822 results

    2014

  • Journal Papers O. Kahramanogullari.

    Interaction and Depth against Nondeterminism in Proof Search,


    Logical Methods in Computer Science,

    2014


    abstract


  • Journal Papers J. Podani,  F. Jordan,  D. Schmera.

    New insights into the architecture of bipartite (interaction) ecological networks,


    Journal of Complex Networks,

    2014



  • Journal Papers S. Lacroix,  M. Juneau,  A. Nigam,  M. Gayda.

    Are Drastic Caloric Restrictions and Moderate- Intensity Physical Activity Still Relevant Lifestyle Interventions for Obese Patients With Type 2 Diabetes?,


    Canadian Journal of Cardiology,

    30:465, 2014


    pdf pdf


  • Journal Papers P. Nguyen,  L. Caberlotto,  M. Morine,  C. Priami.

    Network Analysis of Neurodegenerative Disease Highlights a Role of Toll-Like Receptor Signaling,


    BioMed Research International,

    2014:1-16, 2014



  • technical report R. Zunino,  T. Vo,  C. Priami.

    RSSA: a Rejection-based Stochastic Simulation Algorithm,



    abstract | pdf pdf


  • Journal Papers M. Morine.

    Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life.,


    Genes & nutrition,

    9:1-9, 2014


    abstract


  • proceeding Papers O. Kahramanogullari,  J. Lynch,  C. Priami.

    Algorithmic Systems Ecology: Experiments on Multiple Interaction Types and Patches,


    InSuEdu 2012,

    LNCS 7991, Springer, 2014


    abstract


  • Journal Papers T. Vo,  R. Zunino.

    Adaptive Tree-Based Search for Stochastic Simulation Algorithm,


    International Journal of Computational Biology and Drug Design,

    Inderscience, 2014


    abstract


  • Book Chapter L. Marchetti,  V. Manca,  R. Pagliarini,  A. Bollig-Fischer.

    MP Modelling for Systems Biology: Two Case Studies,


    Applications of Membrane Computing in Systems and Synthetic Biology7,

    7:223-245, Springer International Publishing, 2014


    abstract


  • 2013

  • Journal Papers M. Morine.

    Perspective: a systems approach to diabetes research.,


    2013


    abstract


  • Journal Papers P. Samantha,  B. Llamas,  M. Scott-Boyer,  S. Picard,  F. Robert,  D. Langlais,  B. Haibe-Kains,  D. Faubert,  D. Silversides,  C. Deschepper.

    Novel Effects of Chromosome Y on Cardiac Regulation, Chromatin Remodeling, and Neonatal Programming in Male Mice,


    Endocrinology,

    2013



  • Journal Papers O. Kahramanogullari,  L. Cardelli.

    An Intuitive Modelling Interface for Systems Biology,


    International Journal of Software and Informatics,

    7:4, 2013


    abstract


  • Journal Papers M. Scott-Boyer,  C. Deschepper.

    Genome-wide Detection of Gene Co-expression Domains Showing Linkage to Regions Enriched with Polymorphic Retrotransposons in Recombinant Inbred Mouse Strains,


    G3 (Bethesda, Md.),

    2013


    abstract


  • poster L. Caberlotto,  M. Lauria,  P. Nguyen,  M. Scotti.

    The central role of AMP-kinase and energy homeostasis impairment in Alzheimer’s disease: a multifactor network analysis. ,


    Italian Society for Neuroscience,

    - Rome, 2013


    abstract


  • Journal Papers M. Scotti,  F. Ciocchetta,  F. Jordan.

    Social and landscape effects on food webs: a multi-level network simulation model,


    Journal of Complex Networks,

    1:160-182, 2013


    abstract


  • Book Chapter I. Mura.

    Cell Cycle Modeling, Petri Nets,


    Encyclopedia of Systems Biology,

    DOI 10.1007/978-1-4419-9863-7, Springer, 2013



  • Journal Papers A. Tarca,  M. Lauria,  M. Unger,  E. Bilal,  S. Boue,  K. Dey,  J. Hoeng,  H. Koeppl,  F. Martin,  P. Meyer,  P. Nandy,  R. Norel,  M. Peitsch,  J. Rice,  R. Romero,  G. Stolovitzky,  M. Talikka,  Y. Xiang,  C. Zechne.

    Strengths and limitations of microarray-based phenotype prediction: Lessons learned from the IMPROVER Diagnostic Signature Challenge,


    Bioinformatics,

    29:2892-9, Oxford University Press, 2013


    abstract


  • proceeding Papers D. Tran,  P. Nguyen,  L. Caberlotto,  C. Priami.

    Inference of Autism-Related Genes by Integrating Protein-Protein Interactions and miRNA-Target Interactions,


    Proceedings of the Fifth International Conference KSE 2013,

    Adv in Intelligent Systems and Computing-Springer, 2013



  • Journal Papers I. Nassiri,  Ali Masoudi-Nejad,  Mahdi Jalili,  A. Moeini.

    Normalized Similarity Index: An adjusted index to prioritize article citations,


    Journal of Informetrics,

    7:91-98, 2013


    abstract


  • Journal Papers I. Nassiri,  Ali Masoudi-Nejad,  Mahdi Jalili,  A. Moeini.

    Discovering dominant pathways and signaling response relationships in signaling networks through nonparametric approaches,


    Genomics,

    2013


    abstract


  • PhD Thesis N. Gjata .

    FOOD WEB SIMULATION STUDIES ON AQUATIC ECOSYSTEMS,


    COSBI - DISI - University of Trento,


    abstract | pdf pdf


  • Journal Papers M. Morine.

    Discovery-Based Nutritional Systems Biology: Developing N-of-1 Nutrigenomic Research. ,


    2013


    abstract


  • Book Chapter C. Damiani.

    Modelling the influence of cell signaling on the dynamics of gene regulatory networks,


    Biomechanics of Cells and Tissues Lecture Notes in Computational Vision and Biomechanics ,

    9:103-130, Springer, 2013


    abstract


  • Book Chapter A. Palmisano,  C. Priami.

    Cell Cycle Modeling, Process Algebra,


    DOI 10.1007/978-1-4419-9863-7, 2013


    abstract


  • Journal Papers M. Scotti,  L. Stella,  E. Shearer,  P. Stover.

    Modeling cellular compartmentation in one- carbon metabolism,


    WIREs Systems Biology and Medicine,

    5:343-365, 2013


    abstract


  • Journal Papers M. Scott-Boyer,  G. Imholte,  A. Labbe,  C. Deschepper,  R. Gottardo.

    iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.,


    Bioinformatics (Oxford, England),

    2013


    abstract


  • Journal Papers P. Praveen,  H. Froehlich.

    Boosting Probabilistic Graphical Model Inference by Incorporating Prior Knowledge from Multiple Sources,


    PloS One,

    8:e67410, Public Library of Science, 2013


    abstract


  • Journal Papers L. Caberlotto,  M. Lauria,  P. Nguyen,  M. Scotti.

    The central role of AMP-kinase and energy homeostasis impairment in Alzheimer's disease: a multifactor network analysis ,


    PLOS ONE,

    8:e78919, 2013


    abstract


  • Book Chapter A. Csikasz-Nagy.

    Cell Cycle,


    Encyclopedia of Systems Biology,

    DOI 10.1007/978-1-4419-9863-7, Springer, 2013



  • Journal Papers A. Bajpai,  A. Feoktistova,  J. Chen,  D. McCollum,  M. Sato,  R. Carazo-Salas,  K. Gould,  A. Csikász-Nagy.

    Dynamics of SIN Asymmetry Establishment,


    PLoS Computational Biology,

    9(7): e1003147, 2013


    abstract | pdf pdf


  • Journal Papers M. Lauria.

    Rank-based transcriptional signatures: A novel approach to diagnostic biomarker definition and analysis,


    Systems Biomedicine,

    1:0-10, Landes Bioscience, 2013


    abstract


  • poster P. Nguyen,  L. Caberlotto,  C. Priami.

    An Efficient Method for Predicting Dementia Drug Targets Using Multi- Relational Data Mining,


    European Conference on Computational Biology 2013,

    - Berlin, Germany, 2013



  • Journal Papers I. Nassiri,  E. Azadian,  Ali Masoudi-Nejad.

    Co-occurrence: A gene reference resource for coincidental patterns of gene mutations in human cancers ,


    Journal of Proteomics and Bioinformatics ,

    6:197-201, 2013


    abstract


  • Book Chapter O. Kahramanogullari,  A. Phillips,  F. Vaggi.

    Process Modeling and Rendering of Biochemical Structures: Actin,


    Biomechanics of cells and tissues: experiments, models and simulations, Lecture Notes in Computational Vision and Biomechanics,

    9:45-63, Springer, 2013


    abstract


  • Book Chapter P. Lecca,  G. Constantin,  C. Laudanna,  C. Priami.

    A model predicting rolling cells percentage in inflamed brain venules,


    Biomechanics of cells and tissues: experiments, models and simulations, Lecture Notes in Computational Vision and Biomechanics,

    Springer, 2013


    abstract


  • Journal Papers M. Ortiz,  R. Levins,  L. Campos,  F. Berrios,  F. Campos,  F. Jordan,  B. Hermosillo,  J. Gonzalez,  F. Rodriguez.

    Identifying keystone trophic groups in benthic ecosystems: implications for fisheries management,


    Ecological Indicators,

    25:133-140, 2013



  • Journal Papers M. Pizzol,  M. Scotti,  M. Thomsen.

    Network analysis as a tool for assessing environmental sustainability: applying the ecosystem perspective to a Danish water management system,


    Journal of Environmental Management,

    118:21-31, 2013


    abstract


  • Journal Papers H. Sridhar,  K. Shanker,  F. Jordan.

    Species importance in a heterospecific foraging association network,


    Oikos,

    122:1325-1334, 2013



  • proceeding Papers T. Vo,  R. Zunino.

    Splitting for Rare Event Simulation in Biochemical Systems,


    The 6th International ICST Conference on Simulation Tools and Techniques (SIMUTools),

    2013


    abstract | pdf pdf


  • Journal Papers P. Praveen,  H. Failmezger,  A. Tresch,  H. Froehlich.

    Learning Gene Network Structure from Time Laps Cell Imaging in RNAi Knock-Downs,


    Bioinformatics,

    29:1534-1540, Oxford Journal, 2013


    abstract


  • Journal Papers L. Caberlotto,  L. Carboni,  F. Zanderigo,  F. Andreetta,  M. Andreoli,  G. Gentile,  M. Razzoli.

    Differential effects of glycogen synthase kinase 3 (GSK3) inhibition by lithium or selective inhibitors in the central nervous system.,


    Naunyn Schmiedebergs Arch Pharmacol.,

    386:893-903, 2013


    abstract


  • Journal Papers F. Amara,  R. Colombo,  P. Cazzaniga,  D. Pescini,  A. Csikasz-Nagy,  M. Muzi Falconi,  D. Besozzi,  P. Plevani.

    In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae,


    BMC Systems Biology,

    7:24, 2013


    abstract


  • Journal Papers V. Manca,  A. Castellini,  G. Franco,  L. Marchetti,  R. Pagliarini.

    Metabolic P Systems: A Discrete Model for Biological Dynamics,


    Chinese Journal of Electronics,

    22:717-723, 2013


    abstract


  • Journal Papers A. De Gaetano,  S. Panunzi,  A. Matone,  A. Samson,  J. Vrbikova,  B. Bendlova,  G. Pacini.

    Routine OGTT: A Robust Model Including Incretin Effect for Precise Identification of Insulin Sensitivity and Secretion in a Single Individual ,


    PLOS ONE,

    8, 2013


    abstract


  • Journal Papers I. Nassiri,  E. Azadian,  Ali Masoudi-Nejad.

    A sequence motif associated with intrinsic mutation hot-spots in human cancers ,


    Journal of Proteomics and Bioinformatics ,

    6:173-186, 2013


    abstract


  • Journal Papers O. Kahramanogullari,  J. Lynch.

    Stochastic Flux Analysis of Chemical Reaction Networks,


    BMC Systems Biology,

    7:133, 2013


    abstract


  • Journal Papers M. Morine.

    PBMCs reflect the immune component of the WAT transcriptome - Implications as biomarkers of metabolic health in the postprandial state. ,


    Molecular nutrition & food research,

    2013


    abstract


  • Journal Papers M. Scott-Boyer,  B. Haibe-Kains,  C. Deschepper.

    Network statistics of genetically-driven gene co-expression modules in mouse crosses,


    Frontiers in Genetics,

    4, 2013



  • Book Papers P. Lecca,  I. Laurenzi,  F. Jordan.

    Deterministic versus stochastic modelling in biochemistry and systems biology,


    Woodhead Publishing Series in Biomedicine No. 21 - Cambridge, UK, 2013



  • Journal Papers J. Nieto-Navarro,  M. Zetina-Rejón,  F. Arreguín-Sánchez,  D. Palacios-Salgado,  F. Jordan.

    Seasonal changes in fish assemblages of soft bottom habitats along the eastern coast of the mouth of the Gulf of California,


    Journal of Applied Ichthyology,

    29:1-7, 2013



  • Journal Papers R. De Cegli,  S. Iacobacci,  G. Flore,  G. Gambardella,  L. Mao,  L. Cutillo,  M. Lauria,  J. Klose,  E. Illingworth,  S. Banfi,  D. di Bernardo.

    Reverse engineering a mouse embryonic stem cell-specific transcriptional network reveals a new modulator of neuronal differentiation.,


    Nucleic Acids Res,

    41:711-26, Oxford Journals, 2013


    abstract


  • Journal Papers A. Bhadra,  F. Jordan.

    Cryptic successors unrevealed even by network analysis: A comparative study of two paper wasp species,


    Network Biology,

    3:54-66, 2013


    abstract


  • Journal Papers J. Dodgson,  A. Chessel,  M. Yamamoto,  F. Vaggi,  S. Cox,  E. Rosten,  D. Albrecht,  M. Geymonat,  A. Csikasz-Nagy,  M. Sato,  R. E. Carazo-Salas.

    Spatial segregation of polarity factors into distinct cortical clusters is required for cell polarity control,


    Nature Communications,

    Nature, 2013


    abstract


  • Journal Papers V. Manca,  L. Marchetti.

    An algebraic formulation of inverse problems in MP dynamics,


    International Journal of Computer Mathematics,

    90:845-856, 2013


    abstract


  • Journal Papers S. Lacroix,  C. DesRosiers,  M. Gayda,  E. Thorin,  J. Tardif,  A. Nigam.

    A Single Mediterranean-Type Meal Leads to Postprandial Enrichment in Omega-3 Pufas and Does Not Impair Flow-Mediated Dilatation in Comparison to a High-Saturated Fat Meal in Healthy Men With High- Normal Fasting Triglyceridemia,


    Canadian Journal of Cardiology,

    29:S357, 2013



  • Book Chapter I. Mura.

    Cell Cycle Modeling, Stochastic Methods,


    Encyclopedia of Systems Biology,

    DOI 10.1007/978-1-4419-9863-7, Springer, 2013


    abstract


  • Journal Papers F. Jordan,  A. Báldi.

    Systems-based conservation and the odd conflicts between species-protection programmes,


    Web Ecology,

    13:1-5, 2013



  • PhD Thesis T. Vo.

    On Efficient Algorithms for Stochastic Simulation of Biochemical Reaction Systems,



    abstract | pdf pdf


  • 2012

  • Book Chapter P. Lecca,  A. Palmisano.

    The present and the future perspectives of biological network inference,


    Bioinformatics & Computational Systems Biology: Recent Advances and Applications The present and the future perspectives of biological network inference,

    IGI-Global , 2012


    abstract


  • Journal Papers M. Morine,  E. Brennan,  D. Walsh,  S. Roxburgh,  M. Lindenmeyer,  D. Brazil.

    Next-generation sequencing identifies TGF-ß1- associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy.,


    Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease,

    2012


    abstract


  • Book Papers O. Kahramanogullari.

    Nondeterminism and Language Design in Deep Inference - A Proof Theoretic Approach to Logic Programming,


    Lambert Academic Publishing, 2012


    abstract


  • Journal Papers P. Lecca,  D. Morpurgo.

