@article{cwcsim:cloud:13,
  Author = {Marco Aldinucci and Massimo Torquati and Concetto Spampinato and Maurizio Drocco and Cristina Calcagno and Mario Coppo},
  Journal = {Submitted for pubblication},
  OPTJournal = {Briefings in Bioinformatics},
  Title = {Parallel stochastic systems biology in the cloud},
  Year = {2013},
  Note = {Submitted for pubblication},
}

@article{biocloud:13,
  Author = {Concetto Spampinato and Sebastiano Milardo and Carmelo Pino and Isaak Kavasidis and Marco Aldinucci and Manuela Pennisi},
  Journal = {Submitted for pubblication},
  OPTJournal = {Briefings in Bioinformatics},
  Title = {BioCloud: Discovering Biological Knowledge by Integrating High Throughput Data and Scientific Literature on the Cloud},
  Year = {2013},
  Note = {Submitted for pubblication},
}

@article{cwcsim:ff:multicore:13,
  Author = {Marco Aldinucci and Cristina Calcagno and Mario Coppo and Ferruccio Damiani and Maurizio Drocco and Eva Sciacca and Salvatore Spinella and Massimo Torquati and Angelo Troina},
  Journal = {Submitted for pubblication},
  OPTJournal = {BMC Bioinformatics},
  Title = {On designing multicore-aware simulators for systems biology endowed with on-line statistics},
  Year = {2013},
  Note = {Submitted for pubblication},
}

@article{Gia+Vink:CS2Bio-2013,
  title = {International Workshop on Interactions between Computer Science and Biology, CS2Bio 2012},
  author = {Giannini, Paola and {de Vink}, E.P.},
   year = {2013},
  series    = {EPTCS},
}

@inproceedings{DBLP:journals/corr/abs-1207-7147,
  author    = {Bioglio, Livio and Dezani-Ciancaglini, Mariangiola and Giannini, Paola and Troina, Angelo},
  title     = {A Calculus of Looping Sequences with Local Rules},
  booktitle = {Proceedings 7th International Workshop on Developments of
               Computational Methods},
  series    = {EPTCS},
  volume    = {88},
  year      = {2011},
  pages     = {43-58},
}

@inproceedings{ff_cwc_distr:pdp:13,
  Author = {Aldinucci, Marco and Tordini, Fabio and Drocco, Maurizio and Torquati, Massimo and Coppo, Mario},
  Booktitle = {Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP'13)},
  Publisher = {IEEE},
  Title = {Parallel stochastic simulators in system biology: the evolution of the species},
  Year = {2013}
}


@inproceedings{ff:cwc:pdp:11,
  Author = {Aldinucci, Marco and Coppo, Mario and Damiani, Ferruccio and Drocco, Maurizio and Torquati, Massimo and Troina, Angelo},
  Booktitle = {Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP'11)},
  Pages = {318-325},
  Publisher = {IEEE},
  Title = {On Designing Multicore-Aware Simulators for Biological Systems},
  Url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=5739030},
  Year = {2011},
}


@inproceedings{stochkit-ff:hibb:10,
  Author = {Aldinucci, Marco and Bracciali, Andrea and Li\`o, Pietro and Sorathiya, Anil and Torquati, Massimo},
  Booktitle = {Euro-Par 2010, Workshop on High Performance Bioinformatics and Biomedicine (HiBB)},
  Pages = {167-175},
  Publisher = {Springer},
  Series = {LNCS},
  Title = {{StochKit-FF}: Efficient Systems Biology on Multicore Architectures},
  Url = {http://link.springer.com/chapter/10.1007%2F978-3-642-21878-1_21},
  Volume = {6586},
  Year = {2011}
}

@article{stochkitff:ercimnews:10,
	Author = {Aldinucci, Marco and Bracciali, Andrea and Li\`o, Pietro},
	Journal = {ERCIM News},
	Pages = {40--41},
	Title = {Formal Synthetic Immunology},
	Url = {http://ercim-news.ercim.eu/images/stories/EN82/EN82-web.pdf},
	Volume = {82},
	Year = {2010},
}

@inproceedings{RamTro12,
  booktitle = {International Conference on Membrane Computing (CMC13)},
  author = {Ram\`on, Pablo and Troina, Angelo},
  title = {Modelling Ecological Systems with the Calculus of Wrapped Compartments},
  year = {2012},
  series = {LNCS}
  volume = {7762},
  pages = {358-377},
  url = {http://www.di.unito.it/~troina/publications/cmc13.pdf},
}

