BMES10.pdf}
}
8. [2010, inproceedings]
   R. Umeton, B. Yankama, G. Nicosia, and C. F. Dewey, "OREMP: Ontology Reasoning Engine for Molecular Pathways," in Proceedings of 1st International Workshop on Ontology Repositories and Editors for the Semantic Web (ORES) – Co-located with 7th Extended Semantic Web Conference (ESWC), Heraklion, Crete, Greece, May 30, 2010, pp. 26-30.
   @INPROCEEDINGS{ umeton2010eswc,
  AUTHOR = {Umeton, Renato and Yankama, Beracah and Nicosia, Giuseppe and {Dewey},
  {C.F}},
  TITLE = {OREMP: Ontology Reasoning Engine for Molecular Pathways},
  BOOKTITLE = {Proceedings of 1st International Workshop on Ontology Repositories and Editors for the Semantic Web (ORES) - Co-located with 7th Extended Semantic Web Conference (ESWC), Heraklion, Crete, Greece, May 30},
  YEAR = {2010},
  PAGES = {26--30},
  EDITOR = {D\'Aquin, Mathieu and Castro, Alexander Garcia and Lange, Christoph and Viljanen, Kim},
  VOLUME = {596},
  ISSN = {1613-0073},
  URL = {http://ceur-ws.org/Vol-596/paper-06.pdf},
  PUBLISHER = {CEUR-WS},
  ABSTRACT = {The information about molecular processes is shared continuously in the form of runnable pathway collections and biomedical ontologies provide a semantic context to the majority of those pathways. Recent advances in both fields pave the way for a scalable information integration based on aggregate knowledge repositories, but the lack of overall standard formats impedes this progress. Here we propose a strategy that integrates these resources by means of extended ontologies built on top of a common meta-format. Information sharing, integration and discovery are the primary features provided by the system; additionally, two current field applications of the system are reported.}
}
9. [2010, inproceedings]
   G. Stracquadanio, R. Umeton, A. Papini, P. Liò, and G. Nicosia, "Analysis and Optimization of C3 Photosynthetic Carbon Metabolism," in Proceedings of 10th IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE), Philadelphia, PA, USA, May 31-June 3, 2010, pp. 44-51.
   @INPROCEEDINGS{ umeton2010ieee,
  AUTHOR = {Stracquadanio, Giovanni and Umeton, Renato and Papini, Alessio and Li\`o, Pietro and Nicosia, Giuseppe},
  TITLE = {Analysis and Optimization of C3 Photosynthetic Carbon Metabolism},
  BOOKTITLE = {Proceedings of 10th IEEE International Conference on Bioinformatics and Bioengineering (IEEE BIBE), Philadelphia, PA, USA, May 31-June 3},
  YEAR = {2010},
  PAGES = {44--51},
  EDITOR = {Rigoutsos, Isidore and Floudas, Christodoulos A.},
  PUBLISHER = {IEEE Computer Society},
  DOI = {10.1109/BIBE.2010.17},
  URL = {http://www.umeton.com/papers/Stracquadanio-BIBE10.pdf},
  ABSTRACT = {We have studied the C3 photosynthetic carbon metabolism centering our investigation on the following four design principles. (1) Optimization of the photosynthetic rate by modifying the partitioning of resources between the different enzymes of the C3 photosynthetic carbon metabolism using a constant amount of protein-nitrogen. (2) Identify sensitive and less sensitive enzymes of the studied model. (3) Maximize photosynthetic productivity rate through the choice of robust enzyme concentrations using a new precise definition of robustness. (4) Modeling photosynthetic carbon metabolism as a multi-objective problem of two competing biological selection pressures: light-saturated photosynthetic rate versus total protein-nitrogen requirement. Using the designed single-objective optimization algorithms, PAO and A-CMA-ES, we have obtained an increase in photosynthetic productivity of the 135% from 15.486 µmol m-2 s-1 to 36.382 µmol m-2 s-1 , and improving the previous best-found photosynthetic productivity value (27.261 µmol m-2 s-1 , 76% of enhancement). Optimized enzyme concentrations express a maximal local robustness (100%) and a high global robustness (97.2%), satisfactory properties for a possible “in vitro” manufacturing of the optimized pathway. Morris sensitivity analysis shows that 11 enzymes over 23 are high sensitive enzymes, i.e., the most influential enzymes of the carbon metabolism model. Finally, we have obtained the trade-off between the maximization of the leaf CO2 uptake rate and the minimization of the total protein-nitrogen concentration. This trade-off search has been carried out for the three ci concentrations referring to the estimate of CO2 concentration in the atmosphere characteristic of 25 million years ago, nowadays and in 2100 a.C. Remarkably, the three Pareto frontiers identify the highest photosynthetic productivity rates together with the fewest protein-nitrogen usage.}
}
10. [2008, inproceedings]
    S. Di Gregorio, R. Umeton, A. Bicocchi, and A. Evangelisti, "A Cellular Automata Model for Highway Traffic with Preliminary Results," in Proceedings 5th Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Venice, September 8-10, 2008, pp. 235-244.