    Modelling non-homogeneous stochastic reaction-diffusion systems: the case study of gemcitabine-treated non-small cell lung cancer growth,


    BMC Bioinformatics,

    2012



  • proceeding Papers D. Prandi,  T. Mazza.

    Stability Analysis of Bio-Network Topology during Stochastic Simulation,


    4th International ICST Conference on Simulation Tools and Techniques,

    2012



  • Book Chapter D. Rocchini,  F. Jordan,  Et al..

    Spatial algorithms applied to landscape diversity estimate by remote sensing,


    Models of the ecological hiera, Elsevier - 391-411, 2012



  • Journal Papers S. Lai,  W. Liu,  F. Jordan.

    On the centrality and uniqueness of species from the network perspective,


    Biology Letters,

    8:570-573, 2012



  • Journal Papers M. Scotti,  N. Gjata ,  C. Livi,  F. Jordan.

    Dynamical effects of weak trophic interactions in a stochastic food web simulation,


    Community Ecology,

    13:230-237, 2012


    abstract


  • Book Papers B. Vedres,  M. Scotti.

    Networks in Social Policy Problems,


    Cambridge University Press - Cambridge, 2012


    abstract


  • Journal Papers F. Vaggi,  J. Dodgson,  A. Bajpai,  A. Chessel,  F. Jordan,  M. Sato,  R. Carazo-Salas,  A. Csikasz-Nagy.

    Linkers of cell polarity and cell cycleregulation in the fission yeast protein interaction network,


    PLoS Computational Biology,

    8:e1002732, 2012


    pdf pdf


  • poster P. Nguyen,  C. Priami.

    Inference of crosstalk mechanisms underlying signaling pathway interactions,


    European Conference on Computational Biology 2012,

    - Basel, Switzerland, 2012



  • Journal Papers O. Kahramanogullari,  G. Fantaccini,  P. Lecca,  D. Morpurgo,  C. Priami.

    Algorithmic Modeling Quantifies the Complementary Contribution of Metabolic Inhibitions to Gemcitabine Efficacy,


    PLoS ONE,

    7:12, 2012


    abstract


  • Journal Papers R. Zunino.

    On Computation and Synchronization Costs in Spatial Distributed Simulation,


    Journal of Simulation,

    6:193-204, Operational Research Society, 2012


    abstract


  • proceeding Papers D. Nikolic,  F. Spoto.

    Definite Expression Aliasing Analysis for Java Bytecode,


    The 9th International Colloquium on Theoretical Aspects of Computing (ICTAC 2012),

    7521:74-89, Springer, 2012


    abstract | pdf pdf


  • poster P. Praveen,  E. Younesi,  M. Hofmann-Apitius.

    Modelling three protozoan parasitic diseases using host-parasite protein-protein interaction networks,


    10th Annual Rocky Mountain Bioinformatics Conference,

    - Aspen, CO (USA), 2012



  • Journal Papers A. De Gaetano,  A. Matone,  A. Agnes,  P. Palumbo,  F. Ria,  S. Magalini.

    Modeling rejection immunity,


    Theoretical Biology and Medical Modelling,

    9:18, BioMed Central, 2012


    abstract


  • Book Chapter M. Scotti,  B. Vedres.

    Supply security in the European natural gas pipeline network,


    Networks in Social Policy Problems,

    Cambridge University Press - Cambridge, 2012


    abstract


  • proceeding Papers V. Manca,  L. Marchetti.

    APPLICATION OF THE MP THEORY TO SYSTEMS BIOLOGY,


    International Conference on Bio-inspired Systems and Signal Processing,

    2012


    abstract


  • Journal Papers S. Lueabunchong,  Y. Lenbury,  S. Panunzi,  A. Matone.

    Comparison of Markov Chain Monte Carlo and G eneralized Least Square Methods on a Model of Glucose / Insulin Dynamics with GLP1- DPP4 Interaction ,


    INTERNATIONAL JOURNAL OF MATHEMATICS AND COMPUTERS IN SIMULATION,

    6, 2012


    abstract


  • proceeding Papers P. Lecca.

    Identification of models of brain glucose metabolism from 18F - deoxyglucose PET images,


    CompIMAGE2012 (Computational Modeling of Objects Presented in Images),

    2012



  • Journal Papers P. Lecca,  C. Priami.

    Biological network inference for drug discovery,


    Drug Discovery Today,

    2012


    abstract


  • Journal Papers M. Morine,  E. Allott,  J. Lysaght,  S. McGarrigle,  C. Donohoe,  J. Reynolds,  H. Roche,  G. Pidgeon.

    Elevated tumour expression of PAI-1 and SNAI2 in obese oesophageal adenocarcinoma patients and impact on prognosis.,


    Clinical and Translational Gastroenterology,

    2012


    abstract


  • Journal Papers F. Ferrezuelo,  N. Colomina,  A. Palmisano,  E. Garí,  C. Gallego,  A. Csikasz-Nagy,  M. Aldea.

    The critical size is set at a single-cell level by growth rate to attain homeostasis and adaptation.,


    Nature Communications,

    3:1012, 2012


    pdf pdf


  • technical report C. Damiani,  P. Lecca.

    A novel method for parameter sensitivity analysis of complex stochastic systems.,



    abstract | pdf pdf


  • Journal Papers F. Jordan,  N. Gjata ,  M. Shu,  C. Yule.

    Simulating food web dynamics along a gradient: quantifying human influence,


    PLoS ONE,

    7:e40280, 2012



  • Book Chapter A. Csikasz-Nagy,  M. Cavaliere,  S. Sedwards.

    Combining Game Theory and Graph Theory to Model Interactions between Cells in the Tumor Microenvironment,


    New Challenges for Cancer Systems Biomedicine1,

    Springer, 2012



  • Journal Papers M. Bartoletti,  E. Tuosto,  R. Zunino.

    Contract-Oriented Computing in CO2,


    Scientific Annals of Computer Science,

    22:5-60, A.I. Cuza University Press, 2012


    abstract


  • proceeding Papers D. Nikolic,  C. Priami,  R. Zunino.

    A Rule-based and Imperative Language for Biochemical Modeling and Simulation,


    The 10th International Conference on Software Engineering and Formal Methods (SEFM 2012),

    7504:16 - 32, Springer, 2012


    abstract | pdf pdf


  • Book Chapter F. Ciocchetta,  D. Prandi,  M. Forlin,  F. Jordan.

    A network model of the hierarchical organization of supra-individual biosystems,


    Models of the ecological hiera, Elsevier - 517-532., 2012



  • Book Chapter P. Lecca.

    A process algebra model of the cell mechanics of autoreactive lymphocites recruitment,


    Technologies for Medical Sciences, Lecture Notes in Computational Vision and Biomechanics,

    Volume 1:311-333, Springer, 2012



  • proceeding Papers D. Nikolic,  F. Spoto.

    Automaton-based Array Initialization Analysis,


    The 6th International Conference on Language and Automata Theory and Applications (LATA 2012),

    7183:420-433, Springer, 2012


    abstract | pdf pdf


  • Book Chapter M. Scotti.

    The role of stochastic simulations to extend food web analyses,


    Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances,

    IGI Global, 2012


    abstract


  • Book Chapter L. Marchetti,  V. Manca.

    A Methodology Based on MP Theory for Gene Expression Analysis,


    Lecture Notes in Computer Science (LNCS),

    7184:300-313, 2012


    abstract


  • Journal Papers V. Manca,  L. Marchetti.

    Solving dynamical inverse problems by means of Metabolic P systems,


    BioSystems,

    109:78-86, 2012


    abstract


  • Journal Papers A. Fagiolini,  A. Matone,  C. Gaz,  S. Panunzi,  A. De Gaetano.

    Pharmacoeconomic comparison of ziprasidone with other atypical oral antipsychotic agents in schizophrenia,


    Farmeconomia,

    12:29-40, SEEd Medical Publishers, 2012


    abstract


  • PhD Thesis S. Muppirisetty.

    Ex-vivo and in-silico Study of p53 Transactivation, Dynamics in Budding Yeast,


    COSBI - The Microsoft Research - University of Trento Ce,


    abstract | pdf pdf


  • Journal Papers P. Lecca,  D. Morpurgo,  G. Fantaccini,  A. Casagrande,  C. Priami.

    Inferring biochemical reaction pathways: the case of the gemcitabine pharmacokinetics,


    BMC Systems Biology,

    6:51, BioMed Central, 2012



  • Journal Papers M. Morine,  C. Reynolds,  S. Toomey,  R. McBride,  J. McMonagle,  O. Belton,  A. Moloney,  H. Roche.

    Divergent effects of a CLA-enriched beef diet on metabolic health in ApoE(-/-) and ob/ob mice. ,


    Journal of Nutritional Biochemistry,

    2012


    abstract


  • Book Chapter P. Lecca,  A. Palmisano.

    The present and the future perspectives of biological network inference,


    Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances ,

    Paola Lecca, Dan Tulpan, Rajaraman Kanagasabai, 2012



  • Book Papers F. Jordan,  S. Jorgensen.

    Models of the ecological hierarchy from molecules to the ecosphere,


    Elsevier - Amsterdam, 2012



  • Journal Papers N. Gjata ,  M. Scotti,  F. Jordan.

    The strength of simulated indirect interaction modules in a real food web,


    Ecological Complexity,

    11:160-164, 2012


    abstract


  • Book Chapter F. Vaggi,  A. Csikasz-Nagy.

    Keystone species of the molecular network of cellular functions,


    Models of the Ecological Hierarchy,

    Elsevier, 2012



  • Journal Papers M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    Model Checking Usage Policies,


    Mathematical Structures in Computer Science,

    2012



  • proceeding Papers D. Nikolic,  F. Spoto.

    Reachability Analysis of Program Variables,


    The 6th International Joint Conference on Automated Reasoning (IJCAR 2012),

    7364:423 - 438, Springer, 2012


    abstract | pdf pdf


  • Journal Papers S. Lacroix,  M. Gayda,  V. Gremeaux,  M. Juneau,  J. Tardif,  A. Nigam.

    Reproducibility of near-infrared spectroscopy parameters measured during brachial artery occlusion and reactive hyperemia in healthy men.,


    Journal of biomedical optics,

    17:077010, 2012


    abstract | pdf pdf


  • Journal Papers R. Lombardo,  V. Manca.

    Milieu-M: Visual Manipulation and Programming for Multi-Membranes,


    International Journal of Information Theories and Applications,

    19, 2012


    abstract


  • Journal Papers M. Cavaliere,  S. Sedwards,  C. Tarnita,  M. Nowak,  A. Csikasz-Nagy.

    Prosperity is associated with instability in dynamical networks,


    J Theor Biol ,

    299, 2012


    pdf pdf


  • poster T. Vo,  R. Zunino.

    Tree-Based Search for stochastic simulation algorithm,


    ACM Symposium on Applied Computing (SAC),

    2012


    abstract


  • PhD Thesis A. Bajpai.

    In silico modeling of cell polarity establishment and cell division initiation regulation networks of fission yeast cells,


    COSBI - The Microsoft Research - University of Trento Ce,


    abstract | pdf pdf


  • Journal Papers F. Niola,  X. Zhao,  D. Singh,  A. Castano,  R. Sullivan,  M. Lauria,  H. Nam,  Y. Zhuang,  R. Benezra,  D. di Bernardo,  A. Iavarone,  A. Lasorella.

    Id proteins synchronize stemness and anchorage to the niche of neural stem cells,


    Nature Cell Biology,

    14:477-8, Nature Publishing Group, 2012


    abstract


  • Journal Papers L. Cardelli,  A. Csikasz-Nagy.

    The Cell Cycle switch Computes Approximate Majority,


    Scientific Reports,

    2:656, 2012


    pdf pdf


  • Journal Papers M. Morine,  S. Toomey,  F. McGillicuddy,  C. Reynolds,  K. Power,  J. Browne,  C. Loscher,  K. Mills,  H. Roche.

    Network analysis of adipose tissue gene expression highlights altered metabolic and regulatory transcriptomic activity in high-fat-diet-fed IL-1RI knockout mice.,


    Journal of Nutritional Biochemistry,

    2012


    abstract


  • Book Chapter P. Lecca,  A. Palmisano.

    The present and the future perspectives of biological network inference,


    Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances,

    IGI-Global, 2012



  • Book Chapter O. Kahramanogullari.

    Process algebra models in biology: the case of phagocytosis ,


    Bioinformatics & Computational Systems Biology: Recent Advances and Applications,

    IGI Global, 2012


    abstract


  • Book Chapter A. Navia,  E. Cortes,  F. Jordan,  V. Cruz-Escalona,  P. Mejia-Falla.

    Changes to marine food webs caused by fishing,


    Marine Ecosystems,

    InTech - 417-452, 2012



  • Journal Papers F. Jordan,  P. Nguyen,  W. Liu.

    Studying protein-protein interaction networks: a systems view on disease,


    Briefings in Functional Genomics,

    2012



  • Journal Papers F. Jordan,  M. Scotti.

    From C:P ratios to polar meta-ecosystems,


    Ecological Modelling,

    245:1-2, 2012



  • Book Chapter B. Vedres,  M. Scotti.

    Introduction,


    Networks in Social Policy Problems ,

    Cambridge University Press - Cambridge, 2012



  • proceeding Papers M. Bartoletti,  E. Tuosto,  R. Zunino.

    On the Realizability of Contracts in Dishonest Systems,


    COORDINATION,

    LNCS 7274, Springer, 2012


    abstract


  • proceeding Papers R. Giacobazzi,  I. Mastroeni,  D. Nikolic.

    Strong Preservation by Model Deformation,


    The 6th IEEE International Symposium on Theoretical Aspects of Software Engineering (TASE 2012),

    IEEEE, 2012


    abstract | pdf pdf


  • Journal Papers S. Lacroix,  C. DesRosiers,  J. Tardif,  A. Nigam.

    The role of oxidative stress in postprandial endothelial dysfunction,


    Nutrition Research Reviews,

    25:288 - 301, 2012


    abstract | pdf pdf


  • Journal Papers P. Nguyen,  T. Ho.

    Detecting Disease Genes Based on Semi-Supervised Learning and Protein-Protein Interaction Networks,


    Artificial Intelligence in Medicine,

    Vol. 54 Num.1:63-71, Elsevier, 2012


    abstract


  • Journal Papers P. Toghaw,  A. Matone,  Y. Lenbury,  A. De Gaetano.

    Bariatric surgery and T2DM improvement mechanisms: a mathematical model,


    Theoretical Biology and Medical Modelling,

    9:16, 2012


    abstract


  • proceeding Papers V. Manca,  R. Lombardo.

    Computing with Multi-Membranes,


    12th Conference on Membrane Computing,

    LNCS 7184, 2012


    abstract


  • Journal Papers M. Scott-Boyer,  G. Imholte,  A. Tayeb,  A. Labbe,  C. Deschepper,  R. Gottardo.

    An integrated hierarchical Bayesian model for multivariate eQTL mapping.,


    Statistical applications in genetics and molecular biology,

    11, 2012


    abstract


  • Journal Papers I. Nassiri,  Ali Masoudi-Nejad,  Mahdi Jalili,  A. Moeini.

    Nonparametric simulation of signal transduction networks with semi-synchronized update ,


    PLoS ONE,

    7:e39643, 2012


    abstract


  • Journal Papers A. Romanel,  L. Jensen,  L. Cardelli,  A. Csikasz-Nagy.

    Transcriptional Regulation Is a Major Controller of Cell Cycle Transition Dynamics,


    PLoS ONE,

    7:e29716, 2012


    abstract | pdf pdf


  • proceeding Papers C. Priami,  P. Quaglia,  R. Zunino.

    An imperative language of self-modifying graphs for biological systems.,


    ACM Symposium on Applied Computing (SAC),

    2012


    abstract


  • Book Chapter F. Jordan,  P. Lecca,  C. Livi.

