Publications

Work package 1

Journal Papers

2013

  1. Desir`o, A., Naumann, M., Epis, S., Novero, M., Bandi, C., Genre, A. and Bonfante, P.
    Mollicutes-related Endobacteria thrive inside Liverwort-associated Arbuscular Mycorrhizal Fungi. In Environmental Microbiology, 2013.
    [Web link]  [Bib] 

2011

  1. Bonfante, P. and Requena, N.
    Dating in the dark: how roots respond to fungal signals to establish arbuscular mycorrhizal symbiosis. In Current Opinion in Plant Biology, 14 (4): 451-457, 2011.
    [Web link]  [Bib] 
  2. Ghignone, S., Salvioli, A., Anca, I., Lumini, E., Ortu, G., Petiti, L., Cruveiller, S., Bianciotto, V., Piffanelli, P., Lanfranco, L. and Bonfante, P.
    The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. In The ISME Journal: 1-10, 2011.
    [Web link]  [Bib] 
  3. Chabaud, M., Genre, A., Sieberer, B.J., Faccio, A., Fournier, J., Novero, M., Barker, D.G. and Bonfante, P.
    Arbuscular mycorrhizal hyphopodia and germinated spore exudates trigger Ca2+ spiking in the legume and nonlegume root epidermis. In New Phytologist, 189 (1): 347-355, 2011.
    [Web link]  [Bib] 

2010

  1. Bonfante, P. and Genre, A.
    Mechanisms underlying beneficial plant--fungus interactions in mycorrhizal symbiosis. In Nature Communications, 48 (1), 2010.
    [Web link]  [Bib] 
  2. Naumann, M., Schuessler, A. and Bonfante, P.
    The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes. In The ISME Journal, 2010.
    [Web link]  [Bib] 
  3. Chin, G. and Yeston, J.
    Commentary on "The obligate endobacteria of arbuscular mycorrhizal fungi are ancient heritable components related to the Mollicutes". In Science, 2010.
    [Web link]  [Bib] 
  4. Salvioli, A., Chiapello, M., Fontaine, J., Hadj-Sahraoui, A.L., Grandmougin-Ferjani, A., Lanfranco, L., P., and B.
    Endobacteria affect the metabolic profile of their host Gigaspora margarita, an arbuscular mycorrhizal fungus. In Environmental Microbiology, 2010.
    [Web link]  [Bib] 

Conference Papers

2011

  1. Ghignone, S., Salvioli, A., Anca, I., Lumini, E., Cruveiller, S., Ortu, G., Piffanelli, P., Lanfranco, L. and Bonfante, P.
    The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions. In 26th Fungal Genetics Conference at Asilomar (15-20 March 2011), 2011.
    [Web link]  [Bib] 

2010

  1. Bonfante, P.
    Mycorrhizas as tripartite associations. In Indo-Italian workshop on bacteria and fungi for environmental sustainability, New Delhi, November 29-30 and December 1, 2010.
    [Web link]  [Bib] 
  2. Genre, A.
    Molecular signaling and cellular mechanisms at the basis of root colonization by arbuscular mycorrhizal fungi. In Indo-Italian workshop on bacteria and fungi for environmental sustainability, New Delhi, November 29-30 and December 1, 2010.
    [Web link]  [Bib] 

Work package 2

Journal Papers

2013

  1. Genre, A., Chabaud, M., Balzergue, C., Puech-Pagès, V., Novero, M., Rey, T., Fournier, J., Rochange, S., Bécard, G., Bonfante, P. and Barker, D.G.
    Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca2+ spiking in Medicago truncatula roots and their production is enhanced by strigolactone. In New Phytologist, 2013.
    [Web link]  [Bib] 
  2. Volpe, V., Dell'Aglio, E., Giovannetti, M., Ruberti, C., Costa, A., Genre, A., Guether, M. and Bonfante, P.
    An AM-induced, MYB-family gene of Lotus japonicus (LjMAMI) affects root growth in an AM-independent manner. In The Plant Journal, 73 (3): 442-455, 2013.
    [Web link]  [Bib] 