    @INPROCEEDINGS{ digregorio2008wivace,
  AUTHOR = {Di Gregorio, S and Umeton, R and Bicocchi, A and Evangelisti, A},
  TITLE = {A Cellular Automata Model for Highway Traffic with Preliminary Results},
  BOOKTITLE = {Proceedings 5th Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Venice, September 8-10},
  YEAR = {2008},
  EDITOR = {Serra, Roberto and Villani, Marco and Poli, Irene},
  PUBLISHER = {World Scientific},
  YEAR = {2008},
  PAGES = {235--244},
  URL = {http://ebooks.worldscinet.com/ISBN/9789814287456/9789814287456_0021.html}
}
11. [2008, inproceedings]
    R. Umeton and S. Di Gregorio, "Admissible Method for Improved Genetic Search in Cellular Automata Model (ammisca): a Strategy in Genetic Calibration – Preliminary Results," in Proceedings 5th Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Venice, September 8-10, 2008, pp. 99-108.
    @INPROCEEDINGS{ umeton2008wivace,
  AUTHOR = {Umeton, Renato and Di Gregorio, Salvatore},
  TITLE = {Admissible Method for Improved Genetic Search in Cellular Automata Model (ammisca): a Strategy in Genetic Calibration - Preliminary Results},
  BOOKTITLE = {Proceedings 5th Italian Workshop on Artificial Life and Evolutionary Computation (WIVACE), Venice, September 8-10},
  YEAR = {2008},
  EDITOR = {Serra, Roberto and Villani, Marco and Poli, Irene},
  PUBLISHER = {World Scientific},
  PAGES = {99--108},
  URL = {http://www.umeton.com/papers/Umeton-WIVACE08.pdf},
  ABSTRACT = {Genetic Algorithms (GAs) are widely used to incrementally reach admissible solutions for hard problems such as parameter tuning in Cellular Automata (CA) models. This paper presents a genetic strategy, specifically developed for CA model calibration, exploiting the circumstance that the considered CA parameters have a physical meaning. The proposed approach has proved to be comparable and, in some cases outperforming, if compared with the standard GA proposed by Holland. As a further result, the goodness of the proposed genetic strategy opens the door to genetic tuning algorithms lacking of a standard crossover operator. Results, though preliminary, can be considered encouraging and routes to a wider analysis of the proposed approach.}
}
12. [2008, inproceedings]
    S. Di Gregorio, R. Umeton, A. Bicocchi, A. Evangelisti, and M. Gonzalez, "Highway Traffic Model Based on Cellular Automata: Preliminary Simulation Results with Congestion Pricing Considerations," in Proceedings of 20th European Modeling & Simulation Symposium (EMSS), Campora S.G., CS, Italy, September 17-19, 2008, pp. 665-674.