    Structural and dynamical heterogeneity in ecological networks. ,


    Systemic Approaches in Bioinformatics and Computational Systems Biology: Recent Advances--Chapter 7,

    IGI Global, 2012



  • proceeding Papers S. Lueabunchong,  Y. Lenbury,  S. Panunzi,  A. Matone.

    Statistical Evaluation of a Glucose/Insulin Nonlinear Differential Equation Model with Classical and Bayesian Procedures.,


    Proceedings of the 11th WSEAS international conference on Applied Computer and Applied Computational Science,

    World Scientific and Engineering Academy and Socie, 2012


    abstract


  • 2011

  • Book Chapter P. Lecca.

    Modelling, designing and simulating living systems with BlenX,


    2011



  • Journal Papers Z. Benedek,  A. Nagy,  I. Racz,  F. Jordan,  Z. Varga.

    Landscape metrics as indicators: quantifying habitat network changes of a bush-cricket Pholidoptera transsylvanica in Hungary,


    Ecological Indicators,

    11:930-933, 2011



  • PhD Thesis M. Morine.

    A nutritional systems biology approach to clarifying molecular pathology of metabolic syndrome, diabetes and transcriptomic effects of dietary fatty acid variation. ,



    abstract


  • Journal Papers G. Baranyi,  S. Saura,  J. Podani,  F. Jordan.

    Contribution of habitat patches to network connectivity: redundancy and uniqueness of topological indices,


    Ecological Indicators,

    11:1301-1310, 2011


    abstract


  • Book Chapter P. Nguyen,  T. Ho.

    Mining multiple biological data for reconstructing signal transduction networks,


    Data Mining: Foundations and Intelligent Paradigms ,

    Springer, 2011



  • Journal Papers A. Graudenzi,  R. Serra,  M. Villani,  C. Damiani,  A. Colacci,  S. Kauffman.

    Dynamical properties of a Boolean model of gene regulatory network with memory,


    Journal of Computational Biology,

    18:1-13, Mary Ann Liebert, Inc., 2011


    abstract


  • Journal Papers P. Nguyen,  W. Liu,  F. Jordan.

    Inferring pleiotropy by network analysis: linked diseases in the human PPI network,


    BMC Systems Biology ,

    5:179, The BioMed Central , 2011


    abstract


  • Journal Papers F. Jordan,  M. Scotti,  C. Priami.

    Process algebra-based computational tools in ecological modelling,


    Ecological Complexity,

    8:357-363, 2011


    abstract


  • poster F. Ciocchetta,  F. Jordan.

    A network model of the hierarchical organization of supra-individual biosystems,


    7th ECEM,

    - Riva del Garda, 2011



  • proceeding Papers R. Lombardo,  V. Manca.

    Arithmetical Metabolic P Systems,


    Foundations on Natural and Artificial Computation,

    LNCS 6686, 2011


    abstract


  • technical report P. Lecca.

    Visualizing the analysis of biochemical kinetics models,



    abstract | pdf pdf


  • proceeding Papers M. Bartoletti,  E. Tuosto,  R. Zunino.

    Contracts in distributed systems,


    Interaction and Concurrency Experience (ICE), 2011,

    2011


    abstract


  • Journal Papers M. Vasei,  B. Goliaei,  P. Owlia,  I. Nassiri.

    Normalized impact factor (NIF): An adjusted method for calculating the citation rate of biomedical journals,


    Journal of Biomedical Informatics,

    44:216-220, 2011


    abstract


  • Journal Papers L. Quarta,  C. Leslie,  R. Carletti,  E. Valerio,  L. Caberlotto.

    Central administration of NPY or an NPY- Y5 selective agonist increase in vivo extracellular monoamine levels in mesocorticolimbic projecting areas. ,


    Neuropharmacology. ,

    60:328-35, 2011


    abstract


  • Journal Papers O. Kahramanogullari,  J. Lynch,  F. Jordan.

    CoSBiLab LIME: a language interface for stochastic dynamical modelling in ecology,


    Environmental Modelling and Software,

    26:685-687, 2011


    abstract


  • Journal Papers C. Livi,  F. Jordan,  P. Lecca,  T. Okey.

    Identifying key species in ecosystems with stochastic sensitivity analysis.,


    Ecological Modelling,

    222:2542-2551, 2011


    abstract


  • proceeding Papers P. Lecca,  O. Kahramanogullari,  C. Priami,  R. Soo.

    Modelling the tumor shrinkage pharmacodynamics with BlenX,


    1st IEEE International Conference on Computational Advances in Bio and medical Sciences (ICCABS),

    2011



  • Book Papers F. Jordan,  M. Scotti,  V. Lencioni.

    Ecological hierarchy from the genes to the biosphere. Book of Abstracts, 7th European Conference on Ecological Modelling,


    - Riva del Garda (Trento, Italy), 2011



  • Journal Papers F. Vaggi,  A. Disanza,  F. Milanesi,  P. Di Fiore,  E. Menna,  M. Matteoli,  N. Gov,  G. Scita,  A. Ciliberto.

    The Eps8/IRSp53/VASP Network Differentially Controls Actin Capping and Bundling in Filopodia Formation,


    PLoS Computational Biology,

    2011


    abstract


  • proceeding Papers C. Damiani,  P. Lecca.

    Model identification using correlation-based inference and transfer entropy estimation,


    EMS 2011 UKSim 5th European Modelling Symposium on Mathematical Modelling and Computer Simulation,

    Conference Publishing Service (CPS)., 2011



  • proceeding Papers P. Lecca.

    Calibration of process algebra models of discretely observed stochastic biochemical systems,


    The 23rd European Modeling & Simulation Symposium,

    2011



  • poster P. Nguyen.

    Discovering interaction networks of neurodegenerative diseases,


    Genomics of Common Diseases,

    - Cambridge, UK, 2011



  • Book Chapter A. Csikasz-Nagy,  A. Palmisano,  J. Zamborszky.

    Molecular network dynamics of cell cycle control: transitions to start and finish,


    Methods in Molecular Biology 19,

    Humana Press - Springer, 2011


    pdf pdf


  • Book Chapter F. Jordan.

    Maintaining connectivity: topological considerations on landscape digraphs,


    Sources, Sinks, and Sustainability across Landscapes,

    Cambridge University Press - Cambridge, 2011



  • proceeding Papers R. Zunino.

    Trading computation time for synchronization time in spatial distributed simulation,


    25th ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS),

    2011


    abstract


  • Book Chapter P. Lecca,  P. Nguyen,  C. Priami,  P. Quaglia.

    Network inference from Time-Dependent Omics Data,


    Bioinformatics for Omics data: Methods and Protocols,

    Humana Press Springer Science+Businnes Media, LLC, 2011


    abstract


  • technical report S. Sedwards,  J. Mercader,  M. Puiggròs,  D. Torrents.

    A Computational Framework For Complex Diseases,



    abstract | pdf pdf


  • Journal Papers P. Lecca.

    BlenX models of alpha-synuclein and parkin kinetics in neuropathology of Parkinson's disease,


    Journal of Biological Systems,

    2011



  • Book Chapter M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    Call-by-contract for service discovery, orchestration and recovery,


    Rigorous Software Engineering for Service-Oriented Systems - Results of the SENSORIA project on Software Engineering for Service-Oriented Computing,

    2011



  • proceeding Papers P. Lecca,  O. Kahramanogullari,  D. Morpurgo,  C. Priami,  R. Soo.

    Modelling and estimating dynamics of tumor shrinkage with BlenX and KInfer,


    UKSim 2011 - 13th International Conference on Modelling and Simulation.,

    IEEE Computer Society Digital Library, 2011


    abstract


  • technical report O. Kahramanogullari,  J. Lynch.

    Stochastic Flux Equivalence,



    abstract


  • Journal Papers P. Nguyen,  A. Ihekwaba,  C. Priami.

    EM clustering based approach to decipher functional modules in crosstalk of signalling systems,


    International Journal of Bioscience, Biochemistry and Bioinformatics ,

    1:1-9, ACSIT, 2011


    abstract


  • Journal Papers P. Nguyen,  M. Scotti,  M. Morine,  C. Priami.

    Model-based clustering reveals vitamin D dependent multi-centrality hubs in a network of vitamin-related proteins,


    BMC Systems Biology,

    5:195, 2011


    abstract


  • Book Chapter A. Csikasz-Nagy,  I. Mura.

    Role of mRNA Gestation and Senescence in Noise Reduction During the Cell Cycle,


    Studies in Health Technology and InformaticsISBN: 978-1-60750-703-1,

    Biological, 2011



  • PhD Thesis R. Larcher.

    Optimizing the Execution of Biological Models,



    abstract | pdf pdf


  • Journal Papers H. Moriya,  A. Chino,  O. Kapuy,  A. Csikasz-Nagy,  B. Novák.

    Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico,


    Molecular Systems Biology,

    7:556, 2011


    pdf pdf


  • Journal Papers V. Manca,  L. Marchetti.

    LOG-GAIN STOICHIOMETRIC STEPWISE REGRESSION FOR MP SYSTEMS,


    International Journal of Foundations of Computer Science,

    22:97-106, 2011


    abstract


  • Journal Papers E. Zambello,  L. Zanetti,  G. Hedou,  R. Arban,  O. Angelici,  R. Tasan,  G. Sperk,  L. Caberlotto.

    Neuropeptide Y-Y2 receptor knockout mice: influence of genetic background on anxiety-related behaviors.,


    Neuroscience,

    176:420-30, 2011


    abstract


  • Journal Papers A. Csikasz-Nagy,  L. Cardelli,  O. Soyer.

    Response dynamics of phosphorelays suggest their potential utility in cell signalling,


    J R Soc Interface ,

    8:480-488, 2011


    pdf pdf


  • Book Chapter M. Bartoletti,  L. Caires,  I. Lanese,  F. Mazzanti,  D. Sangiorgi,  H. Vieira,  R. Zunino.

    Tools and Verification,


    Rigorous Software Engineering for Service-Oriented Systems - Results of the SENSORIA project on Software Engineering for Service-Oriented Computing,

    Springer, 2011



  • proceeding Papers P. Nguyen,  A. Ihekwaba,  C. Priami.

    Detecting Crosstalk Modules of Combined Networks: the Case for the NF-kB and p53,


    IEEE International Conference on Bioscience, Biochemistry and Bioinformatics,

    2011



  • Journal Papers C. Damiani,  R. Serra,  M. Villani,  S. Kauffman,  A. Colacci.

    Cell-cell interaction and diversity of emergent behaviours,


    IET Systems Biology,

    5:137-44, 2011


    abstract


  • Journal Papers H. Froehlich,  P. Praveen,  A. Tresch.

    Fast and Efficient Dynamic Nested Effects Models,


    Bioinformatics,

    27:238-44, Oxford University Press , 2011


    abstract


  • Journal Papers Y. Li,  N. Chia,  M. Lauria,  R. Bundschuh.

    A performance enhanced PSI-BLAST based on hybrid alignment.,


    Bioinformatics,

    27:31-37, 2011


    abstract


  • proceeding Papers O. Kahramanogullari,  F. Jordan,  C. Priami.

    Composability: Perspectives in Ecological Modeling,


    Algebraic and Numeric Biology 2010,

    LNCS 6479, Springer, 2011


    abstract


  • Book Chapter J. Zamborszky,  A. Csikasz-Nagy.

    Modeling the cell cycle,


    Encyclopedia of Life Support Systems,

    UNESCO , 2011



  • Journal Papers M. Morine,  T. Audrey C.,  v. Ben,  D. Hannelore,  T. Sinead,  G. Ingrid M. F.,  G. Isobel C.,  P. Pablo,  D. Christian A.,  L. Jose.

    Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health,


    PLoS Comput Biol,

    7:e1002223, Public Library of Science, , 2011


    abstract


  • poster N. Gjata ,  C. Yule,  F. Jordan.

    Stochastic sensitivity analysis of tropical river ecosystem: Kelian river, Borneo,


    12th EEF,

    - Avila, 2011



  • Journal Papers V. Manca,  L. Marchetti,  R. Pagliarini.

    MP Modelling of Glucose-Insulin Interactions in the Intravenous Glucose Tolerance Test,


    International Journal of Natural Computing Research,

    2:13-24, 2011


    abstract


  • 2010

  • proceeding Papers L. Cardelli,  R. Mardare.

    The Measurable Space of Stochastic Processes,


    QEST 2010,

    2010



  • proceeding Papers P. Lecca,  L. Dematté,  A. Ihekwaba,  C. Priami.

    Redi: a simulator of stochastic biochemical reaction-diffusion systems,


    The Second International Conference on Advances in System Simulation (SIMUL 2010),

    IEEE Computer Society CPS, 2010



  • Journal Papers L. Caberlotto,  G. Luniss,  M. Biagetti.

    The identification of a series of novel, soluble non-peptidic neuropeptide Y Y2 receptor antagonists. ,


    Bioorg Med Chem Lett.,

    20:7341-4, 2010


    abstract


  • Journal Papers C. Cazzin,  F. Zanderigo,  V. Costantini,  E. Zambello,  C. Ring,  A. Morrison ,  L. Caberlotto,  J. Kew.

    Adenoviral-mediated Cre expression effectively suppresses GlyT1 binding in the thalamic area of GlyT1 conditional knock-out mice. ,


    J Neurosci Methods.,

    193:254-63, 2010


    abstract


  • technical report I. Mura.

    Modeling Biological Systems with Stochastic Petri Nets,



    abstract | pdf pdf


  • Journal Papers W. Liu,  H. Chen,  F. Jordan,  W. Lin,  W. Liu.

    Quantifying the interaction structure and the topological importance of species in food webs: a signed digraph approach.,


    Journal of Theoretical Biology,

    267:355-362, 2010



  • proceeding Papers M. Bartoletti,  R. Zunino.

    A Calculus of Contracting Processes,


    Logic in Computer Science (LICS),

    IEEE, 2010


    abstract


  • Journal Papers R. De Cegli,  A. Romito,  S. Iacobacci,  L. Mao,  M. Lauria,  A. Fedele,  J. Klose,  C. Borel,  P. Descombes,  S. Antonarakis,  D. di Bernardo,  S. Banfi,  A. Ballabio,  G. Cobellis.

    A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes,


    Genome Biology,

    11:R64, 2010


    abstract


  • Journal Papers M. Morine,  M. Jolene,  T. Sinead,  R. Clare M.,  M. AidanP,  G. Isobel C,  G. Peadar O..

    Bi-directional gene set enrichment and canonical correlation analysis identify key diet- sensitive pathways and biomarkers of metabolic syndrome,


    BMC Bioinformatics,

    11:499, BioMed Central, , 2010


    abstract


  • PhD Thesis M. Forlin.

    Knowledge discovery for stochastic models of biological systems,



    abstract | pdf pdf


  • Journal Papers V. Manca,  L. Marchetti.

    Metabolic approximation of real periodical functions,


    The Journal of Logic and Algebraic Programming,

    79:363-373, 2010


    abstract


  • Journal Papers R. Larcher,  C. Priami,  A. Romanel.

    Modelling self-assembly in BlenX,


    Transactions on Computational Systems Biology XII,

    5945:163-198, Springer-Verlag, 2010


    abstract


  • technical report P. Lecca,  A. Ihekwaba,  L. Dematté,  C. Priami.

    Spatio-temporal dynamics of reaction diffusion systems: stochastic simulation of the bicoid gradient in Drosophila embryo,



    abstract | pdf pdf


  • proceeding Papers F. Ciocchetta,  M. Guerriero,  J. Hillston.

    Investigating modularity in the analysis of process algebra models of biochemical systems,


    3rd Workshop From Biology To Concurrency and back,

    2010



  • technical report R. Mardare,  L. Cardelli.

    The Measurable Space of Stochastic Processes,



    abstract | pdf pdf


  • Journal Papers R. Conradie,  F. Bruggeman,  A. Ciliberto,  A. Csikasz-Nagy,  B. Novák,  H. Westerhoff,  J. Snoep.

    Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex,


    FEBS Journal,

    277:357-367, 2010


    abstract | pdf pdf


  • Journal Papers P. Nguyen,  F. Jordan.

