Publications
  • Bianco L, Castellini A. Psim: A computational platform for metabolic P systems. LNCS 4860, 1-20, Springer 2007
  • Bianco L, Castellini A. (2008) Psim: A computational platform for metabolic P systems. LNCS 4860, 1-20, Springer 2007.
  • Bianco L, Castellini A. Psim: A computational platform for metabolic P systems. LNCS 4860, 1-20, Springer 2007
  • Bianco L, Fontana F, Franco G, Manca V. (2006) P systems for biological dynamics. In Applications of Membrane Computing, Chapter 2, G. Ciobanu, G. Paun, M. J. Perez-Jimenez (eds). Springer, 2006.
  • Bianco L. (2008) Membrane models of biological systems. Ph.D. Thesis, University of Verona, April, 2007.
  • Bianco L., Manca V., Marchetti L., Petterlini M. (2006), Psim: a simulator for biochemical dynamics based on P systems. 2007 IEEE Congress on Evolutionary Computation. The Institute of Electrical and Electronics Engineers, 25, 2007.
  • Biarnés X.; Marchiori A.; Giorgetti A.; Lanzara C.; Gasparini P.; Carloni P.; Born S.; Brockhoff A.; Behrens M.; Meyerhof W. Insights into the Binding of Phenyltiocarbamide (PTC) Agonist to Its Target Human TAS2R38 Bitter Receptor. PLoS ONE , vol. 5 , n. 8 - e12394 , pp. 1-6, 2010
  • Bicego M. , Lovato P., Perina A. , Fasoli M., Delledonne M. , Pezzotti M. , Polverari A., Murino V.: IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1831-6. doi: 10.1109/TCBB.2012.121.
  • Blin G, Morel P, Rizzi R, Vialette S. Towards unlocking the full potential of Multileaf Collimators
  • Blin G., Rizzi R., Vialette S.: A Faster Algorithm for Finding Minimum Tucker Submatrices. CiE 2010
  • Bolognin S, Zatta P, Lorenzetto E, Valenti MT, Buffelli M. β-Amyloid-aluminum complex alters cytoskeletal stability and increases ROS production in cortical neurons. Neurochem Int. 2013 Apr;62(5):566-74. doi: 10.1016
  • Bolomini-Vittori M, Montresor A, Giagulli C, Staunton D, Rossi B, Martinello M, Constantin G, Laudanna C. Regulation of conformer-specific activation of the integrin LFA-1 by a chemokine-triggered Rho signaling module. Nat Immunol. 2009 Feb;10(2):185-94. Epub 2009 Jan 11. PubMed PMID: 19136961.
  • Bonizzoni P., Della Vedova G-, Dondi R., Pirola Y., Rizzi R-: Pure Parsimony Xor Haplotyping. IEEE/ACM Trans. Comput. Biology Bioinform. 7(4): 598-610 (2010)
  • Bonizzoni P., Della Vedova G., Dondi R., Pirola Y., Rizzi R.: Pure Parsimony Xor Haplotyping. ISBRA 2009: 186-197
  • Brelstaff, G., Bicego M., Culeddu, N., Chessa M.: Bag of Peaks: interpretation of NMR spectrometry, Bioinformatics, vol. 25, pp 258-264, (2009) pdf
  • Castellini A, Franco G, and Manca V. (2007) Toward a representation of Hybrid Functional Petri Nets by MP systems. In Proceedings of the 2nd International Workshop on Natural Computing, IWNC 2007, Nagoya University, Japan. Springer Verlag Tokyo
  • Castellini A, Manca V, Marchetti L. (2008) MP systems and Hybrid Petri Nets. In: Proceedings of International Workshop on Nature Inspired Cooperative Strategies for Optimization - NICSO 2007, Acireale, Italy, 2007.
  • Castellini A, Manca V. (2008) MetaPlab: A Computational Framework for Metabolic P Systems. In: Pre-proceedings of Workshop on membrane computing, 9th International Workshop, WMC 2008, Edinburgh, Scotland, 2008.