    @INPROCEEDINGS{ digregorio2008emss,
  AUTHOR = {Di Gregorio, S. and Umeton, R. and Bicocchi, A. and Evangelisti, A. and Gonzalez, M.},
  TITLE = {Highway Traffic Model Based on Cellular Automata: Preliminary Simulation Results with Congestion Pricing Considerations},
  BOOKTITLE = {Proceedings of 20th European Modeling & Simulation Symposium (EMSS), Campora S.G., CS, Italy, September 17-19},
  YEAR = {2008},
  PAGES = {665--674},
  EDITOR = {Castilla Rodriguez, Ivan and Longo, Francesco},
  PUBLISHER = {Inder Science},
  URL = {http://www.umeton.com/papers/DiGregorio-EMSS08.pdf},
  ABSTRACT = {Cellular Automata are a reputable formal support for traffic modelling and simulation. STRATUNA is a Cellular Automata model for simulating the evolution of two/three lane highways. It encodes the wide specification of driver’s response to the events in his sight range. Encouraging comparison between simulated events and their corresponding in the reality bring to the specification of a theoretical general model characterized by an increased expression power and a significantly deeper forecasting potential, whose application fields are numerous and varied. Fair results in flow forecasting lead to the implementation of an established cost system in which simulation directly provides cost forecasting in terms of congestion toll.}
}
13. [2007, inproceedings]
    M. V. Avolio, G. M. Crisci, S. Di Gregorio, R. Rongo, and R. Umeton, "Introduction of More Physical Features in the Cellular Automata Model for Lava Flows SCIARA: Preliminary Results Regarding the Viscosity," in Proceedings of Asia Oceania Geosciences Conference (AOGS), Bangkok, Thailand, July 30-August 4, 2007.
    @INPROCEEDINGS{ avolio2007,
  AUTHOR = {Avolio, M. V. and Crisci, G. M. and Di Gregorio, S. and Rongo, R. and Umeton, R.},
  TITLE = {Introduction of More Physical Features in the Cellular Automata Model for Lava Flows SCIARA: Preliminary Results Regarding the Viscosity},
  BOOKTITLE = {Proceedings of Asia Oceania Geosciences Conference (AOGS), Bangkok, Thailand, July 30-August 4},
  YEAR = {2007},
  URL = {http://www.cosis.net/abstracts/EGU2007/04208/EGU2007-J-04208.pdf}
}

Posters

1. [2011, misc]
   R. Umeton, R. Pizzolato, G. Nicosia, and C. F. Dewey, OREMPdb, System Overview and First Queries in the Neurology Field, 2011.
   @MISC{ umeton2011posterb,
  AUTHOR = {Umeton, Renato and Pizzolato, Raffaella and Nicosia, Giuseppe and {Dewey},
  {C.F}},
  TITLE = {OREMPdb, System Overview and First Queries in the Neurology Field},
  HOWPUBLISHED = {Poster at 3rd Int. Workshop on Bio-Design Automation (IWBDA) San Diego, CA, USA, 5-9 June 2011},
  Month = {June},
  YEAR = {2011},
  URL = {http://wiki.bu.edu/ece-cidar/index.php/IWBDA_2011}
}
2. [2011, misc]
   R. Umeton, V. Annibali, D. Vittori, R. Mechelli, S. Romano, C. Policano, G. Coarelli, C. Mattei, G. Ristori, and M. Salvetti, MicroRNA expression profile of B lymphocytes in Multiple Sclerosis, 2011.
   @MISC{ umeton2011posterms1,
  AUTHOR = {Umeton, R. and Annibali, V. and Vittori, D. and Mechelli, R. and Romano, S. and Policano, C. and Coarelli, G. and Mattei, C. and Ristori, G. and Salvetti, M.},
  TITLE = {MicroRNA expression profile of B lymphocytes in Multiple Sclerosis},
  HOWPUBLISHED = {Poster at 21st Conference of the Italian Neuroimmunology Society (AINI) Pollenzo, CN, Italy, 22-25 September 2011},
  Month = {September},
  YEAR = {2011},
  URL = {http://www.umeton.com/papers/Umeton-AINI11.pdf}
}
3. [2011, misc]
   A. Koo, C. F. Dewey, D. Nordsletten, B. Yankama, R. Umeton, and S. Ayyadurai, Mapping and Simulating Flow-dependent Signaling Pathways in Endothelial Cells, 2011.