2012

  1. Giovannetti, M., Balestrini, R., Volpe, V., Guether, M., Straub, D., Costa, A., Ludewig, U. and Bonfante, P.
    Two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in Lotus japonicus. In BMC Plant Biology, 12: 186, 2012.
    [Bib] 
  2. Ortu, G., Balestrini, R., Pereira, P.A., Becker, J.D., Küster, H. and Bonfante, P.
    Plant genes related to gibberellin biosynthesis and signaling are differentially regulated during the early stages of AM fungal interactions. In Molecular Plant, 5 (4): 951-954, 2012.
    [Web link]  [Bib] 
  3. Montani, S., Leonardi, G., Ghignone, S. and Lanfranco, L.
    Flexible case-based retrieval for comparative genomics. In Applied Intelligence, 2012.
    [Web link]  [Bib] 

2011

  1. Guether, M., Volpe, V., Balestrini, R., Requena, N., Wipf, D. and Bonfante, P.
    LjLHT1.2 - a mycorrhiza-inducible plant amino acid transporter from Lotus japonicus. In Biology and Fertility of Soils, 47 (8): 925-936, 2011.
    [Bib] 
  2. Bonfante, P., Cordero, F., Ghignone, S., Ienco, D., Lanfranco, L., Leonardi, G., Meo, R., Montani, S., Roversi, L. and Visconti, A.
    A Modular Database Architecture Enabled to Comparative Sequence Analysis. In LNCS journal Transactions on Large-Scale Data and Knowledge-Centered Systems: 124-147, 2011.
    [Web link]  [Bib] 
  3. Tisserant, E., Kohler, A., Dozolme-Seddas, P., Balestrini, R., Benabdellah, K., Colard, A., Croll, D., C., Da S., Gomez, S.K., Koul, R., Ferrol, N., Fiorilli, V., Formey, D., Franken, P., Helber, N., Hijri, M., Lanfranco, L., Lindquist, E., Liu, Y., Malbreil, M., Morin, E., Poulain, J., Shapiro, H., Tuinen, D. v., Waschke, A., Azcón-Aguilar, C., Bécard, G., Bonfante, P., Harrison, M.J., Küster, H., Lammers, P., Paszkowski, U., Requena, N., Rensing, S.A., Roux, C., Sanders, I.R., Shachar-Hill, Y., Tuskan, G., Young, J.P.W., Gianinazzi-Pearson, V. and Martin, F.
    The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont. In New Phytologist, 2011.
    [Web link]  [Bib] 

2010

  1. Salvioli, A., Chiapello, M., Fontaine, J., Hadj-Sahraoui, A.L., Grandmougin-Ferjani, A., Lanfranco, L., P., and B.
    Endobacteria affect the metabolic profile of their host Gigaspora margarita, an arbuscular mycorrhizal fungus. In Environmental Microbiology, 2010.
    [Web link]  [Bib] 

2009

  1. Guether, M., Balestrini, R., Hannah, M., He, J., Udvardi, M.K and Bonfante, P.
    Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus. In New Phytologist, 182 (1): 200-212, 2009.
    [Web link]  [Bib] 
  2. Guether, M., Neuhäuser, B., Balestrini, R., Dynowski, M., Ludewig, U. and Bonfante, P.
    A mycorrhizal-specific ammonium transporter from Lotus japonicus acquires nitrogen released by arbuscular mycorrhizal fungi. In Plant Physiology, 150 (1): 73-83, 2009.
    [Web link]  [Bib] 

Book chapters

2011

  1. Lanfranco, L., Guether, M. and Bonfante, P.
    Arbuscular mycorrhizas and N acquisition by plants.
    [Web link]  [Bib] 
  2. Cordero, F., Ghignone, S., Lanfranco, L., Leonardi, G., Meo, R., Montani, S. and Roversi, L.
    BIOBITS: A Study on Candidatus Glomeribacter Gigasporarum with a Data Warehouse.
    [Web link]  [Bib] 

Conference Papers

2011

  1. Montani, S., Leonardi, G., Ghignone, S. and Lanfranco, L.
    Flexible and interactive retrieval for supporting comparative genomics studies on endobacteria. In Proc. Workshop on Human-centered Case-Based Reasoning, International Conference on Case-Based Reasoning (ICCBR), 2011.
    [Web link]  [Bib] 
  2. Montani, S., Leonardi, G., Ghignone, S. and Lanfranco, L.
    Flexible and interactive retrieval for supporting in-silico studies of endobacteria. In Proc. IEEE International Conference on Tools with Artificial Intelligent (ICTAI), 2011.
    [Web link]  [Bib] 