  • Castellini A., Franco G., Manca V.: A dictionary based informational genome analysis. BMC Genomics. 13 (1) 485, 2012
  • Castellini A., Franco G., Milanese A. (submitted) A genome analysis based on repeat sharing gene networks
  • Castellini A., Manca V., Zucchelli M. (submitted) An evolutionary procedure for inferring MP systems regulation functions of biological networks
  • Castellini A., Zucchelli M., Busato M., Manca V.: From time series to biological network regulations: an evolutionary approach. Molecular BioSystems, 2013
  • Constantin G, Laudanna C. A deadly migration. Immunity. 2010 Feb 26;32(2):147-9. PubMed PMID: 20189478.
  • Constantin G, Laudanna C. Leukocyte chemotaxis: from lysosomes to motility. Nat Immunol. 2010 Jun;11(6):463-4. PubMed PMID: 20485271
  • Constantin G, Laudanna C. Transmigration of effector T lymphocytes: changing the rules. Nat Immunol. 2011 Dec 16;13(1):15-6. doi: 10.1038/ni.2188. PubMed PMID: 22179273.
  • De Franceschi L, Biondani A, Carta F, Turrini F, Laudanna C, Deana R, Brunati AM, Turretta L, Iolascon A, Perrotta S, Elson A, Bulato C, Brugnara C. PTPepsilon has a critical role in signaling transduction pathways and phosphoprotein network topology in red cells. Proteomics. 2008 Nov;8(22):4695-708. PubMed PMID: 18924107; PubMed Central PMCID: PMC3008556.
  • De Franceschi L, Scardoni G, Tomelleri C, Danek A, Walker RH, Jung HH, Bader B, Mazzucco S, Dotti MT, Siciliano A, Pantaleo A, Laudanna C. Computational identification of phospho-tyrosine sub-networks related to acanthocyte generation in neuroacanthocytosis. PLoS One. 2012;7(2):e31015. doi: 10.1371/journal.pone.0031015. Epub 2012 Feb 15. PubMed PMID: 22355334; PubMed Central PMCID: PMC3280254.
  • Della Peruta M, Giagulli C, Laudanna C, Scarpa A, Sorio C. RHOA and PRKCZ control different aspects of cell motility in pancreatic cancer metastatic clones. Mol Cancer. 2010 Mar 17;9:61. PubMed PMID: 20236512; PubMed Central PMCID: PMC2846889
  • e.g., Bianco L, Castellini A. (2008) Psim: A computational platform for metabolic P systems. LNCS 4860, 1-20, Springer 2007
  • Fabene PF, Laudanna C, Constantin G. Leukocyte trafficking mechanisms in epilepsy. Mol Immunol. 2013 Aug;55(1):100-4. doi: 10.1016/j.molimm.2012.12.009. Epub 2013 Jan 23. PubMed PMID: 23351392.
  • Farinelli A., Denitto M., and Bicego M., Biclustering of Expression Microarray Data Using Affinity Propagation, In PRIB, pp. 13-24, 2011
  • Feigelson SW, Pasvolsky R, Cemerski S, Shulman Z, Grabovsky V, Ilani T, Sagiv A, Lemaitre F, Laudanna C, Shaw AS, Alon R. Occupancy of lymphocyte LFA-1 by surface-immobilized ICAM-1 is critical for TCR- but not for chemokine-triggered LFA-1 conversion to an open headpiece high-affinity state. J Immunol. 2010 Dec 15;185(12):7394-404. doi: 10.4049/jimmunol.1002246. Epub 2010 Nov 15. PubMed PMID: 21078912.
  • Fontana F, Manca V. (2008) Predator-prey dynamics in P systems ruled by metabolic algorithm. Biosystems 91, 545-557, 2008.
  • Fontana F., Manca V. (2008) Discrete solutions to differential equations by metabolic P systems. Theoretical Computer Science 372, 165-182. 2007.