   @MISC{ umeton2011postera,
  AUTHOR = {Koo, Andrew and {Dewey},
  {C.F} and Nordsletten, David and Yankama, Beracah and Umeton, Renato and Ayyadurai, Shiva},
  TITLE = {Mapping and Simulating Flow-dependent Signaling Pathways in Endothelial Cells},
  HOWPUBLISHED = {Poster at 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology (ISMB-ECCB), Vienna, Austria, 17-19 July 2011},
  Month = {July},
  YEAR = {2011},
  URL = {https://www.iscb.org/cms_addon/conferences/ismbeccb2011/posterlist.php?cat=X},
  ABSTRACT = {Nitric Oxide (NO) produced by endothelial cells plays multiple roles in vascular stasis including being an anti-oxidant, a mediator of inflammation, and a potent vasodilator. Not surprisingly, NO production is complexly regulated by multiple pathways. In order to understand the rich diversity of responses that have been observed experimentally, it is necessary to account for an ensemble of these pathways acting simultaneously- a systems biology problem. We have assembled four different quantitative molecular pathways appearing in the literature that have been proposed for shear stress-induced NO production. In these pathways, endothelial nitric oxide synthase (eNOS) is activated (a) via calcium influx, (b) via phosphorylation reactions, via enhanced eNOS protein expression through (d) the MAP kinase pathway, and (d) the NFkB pathway. To these we added a fifth pseudo-pathway describing the actual NO production from different calcium-bound or phosphorylated states of eNOS. All five components were combined using Cytosolve, a new computational environment for combining independent pathway calculations to create complexes of simultaneous biological reactions. The integrated model is able to describe the changes in NO concentration with time following the application of fluid shear stress to endothelial cells. The complex time history, arising from interaction between various pathways, is computed. The results agree favorably with experimental data. The complete model can also be used to predict the specific effects on NO production following interventional pharmacological and genetic changes to the cell.}
}
4. [2011, misc]
   C. Eleuteri, C. Veroni, R. Umeton, M. Salvetti, and C. Agresti, An extensive in vitro and ex vivo screening of registered drugs to identify new enhancer of endogenous remyelination, 2011.
   @MISC{ umeton2011posterms2,
  AUTHOR = {Eleuteri, C. and Veroni, C. and Umeton, R. and Salvetti, M. and Agresti, C.},
  TITLE = {An extensive in vitro and ex vivo screening of registered drugs to identify new enhancer of endogenous remyelination},
  HOWPUBLISHED = {Poster at 10th Europeglia Meeting on Glial Cells in Health and Diseases (GLIA) Prague, Czech Republic, 13-17 September 2011},
  Month = {September},
  YEAR = {2011},
  URL = {http://www.umeton.com/papers/Eleuteri-GLIA11.pdf}
}
5. [2011, misc]
   G. Stracquadanio, R. Umeton, A. Papini, P. Liò, and G. Nicosia, Automating the Biological Design of C3 Carbon Metabolism for Enhanced Photosynthetic Productivity Minimizing the Nitrogen Employed, 2011.
   @MISC{ umeton2011posterc,
  AUTHOR = {Stracquadanio, Giovanni and Umeton, Renato and Papini, Alessio and Li\`o, Pietro and Nicosia, Giuseppe},
  TITLE = {Automating the Biological Design of C3 Carbon Metabolism for Enhanced Photosynthetic Productivity Minimizing the Nitrogen Employed},
  HOWPUBLISHED = {Poster at Int. Workshop Modeling Natural and Artificial Photosynthesis, Lorentz Center - Leiden, The Netherlands, 7-11 March 2011},
  Month = {March},
  YEAR = {2011},
  URL = {http://www.lorentzcenter.nl/lc/web/2011/432/info.php3?wsid=432}
}
6. [2010, misc]
   G. Stracquadanio, R. Umeton, A. Papini, P. Liò, and G. Nicosia, Towards Artificial Photosynthesis: Analysis and Optimization of C3 Photosynthetic Carbon Metabolism, 2010.
   @MISC{ umeton2010poster5,
  AUTHOR = {Stracquadanio, Giovanni and Umeton, Renato and Papini, Alessio and Li\`o, Pietro and Nicosia, Giuseppe},
  TITLE = {Towards Artificial Photosynthesis: Analysis and Optimization of C3 Photosynthetic Carbon Metabolism},
  HOWPUBLISHED = {Poster at MIT-BEIW 2010, MIT Biological Engineering Interview Weekend, March 21, 2010, Cambridge, MA, USA},
  YEAR = {2010}
}
7. [2010, misc]
   G. Stracquadanio, R. Umeton, A. Papini, P. Liò, and G. Nicosia, Key enzymes for the optimization of CO2 uptake rate and nitrogen concentration in the C3 photosynthetic Carbon metabolism, 2010.