2010

  1. Montani, S., Leonardi, G., Ghignone, S. and Lanfranco, L.
    Flexible genome retrieval for supporting in-silico studies of endobacteria-AMFs. In World Computer Congress - International Federation for Information Processing (IFIP) IFIP-AICT 335, pages 138-147, Springer, Berlin, 2010.
    [Bib] 
  2. Lanfranco, L.
    Symbiosis in the -OMICS era: a glance into the arbuscular mycorrhizal symbiosis. In Indo-Italian workshop on bacteria and fungi for environmental sustainability, New Delhi, November 29-30 and December 1, 2010.
    [Web link]  [Bib] 

Work package 3

Journal Papers

2013

  1. Aldinucci, M., Torquati, M., Spampinato, C., Drocco, M., Calcagno, C. and Coppo, M.
    Parallel stochastic systems biology in the cloud. In Submitted for pubblication, 2013.
    [Bib] 
  2. Spampinato, C., Milardo, S., Pino, C., Kavasidis, I., Aldinucci, M. and Pennisi, M.
    BioCloud: Discovering Biological Knowledge by Integrating High Throughput Data and Scientific Literature on the Cloud. In Submitted for pubblication, 2013.
    [Bib] 
  3. Aldinucci, M., Calcagno, C., Coppo, M., Damiani, F., Drocco, M., Sciacca, E., Spinella, S., Torquati, M. and Troina, A.
    On designing multicore-aware simulators for systems biology endowed with on-line statistics. In Submitted for pubblication, 2013.
    [Bib] 
  4. Giannini, P. and E.P., de V.
    International Workshop on Interactions between Computer Science and Biology, CS2Bio 2012.
    [Bib] 

2012

  1. Bioglio, L., Dezani-Ciancaglini, M., Giannini, P. and Troina, A.
    Type Stochastic Semantics for the Calculus of Looping Sequences. In Theoretical Computer Science, 2012.
    [Bib] 
  2. Coppo, M., Damiani, F., Drocco, M., Grassi, E., Sciacca, E., Spinella, S. and Troina, A.
    Simulation Techniques for the Calculus of Wrapped Compartments. In Theoretical Computer Science, 2012.
    [Bib] 

2011

  1. Giannini, P. and Krivine, J.
    International Workshop on Interactions between Computer Science and Biology, CS2Bio 2011. In Electr. Notes Theor. Comput. Sci., 277: 1-2, 2011.
    [Web link]  [Bib] 
  2. Bioglio, L., Dezani-Ciancaglini, M., Giannini,Paola and Troina, A.
    Type Directed Semantics for the Calculus of Looping Sequences. In International Journal of Software and Informatics, 2011.
    [Web link]  [Bib] 
  3. Bioglio, L.
    Enumerated Type Semantics for the Calculus of Looping Sequences. In RAIRO - Theoretical Informatics and Applications, 45 (1): 35-58, 2011.
    [Web link]  [Bib] 

2010

  1. Aldinucci, M., Bracciali, A. and Li`o, P.
    Formal Synthetic Immunology. In ERCIM News, 82: 40-41, 2010.
    [Web link]  [Bib] 
  2. Barbuti, R., Dezani-Ciancaglini, M., Maggiolo-Schettini, A., Milazzo, P. and Troina, A.
    A Formalism for the Description of Protein Interaction. In Fundamenta Informaticae, XX: 1-29, 2010.
    [Web link]  [Bib] 

Book chapters

2011

  1. Cordero, F., Ghignone, S., Lanfranco, L., Leonardi, G., Meo, R., Montani, S. and Roversi, L.
    BIOBITS: A Study on Candidatus Glomeribacter Gigasporarum with a Data Warehouse.
    [Web link]  [Bib] 

Conference Papers

2013

  1. Aldinucci, M., Tordini, F., Drocco, M., Torquati, M. and Coppo, M.
    Parallel stochastic simulators in system biology: the evolution of the species. In Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP'13), IEEE, 2013.
    [Bib] 

2012

  1. Ram`on, P. and Troina, A.
    Modelling Ecological Systems with the Calculus of Wrapped Compartments. In International Conference on Membrane Computing (CMC13), pages 358-377, 2012.
    [Web link]  [Bib] 
  2. Ciobanu, G. and Troina, A.
    Rate-Based Stochastic Fusion Calculus and Continuous Time Markov Chains. In Italian Conference on Theoretical Computer Science (ICTCS'12), pages 86-89, 2012.
    [Web link]  [Bib] 
  3. Compagnoni, A., Dezani-Ciancaglini, M., Giannini, P., Sauer, K., Sharma, V. and Troina, A.
    Parallel BioScape: A Stochastic and Parallel Language for Mobile and Spatial Interactions. In International Meeting on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC'12), pages 101-106, 2012.
    [Web link]  [Bib] 
  4. Sciacca, E., Spinella, S., Calcagno, C., Damiani, F. and Coppo, M.
    Parameter Identification and Assessment of Nutrient Transporters in AM Symbiosis through Stochastic Simulations. In International Workshop on Interactions between Computer Science and Biology, CS2Bio 2012, 2012.
    [Bib] 