  • Franco G. , Manca V. : Algorithmic Applications of XPCR. NATURAL COMPUTING, vol. 10, p. 805-819, 2011
  • Gagie T, Makinen V, Popa A, Tomescu A I. Approximations for the Transcript Expression Problem
  • Graziano F, Elia C, Laudanna C, Poli G, Alfano M. Urokinase plasminogen activator inhibits HIV virion release from macrophage-differentiated chronically infected cells via activation of RhoA and PKCε. PLoS One. 2011;6(8):e23674. doi: 10.1371/journal.pone.0023674. Epub 2011 Aug 17. PubMed PMID: 21858203; PubMed Central PMCID: PMC3157461.
  • Griguoli,M., Maul, A., Chuong Nguyen, Giorgetti,A., Carloni, P. and Cherubini,E. Nicotine blocks the hyperpolarization-activated current Ih and severely impairs the oscillatory behaviour of O-LM interneurons. Journal of Neuroscience. vol. 30 , n. 32 , pp. 10773-10783, 2010
  • Guillaume Blin, Romeo Rizzi, Stéphane Vialette: A Polynomial-Time Algorithm for Finding a Minimal Conflicting Set Containing a Given Row. CSR 2011: 373-384
  • Guillaume Fertin, Danny Hermelin, Romeo Rizzi, Stéphane Vialette: Finding common structured patterns in linear graphs. Theor. Comput. Sci. 411(26-28): 2475-2486
  • Guillaume Fertin, Danny Hermelin, Romeo Rizzi, Stéphane Vialette: Finding common structured patterns in linear graphs. Theor. Comput. Sci. 411(26-28): 2475-2486 (2010)
  • Guillaume Fertin, Romeo Rizzi, Stéphane Vialette: Finding occurrences of protein complexes in protein-protein interaction graphs. J. Discrete Algorithms 7(1): 90-101
  • Heller, D.M., Giorgetti, A. NMR Constraints Analyser: a web-server for the graphical analysis of NMR experimental constraints. Nucleic Acids Research, vol. 38 pp. W628-W632, 2010
  • Karnovsky A, Weymouth T, Hull T, V. Tarcea G, Overmyer K, Shellman E, Scardoni G, Laudanna C, Sartor M, Stringer K, Athey B, S. Omenn G & Burant C. Development and Application of the Metscape 2.X Bioinformatics Tool for the Analysis and Visualization of Metabolomics and Gene expression Data. Bioinformatics. 2012 Feb 1;28(3):373-80. doi: 10.1093/bioinformatics/btr661. Epub 2011 Nov 30. PMID: 22135418
  • Kempf T, Zarbock A, Widera C, Butz S, Stadtmann A, Rossaint J, Bolomini-Vittori M, Korf-Klingebiel M, Napp LC, Hansen B, Kanwischer A, Bavendiek U, Beutel G, Hapke M, Sauer MG, Laudanna C, Hogg N, Vestweber D, Wollert KC. GDF-15 is an inhibitor of leukocyte integrin activation required for survival after myocardial infarction in mice. Nat Med. 2011 May;17(5):581-8. doi: 10.1038/nm.2354. Epub 2011 Apr 24. PubMed PMID: 21516086.
  • Lapilla M, Gallo B, Martinello M, Procaccini C, Costanza M, Musio S, Rossi B, Angiari S, Farina C, Steinman L, Matarese G, Constantin G, Pedotti R. Histamine Regulates autoreactive T cell activation and adhesiveness in inflamed brain microcirculation. J Leukoc Biol. 2011 Feb;89(2):259-67. Epub 2010 Nov 11
  • Laudanna C., Bolomini-Vittori M. Integrin activation in the immune system: a systems biology perspective. Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug;1(1):116-27. Review. PubMed PMID: 20835985.