@inproceedings{CioTro12,
  booktitle = {Italian Conference on Theoretical Computer Science (ICTCS'12)},
  author = {Ciobanu, Gabriel and Troina, Angelo},
  title = {Rate-Based Stochastic Fusion Calculus and Continuous Time Markov Chains},
  year = {2012},
  pages = {86--89},
  url = {http://www.di.unito.it/~troina/publications/ictcs12.pdf},
}

@inproceedings{CDGSST12,
  booktitle = {International Meeting on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC'12)},
  volume = {100},
  author = {Compagnoni, Adriana and Dezani-Ciancaglini, Mariangiola and Giannini, Paola and Sauer, Karin and Sharma, Vishakha and Troina, Angelo},
  title = {Parallel BioScape: A Stochastic and Parallel Language for Mobile and
           Spatial Interactions},
  year = {2012},
  series = {EPTCS},
  pages = {101--106},
  url = {http://www.di.unito.it/~troina/publications/mecbic12.pdf},
}

@inproceedings{SciSpiCalDamCop,
  booktitle = {International Workshop on Interactions between Computer Science and Biology, CS2Bio 2012},
  author = {Sciacca, Eva and Spinella, Salvatore and Calcagno, Cristina and Damiani, Ferruccio and Coppo, Mario},
  title = {Parameter Identification and Assessment of Nutrient Transporters in AM Symbiosis through Stochastic Simulations},
  year = {2012},
}

@inproceedings{DBLP:conf/spire/EgidiM11,
  author    = {Egidi, Lavinia and Manzini, Giovanni},
  title     = {Spaced Seeds Design Using Perfect Rulers},
  booktitle = {Proceedings SPIRE: String Processing and Information Retrieval},
  publisher = {Springer},
  series    = {Lecture Notes in Computer Science},
  volume    = {7024},
  year      = {2011},
  isbn      = {978-3-642-24582-4}, 
  pages     = {32-43}
}

@misc{CSA_Prot,
  title = {A(S)CFG generator (Prototypal Software)},
  author = {Sciacca, Eva and Spinella, Salvatore and Giannini, Paola},
  year = {2011},
  howpublished = {Prototypal Software},
  url = {},
}

@misc{CWCSL_Prot,
  title = {CWC Surface Language Software (Prototypal Software)},
  author = {Bioglio, Livio and Coppo, Mario and Damiani, Ferruccio and Sciacca, Eva and Spinella, Salvatore and Troina, Angelo},
  year = {2011},
  howpublished = {Prototypal Software},
  url = {},
}

@misc{CSA_Prot,
  title = {Calcium Spiking Analyser (Prototypal Software)},
  author = {Sciacca, Eva and Spinella, Salvatore},
  year = {2011},
  howpublished = {Prototypal Software},
  url = {},
}

@misc{CWC_Sim,
  title = {CWC Simulator (Public Software)},
  author = {Aldinucci, Marco and Coppo, Mario and Damiani, Ferruccio and Drocco, Maurizio and Giovannetti, Elio and Grassi, Elena and Sciacca, Eva and Spinella, Salvatore and Troina, Angelo},
  year = {2010},
  url = {http://cwcsimulator.sourceforge.net/},
}

@article{BDGT_TCS12,
  title = {Type Stochastic Semantics for the Calculus of Looping Sequences},
  author = {Bioglio, Livio and Dezani-Ciancaglini, Mariangiola and Giannini, Paola and Troina, Angelo},
  journal = {Theoretical Computer Science},
  year = {2012},
  note = {to appear},
}

@article{CDDG_TCS12,
  title = {Simulation Techniques for the Calculus of Wrapped Compartments},
  author = {Coppo, Mario and Damiani, Ferruccio and Drocco, Maurizio and Grassi, Elena and Sciacca, Eva and Spinella, Salvatore and Troina, Angelo},
  journal = {Theoretical Computer Science},
  year = {2012},
  note = {to appear},
}

@inproceedings{sciacca2011ascfg,
  booktitle = {Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. Springer LNCS},
  volume = {6623},
  author = {Sciacca, Eva and Spinella, Salvatore and Ienco, Dino and Giannini, Paola},
  title = {Annotated Stochastic Context Free Grammars for Analysis and Synthesis of Proteins},
  year = {2011},
}