2011

  1. Bioglio, L., Dezani-Ciancaglini, M., Giannini, P. and Troina, A.
    A Calculus of Looping Sequences with Local Rules. In Proceedings 7th International Workshop on Developments of Computational Methods, pages 43-58, 2011.
    [Bib] 
  2. Aldinucci, M., Coppo, M., Damiani, F., Drocco, M., Torquati, M. and Troina, A.
    On Designing Multicore-Aware Simulators for Biological Systems. In Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP'11), pages 318-325, IEEE, 2011.
    [Web link]  [Bib] 
  3. Aldinucci, M., Bracciali, A., Li`o, P., Sorathiya, A. and Torquati, M.
    StochKit-FF: Efficient Systems Biology on Multicore Architectures. In Euro-Par 2010, Workshop on High Performance Bioinformatics and Biomedicine (HiBB), pages 167-175, Springer, 2011.
    [Web link]  [Bib] 
  4. Egidi, L. and Manzini, G.
    Spaced Seeds Design Using Perfect Rulers. In Proceedings SPIRE: String Processing and Information Retrieval, pages 32-43, Springer, 2011.
    [Bib] 
  5. Sciacca, E., Spinella, S., Ienco, D. and Giannini, P.
    Annotated Stochastic Context Free Grammars for Analysis and Synthesis of Proteins. In Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. Springer LNCS, 2011.
    [Bib] 
  6. Sciacca, E., Spinella, S., Genre, A. and Calcagno, C.
    Analysis of Calcium Spiking in Plant Root Epidermis through CWC Modeling. In CS2BIO 2011, 2011.
    [Bib] 
  7. Calcagno, C., Coppo, M., Damiani, F., Drocco, M., Sciacca, E., Spinella, S. and Troina, A.
    Modelling Spatial Interactions in the Arbuscular Mycorrhizal Symbiosis using the Calculus of Wrapped Compartments. In 3rd International Workshop on Computational Models for Cell Processes (CompMod'11), EPTCS, pages 3-18, 2011.
    [Bib] 
  8. Bioglio, L., Calcagno, C., Coppo, M., Damiani, F., Sciacca, E., Spinella, S. and Troina, A.
    A Spatial Calculus of Wrapped Compartments. In 5th International Meeting on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC'11), pages 25-39, 2011.
    [Bib] 
  9. Bioglio, L.
    A Minimal OO Calculus for Modelling Biological Systems. In Computational Models for Cell Processes (CompMod) 2011, 2011.
    [Bib] 
  10. Aldinucci, M., Coppo, M., Damiani, F., Drocco, M., Sciacca, E., Spinella, S., Torquati, M. and Troina, A.
    On Parallelizing On-Line Statistics for Stochastic Biological Simulations. In 2nd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB'11), Springer LNCS, 2011.
    [Bib] 

2010

  1. Coppo, M., Damiani, F., Drocco, M., Grassi, E., Sciacca, E., Spinella, S. and Troina, A.
    Hybrid Calculus of Wrapped Compartments. In Membrane Computing and Biologically Inspired Process Calculi 2010, pages 98-116, 2010.
    [Bib] 
  2. Spinella, S., Sciacca, E. and Giannini, P.
    Sequence-Function Protein Analysis Using Annotated Context Free Grammars. In ICTCS 2010, 2010.
    [Bib] 
  3. Capecchi, S. and Troina, A.
    Types for BioAmbients. In 3rd Workshop From Biology To Concurrency and back, pages 103-115, 2010.
    [Web link]  [Bib] 
  4. Coppo, M., Damiani, F., Drocco, M., Grassi, E. and Troina, A.
    Stochastic Calculus of Wrapped Compartment. In QAPL (affiliated with ETAPS 2010), 2010.
    [Web link]  [Bib] 