    A quantitative approach to study indirect effects among disease proteins in the human protein interaction network,


    BMC Systems Biology,

    4, BioMed Central Ltd, 2010


    abstract


  • Journal Papers D. Prandi,  L. Dematté.

    GPU computing for systems biology ,


    Briefings in Bioinformatics,

    11:323, 2010


    abstract


  • PhD Thesis A. Romanel.

    Dynamic Biological Modelling: a language-based approach,



    abstract | pdf pdf


  • technical report D. Prandi,  L. Dematté.

    GPU Computing for Systems Biology,



    abstract | pdf pdf


  • Journal Papers E. Zambello,  E. Fuchs,  N. Abumaria,  R. Rygula,  E. Domenici,  L. Caberlotto.

    Chronic psychosocial stress alters NPY system: different effects in rat and tree shrew.,


    Prog Neuropsychopharmacol Biol Psychiatry.,

    34:122-30, 2010


    abstract


  • proceeding Papers H. Kuwahara,  C. Madsen,  C. Meyers,  I. Mura,  A. Tejeda,  C. Winstead.

    Efficient Stochastic Simulation to Analyze Targeted Properties of Biological Systems ,


    SCIYO Open Access Publisher, 2010



  • Book Chapter I. Mura.

    Stochastic Modeling,


    Modeling in Systems Biology, Computational Biology Series, 16Stochastic Modeling,

    Springer-Verlag, 2010


    abstract


  • technical report P. Lecca.

    On parameter identifiability of non-linear time-continuous systems,



    abstract | pdf pdf


  • proceeding Papers S. Kauffman,  C. Damiani,  R. Serra,  M. Villani,  A. Colacci.

    Information transfer among coupled Random Boolean Networks,


    Cellular Automata, 9th International Conference on Cellular Automata for Research and Industry,

    LNCS 6350:1-11, Springer-Verlag Berlin Heidelberg, 2010


    abstract


  • poster P. Praveen,  A. Tresch,  H. Frohlich.

    Efficient learning of signaling networks from perturbation time series via dynamic nested effects model,


    European Conference on Computational Biology 2010,

    - Gent, (Belgium), 2010



  • Journal Papers F. Ciocchetta,  J. Hillston.

    Bio-PEPA for epidemiological models ,


    ENTCS (Proc. of PASM 2009),

    261:43-69 , - London, 2010



  • Journal Papers P. Lecca,  A. Palmisano,  A. Ihekwaba,  C. Priami.

    Calibration of dynamic models of biological systems with KInfer,


    Eur. Biophysics J. ,

    39:1019-1039, Springer Berlin / Heidelberg, 2010


    abstract


  • PhD Thesis A. Palmisano.

    Modelling and Inference strategies for Biological Systems,



    abstract | pdf pdf


  • proceeding Papers P. Lecca,  A. Palmisano,  A. Ihekwaba.

    Correlation-based network inference and modelling in systems biology: the NF-kB signalling network case study,


    Int. Conf. on Intelligent Systems, Modelling and Simulation, pp170-175,

    IEEE Computer Society - Liverpool, England, 2010



  • Journal Papers S. Vallian,  I. Nassiri.

    Development of a sensitive deaminated single-strand conformation polymorphism (DSSCP),


    Applied Biochemistry and Biotechnology,

    160:927-931, 2010


    abstract


  • Book Chapter L. Dematté,  R. Larcher,  A. Palmisano,  C. Priami,  A. Romanel.

    Programming Biology in BlenX,


    Systems Biology for Signaling Networks,

    1:777-820, Springer, 2010



  • technical report R. Mardare,  L. Cardelli.

    Continuous Markovian Logic,



    abstract | pdf pdf


  • technical report F. Ciocchetta,  F. Jordan.

    Modelling and analysing hierarchical ecological systems in BlenX,



    abstract | pdf pdf


  • Journal Papers D. Pizzi,  C. Leslie,  A. Mazzali,  C. Seri,  M. Biagetti,  J. Bentley,  T. Genski,  R. Di Fabio,  S. Contini,  L. Zonzini,  L. Caberlotto.

    Design, synthesis and SAR of a novel series of benzimidazoles as potent NPY Y5 antagonists. ,


    Bioorg Med Chem Lett.,

    20:7120-3, 2010


    abstract


  • Journal Papers M. Biagetti,  C. Leslie,  A. Mazzali,  C. Seri,  D. Pizzi,  J. Bentley,  T. Genski,  R. Di Fabio,  L. Zonzini,  L. Caberlotto.

    Synthesis and structure-activity relationship of N-(3-azabicyclo[3.1.0]hex-6-ylmethyl)-5-(2-pyridinyl)-1,3-thiazol-2-amines derivatives as NPY Y5 antagonists. ,


    Bioorg Med Chem Lett. ,

    20:4741-4, 2010


    abstract


  • Editor T. Mazza.

    Editorial: Accelerating systems biology,


    Briefings in Bioinformatics,

    11:267-269, 2010


    pdf pdf


  • Book Chapter F. Jordan,  G. Baranyi,  F. Ciocchetta.

    A hierarchy of networks spanning from individual organisms to ecological landscapes,


    Complex Networks across the Natural and Technological Sciences,

    Springer - Berlin, 2010



  • Journal Papers M. Scotti,  F. Jordan.

    Relationships between centrality indices and trophic positions in food webs,


    Community Ecology,

    11:59-67, 2010


    abstract


  • Journal Papers P. Lecca,  A. Ihekwaba,  L. Dematté,  C. Priami.

    Stochastic simulation of the spatio- temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient,


    Journal of Integrative Bioinformatics,

    7, 2010



  • PhD Thesis L. Dematté.

    Scaling up Systems Biology: Model Construction, Simulation and Visualization,



    abstract | pdf pdf


  • proceeding Papers M. Forlin,  T. Mazza,  D. Prandi.

    Predicting the effects of parameters changes in stochastic models through parallel synthetic experiments and multivariate analysis,


    HiBi 2010,

    IEEE Computer Society CPS, 2010


    abstract | pdf pdf


  • technical report P. Nguyen,  A. Ihekwaba,  C. Priami.

    Inferring Crosstalk Modules of Combined Networks by Using Multi-relational Clustering,



    abstract | pdf pdf


  • technical report P. Lecca.

    BlenX for modelling and simulating living systems,



    abstract | pdf pdf


  • proceeding Papers M. Bartoletti,  R. Zunino.

    Static Enforcement of Service Deadlines,


    Software Engineering and Formal Methods (SEFM), IEEE International Conference on,

    IEEE, 2010



  • Journal Papers B. Bauer,  F. Jordan,  J. Podani.

    Node centrality indices in food webs: rank orders versus distributions,


    Ecological Complexity,

    7:471-477, 2010



  • Journal Papers F. Ciocchetta,  A. Degasperi,  J. Heath,  J. Hillston.

    Modelling and Analysis of the NF-$kappa$B pathway in Bio-PEPA,


    Transactions on Computational Systems Biology XII, LNBI,

    5945:229-262, Springer-Verlag, 2010



  • proceeding Papers I. Mastroeni,  D. Nikolic.

    Abstract Program Slicing: From Theory Towards an Implementation,


    The 12th International Conference on Formal Engineering Methods (ICFEM 2010),

    6447:452-467, Springer, 2010


    abstract | pdf pdf


  • Book Chapter V. Manca,  L. Marchetti.

    Goldbeter's Mitotic Oscillator Entirely Modeled by MP Systems,


    Lecture Notes in Computer Science (LNCS),

    6501:273-284, 2010


    abstract


  • proceeding Papers A. Palmisano.

    Coding biological systems in a stochastic framework: the case study of budding yeast cell cycle,


    1st International Conference on Bioinformatics (Bioinformatics 2010),

    - Valencia, Spain, 2010



  • proceeding Papers O. Kahramanogullari.

    Flux Analysis in Process Models via Causality,


    Proceedings of the 3rd Workshop From Biology To Concurrency and back (FBTC),

    19:20-39, EPTCS, 2010


    abstract


  • Journal Papers A. Csikasz-Nagy,  I. Mura.

    Role of mRNA gestation and senescence in noise reduction during the cell cycle,


    In Silico Biology,

    10:81-88, 2010


    abstract | pdf pdf


  • Journal Papers P. Lecca,  A. Palmisano,  A. Ihekwaba.

    Inferring the kinetic constants of cyclin-triggered expression of Cdc20 gene in eukaryotic cell cycle,


    Online Journal of Bioinformatics,

    11:177-216, 2010



  • Journal Papers P. Lecca,  A. Palmisano.

    Identification of biochemical chaotic systems with KInfer,


    Int. Journal of Simulation: Systems, Science & Technology,

    11, United Kingdom Simulation Society, 2010



  • Journal Papers C. Leslie,  J. Bentley,  M. Biagetti,  S. Contini,  R. Di Fabio,  D. Donati,  T. Genski,  S. Guery,  A. Mazzali,  G. Merlo ,  D. Pizzi,  F. Sacco,  C. Seri,  M. Tessari,  L. Zonzini,  L. Caberlotto.

    Discovery and structure-activity relationship of a novel spirocarbamate series of NPY Y5 antagonists. ,


    Bioorg Med Chem Lett.,

    20:6103-7, 2010


    abstract


  • technical report S. Sedwards,  A. Ihekwaba.

    Crosstalk in oscillatory pathways: Frequency Domain Analysis,



    abstract | pdf pdf


  • proceeding Papers L. Dematté.

    Parallel particle-based reaction diffusion: a GPU implementation,


    PDMC/HiBi Workshop,

    IEEE - Twente, NL, 2010


    abstract | pdf pdf


  • proceeding Papers D. Prandi.

    Particle Swarm Optimization for Stochastic Process Calculi,


    9th Workshop on Process Algebra and Stochastically Timed Activities PASTA/Bio-PASTA 2010,

    - Imperial College, London, 2010


    abstract


  • proceeding Papers M. Bartoletti,  R. Zunino.

    Primitives for Contract-based Synchronization,


    Interaction and Concurrency Experience (ICE),

    EPTCS, 2010



  • Journal Papers T. Mazza,  A. Romanel,  F. Jordan.

    Estimating the divisibility of complex biological networks by sparseness indices,


    Briefings in Bioinformatics,

    11:364-374, 2010


    abstract | pdf pdf


  • Journal Papers A. Romanel,  C. Priami.

    On the Computational Power of BlenX,


    Theoretical Computer Science,

    411:542-565, 2010


    abstract


  • PhD Thesis J. Zamborszky.

    Compositional Modeling of biological Systems,



    abstract | pdf pdf


  • Journal Papers R. Valentini,  F. Jordan.

    CoSBiLab Graph: the network analysis module of CoSBiLab,


    Environmental Modelling and Software,

    25:886-888, 2010



  • technical report F. Jordan,  R. Valentini.

    Network analysis in CoSBiLab Graph,



    abstract | pdf pdf


  • Journal Papers T. Mazza,  G. Iaccarino,  C. Priami.

    Snazer: the simulations and networks analyzer,


    BMC Systems Biology,

    4, 2010


    abstract | pdf pdf


  • 2009

  • Journal Papers M. Scotti,  C. Bondavalli,  A. Bodini,  S. Allesina.

    Using trophic hierarchy to understand food web structure,


    Oikos,

    118:1695-1702, 2009


    abstract


  • Journal Papers E. DiDaniel,  M. Mok,  E. Mead ,  C. Mutinelli,  E. Zambello,  L. Caberlotto,  T. Pell,  C. Langmead,  A. Shah,  G. Duddy,  J. Kew,  P. Maycox.

    Evaluation of expression and function of the H+/myo-inositol transporter HMIT. ,


    BMC Cell Biol. ,

    10:54, 2009


    abstract


  • Journal Papers A. Csikasz-Nagy.

    Computational systems biology of the cell cycle,


    Briefings in Bioinformatics,

    10:424-434, 2009


    abstract | pdf pdf


  • Journal Papers F. Jordan,  W. Liu,  A. Mike.

    Trophic field overlap: a new approach to quantify keystone species,


    Ecological Modelling,

    220:2899-2907, 2009



  • technical report S. Sedwards.

    Fourier analysis of stochastic simulations,



    abstract | pdf pdf


  • technical report P. Lecca.

    On the mathematical structure of chemical kinetic models,



    abstract | pdf pdf


  • Journal Papers O. Soyer,  H. Kuwahara,  A. Csikasz-Nagy.

    Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses,


    FEBS Journal,

    276:3290, 2009


    abstract | pdf pdf


  • proceeding Papers P. Lecca.

    Deterministic chemical chaos identification in models and experiments,


    The 2009 International Conference on Bioinformatics & Computational Biology,

    CSREA Press - Las Vegas, Nevada (USA), 2009



  • proceeding Papers G. Iaccarino,  T. Mazza.

    Fastest Parallel Molecular Algorithms for the Elliptic Curve Discrete Logarithm Problem over GF(2n),


    BADS 2009,

    ACM press, pp. 95-104 - Barcellona, 2009


    abstract | pdf pdf


  • technical report P. Lecca,  A. Palmisano,  C. Priami,  A. Ihekwaba.

    A noise-robust method for parameter inference in biochemical network models: an NF-kappaB case study,



    abstract | pdf pdf


  • PhD Thesis S. Sedwards.

    A Natural Computation Approach To Biology: Modelling Cellular Processes and Populations of Cells With Stochastic Models of P Systems,


    PhD Thesis,

    UNITN,


    abstract


  • Journal Papers M. Bartoletti,  G. Costa,  P. Degano,  F. Martinelli,  R. Zunino.

    Securing Java with Local Policies,


    Journal of Object Technology,

    8:5-32, 2009



  • Journal Papers F. Ciocchetta,  J. Hillston.

    Bio-PEPA: a Framework for the Modelling and Analysis of Biological Systems,


    Theoretical Computer Science,

    410:3065-3084, 2009



  • Journal Papers F. Ciocchetta,  A. Degasperi,  J. Hillston,  M. Calder.

    Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA ,


    Proc. of FBTC 2008. Also in Electr. Notes Theor. Comput. Sci.,

    229:145-163, 2009



  • proceeding Papers A. Romanel.

    Towards a process calculi approach to study the evolution of biological networks,


    8th Workshop on Process Algebra and Stochastically Timed Activities (PASTA) ,

    2009



  • proceeding Papers P. Lecca,  L. Dematté,  M. Lecca,  C. Priami.

    Stochastic modelling of diffusion systems. Video image simulation of tubulin diffusion in cytoplasm: a case study,


    II Eccomas Thematic Conference on Computaional Vision and Medical Image Processing,

    Taylor & Francis (ISBN: 978-0-415570-41-1 ) - Porto, Portugal, 2009



  • Journal Papers O. Kahramanogullari,  L. Cardelli,  E. Caron,  P. Gardner,  A. Phillips.

    A Process Model of Rho GTP-Binding Proteins,


    Theoretical Computer Science,

    410:3166-3185, Elsevier, 2009



  • Journal Papers V. Vasas,  T. Magura,  F. Jordan,  B. Tóthmérész.

    Graph theory in action: evaluating planned highway tracks based on connectivity measures of a fragmented forest landscape,


    Landscape Ecology,

    24:581-586, 2009


    pdf pdf


  • proceeding Papers C. Priami,  P. Ballarini,  P. Quaglia.

    BlenX4Bio BlenX for biologists,


    Proc. 7th International Conference on Computational Methods in Systems Biology, CMSB 2009, volume 5688 of LNCS/LNBI,

    2009



  • proceeding Papers P. Ballarini,  M. Forlin,  T. Mazza,  D. Prandi.

    Efficient Parallel Statistical Model Checking of Biochemical Networks,


    Parallel and Distributed Methods in verifiCation (PDMC 09),

    EPTCS, 14:47-61, 2009


    abstract | pdf pdf


  • Journal Papers F. Jordan.

    Keystone species and food webs,


    Phil. Trans. Roy. Soc. London, series B,

    364:1733-1741, 2009


    pdf pdf


  • Journal Papers C. Priami.

    Algorithmic Systems Biology,


    Communications of the ACM,

    52:80-88, ACM, 2009


    abstract


  • proceeding Papers P. Lecca.