@inproceedings{sciacca2011,
  booktitle = {CS2BIO 2011},
  location = {Reykjavik, Iceland},
  title = {Analysis of Calcium Spiking in Plant Root Epidermis through CWC Modeling},
  author = {Sciacca, Eva and Spinella, Salvatore and Genre, Andrea and Calcagno, Cristina},
  year = {2011},
}

@article{Gia+Kri:CS2Bio-2011,
  volume = {277},
  url = {http://dx.doi.org/10.1016/j.entcs.2011.09.030},
  title = {International Workshop on Interactions between Computer Science and Biology, CS2Bio 2011},
  author = {Paola Giannini and Jean Krivine},
  pages = {1-2},
  year = {2011},
  journal = {Electr. Notes Theor. Comput. Sci.},
}

@inproceedings{calcagno2011,
  booktitle = {3rd International Workshop on Computational Models for Cell Processes (CompMod'11), EPTCS},
  volume = {67},
  title = {Modelling Spatial Interactions in the Arbuscular Mycorrhizal Symbiosis using the Calculus of Wrapped Compartments},
  author = {Calcagno, Cristina and Coppo, Mario and Damiani, Ferruccio and Drocco, Maurizio and Sciacca, Eva and Spinella, Salvatore and Troina, Angelo},
  year = {2011},
  pages = {3--18},
}

@inproceedings{bioglio2011spatialcwc,
  booktitle = {5th International Meeting on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC'11)},
  location = {Paris (Fontainebleau), France},
  title = {A Spatial Calculus of Wrapped Compartments},
  author = {Bioglio, Livio and Calcagno, Cristina and Coppo, Mario and Damiani, Ferruccio and Sciacca, Eva and Spinella, Salvatore and Troina, Angelo},
  year = {2011},
  pages = {25--39},
}

@inproceedings{B11,
  booktitle = {Computational Models for Cell Processes (CompMod) 2011},
  url = {},
  author = {Bioglio, Livio},
  title = {A Minimal OO Calculus for Modelling Biological Systems},
  year = {2011},
}

@inproceedings{aldinucci2011parcwc,
  booktitle = {2nd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB'11), Springer LNCS},
  title = {On Parallelizing On-Line Statistics for Stochastic Biological Simulations},
  author = {Aldinucci, Marco and Coppo, Mario and Damiani, Ferruccio and Drocco, Maurizio and Sciacca, Eva and Spinella, Salvatore and Torquati, Massimo and Troina, Angelo},
  year = {2011},
}

@article{BDGT10,
  url = {http://www.di.unito.it/~dezani/papers/bdgt.pdf},
  title = {{Type Directed Semantics for the Calculus of Looping Sequences}},
  author = {Bioglio, Livio and Dezani-Ciancaglini, Mariangiola and Giannini,Paola and Troina, Angelo},
  year = {2011},
  note = {to appear},
  journal = {International Journal of Software and Informatics},
}

@article{B10,
  url = {http://www.di.unito.it/~biogliol/papers/enumerated_type_semantics_for_cls.pdf},
  title = {{Enumerated Type Semantics for the Calculus of Looping Sequences}},
  author = {Bioglio, Livio},
  year = {2011},
  journal = {RAIRO - Theoretical Informatics and Applications},
  volume = {45},
  number = {1},
  pages = {35--58},
}

@inbook{CorGhiLanLeoMeoMonRov:2011-BIOBITS,
  place = {{Singapore}},
  author = {{Cordero, Francesca and Ghignone, Stefano and Lanfranco, Luisa and Leonardi, Giorgio and Meo, Rosa and Montani, Stefania and Roversi, Luca}},
  note = {{Pubblication date: scheduled Summer 2011}},
  booktitle = {{Database Technology for Life Sciences and Medicine}},
  editor = {Plant, Claudia and B\"ohm, Christian},
  url = {http://www.di.unito.it/~rover/RESEARCH/PUBLICATIONS/2011-BIOBITSChapter/CorGhiLanLeoMeoMonRovBIOBITS-chapter-book.pdf},
  title = {{BIOBITS: A Study on Candidatus Glomeribacter Gigasporarum with a Data Warehouse}},
  address = {{Singapore}},
  isbn = {978-981-4307-70-3},
  publisher = {{World Scientific Publishing}},
  pages = {203 --- 220},
  year = {2011},
}