  • Lecca P., Constantin G., Laudanna C. and Priami C.. A Model Predicting Rolling Cells Percentage in Inflamed Brain Venules. Biomechanics of Cells and Tissues, Lecture Notes in Computational Vision and Biomechanics 9, DOI: 10.1007/978-94-007-5890-2_3 2013
  • Lorenzetto E, Ettorre M, Pontelli V, Bolomini-Vittori M, Bolognin S, Zorzan S, Laudanna C, Buffelli M, Selective Rac1 mutants promote retina ganglion cells survival and regeneration by ERK1/2 and PAK activation after optic nerve injury. Proceedings of
  • Lorenzetto E, Moratti E, Vezzalini M, Harroch S, Sorio C, Buffelli M. Distribution of different isoforms of receptor protein tyrosine phosphatase γ (Ptprg-RPTP γ) in adult mouse brain: upregulation during neuroinflammation. Brain Struct Funct. 2013 Mar 28
  • Lorenzetto E., Ettorre M., Pontelli V., Bolomini-Vittori M., Bolognin S., Zorzan S., Laudanna C., Buffelli M. "Rac1 selective activation improves retina ganglion cell survival and regeneration". PLOS ONE 2013 (in print)
  • Lupieri P-, Chuong Ha Hung Nguyen, Zhaleh Ghaemi Bafghi, Giorgetti A., Carloni P.: Computational molecular biology approaches to ligand-target interactions. HFSP Journal. 3(4):228-39, 2009
  • Manca V. (2009). Metabolic P Dynamics, Gh. Paun, G. Rozenberg, A. Salomaa (eds). Handbook of Membrane Computing, CHAPTER 20, OXFORD UNIVERSITY PRESS, 2009
  • Manca V, Pagliarini R, and Zorzan S. (2008) Towards an MP model of non-photochemical quenching. In: Pre-proceedings of Workshop on membrane computing, 9th International Workshop, WMC 2008, Edinburgh, Scotland, 2008.
  • Manca V. (2007) Metabolic P systems for biochemical dynamics. Progress in Natural Sciences 17 (4), 384-391. 2007.
  • Manca V. (2008) Discrete simulations of biochemical dynamics. In DNA 13, M. H. Garzon, H. Yan (eds). LNCS 4848, 231-235. Springer, 2008.
  • Manca V. (2008) The metabolic algorithm: principles and applications. THEORETICAL COMPUTER SCIENCE, vol. 404, n. 1-2, 2008, pp. 142-155
  • Manca V. (2009) Fundamentals of Metabolic P Systems, Gh. Paun, G. Rozenberg, A. Salomaa (eds), Handbook of Membrane Computing, CHAPTER 19, OXFORD UNIVERSITY PRESS, 2009.
  • Manca V. (2009). Log-Gain Principles for Metabolic P Systems, CHAPTER 28, A. Condon et al. (eds), Algorithmic Bioprocesses, Natural Computing Series, SPRINGER-VERLAG, Berlin Heidelberg 2009
  • Manca V. , Marchettii L., Pagliarini R., MP Modelling of Glucose-Insulin Interactions in the Intravenous Glucose Tolerance Test. Int. J. Found. C.S. 1(2) 13-24, 2011
  • Manca V. Infobiotics: Information in biotic systems. Springer, Heidelberg, Berlin, New-York, 2013
  • Manca V., Marchetti.L., Solving dynamical inverse problems by means of Metabolic P systems BioSystems 109(1) 78-86, 2012
  • Manca V., Bianco L. (2008) Biological Networks in metabolic P systems. Biosystems 91 (3), 489-498. 2008.
  • Manca V., et al. Evolution and Oscillation in P systems: Applications to biological phenomena, G. Mauri et al. (eds), WMC5 (Milano, Italy, June, 2004). LNCS 3365, pp. 63-84, SPRINGER-VERLAG, Berlin, Heidelberg 2005.