    On the mathematical structure and algorithmic implementation of biochemical network models,


    In Procs of Int. Conference on Cellular and Molecular Biology, vol. 40 pp. 345-368,

    World Academy of Science, Engineering and Technol - Rome, 2009



  • proceeding Papers P. Lecca,  A. Palmisano,  C. Priami.

    Deducing chemical reaction rate constants and their regions of confidence from noisy measurements of time series of concentration,


    UKSim 2009: 11th International Conference on Computer Modelling and Simulation, pp. 200-205,

    IEEE Computer Society - Cambridge - England, 2009



  • Journal Papers M. Cavaliere,  O. Egecioglu,  O. Ibarra,  M. Ionescu,  G. Paun,  S. Woodworth.

    Asynchronous Spiking Neural P Systems,


    2009



  • Journal Papers N. Barker,  C. Myers,  H. Kuwahara.

    Learning Genetic Regulatory Network Connectivity From Time Series Data,


    IEEE/ACM Transactions on Computational Biology and Bioinformatics,

    2009



  • technical report P. Lecca,  C. Priami.

    Deterministic chemical chaos,



    abstract | pdf pdf


  • technical report P. Nguyen,  T. Ho.

    Detecting Disease Genes Based on Protein Interaction Networks,



    abstract | pdf pdf


  • technical report P. Ballarini,  R. Guido,  T. Mazza,  D. Prandi.

    Taming the complexity of biological pathways through parallel computing,



    abstract | pdf pdf


  • Book Chapter M. Cavaliere,  D. Sburlan.

    Time in Membrane Computing,


    2009



  • Book Chapter H. Kuwahara,  C. Myers.

    Abstraction Methods for Analysis of Gene Regulatory Networks ,


    2009



  • proceeding Papers O. Akman,  F. Ciocchetta,  A. Degasperi,  M. Guerriero.

    Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora Crassa Circadian Network. ,


    Proc. of CMSB 2009, LNCS/LNBI,

    5688, Springer-Verlag, 2009



  • Journal Papers F. Ciocchetta,  S. Gilmore,  M. Guerriero,  J. Hillston.

    Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems,


    Proc. of PASM 2008. Also in Electr. Notes Theor. Comput. Sci. ,

    232:17-38 , 2009



  • Journal Papers M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    Hard Life with Weak Binders,


    Electr. Notes Theor. Comput. Sci.,

    242:49-72, 2009



  • proceeding Papers M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    nu-Types for Effects and Freshness Analysis,


    International Conference on Theoretical Aspects of Computing (ICTAC),

    Springer, 2009



  • Journal Papers M. Lauria,  F. Iorio,  D. di Bernardo.

    NIRest: a tool for gene network and mode of action inference,


    Annals of the New York Academy of Sciences,

    1158:257-264, 2009


    abstract


  • Journal Papers O. Kahramanogullari.

    On Linear Logic Planning and Concurrency,


    Information and Computation,

    207:1229 - 125, Elsevier, 2009



  • technical report P. Nguyen,  F. Jordan.

    Quantifying indirect effects among human disease genes,



    abstract | pdf pdf


  • technical report A. Csikasz-Nagy,  I. Mura.

    Role of mRNA gestation and senescence in noise reduction during the cell cycle,



    abstract | pdf pdf


  • Journal Papers M. Cavaliere,  N. Jonoska,  P. Leupold.

    DNA Splicing: Computing by Observing,


    Natural Computing ,

    8, 2009



  • Journal Papers A. Ihekwaba,  P. Nguyen,  C. Priami.

    Elucidation of Functional Consequences of Signalling Pathway Interactions ,


    BMC Bioinformatics,

    10, BioMed Central, 2009



  • proceeding Papers P. Ballarini,  M. Guerriero,  J. Hillston.

    Qualitative Reasoning of Stochastic Models and the Role of Flux,


    8th Workshop on Process Algebra and Stochastically Timed Activities (PASTA 2009),

    - Edinburgh, 2009


    abstract | pdf pdf


  • Journal Papers A. Bhadra,  F. Jordan,  A. Sumana,  S. Deshpande,  R. Gadagkar.

    A comparative social network analysis of wasp colonies and classrooms: linking network structure to functioning,


    Ecological Complexity,

    6:48-55, 2009


    pdf pdf


  • Book Chapter C. Priami.

    Algorithmic Systems Biology,


    Handbook of Natural Computing,

    Elsevier, 2009



  • technical report M. Scotti,  F. Jordan.

    Centrality and trophic height in ecosystems,



    abstract | pdf pdf


  • technical report P. Lecca,  A. Palmisano.

    Inferring the kinetic constants of cyclin-triggered Cdc20 gene expression from mRNA experimental time-course data,



    abstract | pdf pdf


  • Journal Papers A. Csikasz-Nagy,  O. Kapuy,  A. Tóth,  C. Pal,  L. Jensen,  F. Uhlmann,  J. Tyson,  B. Novák.

    Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation,


    Molecular Systems Biology,

    5:236, 2009


    abstract | pdf pdf


  • Journal Papers M. Scotti,  C. Bondavalli,  A. Bodini.

    Ecological Footprint as a tool for local sustainability: The municipality of Piacenza (Italy) as a case study,


    Environmental Impact Assessment Review,

    29:39-50, 2009


    abstract


  • proceeding Papers M. Cavaliere,  S. Krishna,  A. Paun,  G. Paun.

    P Systems with Objects on Membranes,


    2009



  • technical report R. Mardare,  I. Mura.

    Modular probabilistic logic for compositional Harsanyi type spaces,



    abstract | pdf pdf


  • Journal Papers M. Guerriero,  A. Dudka,  N. Underhill-Day,  J. Heath,  C. Priami.

    Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway BMC Systems Biology 2009, 3:40,


    BMC Systems Biology,

    2009


    abstract


  • technical report P. Lecca,  A. Palmisano,  C. Priami.

    Inferring kinetic parameters and their variances from a time series of concentrations,



    abstract | pdf pdf


  • proceeding Papers C. Priami.

    Computer Science and Systems Biology: A Cross Road,


    2nd AFI Symposium, October 2008,

    Innsbruck University Press - Innsbruck, 2009



  • Journal Papers F. Ciocchetta.

    Bio-PEPA with Events,


    Transactions on Computational Systems Biology, LNBI ,

    XI:45-68, Springer-Verlag, 2009



  • proceeding Papers A. Graudenzi,  R. Serra,  C. Damiani,  M. Villani,  A. Colacci,  S. Kauffman.

    Timing of molecular processes in a synchronous Boolean model of genetic regulatory network,


    European Conference on Complex Systems, ECCS 09, Warwick 21-25 ,

    2009


    abstract


  • Journal Papers M. Bartoletti,  G. Costa,  R. Zunino.

    Jalapa: Securing Java with Local Policies: Tool Demonstration,


    Electr. Notes Theor. Comput. Sci.,

    253:145-151, 2009



  • technical report R. Larcher,  C. Priami,  A. Romanel.

    Programming self-assembly in BlenX,



    abstract | pdf pdf


  • Journal Papers F. Ciocchetta,  A. Duguid,  M. Guerriero.

    A compartmental model of the cAMP/PKA/MAPK pathway in Bio-PEPA,


    MeCBIC 2009,

    EPTCS , 2009



  • proceeding Papers M. Forlin.

    A computational design for high dimensional biochemical experiments,


    6th Workshop on Simulation,

    - St. Petersburg, 2009


    abstract


  • Journal Papers T. Gurry,  O. Kahramanogullari,  R. Endres.

    Biophysical Mechanism for Ras-Nanocluster Formation and Signaling in Plasma Membrane,


    PLoS ONE,

    4, 2009



  • proceeding Papers T. Ho,  K. Takabayashi,  T. Pham,  P. Nguyen,  S. Kawasaki,  D. Tran.

    Towards service-oriented knowledge discovery in biomedicine research,


    International Workshop on Third Generation Data Mining, ECML/PKDD 2009,

    2009



  • proceeding Papers P. Lecca,  A. Palmisano.

    On the parameter inference in chaotic chemical systems,


    2009 Third UKSim European Symposium on Computer Modeling and Simulation, pp. 175-180,

    IEEE Computer Society - Athens, Greece, 2009



  • Journal Papers E. Chiefari,  F. Paonessa,  S. Tanyolac,  C. Capula,  T. Mazza,  M. Forlin,  S. Iritano,  F. Alfredo,  D. Foti,  I. Goldfine,  A. Brunetti.

    Functional Variants of the Gene for the Architectural Transcription Factor HMGA1 are Frequent and Confer a High Risk for Type 2 Diabetes Mellitus [Abstract],


    Diab Vasc Dis Res,

    7:95-96, 2009


    pdf pdf


  • proceeding Papers P. Ballarini,  A. Horvàth.

    Memory Efficient Analysis for a Class of Large Structured Markov Chains,


    The 4th International Workshop on Tools for solving,

    - Pisa, Italy, 2009


    abstract | pdf pdf


  • proceeding Papers V. Manca,  L. Marchetti.

    XML Representation of Metabolic P Systems,


    IEEE Congress on Evolutionary Computation (CEC 2009),

    2009


    abstract


  • Journal Papers I. Nassiri,  M. Faghihi,  M. Tavassoli.

    Pharmacogenomic profiling of the PI3K/PTEN pathway in sporadic breast cancer,


    Iranian Biomedical Journal ,

    13:79-86, 2009


    abstract


  • Journal Papers M. Scotti,  C. Bondavalli,  C. Bodini.

    Linking trophic positions and flow structure constraints in ecological networks: energy transfer efficiency or topology effect?,


    Ecological Modelling,

    220:3070-3080, 2009


    abstract


  • Journal Papers G. Luniss,  A. Barness,  N. Barton,  M. Biagetti,  F. Bianchi,  S. Blowers,  L. Caberlotto,  A. Emmons,  I. Holmes,  D. Montanari,  R. Norris,  D. Walters,  S. Watson.

    The identification and optimisation of novel and selective diamide neuropeptide Y Y2 receptor antagonists,


    Bioorg Med Chem Lett. ,

    19:4022-5, 2009


    abstract


  • Book Chapter M. Guerriero,  D. Prandi,  C. Priami,  P. Quaglia.

    Process Calculi Abstractions for Biology,


    Algorithmic BioprocessesProcess Calculi Abstractions for Biology,

    Springer, 2009


    abstract


  • technical report B. Bauer,  F. Jordan,  J. Podani.

    Distribution of node centrality indices in food webs,



    abstract | pdf pdf


  • Journal Papers P. Ballarini,  R. Guido,  T. Mazza,  D. Prandi.

    Taming the complexity of biological pathways through parallel computing,


    Briefings in Bioinformatics,

    10:278-288, 2009


    abstract | pdf pdf


  • Journal Papers I. Mura,  D. Prandi,  C. Priami,  A. Romanel.

    Exploiting non-Markovian Bio-Processes,


    Electronic Notes in Theoretical Computer Science,

    253:83-98, Elsevier, 2009


    abstract


  • Journal Papers P. Ballarini,  T. Mazza,  A. Palmisano,  A. Csikasz-Nagy.

    Studying irreversible transitions in a model of cell cycle regulation.,


    ENTCS,

    232:39-53, 2009


    abstract | pdf pdf


  • Journal Papers M. Morine,  H. Gu,  R. Myers,  J. Bielawski.

    Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth.,


    Journal of Molecular Evolution,

    2009


    abstract


  • technical report R. Mardare.

    A Survey on Approximating Methods for Quantitative Model Checking,



    abstract | pdf pdf


  • technical report D. Prandi,  R. Zunino.

    Computing by Complexes,



    abstract | pdf pdf


  • proceeding Papers E. Chiefari,  F. Paonessa,  S. Tanyolac,  C. Capula,  T. Mazza,  M. Forlin,  S. Iritano,  B. Arcidiacono,  K. Possidente,  A. Nocera,  D. Foti,  I. Goldfine,  A. Brunetti.

    Genetic syndromes of extreme insulin resistance and diabetes mellitus due to defect in insulin receptor gene transcription,


    XV Scientific Telethon Convention,

    p. 282 - Riva del Garda, 2009


    pdf pdf


  • technical report A. Ihekwaba,  C. Priami,  P. Nguyen.

    Elucidation of Functional Consequences of Interaction Networks,



    abstract | pdf pdf


  • proceeding Papers A. Palmisano,  I. Mura,  C. Priami.

    From Odes to Language-based, executable models of Biological Systems,


    Pacific Symposium on Biocomputing (PSB 2009),

    2009



  • Journal Papers I. Cappello,  P. Quaglia.

    A translation of Beta-binders in a prioritized pi-calculus,


    ENTCS,

    229:109-125, Elsevier, 2009



  • proceeding Papers S. Sedwards,  P. Ballarini,  A. Csikasz-Nagy,  F. Jordan,  R. Larcher,  P. Lecca,  T. Mazza,  I. Mura,  A. Palmisano,  A. Romanel,  J. Zamborszky,  F. Adrien,  H. Siebert,  S. Soliman,  D. Thieffry.

    Analyzing various models of Circadian Clock and Cell Cycle coupling,


    Dagstuhl Seminar Proceedings,

    09091, Leibniz-Zentrum für Informatik, 2009


    abstract


  • proceeding Papers P. Lecca,  A. Palmisano.

    Estimating the parameters of cyclin-triggered gene expression in cell cycle control network,


    2009 International Conference on Computational Intelligence, Modelling and Simulation, pp. 164-169,

    IEEE Computer Society - Brno, Czech Republic, 2009



  • proceeding Papers F. Ciocchetta,  A. Duguid,  S. Gilmore,  M. Guerriero,  J. Hillston.

    The Bio-PEPA Tool Suite,


    proc. of QEST 2009 (tool session),

    2009



  • Journal Papers F. Ciocchetta,  M. Guerriero.

    Modelling Biological Compartments in Bio-PEPA,


    Proc. of MeCBIC 2008. Electr. Notes Theor. Comput. Sci.,

    227:77-95, 2009



  • proceeding Papers C. Damiani,  A. Graudenzi,  R. Serra,  M. Villani,  A. Colacci,  S. Kauffman.

    On the fate of perturbations in critical random Boolean networks,


    the European Conference on Complex Systems, ECCS 09, Warwick 21-25,

    2009


    abstract


  • Journal Papers M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    Local policies for resource usage analysis,


    Trans. Program. Lang. Syst.,

    31:1-43, ACM, 2009



  • Journal Papers A. Rubaiyat Islam Sadat ,  P. Lecca.

    On the performances in simulation of parallel databases: an overview on the most recent techniques for query optimization,


    High Performance computational systems biology,

    - Trento, Italy, 2009



  • technical report P. Ballarini,  A. Horvàth.

    Memory Efficient Calculation of Path Probabilities in Large Structured Markov Chains,



    abstract | pdf pdf


  • proceeding Papers C. Priami,  P. Quaglia,  A. Romanel.

    BlenX - Static and Dynamic Semantics,


    In Proceedings of 20th International Conference on Concurrency Theory (CONCUR),

    Springer-Verlag, 2009


    abstract


  • technical report R. Larcher,  L. Dematté.

    Custom visualization of biological structures: an application to BlenX complexes,



    abstract | pdf pdf


  • proceeding Papers O. Kahramanogullari,  L. Cardelli,  E. Caron,  P. Gardner,  A. Phillips.

    A Process Model of Actin Polymerisation ,


    Proceedings of the Second International Workshop From Biology To Concurrency (FBTC 2008), ENTCS,

    229, Elsevier, 2009



  • Journal Papers A. Moreh,  F. Jordan,  A. Szilagyi,  I. Scheuring.

    Overfishing and regime shifts in minimal food web models,


    Community Ecology,

    10:236-243., 2009



  • Journal Papers F. Jordan,  G. Osvath.

    The sensitivity of food web topology to temporal data aggregation,


    Ecological Modelling,

    220:3141-3146, 2009


    pdf pdf


  • proceeding Papers O. Kahramanogullari,  L. Cardelli,  E. Caron.