2009

  1. Dezani-Ciancaglini, M., Giannini, P. and Troina, A.
    A Type System for Required/Excluded Elements in CLS. In DCM'09, pages 38-48, 2009.
    [Web link]  [Bib] 
  2. Bioglio, L.
    Typeed Reductions of CLS. In Italian Conference on Theoretical Computer Science (ITCTS) 2009, 2009.
    [Web link]  [Bib] 
  3. Dezani-Ciancaglini, M., Giannini, P. and Troina, A.
    A Type System for a Stochastic CLS. In MeCBIC'09, 2009.
    [Web link]  [Bib] 
  4. Coppo, M., Damiani, F., Grassi, E., Guether, M. and Troina, A.
    Modelling an Ammonium Transporter with SCLS. In CompMod 2009 (affiliated with FM 2009), 2009.
    [Web link]  [Bib] 
  5. Aman, B., Dezani-Ciancaglini, M. and Troina, A.
    Type Disciplines for Analysing Biologically Relevant Properties. In MeCBIC'08, pages 97-111, Elsevier, 2009.
    [Web link]  [Bib] 

Misc

2011

  1. Sciacca, E., Spinella, S. and Giannini, P.
    A(S)CFG generator (Prototypal Software).
    [Bib] 
  2. Bioglio, L., Coppo, M., Damiani, F., Sciacca, E., Spinella, S. and Troina, A.
    CWC Surface Language Software (Prototypal Software).
    [Bib] 
  3. Sciacca, E. and Spinella, S.
    Calcium Spiking Analyser (Prototypal Software).
    [Bib] 

2010

  1. Aldinucci, M., Coppo, M., Damiani, F., Drocco, M., Giovannetti, E., Grassi, E., Sciacca, E., Spinella, S. and Troina, A.
    CWC Simulator (Public Software).
    [Web link]  [Bib] 

Work package 4

Journal Papers

2012

  1. Gaiji, N., Cardinale, F., Prandi, C., Bonfante, P. and Ranghino, G.
    The computational-based structure of Dwarf14 provides evidence for its role as potential strigolactone receptor in plants. In BMC Research Notes, 5 (307), 2012.
    [Web link]  [Bib] 

Conference Papers

2012

  1. Gaiji, N., Cardinale, F., Prandi, C., Bonfante, P. and Ranghino, G.
    The computational-based structure of Dwarf14 provides evidence for its role as potential strigolactone receptor in plants. In Bioinformatica Indica, 2012.
    [Bib] 

2011

  1. Gaiji, N., Cardinale, F., Prandi, C., Bonfante, P. and Ranghino, G.
    The computational-based structure of Dwarf14 provides evidence for its role as potential strigolactone receptor in plants. In International Interdisciplinary Science Conference 2011 on Bioinformatics: An Interface between Computer Science and Biology, 2011.
    [Bib] 

Work package 5

Journal Papers

2011

  1. Prandi, C., Occhiato, E.G., Tabasso, S., Bonfante, P., Novero, M., Scarpi, D., Bova, M.E. and Miletto, I.
    New Potent Fluorescent Analogues of Strigolactones: Synthesis and Biological Activity in Parasitic Weed Germination and Fungal Branching. In European Journal of Organic Chemistry: 3781-3793, 2011.
    [Web link]  [Bib] 

2009

  1. Bhattacharya, C., Bonfante, P., Deagostino, A., Kapulnik, Y., Larini, P., Occhiato, E. G., Prandi, C. and Venturello, P.
    A new class of conjugated strigolactones analogues with fluorescent properties: synthesis and biological activity.
    [Web link]  [Bib] 

Work package 6

Journal Papers

2013

  1. Borriello, R, Bisignano, A, Bianciotto, V and Beruto, M.
    I funghi micorrizici arbuscolari utili alleati nella produzione del Ranuncolo clonato in vitro. In Il Floricultore, Gennaio--Febbraio: 2-7, 2013.
    [Web link]  [Bib] 

Collections

2011

  1. Giovannetti, G.
    I batteri e il loro rapporto con le coltivazioni e con la salute umana, In Systemic Design, progettare la sostenibilità produttiva e l'ambiente: 214--223, Slow Food Editore, 2011.
    [Web link]  [Bib] 

Misc

2012

  1. Bianciotto, V.
    Applicazione di inoculi micorrizici alle piante ornamentali, In Summer School in Micropropagazione e Tecniche Avanzate di Coltura, Vitro Sanremo-Pescia, 10–-14 September, invited speaker.
    [Bib] 

2011

  1. Giovannetti, G.
    Biotecnologie Agrarie basate sui Consorzi Microbici: Vicende Affermative del Microsat F (Report).
    [Web link]  [Bib]