  • Manca, V., Marchetti L., Goldbeter's Mitotic Oscillator Entirely Modeled by MP Systems. Membrane Computing - CMC 2010, LNCS 2010. vol. 6501, p. 273-284
  • Marchetti L. , Manca V. (2012). A Methodology Based on MP Theory for Gene Expression Analysis. In: Membrane Computing, CMC 2011. vol. 7184, p. 300-313, Springer-Verlag Berlin, Heidelberg
  • Marcin Kubica, Romeo Rizzi, Stéphane Vialette, Tomasz Walen: Approximation of RNA multiple structural alignment. J. Discrete Algorithms 9(4): 365-376 (2011)
  • Martino A, Ettorre M, Musilli M, Lorenzetto E, Buffelli M and Diana G (2013). Rho GTPase-dependent plasticity of dendritic spines in the adult brain. Front. Cell. Neurosci.7:62. doi: 10.3389/fncel.2013.00062
  • Maullu C, Raimondo D, Caboi F, Giorgetti A, Sergi M, Valentini M, Tonon G, Tramontano A. Site-directed enzymatic PEGylation of the human granulocyte colony-stimulating factor. FEBS J. 276(22):6741-50, 2009
  • Mazzolini M, Marchesi A, Giorgetti A, Torre V. Gating in CNGA1 channels. Pflugers Arch. 459(4):547-55, 2010
  • Mirenda M, Toffali L, Montresor A, Scardoni G, Sorio C and Laudanna C. Protein tyrosine phosphatase, receptor type, gamma (PTPRG) is a JAK phosphatase and negatively regulates leukocyte integrin activation. Journal of Immunology 2015 PubMed PMID: 25624455.
  • Modena, D.; Trentini, M.; Corsini, M.; Bombaci, A.; Giorgetti, A. OlfactionDB: A Database of Olfactory Receptors and Their Ligands. Advances in Life Sciences, 2011; 1(1): 9-13
  • Molteni R, Crespo CL, Feigelson S, Moser C, Fabbri M, Grabovsky V, Krombach F, Laudanna C, Alon R, Pardi R. Beta-arrestin 2 is required for the induction and strengthening of integrin-mediated leukocyte adhesion during CXCR2-driven extravasation. Blood. 2009 Jul 30;114(5):1073-82. Epub 2009 May 8. PubMed PMID: 19429870
  • Montresor A, Bolomini-Vittori M, Simon SI, Rigo A, Vinante F, Laudanna C. Comparative analysis of normal versus CLL B-lymphocytes reveals patient-specific variability in signaling mechanisms controlling LFA-1 activation by chemokines. Cancer Res. 2009 Dec 15;69(24):9281-90. Epub . PubMed PMID: 19934331
  • Montresor A, Bolomini-Vittori M, Toffali L, Rossi B, Constantin G, Laudanna C. JAK tyrosine kinases promote hierarchical activation of Rho and Rap modules of integrin activation. J Cell Biol. 2013 Dec 23;203(6):1003-19. doi: 10.1083/jcb. 01303067. PubMed PMID: 24368807
  • Montresor A, Toffali L, Constantin G, Laudanna C. Chemokines and the signaling modules regulating integrin affinity. Front Immunol. 2012;3:127. doi: 10.3389/fimmu.2012.00127. Epub 2012 May 25. PubMed PMID: 22654882; PubMed Central PMCID: PMC3360201.
  • Pasvolsky R, Grabovsky V, Giagulli C, Shulman Z, Shamri R, Feigelson SW, Laudanna C, Alon R. RhoA is involved in LFA-1 extension triggered by CXCL12 but not in a novel outside-in LFA-1 activation facilitated by CXCL9. J Immunol. 2008 Mar 1;180(5):2815-23. PubMed PMID: 18292502
  • Rizzi R, Tomescu A I, Veli Makinen V: On the Complexity of Minimum Path Cover with Subpath Constraints for Multi-Assembly
  • Rougerie P, Largeteau Q, Megrelis L, Carrette F, Lejeune T, Toffali L, Rossi B, Zeghouf M, Cherfils J, Constantin G, Laudanna C, Bismuth G, Mangeney M, Delon J. Fam65b is a new transcriptional target of FOXO1 that regulates RhoA signaling for T lymphocyte migration. J Immunol. 2013 Jan 15;190(2):748-55. doi: 10.4049/jimmunol.1201174. Epub 2012 Dec 14. PubMed PMID: 23241886.