    An Intuitive Automated Modelling Interface for Systems Biology,


    Proceedings of Developments in Computational Models 2009,

    9:73-86, EPTCS, 2009



  • Journal Papers S. Vallian,  M. Sedaghat,  I. Nassiri,  A. Frazmand.

    Methylation status of p16 INK4A tumor suppressor gene in Iranian patients with sporadic breast cancer,


    Journal of Cancer Research and Clinical Oncology ,

    135:991-996, 2009


    abstract


  • proceeding Papers P. Lecca,  A. Palmisano,  C. Priami,  G. Sanguinetti.

    A new probabilistic generative model of parameter inference in biochemical networks,


    Proceedings of the24th Annual ACM, Symposium on Applied Computing, pp. 758-765 ,

    ACM New York USA - Honolulu, Hawaii, USA, 2009



  • Journal Papers F. Jordan.

    Children in time: community organization in social and ecological systems,


    Current Science,

    97:1579-1585, 2009


    pdf pdf


  • 2008

  • proceeding Papers P. Ballarini,  R. Mardare,  I. Mura.

    Analysing Biochemical Oscillations through Probabilistic Model Checking.,


    2008


    abstract


  • technical report A. Palmisano,  C. Priami.

    From Solvable to Executable Models of Biological Systems,



    abstract | pdf pdf


  • Journal Papers P. Lecca,  L. Dematté.

    Stochastic Simulation of Reaction-diffusion Systems,


    Int. Journal of Medical and Biological Engineering,

    1:211-231, WASET, 2008



  • proceeding Papers M. Cavaliere,  O. Egecioglu,  O. Ibarra,  M. Ionescu,  G. Păun,  S. Woodworth.

    Asynchronous Spiking Neural P Systems; Decidability and Undecidability.,


    2008



  • Journal Papers A. Lovrics,  I. Zsély,  A. Csikasz-Nagy,  J. Zádor,  T. Turányi,  B. Novák.

    Analysis of a Budding Yeast Cell Cycle Model Using the Shapes of Local Sensitivity Functions,


    2008



  • proceeding Papers P. Lecca,  L. Dematté,  C. Priami.

    Modeling and simulating reaction-diffusion systems with state-dependent diffusion coefficients,


    2008



  • Journal Papers M. Salathé,  O. Soyer.

    Parasites lead to evolution of robustness against gene loss in host signaling networks,


    2008



  • proceeding Papers L. Dematté,  T. Mazza.

    On Parallel Stochastic Simulation of Diffusive Systems,


    2008


    pdf pdf


  • technical report R. Mardare,  A. Policriti.

    Towards a Complete Axiomatization for Spatial Logic,



    abstract | pdf pdf


  • technical report C. Priami.

    Algorithmic Systems Biology,



    abstract | pdf pdf


  • Book Chapter P. Quaglia.

    On Beta-Binders Communications,


    Concurrency, Graphs and Models,

    Concurrency, Graphs and Models (LNCS 5065),

    Springer, 2008



  • Journal Papers F. Ciocchetta,  C. Priami,  P. Quaglia.

    An automatic translation of SBML into Beta-Binders.,


    2008



  • proceeding Papers R. Serra,  M. Villani,  C. Damiani,  A. Graudenzi,  A. Colacci.

    The diffusion of perturbations in a model of coupled random Boolean networks,


    8th International Conference on Cellular Auotomata ACRI 2008, Yokohama,

    LNCS 5191/:315-322, Berlin-Springer, 2008


    abstract


  • Journal Papers F. Ciocchetta,  J. Hillston.

    Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks. ,


    Proc. of FBTC 2007. Also in Electr. Notes Theor. Comput. Sci. ,

    194:103-117, 2008



  • Journal Papers A. Csikasz-Nagy,  B. Novák,  J. Tyson.

    Reverse Engineering Models of Cell Cycle Regulation.,


    Adv Exp Med Biol,

    641:88-97, 2008


    pdf pdf


  • Journal Papers R. Serra,  M. Villani,  C. Damiani,  A. Graudenzi,  A. Colacci.

    Comunicazione cellulare, livelli e strutture ordinate,


    Sistemi Intelligenti,

    XX:209-220, 2008


    abstract


  • proceeding Papers P. Nguyen,  K. Satou,  T. Ho,  K. Takabayashi.

    Constructing Signal Transduction Networks Using Multiple Signaling Feature Data,


    2008



  • technical report M. Cavaliere,  A. Baralla,  A. de la Fuente.

    Modeling and parameter estimation of the SOS response network in E.coli,



    abstract | pdf pdf


  • proceeding Papers O. Kahramanogullari.

    On Linear Logic Planning and Concurrency ,


    2nd International Conference on Language and Automata Theory and Applications,

    LNCS, Springer, 2008



  • Journal Papers D. Prandi,  C. Priami,  P. Quaglia.

    Communicating by Compatibility,


    2008



  • Journal Papers F. Jordan,  T. Wey,  D. Blumstein,  W. Shen.

    Social network analysis of animal behaviour: a promising tool for the study of sociality,


    2008



  • technical report A. Romanel,  C. Priami.

    On the Computational Power of BlenX,



    abstract | pdf pdf


  • proceeding Papers P. Lecca,  M. Lecca.

    A model of the Ca2+ and Na+ waves kinetics in astrocytes and its relevance to functional brain imaging,


    2008



  • Journal Papers M. Cavaliere,  S. Sedwards.

    Decision Problems in Membrane Systems with Peripheral Proteins, Transport and Evolution.,


    2008


    pdf pdf


  • Journal Papers I. Mura,  A. Csikasz-Nagy.

    Stochastic Petri Net Extension of a Yeast Cell Cycle Model,


    Journal of Theoretical Biology,

    254:850-860, 2008


    abstract | pdf pdf


  • technical report P. Ballarini,  A. Csikasz-Nagy,  T. Mazza,  A. Palmisano.

    An analysis of irreversible transitions in a model of the buddying yeast cell cycle,



    abstract | pdf pdf


  • Journal Papers H. Chen,  W. Liu,  A. Davis,  F. Jordan,  M. Hwang,  K. Shao.

    Network position of hosts in food webs and their parasite diversity,


    Oikos,

    117:1847-1855, 2008



  • technical report S. Sedwards,  T. Mazza.

    Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes,



    abstract | pdf pdf


  • proceeding Papers T. Mazza,  A. Nocera.

    A formal lightweight view of the p53-dependent G1/S checkpoint control,


    2008


    pdf pdf


  • proceeding Papers P. Lecca.

    Stochastic pi-calculus models of the molecular bases of Parkinson's disease,


    CSREQ Press, 2008



  • Journal Papers E. Zambello,  P. Jimenez,  A. ElKhoury,  A. Mathè,  L. Caberlotto.

    Acute stress differentially affects corticotropin-releasing hormone mRNA expression in the central amygdala of the depressed flinders sensitive line and the control flinders resistant line rats. ,


    Prog Neuropsychopharmacol Biol Psychiatry. ,

    32:651-61, 2008


    abstract


  • Book Chapter M. Scotti.

    Ecological Indicators - Development Capacity,


    Encyclopedia of Ecology,

    2:911-920, Oxford: Elsevier, 2008



  • proceeding Papers D. Prandi,  P. Quaglia,  N. Zannone.

    Formal analysis of BPMN via a translation into COWS,


    2008



  • proceeding Papers D. Aliotta,  P. Buffa,  G. Iaccarino.

    An Evolutionary General Purpose WebGIS to Disclose EGFR Mutations in Lung Cancer. ,


    Proceedings of the 10th International Conference on Visual Information Systems (VISUAL08). LNCS,

    5188:247-258, Springer-Verlag Berlin Heidelberg - Salerno, Italy, 2008


    pdf pdf


  • Journal Papers R. Brijder,  M. Cavaliere,  A. Núñez,  G. Rozenberg,  D. Sburlan.

    Membrane Systems with Proteins embedded in Membranes.,


    2008



  • Journal Papers T. Mazza,  M. Cavaliere.

    Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins,


    MeCBIC 2008,

    Elsevier Science Publishers B. V. Amsterdam, The - Iasi, Romania, 2008


    pdf pdf


  • technical report H. Kuwahara,  I. Mura.

    An Efficient and Exact Stochastic Simulation Method to Analyze Rare Events in Biochemical Systems,



    abstract | pdf pdf


  • technical report R. Mardare,  A. Policriti.

    Decision problems for Spatial Logics revisited,



    abstract | pdf pdf


  • technical report P. Lecca,  A. Palmisano,  C. Priami.

    Inferring rate coefficents of biochemical reactions from noisy data with KInfer,



    abstract | pdf pdf


  • proceeding Papers M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    Model checking usage policies,


    Trustworthy Global Computing (TGC),

    Springer, 2008



  • Journal Papers M. Forlin,  I. Poli,  D. De March,  N. Packard,  G. Gazzola,  R. Serra.

    Evolutionary experiments for self-assembling amphiphilic systems.,


    2008



  • Journal Papers A. Csikasz-Nagy,  B. Győrffy,  A. Wolfgang,  J. Tyson,  B. Novák.

    Spatial controls for growth zone formation during the fission yeast cell cycle.,


    Yeast,

    25:59-69, 2008


    pdf pdf


  • Journal Papers M. Cavaliere,  I. Mura.

    Experiments on the reliability of stochastic spiking neural P systems,


    2008



  • proceeding Papers O. Kahramanogullari,  L. Cardelli,  P. Gardner.

    A Process Model of Rho GTP-binding Proteins in the Context of Phagocytosis ,


    Proceedings of the Workshop From Biology To Concurrency and back (FBTC 2007), ENTCS,

    194:87-102 , Elsevier, 2008



  • Journal Papers L. Dematté,  C. Priami,  A. Romanel.

    Modelling and simulation of biological processes in BlenX,


    2008



  • Journal Papers F. Jordan,  T. Okey,  B. Bauer,  S. Libralato.

    Identifying important species: a comparison of structural and functional indices,


    2008



  • technical report M. Forlin,  I. Mura.

    Independent Component Analysis for the Aggregation of Stochastic Simulation Output,



    abstract | pdf pdf


  • Journal Papers L. Dematté,  C. Priami,  A. Romanel.

    The Beta Workbench: a computational tool to study the dynamics of biological systems,


    2008



  • proceeding Papers M. Cavaliere.

    Computing by Observing: A Brief Survey,


    2008



  • technical report P. Ballarini,  I. Mura,  R. Mardare.

    Query-based Verification of Biochemical Oscillations through Probabilistic Model Checking,



    abstract | pdf pdf


  • Journal Papers H. Kuwahara,  I. Mura.

    An Efficient and Exact Stochastic Simulation Method to Analyze Rare Events in Biochemical Systems ,


    2008



  • proceeding Papers P. Ballarini,  A. Horvàth.

    Memory Efficient Calculation of Path Probabilities in Large Structured Markov Chains,


    2008


    abstract


  • technical report D. Prandi,  C. Priami,  A. Romanel.

    Simulation of non-Markovian Processes in BlenX,



    abstract | pdf pdf


  • Journal Papers C. Sandi,  M. Cordero,  A. Ugolini,  E. Varea,  L. Caberlotto,  C. Large.

    Chronic stress-induced alterations in amygdala responsiveness and behavior--modulation by trait anxiety and corticotropin-releasing factor systems. ,


    Eur J Neurosci. ,

    28:1836-48, 2008


    abstract


  • technical report P. Lecca,  L. Dematté,  C. Priami.

    Modeling and simulating bio-molecule diffusion in non-homogeneous solutions. Diffusive spatial effects on chaperone-assisted protein folding: a case study,



    abstract | pdf pdf


  • Journal Papers M. Cavaliere,  R. Mardare,  S. Sedwards.

    A Multiset-Based Model of Synchronizing Agents: Computability and Robustness,


    2008


    abstract | pdf pdf


  • Journal Papers H. Kuwahara,  C. Myers.

    Production-Passage-Time Approximation: A New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions,


    2008



  • technical report R. Larcher,  C. Priami.

    From BlenX to chemical reactions via SBML,



    abstract | pdf pdf


  • proceeding Papers R. Mardare,  A. Policriti.

    A Complete Axiomatic System for Process-based Spatial Logic,


    2008


    pdf pdf


  • Journal Papers F. Ciocchetta.

    The BlenX Language with Biological Transactions.,


    Transactions on Computational Systems Biology IX, LNBI,

    5121, 2008



  • Book Chapter F. Ciocchetta,  J. Hillston.

    Process Algebras in Systems Biology,


    SFM 2008,

    Springer, 2008


    abstract


  • Journal Papers M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    Semantics-Based Design for Secure Web Services,


    IEEE Trans. Software Eng.,

    34:33-49, 2008



  • proceeding Papers C. Damiani,  A. Graudenzi,  M. Villani.

    How critical random Boolean networks may be affected by the interaction with others,


    Artificial Life and evolutionary computation, proceeding of WIVACE 2008,

    World Scientific, 2008


    abstract


  • Journal Papers M. Morine.

    Session 2: Personalised nutrition. Transcriptomic signatures that have identified key features of metabolic syndrome.,


    The Proceedings of the Nutrition Society,

    67:395-403, 2008



  • proceeding Papers O. Kahramanogullari.

    Maude as a Platform for Designing and Implementing Deep Inference Systems,


    Proceedings of the Eighth International Workshop on Rule-Based Programming (RULE 2007), ENTCS,

    219:35-50, Elsevier, 2008



  • technical report V. Passini,  C. Lhoussaine,  M. Nebut,  C. Kuttler.

    Rule based modeling of gene regulation and biosynthesis of tryptophan in E. coli,



    abstract | pdf pdf


  • Journal Papers M. Cavaliere,  R. Mardare,  S. Sedwards.

    A Logical Characterization of Robustness, Mutants and Species in Colonies of Synchronizing Agents,


    2008


    pdf pdf


  • Journal Papers A. Romanel,  C. Priami.

    On the Decidability and Complexity of the Structural Congruence for Beta-binders.,


    2008



  • Journal Papers F. Jordan.

    Predicting target selection by terrorists: A network analysis of the 2005 London underground attacks,


    2008



  • technical report L. Dematté,  T. Mazza.

    Study on an Optimistic Reaction-Di usion Simulator based on Gillespie SSA,



    abstract | pdf pdf


  • Journal Papers A. Csikasz-Nagy,  O. Soyer.

    Adaptive dynamics with a single two-state protein,


    Journal of the Royal Society Interface Focus,

    Suppl 1:541-7, 2008


    abstract | pdf pdf


  • Journal Papers L. Dematté,  C. Priami,  A. Romanel,  O. Soyer.

    Evolving BlenX programs to simulate the evolution of biological networks,


    2008



  • technical report F. Polo,  C. Priami.

    Automated generation of narrative language programs from NCI-Nature's Pathway Interaction Database,



    pdf pdf


  • technical report M. Cavaliere,  A. Csikasz-Nagy,  F. Jordan.

    Graph Transformations and Game Theory: A Generative Mechanism for Network Formation,



    abstract | pdf pdf


  • Journal Papers M. Lercher,  C. Pal.

    Integration of horizontally transferred genes into regulatory interaction networks takes many millions of years,


    2008



  • Book Chapter A. Kun,  S. Pongor,  F. Jordan,  E. Szathmáry.

    Catalytic propensity of amino acids and the origins of the genetic code and proteins,


    The Codes of Life,

    Springer Verlag, Berlin, 2008



  • technical report I. Mura.

    Exactness and Approximation of the Stochastic Simulation Algorithm,



    abstract | pdf pdf


  • Book Chapter M. Cavaliere,  T. Mazza.

    A (Natural) Computing Perspective on Cellular Processes,


    2008


    pdf pdf


  • technical report T. Mazza,  M. Cavaliere.

    Cell Cycle and Tumor Growth in Membrane Systems with Peripheral Proteins,



    abstract | pdf pdf


  • technical report P. Lecca,  A. Palmisano,  C. Priami,  G. Sanguinetti.

    Calibration of biochemical network models,



    abstract | pdf pdf


  • Journal Papers H. Kuwahara,  I. Mura.

    An Efficient and Exact Stochastic Simulation Method to Analyze Rare Events in Biochemical Systems ,


    2008



  • technical report P. Lecca,  S. Teso.