@inproceedings{coppo2010hybrid,
  title = {{Hybrid Calculus of Wrapped Compartments}},
  author = {Coppo, Mario and Damiani, Ferruccio and Drocco, Maurizio and Grassi, Elena and 
Sciacca, Eva and Spinella, Salvatore and Troina, Angelo},
  BOOKTITLE = {Membrane Computing and Biologically Inspired Process Calculi 2010},
  pages = {98--116},
  year = {2010}
}

@inproceedings{spinella2010acfg,
  author = {Spinella, Salvatore and Sciacca, Eva and Giannini, Paola}
  title = {{Sequence-Function Protein Analysis Using Annotated Context Free Grammars}},
  BOOKTITLE = {ICTCS 2010},
  location = {Camerino, Italy},
  year = {2010}
}

@inproceedings{CT10,
  booktitle = {3rd Workshop From Biology To Concurrency and back},
  volume = {EPTCS 19},
  url = {http://www.di.unito.it/~troina/publications/fbtc10.pdf},
  title = {Types for BioAmbients},
  author = {Capecchi, Sara and Troina, Angelo },
  year = {2010},
  pages = {103--115},
}

@inproceedings{tipoW-Coppo-Damiani-Drocco-Grassi-Troina:QAPL-10,
  booktitle = {QAPL (affiliated with ETAPS 2010)},
  url = {http://qav.comlab.ox.ac.uk/qapl10/},
  tag = {Workshop QAPL (affiliated with ETAPS 2010)},
  title = {{Stochastic Calculus of Wrapped Compartment}},
  author = {Mario Coppo and Ferruccio Damiani and Maurizio Drocco and Elena Grassi and Angelo Troina},
  year = {2010},
}

@article{BDMMT10,
  volume = {XX},
  url = {http://www.di.unito.it/~dezani/papers/bdmmt.pdf},
  title = {{A Formalism for the Description of Protein Interaction}},
  author = {Barbuti, Roberto and Dezani-Ciancaglini, Mariangiola and Maggiolo-Schettini, Andrea and Milazzo, Paolo and Troina, Angelo},
  year = {2010},
  pages = {1--29},
  journal = {Fundamenta Informaticae},
}

@inproceedings{DGT09a,
  volume = {9},
  author = {Dezani-Ciancaglini, Mariangiola and Giannini, Paola and Troina,
            Angelo},
  series = {EPTCS},
  booktitle = {DCM'09},
  url = {http://www.di.unito.it/~dezani/papers/dgtA.pdf},
  title = {{A Type System for Required/Excluded Elements in CLS}},
  year = {2009},
  pages = {38--48},
}

@inproceedings{B09,
  booktitle = {Italian Conference on Theoretical Computer Science (ITCTS) 2009},
  url = {http://www.di.unito.it/~biogliol/papers/typed_reductions_of_cls.pdf},
  title = {{Typeed Reductions of CLS}},
  author = {Bioglio, Livio},
  year = {2009}
}

@inproceedings{DGT09b,
  booktitle = {MeCBIC'09},
  url = {http://www.di.unito.it/~dezani/papers/dgtB.pdf},
  title = {{A Type System for a Stochastic CLS}},
  author = {Dezani-Ciancaglini, Mariangiola and Giannini, Paola and Troina,
            Angelo},
  year = {2009},
  series = {EPTCS},
  note = {to appear},
}

@inproceedings{tipoW-Coppo-Damiani-Grassi-Guether-Troina:CompMod-09,
  booktitle = {CompMod 2009 (affiliated with FM 2009)},
  url = {http://published.eptcs.org/},
  tag = {Workshop CompMod 2009 (affiliated with FM 2009), EPTCS
         (http://published.eptcs.org/)},
  title = {{Modelling an Ammonium Transporter with SCLS}},
  author = {Mario Coppo and Ferruccio Damiani and Elena Grassi and Mike Guether
            and Angelo Troina},
  series = {EPTCS (http://eptcs.org/)},
  year = {2009},
}

@inproceedings{ADT08,
  volume = {227},
  author = {Aman, Bogdan and Dezani-Ciancaglini, Mariangiola and Troina,
            Angelo},
  series = {ENTCS},
  booktitle = {MeCBIC'08},
  editor = {Gabriel Ciobanu},
  url = {http://www.di.unito.it/~dezani/papers/adt.pdf},
  title = {{Type Disciplines for Analysing Biologically Relevant Properties}},
  publisher = {Elsevier},
  year = {2009},
  pages = {97--111},
}