   @MISC{ umeton2010poster2,
  AUTHOR = {Stracquadanio, Giovanni and Umeton, Renato and Papini, Alessio and Li\`o, Pietro and Nicosia, Giuseppe},
  TITLE = {Key enzymes for the optimization of CO2 uptake rate and nitrogen concentration in the C3 photosynthetic Carbon metabolism},
  HOWPUBLISHED = {Poster at IBS 2010, 14th International Biotechnology Symposium, September 14-18, 2010, Rimini, Italy},
  YEAR = {2010}
}
8. [2010, misc]
   R. Umeton, B. Yankama, C. Pujol, S. Ayyadurai, G. Nicosia, and C. F. Dewey, A Cross-format Framework for Consistent Information Integration among Molecular Pathways and Ontologies, 2010.
   @MISC{ umeton2010poster3,
  AUTHOR = {Umeton, Renato and Yankama, Beracah and Pujol, Cristina and Ayyadurai, Shiva and Nicosia, Giuseppe and {Dewey},
  {C.F}},
  TITLE = {A Cross-format Framework for Consistent Information Integration among Molecular Pathways and Ontologies},
  HOWPUBLISHED = {Poster at MIT Biological Engineering Department Retreat, March 22-23, 2010, Newport, RI, USA},
  YEAR = {2010},
  }
9. [2010, misc]
   R. Umeton, B. Yankama, G. Nicosia, and C. F. Dewey, System Demo – OREMP, Ontology Reasoning Engine for Molecular Pathways, 2010.
   @MISC{ umeton2010demo,
  AUTHOR = {Umeton, Renato and Yankama, Beracah and Nicosia, Giuseppe and {Dewey},
  {C.F}},
  TITLE = {System Demo - OREMP, Ontology Reasoning Engine for Molecular Pathways},
  HOWPUBLISHED = {Demo at ORES 2010, 1st International Workshop on Ontology Repositories and Editors for the Semantic Web - satellite conference in ESWC 2010, 7th Extended Semantic Web Conference, May 30, 2010, Heraklion, Crete, Greece},
  YEAR = {2010}
}
10. [2010, misc]
    G. Stracquadanio, R. Umeton, A. Papini, P. Liò, and G. Nicosia, Enhancing Photosynthesis, 2010.
    @MISC{ umeton2010poster1,
  AUTHOR = {Stracquadanio, Giovanni and Umeton, Renato and Papini, Alessio and Li\`o, Pietro and Nicosia, Giuseppe},
  TITLE = {Enhancing Photosynthesis},
  HOWPUBLISHED = {Poster at ICSB 2010, 11th Int. Conf. on Systems Biology, Edinburgh 10-15 October 2010},
  YEAR = {2010}
}
11. [2010, misc]
    R. Umeton, B. Yankama, C. Pujol, S. Ayyadurai, G. Nicosia, and C. F. Dewey, OREMP: Ontology Reasoning Engine for Molecular Pathways, 2010.
    @MISC{ umeton2010poster6,
  AUTHOR = {Umeton, Renato and Yankama, Beracah and Pujol, Cristina and Ayyadurai, Shiva and Nicosia, Giuseppe and {Dewey},
  {C.F}},
  TITLE = {OREMP: Ontology Reasoning Engine for Molecular Pathways},
  HOWPUBLISHED = {Poster at MIT-CSBIW 2010, MIT Computational and Systems Biology Interview Weekend, February 13, 2010, Cambridge, MA, USA},
  YEAR = {2010}
}
12. [2010, misc]
    S. Ayyadurai, C. F. Dewey, C. Pujol, E. Sciacca, R. Umeton, and B. Yankama, Cytosolve: Distributed Simulation of Multiple Biological Pathway Models, 2010.
    @MISC{ umeton2010poster4,
  AUTHOR = {Ayyadurai, Shiva and {{Dewey}},
  {{C.F}} and Pujol, Cristina and Sciacca, Eva and Umeton, Renato and Yankama, Beracah},
  TITLE = {Cytosolve: Distributed Simulation of Multiple Biological Pathway Models},
  HOWPUBLISHED = {Poster at MIT Biological Engineering Department Retreat, March 22-23, 2010, Newport, RI, USA},
  YEAR = {2010}
}

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