    Notes on stochastic simulation of chemical kinetics with cycle-leaping,



    abstract | pdf pdf


  • Journal Papers F. Ciocchetta,  J. Hillston,  M. Kos,  D. Tollervey.

    Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA.,


    Theoretical Computer Science,

    408:41-54, 2008



  • Journal Papers P. Nguyen,  T. Ho.

    An Integrative Domain-based Approach to Predicting Protein-Protein Interactions,


    Journal of Bioinformatics and Computational Biology,

    6:1115-1132, Imperial College Press, 2008



  • proceeding Papers C. Damiani,  M. Villani,  C. Darabos,  M. Tomassini.

    Dynamics of Interconnected Boolean Networks with scale-free topology,


    Artificial Life and evolutionary computation, proceeding of WIVACE 2008, Venice, 8-10 September 2008,

    World Scientific, 2008


    abstract


  • Book Chapter A. Castellini,  V. Manca,  L. Marchetti.

    MP Systems and Hybrid Petri Nets,


    Studies in Computational Intelligence (SCI),

    129:53-62, 2008


    abstract


  • Journal Papers O. Kahramanogullari.

    System BV is NP-Complete,


    Annals of Pure and Applied Logic,

    152 :107-121 , Elsevier, 2008



  • Journal Papers R. Goldstein,  O. Soyer.

    Evolution of taxis responses in bacteria: non-adaptive dynamics ,


    2008


    abstract


  • Book Chapter F. Jordan.

    Network analysis: linking parts to the whole in nature and society,


    2008



  • Book Chapter L. Dematté,  C. Priami,  A. Romanel.

    The BlenX Language: A Tutorial,


    2008



  • technical report L. Dematté,  C. Priami,  A. Romanel.

    The BlenX Language: A Tutorial,



    abstract | pdf pdf


  • Book Chapter O. Soyer.

    Fate of a duplicate gene in a network context,


    2008



  • proceeding Papers T. Mazza,  R. Guido.

    Guidelines for parallel simulation of biological reactive systems,


    2008


    pdf pdf


  • Journal Papers P. Lecca.

    In silico experiments on a faulty ubiquitin-proteaosome system in the pathogenesis of Parkinson's disease,


    2008



  • technical report A. Dudka,  M. Guerriero,  J. Heath,  C. Priami,  N. Underhill-Day.

    Narrative-based Computational Modelling of the Gp130/JAK/STAT Signalling Pathway,



    abstract | pdf pdf


  • 2007

  • technical report P. Lecca,  M. Lecca.

    Molecular mechanism of energy metabolism in astrocytes: a parametric model from FDG PET images,



    abstract | pdf pdf


  • technical report P. Lecca,  L. Dematté,  C. Priami.

    Simulating reaction-diffusion with state-dependent diffusion coefficients,



    abstract | pdf pdf


  • technical report N. Segata,  E. Blanzieri,  C. Priami.

    Towards the integration of computational systems biology and high-throughput data: a way to support differential analysis of microarray gene expression data,



    abstract | pdf pdf


  • proceeding Papers M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    Types and Effects for Resource Usage Analysis,


    Foundations of Software Science and Computation Structures (FoSSaCS),

    Springer, 2007



  • proceeding Papers R. Mardare.

    Observing Distributed Computation. A Dynamic-Epistemic Approach,


    2007


    abstract | pdf pdf


  • Journal Papers A. Ihekwaba,  S. Wilkinson,  D. Waithe,  D. Broomhead,  P. Li,  R. Grimley,  N. Benson.

    Bridging the gap between in silico and cell based analysis of the NF-kB signalling pathway by in vitro studies of IKK2,


    2007



  • proceeding Papers M. Guerriero,  J. Heath,  C. Priami.

    An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra,


    2007



  • proceeding Papers P. Nguyen,  T. Ho.

    A Semi-Supervised Learning Approach to Disease Gene Prediction,


    2007



  • technical report I. Mura.

    Simplifying the Stochastic Petri Net Formalism for Representing Biological Phenomena,



    abstract | pdf pdf


  • technical report A. Ihekwaba,  R. Mardare.

    A Process Algebraical Approach to Modelling Compartmentalized Biological Systems,



    abstract | pdf pdf


  • proceeding Papers I. Ardelean,  M. Cavaliere.

    Modelling Respiration in Bacteria and Respiration/Photosynthesis Interaction in Cyanobacteria by Using a P System Simulator,


    2007



  • technical report I. Fronza,  P. Lecca.

    Solving a system of Master Equations for parallel chemical interactions,



    abstract | pdf pdf


  • Book Chapter F. Jordan.

    Topology and vulnerability of the London underground system,


    2007



  • Journal Papers F. Jordan,  V. Vasas,  C. Lancelot,  V. Rousseau.

    Eutrophication and overfishing in temperate nearshore pelagic food webs: a network perspective,


    2007



  • technical report R. Larcher,  A. Ihekwaba,  C. Priami.

    A BetaWB model for the NFkB pathway,



    abstract | pdf pdf


  • Journal Papers K. Ghaedi,  I. Nassiri.

    Molecular Characterization of Peroxisome Biogenesis Disorders with Zellweger Syndrome Spectrum,


    Iranian Journal of Pediatrics,

    17:275-282, 2007


    abstract


  • Journal Papers M. Cavaliere,  R. Freund,  M. Oswald,  D. Sburlan.

    Multiset random context grammars, checkers, and transducers,


    2007


    abstract | pdf pdf


  • PhD Thesis O. Kahramanogullari.

    Nondeterminism and language design in deep inference,


    - . Dresden University of Technology,


    abstract


  • technical report M. Cavaliere,  O. Egecioglu,  O. Ibarra,  S. Woodworth,  M. Ionescu,  G. Păun.

    Asynchronous Spiking Neural P Systems,



    abstract | pdf pdf


  • technical report L. Dematté,  D. Prandi,  C. Priami,  A. Romanel.

    Effective Index: a formal measure of drug effects,



    abstract | pdf pdf


  • technical report R. Mardare.

    Dynamic-Epistemic reasoning on distributed systems,



    abstract | pdf pdf


  • Journal Papers R. Brijder,  M. Cavaliere,  A. Núñez,  G. Rozenberg,  D. Sburlan.

    Membrane Systems with Marked Membranes,


    2007


    abstract | pdf pdf


  • proceeding Papers F. de Santis,  G. Iaccarino.

    A Conventional Strands Evaluator for DNA Computations,


    2007



  • proceeding Papers M. Bartoletti,  P. Degano,  G. Ferrari,  R. Zunino.

    Secure Service Orchestration,


    LNCSFoundations of Security Analysis and Design IV (FOSAD),

    4677:24-74, Springer, 2007



  • technical report R. Goldstein,  O. Soyer.

    Chemotaxis mediated by non-adaptive dynamics,



    abstract | pdf pdf


  • Journal Papers B. Novák,  J. Tyson,  B. Győrffy,  A. Csikasz-Nagy.

    Irreversible cell cycle transitions due to systems-level feedback,


    Nature Cell Biology,

    9:724-728, 2007


    pdf pdf


  • proceeding Papers F. Ciocchetta,  J. Hillston,  M. Kos,  D. Tollervey.

    Modelling Yeast Pre-rRNA Processing,


    CMSB 2007,

    2007



  • Book Chapter R. Mardare.

    Bio-Logics,


    2007


    abstract | pdf pdf


  • proceeding Papers L. Dematté,  D. Prandi,  C. Priami,  A. Romanel.

    Effective index: A formal measure of drug effects,


    2007



  • proceeding Papers R. Serra,  M. Villani,  C. Damiani,  A. Graudenzi,  P. Ingrami.

    Interacting Random Boolean Networks,


    Proceedings of the European Conference on Complex Systems (ECCS 07 Dresden, October 2007),

    2007


    abstract


  • proceeding Papers P. Nguyen,  T. Ho.

    Combining Domain Fusions And Domain-Domain Interactions To Predict Protein-Protein Interactions,


    2007



  • Book Chapter T. Ho,  P. Nguyen,  T. Tran.

    Study of protein-protein interactions from multiple data sources,


    2007



  • proceeding Papers T. Mazza.

    Towards a Complete Covering of SBML Functionalities,


    2007


    pdf pdf


  • technical report S. Leye,  C. Priami,  A. Uhrmacher.

    A Parallel Beta-binders Simulator,



    abstract | pdf pdf


  • proceeding Papers P. Faccioli,  D. Laforenza,  R. Lombardo,  M. Scarpellini,  M. Serranò,  F. Silvestri.

    Biological Experiments on the Grid: a Novel Workflow Management Platform,


    20th IEEE International Symposium on Computer-Based Medical Systems,

    2007


    abstract


  • Journal Papers M. Cannataro,  P. Guzzi,  T. Mazza,  P. Veltri.

    Using Ontologies for Preprocessing and Mining Spectra Data on the Grid,


    2007


    pdf pdf


  • technical report M. Cavaliere,  I. Mura.

    Experiments on the Reliability of Stochastic Spiking Neural P Systems,



    abstract | pdf pdf


  • technical report I. Fronza,  A. Quattrone,  A. Re.

    An integration of miRNA target predictions for the characterization of human miRNAs,



    abstract | pdf pdf


  • Journal Papers F. Jordan,  T. Magura,  B. Tóthmérész,  V. Ködöböcz,  V. Vasas.

    Carabids (Coleoptera: Carabidae) in a forest patchwork: a connectivity analysis of the Bereg Plain landscape graph,


    2007



  • Journal Papers F. Jordan,  Z. Benedek,  J. Podani.

    Quantifying positional importance in food webs: a comparison of centrality indices,


    2007



  • proceeding Papers L. Bianco,  V. Manca,  L. Marchetti,  M. Petterlini.

    Psim: a simulator for biomolecular dynamics based on P systems,


    IEEE Congress on Evolutionary Computation (CEC 2007),

    2007


    abstract


  • Journal Papers S. Pilati,  M. Perazzolli,  A. Malossini,  A. Cestaro,  L. Dematté,  P. Fontana,  A. Dal Rì,  R. Viola,  R. Velasco,  C. Moser.

    Genome-wide transcriptional analysis of grape berry development,


    2007



  • proceeding Papers A. Ihekwaba,  R. Larcher,  R. Mardare,  C. Priami.

    BetaWB - A language for modular representation of biological systems,


    2007



  • Journal Papers J. Zamborszky,  A. Csikasz-Nagy,  C. Hong.

    Computational Analysis of Mammalian Cell Division Gated by a Circadian Clock: Quantized Cell Cycles and Cell Size,


    Journal of Biological Rhythms,

    22:542-53, 2007


    abstract | pdf pdf


  • proceeding Papers D. Prandi,  P. Quaglia.

    Stochastic COWS,


    2007



  • technical report O. Soyer.

    Emergence and Maintanence of Functional Modules in Signaling Pathways,



    abstract | pdf pdf


  • Journal Papers U. Erra,  G. Iaccarino,  D. Malandrino,  V. Scarano.

    Personalizable Edge Services for Web Accessibility (long paper),


    Universal Access in the Information Society,

    6:285-306, - Springer Berlin Heidelberg, 2007


    pdf pdf


  • Journal Papers P. Lecca,  C. Priami.

    Cell Cycle Control in Eukaryotes: a BioSpi model,


    2007



  • technical report C. Priami.

    Computational Thinking in Biology,



    abstract | pdf pdf


  • technical report A. Romanel,  L. Dematté,  C. Priami.

    The Beta Workbench,



    abstract | pdf pdf


  • proceeding Papers M. Guerriero,  C. Priami,  A. Romanel.

    Modeling Static Biological Compartments with Beta-binders,


    2007


    abstract | pdf pdf


  • Journal Papers F. Ciocchetta,  C. Priami.

    Biological transactions for quantitative models,


    2007


    abstract | pdf pdf


  • Journal Papers M. Cavaliere,  S. Sedwards.

    Membrane Systems with Peripheral Proteins: Transport and Evolution,


    2007


    pdf pdf


  • Journal Papers A. Csikasz-Nagy,  O. Kapuy,  B. Győrffy,  B. Novák,  J. Tyson.

    Modeling the Septation Initiation Network (SIN) in Fission Yeast Cells,


    Current Genetics,

    51:245-55, 2007


    pdf pdf


  • proceeding Papers P. Lecca,  M. Lecca.

    Molecular mechanism of glutamate-triggered brain glucose metabolism: a parametric model from FDG PET-scans,


    Brain, Vision and Artificial Intelligence, LNCS,

    2007



  • proceeding Papers H. Kuwahara,  C. Myers.

    Production-passage-time approximation: A new approximation method to accelerate the simulation process of enzymatic reactions,


    2007



  • technical report M. Cavaliere,  R. Mardare,  S. Sedwards.

    Colonies of Synchronizing Agents,



    abstract | pdf pdf


  • technical report P. Lecca.

    Simulating a faulty mechanism of protein folding in the pathogenesis of familial Parkinson's disease,



    abstract | pdf pdf


  • proceeding Papers M. Cavaliere,  R. Mardare,  S. Sedwards.

    Colonies of synchronizing agents: An abstract model of intracellular and intercellular processes,


    2007



  • proceeding Papers L. Dematté,  C. Priami,  A. Romanel.

    BetaWB: modelling and simulating biological processes,


    2007



  • proceeding Papers R. Serra,  M. Villani,  C. Damiani,  A. Graudenzi,  P. Ingrami,  A. Colacci.

    Investigating cell criticality,


    Towards a general theory of emergence,

    World Scientific, 2007


    abstract


  • proceeding Papers P. Nguyen,  T. Ho.

    Prediction of protein-protein interactions and disease genes by machine learning,


    2007



  • technical report P. Lecca,  G. Sanguinetti,  A. Palmisano,  C. Priami.

    A new model for kinetic parameter estimation in biochemical reactions,



    abstract | pdf pdf


  • technical report P. Lecca,  W. Ooi,  C. Priami.

    Rate sensitivity analysis of a Beta binders model of lymphocyte recruitment control mechanism,



    abstract | pdf pdf


  • Journal Papers P. Lecca.

    Simulating the cellular passive transport of glucose using a time-dependent extension of Gillespie algorithm for stochastic pi-calculus,


    2007



  • Journal Papers R. Velasco,  A. Zharkikh,  M. Troggio,  D. Cartwright,  A. Cestaro,  L. Dematté.

    A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety,


    2007



  • technical report R. Mardare,  M. Cavaliere,  S. Sedwards.

    A Logical Characterization of Robustness, Mutants and Species in Colonies of Agents,



    abstract | pdf pdf


  • Journal Papers F. Jordan,  Z. Benedek,  A. Báldi.

    Topological keystone species complexes in ecological interaction networks,


    2007



  • proceeding Papers M. Scotti,  F. Jordan.

    On the relation between centralities and trophic positions in ecological networks,


    Ecologia, limnologia e oceanografia,

    AIOL - SItE, 2007


    abstract


  • proceeding Papers P. Ballarini,  A. Horvàth.

    Compositional model checking of product-form CTMCs,


    2007



  • Journal Papers C. Priami,  A. Romanel.

    The Decidability of the Structural Congruence for Beta-binders,


    2007


    abstract | pdf pdf


  • Journal Papers F. Nielson,  H. Nielson,  C. Priami,  D. Schuch da Rosa.

    Control Flow Analysis for BioAmbients,


    2007



  • proceeding Papers L. Brodo,  P. Degano,  C. Priami.

    A stochastic semantics for BioAmbients,


    2007



  • technical report N. Segata,  E. Blanzieri,  C. Priami.

    Stochastic pi-calculus modelling of multisite phosphorylation based signaling: in silico analysis of the Pho4 transcription factor and the PHO pathway in Saccharomyces cerevisiae,



    abstract | pdf pdf


  • proceeding Papers C. Kuttler,  C. Lhoussaine,  J. Niehren.

    A stochastic pi-calculus for concurrent objects,


    2007



  • proceeding Papers F. de Santis,  N. Di Luca,  G. Iaccarino.

    Exploiting Constraints in the Codeword Design,


    2007



  • technical report M. Guerriero,  J. Heath,  C. Priami.