  • Ruggerone P., Pantano S., Carloni P,: Advanced Computational Methods in Molecular Medicine. Journal of Biomedicine and Biotechnology, 709085, 2013
  • Rui A. Ferreira, Roberto Grossi, Romeo Rizzi: Output-Sensitive Listing of Bounded-Size Trees in Undirected Graphs. ESA 2011: 275-286
  • Scardoni G , Montresor A, Tosadori G, Laudanna, C. Node Interference and Robustness: Performing Virtual Knock-Out Experiments on Biological Networks: The Case of Leukocyte Integrin Activation Network. February 20, 2014DOI: 10.1371/journal.pone.0088938
  • Scardoni G, Petterlini M, Laudanna C. Analyzing biological network parameters with CentiScaPe. Bioinformatics. 2009 Nov 1;25(21):2857-9. Epub 2009 Sep 2. PubMed PMID: 19729372; PubMed Central PMCID: PMC2781755
  • Scardoni G. Analyzing Biological Pathways by Abstract Interpretation. Proceedings of the First international workshop on Emerging Application of Abstract Interpretation, Electronic Notes in Theoretical Computer Science, Elsevier 2006
  • Scardoni G. and Laudanna C. Graph Theory, book chapter: Centralities based analysis of networks. InTech, open access publisher 2012
  • Scardoni G. and Laudanna C. Identifying critical road network areas with node centralities interference and robustness. Springer Berlin Heidelberg, Studies in Computational Intelligence Volume 424, 2013, pp 245-255 Springer Berlin Heidelberg (proceedings of the Complenet 2012 conference).
  • Scardoni G. and Laudanna C. Network centralities Interference and Robustness. 24 October 2011 (5 pages) Int.J.Comp.Syst.Sci. vol.1(2), pp.164-168 (2011)
  • Scardoni G. Computational Analysis of Biological networks, Topological and dynamic approaches. Lap Lambert Academic publishing (2011-12-07) – ISBN-13: 978-3-8465-9008-9
  • Scardoni, G and Laudanna C. Identifying critical traffic jam areas with node centralities interference and robustness. Networks and heterogeneous media. American Institute of Mathematical Sciences
Volume 7, Num-ber 3, September 2012
  • Shulman Z, Shinder V, Klein E, Grabovsky V, Yeger O, Geron E, Montresor A, Bolomini-Vittori M, Feigelson SW, Kirchhausen T, Laudanna C, Shakhar G, Alon R. Lymphocyte crawling and transendothelial migration require chemokine triggering of high-affinity LFA-1 integrin. Immunity. 2009 Mar 20;30(3):384-96. Epub 2009 Mar 5. PubMed PMID: 19268609.
  • Stadtmann A, Brinkhaus L, Mueller H, Rossaint J, Bolomini-Vittori M, Bergmeier W, Van Aken H, Wagner DD, Laudanna C, Ley K, Zarbock A. Rap1a activation by CalDAG-GEFI and p38 MAPK is involved in E-selectin-dependent slow leukocyte rolling. Eur J Immunol. 2011 Jul;41(7):2074-85. doi: 10.1002/eji.201041196. Epub 2011 Jun 7. PubMed PMID: 21480213; PubMed Central PMCID: PMC3124568.
  • Zanzoni, S.; Assfalg, M.; Giorgetti, A.; D'Onofrio, M.; Molinari, H. Structural Requirements for Cooperativity in Ileal Bile Acid Binding Proteins. The Journal of biological chemistry. 2011 Nov 11;286(45):39307-17.
  • Zorzan S, Buffelli M, Laudanna M, Analysis of antibody microarrays high throughput data: from data processing to network inference. The case of B-cell chronic lymphocytic leukemia. Proceedings of
  • Zorzan S., Laudanna C., Lorenzetto E., Ettorre M., Bolognin S., Pontelli V., Buffelli M. HOMECAT: a tool for comparative enrichment of experimental data based on consensus homology. Proceedings of "ECCB'12 - the European Conference on Computational Biology" , Basel, Switzerland 2012
  • Zorzan S., Lorenzetto E., Ettorre M., Pontelli V., Laudanna C., Buffelli M. HOMECAT: consensus homologs mapping for interspecific knowledge transfer and functional genomic data integration. Bioinformatics 2013; doi: 10.1093/bioinformatics/btt189