    An Automated Translation from a Narrative Language for Biological Modelling into Process Algebra,



    abstract | pdf pdf


  • proceeding Papers N. Nguyen,  H. Kuwahara,  C. Myers,  J. Keener.

    The design of a genetic muller C-element,


    2007



  • technical report L. Dematté,  C. Priami,  A. Romanel,  O. Soyer.

    A formal and integrated framework to simulate evolution of biological pathways,



    abstract | pdf pdf


  • proceeding Papers P. Nguyen,  T. Ho,  N. Nguyen.

    Prediction of Protein-Protein Interactions Using Bayesian Networks,


    2007



  • proceeding Papers A. Ihekwaba,  R. Mardare.

    A Calculus for Modelling, Simulating and Analysing Compartmentalized Biological Systems,


    2007


    abstract | pdf pdf


  • proceeding Papers L. Dematté,  C. Priami,  A. Romanel,  O. Soyer.

    A Formal and Integrated Framework to Simulate Evolution of Biological Pathways,


    2007



  • technical report I. Mura,  A. Csikasz-Nagy.

    Stochastic Modeling of Budding Yeast Cell Cycle,



    abstract | pdf pdf


  • proceeding Papers P. Lecca,  G. Sanguinetti,  A. Palmisano,  C. Priami.

    A new method for inferring rate coefficients from experimental time-consecutive measurements of reactant concentrations,


    2007



  • Journal Papers S. Sedwards,  T. Mazza.

    Cyto-Sim: A Formal Language Model and Stochastic Simulator of Membrane-Enclosed Biochemical Processes,


    2007


    pdf pdf


  • proceeding Papers M. Forlin,  I. Poli,  D. De March,  M. Hanczyc,  N. Packard,  R. Serra.

    Evolving the experimental design for self-assembling amphiphilic systems,


    2007



  • Journal Papers N. Segata,  E. Blanzieri,  C. Priami.

    Towards the integration of computational systems biology and high-throughput data: supporting differential analysis of microarray gene expression data,


    2007



  • proceeding Papers O. Soyer.

    Emergence and maintenance of functional modules in signaling pathways,


    2007



  • Journal Papers F. Jordan,  J. Podani.

    Weighting, scale dependence and indirect effects in ecological networks: a comparative study,


    2007



  • Journal Papers F. Jordan,  W. Liu,  W. Lin,  A. Davis,  H. Yang,  M. Hwang.

    A network perspective on the topological importance of enzymes and their phylogenetic conservation,


    2007



  • Journal Papers M. Scotti,  J. Podani,  F. Jordan.

    Weighting, scale dependence and indirect effects in ecological networks: A comparative study,


    Ecological Complexity,

    4:148-159, 2007


    abstract


  • Journal Papers J. Zamborszky,  A. Csikasz-Nagy,  C. Hong.

    Connection Between the Cell Cycle and the Circadian Rhythm in Mammalian Cells,


    2007



  • 2006

  • Journal Papers P. Degano,  D. Prandi,  C. Priami,  P. Quaglia.

    Beta-binders for biological quantitative experiments,


    2006



  • proceeding Papers F. Di Giandomenico,  S. Chiaradonna,  E. Galliano,  I. Mura.

    Model-based dimensioning of CAUTION++,


    2006



  • proceeding Papers P. Ballarini,  A. Miller.

    Model Checking Medium Access Control for Sensor Networks,


    2006


    abstract


  • technical report M. Cavaliere,  S. Sedwards.

    Modelling Cellular Processes using Membrane Systems with Peripheral and Integral Proteins,



    abstract | pdf pdf


  • proceeding Papers M. Cavaliere,  R. Mardare.

    Playing with partial knowledge in membrane systems: A logical approach,


    2006


    pdf pdf


  • proceeding Papers M. Cavaliere,  P. Frisco,  H. Hoogeboom.

    Computing by Only Observing,


    2006


    abstract | pdf pdf


  • technical report M. Guerriero,  C. Priami,  V. Manca.

    Causality and Concurrency in Beta-binders,



    abstract | pdf pdf


  • Journal Papers A. Csikasz-Nagy,  D. Battogtokh,  K. Chen,  B. Novák,  J. Tyson.

    Analysis of a generic model of eukaryotic cell cycle regulation,


    2006



  • proceeding Papers G. Iaccarino,  D. Malandrino,  V. Scarano.

    Personalizable Edge-Services for Web Accessibility (short paper),


    2006


    pdf pdf


  • proceeding Papers F. de Santis,  G. Iaccarino.

    B-Splines for Genomic Signature,


    2006


    pdf pdf


  • proceeding Papers H. Kuwahara,  C. Myers,  M. Samoilov.

    Abstracted stochastic analysis of type 1 pili expression in E. coli,


    2006



  • Journal Papers P. Nguyen,  T. Ho.

    Discovering Signal Transduction Networks Using Signaling Domain-Domain Interactions,


    2006



  • proceeding Papers R. Brijder,  M. Cavaliere,  A. Núñez,  G. Rozenberg,  D. Sburlan.

    Membrane Systems with External Control,


    2006



  • technical report F. Ciocchetta,  C. Priami.

    Beta-binders with Biological Transactions,



    abstract | pdf pdf


  • Journal Papers C. Kuttler,  J. Niehren.

    Gene regulation in the pi calculus:simulating cooperativity at the lambda switch,


    2006



  • Journal Papers M. Cannataro,  P. Guzzi,  T. Mazza,  G. Tradigo,  P. Veltri.

    Managing Ontologies for Grid Computing,


    2006


    pdf pdf


  • Journal Papers F. Jordan.

    Topological keystone species in ecological interaction networks: considering link quality and non-trophic effects,


    2006



  • technical report M. Cavaliere,  N. Jonoska,  P. Leupold.

    DNA Splicing: Computing by Observing,



    abstract | pdf pdf


  • proceeding Papers A. Sboner,  A. Romanel,  A. Malossini,  F. Ciocchetta,  F. Demichelis,  I. Azzini,  E. Blanzieri,  R. Dell'Anna.

    Simple Methods for Peak and Valley Detection in Time Series Microarray Data,


    2006



  • proceeding Papers O. Kahramanogullari.

    Reducing Nondeterminism in the Calculus of Structures ,


    Proceedings of Logic for Programming Artificial Intelligence and Reasoning 2006 (LPAR 2006), LNCS 4246,

    Springer - Phnom Penh, Cambodia, 2006



  • Journal Papers J. Zamborszky,  A. Csikasz-Nagy,  C. Hong.

    Mathematical model for the coupling between the cell cycle and the circadian rhythm in mammalian cells,


    2006



  • technical report M. Guerriero,  D. Prandi,  C. Priami,  P. Quaglia.

    Process Calculi Abstractions for Biology,



    abstract | pdf pdf


  • Journal Papers A. Csikasz-Nagy.

    Central and Eastern Europe come into view,


    2006



  • Journal Papers D. Prandi,  C. Priami,  P. Quaglia.

    Process calculi in a biological context,


    2006



  • proceeding Papers R. Mardare,  C. Priami.

    Decidable extensions of Hennessy-Milner Logic,


    2006


    abstract | pdf pdf


  • Journal Papers R. Brijder,  M. Cavaliere,  A. Núñez,  G. Rozenberg,  D. Sburlan.

    Communication Membrane Systems with Active Symports,


    2006


    abstract | pdf pdf


  • technical report R. Mardare,  C. Priami.

    Dynamic Epistemic Spatial Logic,



    abstract | pdf pdf


  • proceeding Papers P. Nguyen,  A. Ihekwaba,  C. Priami.

    Modelling and Simulating Biological Processes with Stochastic Multiset Rewriting,


    Dagstuhl Seminar Proceedings,

    06161, Leibniz-Zentrum fur Informatik, 2006


    abstract


  • Journal Papers H. Kuwahara,  C. Myers,  M. Samoilov,  N. Barker,  A. Arkin.

    Automated abstraction methodology for genetic regulatory networks,


    2006



  • technical report F. Ciocchetta,  C. Priami.

    The pi-calculus with biological transactions,



    abstract | pdf pdf


  • Journal Papers M. Cavaliere,  R. Freund,  A. Leitsch,  G. Păun.

    Event-Related Outputs of Computations in P Systems,


    2006



  • Journal Papers C. Kuttler.

    Simulating bacterial transcription and translation in a stochastic pi-calculus,


    2006



  • proceeding Papers M. Cavaliere,  N. Jonoska,  P. Leupold.

    Recognizing DNA Splicing,


    2006



  • Journal Papers F. Jordan,  T. Wyatt.

    A graph theory examination of the global spreading hypothesis,


    2006



  • Journal Papers F. Jordan,  W. Liu,  A. Davis.

    Topological keystone species: measures of positional importance in food webs,


    2006


    abstract


  • proceeding Papers P. Lecca.

    A stochastic description of the molecular mechanisms of hereditary parkinsonism,


    2006



  • proceeding Papers O. Kahramanogullari.

    System BV is NP-Complete,


    Proceedings of the 12th Workshop on Logic, Language, Information and Computation (WoLLIC 2005), ENTCS,

    143:87-99, Elsevier, 2006



  • proceeding Papers P. Ballarini,  M. Fisher,  M. Wooldridge.

    Automated Game Analysis via Probabilistic Model-Checking: a case study.,


    2006


    abstract


  • Editor C. Priami.

    Preface,


    2006



  • technical report C. Priami,  A. Romanel.

    On the Decidability and Complexity of the Structural Congruence for Beta-binders,



    abstract | pdf pdf


  • technical report M. Cavaliere,  S. Sedwards.

    Membrane Systems with Peripheral Proteins: Transport and Evolution,



    abstract | pdf pdf


  • Journal Papers M. Cavaliere,  V. Deufemia.

    Further Results on Time-Free P Systems,


    2006



  • Journal Papers C. Priami.

    Process Calculi and Life Sciences,


    2006



  • proceeding Papers M. Forlin,  I. Poli,  D. De March,  N. Packard,  R. Serra.

    Evolving Complex Biochemical Experimentation,


    2006



  • proceeding Papers P. Nguyen,  T. Ho.

    Prediction of Domain-Domain Interactions Using Inductive Logic Programming from Multiple Genome Databases,


    2006



  • Journal Papers O. Soyer,  T. Pfeiffer,  S. Bonhoeffer.

    Simulating the evolution of signal transduction pathways,


    2006


    abstract | pdf pdf


  • proceeding Papers T. Mazza,  M. Gaspari,  M. Cannataro,  G. Cuda,  P. Guzzi,  G. Tradigo,  P. Veltri.

    A novel approach to integrate MS/MS sequence information from multiple proteomic experiments performed by ICAT labelling and LC-MS/MS analysis,


    2006


    pdf pdf


  • proceeding Papers N. Ali,  M. Lauria.

    Improving the Performance of Remote I/O Using Asynchronous Primitives,


    15th IEEE International Conference on High Performance Distributed Computing (HPDC-15),

    IEEE, 2006


    abstract


  • poster R. Lombardo,  P. Faccioli,  D. Laforenza,  M. Scarpellini,  M. Serranò,  M. Maggini.

    ESCOGITARE Project: Towards Grid-based E-Science Infrastructure for the Italian Agricultural Research Council (CRA),


    NETTAB 2006,

    2006



  • technical report L. Cardelli.

    Artificial Biochemistry,



    abstract | pdf pdf


  • Journal Papers F. Jordan,  B. Field,  A. Osbourne.

    Tansley Review: First encounters – Deployment of defense-related natural products by plants,


    2006



  • Journal Papers F. Jordan,  V. Vasas,  J. Podani,  I. Scheuring.

    Architectural classes of aquatic food webs based on link distribution,


    2006



  • Journal Papers M. Scotti,  S. Allesina,  C. Bondavalli,  A. Bodini,  L. Abarca-Arenas.

    Effective trophic positions in ecological acyclic networks,


    Ecological Modelling,

    198:495-505, 2006


    abstract


  • proceeding Papers D. Prandi,  C. Priami,  P. Lecca,  J. Himmelspach,  A. Uhrmacher,  P. Quaglia.

    Developing an hierarchical simulator for beta-binders,


    2006



  • proceeding Papers P. Lecca.

    A time-dependent extension of Gillespie algorithm for biochemical stochastic pi-calculus,


    2006



  • proceeding Papers D. Prandi.

    A Formal Approach to Molecular Docking,


    2006



  • Journal Papers C. Eccher,  C. Priami.

    Design and implementation of a tool for translating SBML into the biochemical stochastic π-calculus,


    2006



  • proceeding Papers M. Cavaliere,  S. Sedwards.

    Modelling Cellular Processes using Membrane Systems with Peripheral and Integral Proteins,


    2006


    pdf pdf


  • technical report M. Cavaliere,  A. Csikasz-Nagy,  I. Cappello,  D. Walker,  U. Montanari,  J. Hillston,  A. Baralla,  C. Priami,  I. Mura,  M. Morine,  T. Puntip.

    Book of abstracts Scientific Opening,



    abstract | pdf pdf


  • proceeding Papers M. Del Percio,  G. Iaccarino,  D. Malandrino,  V. Scarano.

    Efficient Edge-Services for Colorblind Users,


    2006


    pdf pdf


  • Journal Papers A. Lovrics,  A. Csikasz-Nagy,  I. Zsély,  J. Zádor,  T. Turányi,  B. Novák.

    Time scale and dimension analysis of a budding yeast cell cycle model,


    2006



  • Journal Papers M. Cavaliere,  P. Leupold.

    Observation of String-Rewriting Systems,


    2006



  • proceeding Papers M. Theis,  G. Gazzola,  M. Forlin,  I. Poli,  M. Hanczyc,  M. Bedau.

    Optimal Formulation of Complex Chemical Systems with a Genetic Algorithm,


    2006



  • Journal Papers O. Soyer,  M. Salathé,  S. Bonhoeffer.

    Signal transduction networks: topology, response, and biochemical reactions,


    2006


    abstract | pdf pdf


  • proceeding Papers G. Franco,  P. Guzzi,  T. Mazza,  V. Manca.

    Mitotic Oscillators as MP Graphs,


    2006


    pdf pdf


  • technical report M. Guerriero,  C. Priami,  A. Romanel.

    Beta-binders with Static Compartments,



    abstract | pdf pdf


  • Journal Papers O. Soyer,  S. Bonhoeffer.

    Evolution of Complexity in Signaling Pathways,


    2006


    abstract | pdf pdf


  • Journal Papers F. Jordan.

    Bornholdt and Schuster (eds.): Handbook of Graphs and Networks,


    2006



  • technical report M. Cavaliere,  S. Sedwards.

    Decision Problems in Membrane Systems with Peripheral Proteins, Transport and Evolution,



    abstract | pdf pdf


  • Journal Papers F. Bacchi,  A. Mathè,  P. Jimenez,  L. Stasi,  R. Arban,  P. Gerrard,  L. Caberlotto.

    Anxiolytic-like effect of the selective neuropeptide Y Y2 receptor antagonist BIIE0246 in the elevated plus-maze. ,


    Peptides.,

    27:3202-7, 2006


    abstract


  • 2005

  • Journal Papers A. Chakravarti,  G. Baumgartner,  M. Lauria.

    The organic grid: self-organizing computation on a peer-to-peer network,


    IEEE Transactions on Systems, Man and Cybernetics - Part A: Systems and Humans,

    35:373-384, IEEE, 2005


    abstract


  • Journal Papers C. Bodei,  M. Buchholtz,  P. Degano,  M. Curti,  C. Priami,  F. Nielson,  H. Nielson.

    Performance Evaluation of Security Protocols specified in LiSa,


    2005



  • Journal Papers C. Priami,  P. Quaglia.

    Operational patterns in Beta-binders,


    2005



  • Journal Papers P. Quaglia,  D. Walker.

    Types and full abstraction for polyadic pi-calculus,


    Information and Computation,

    200:215-246, 2005



  • proceeding Papers N. Barker,  C. Myers,  H. Kuwahara.

    Learning genetic regulatory network connectivity from time series data,


    2005



  • proceeding Papers K. Pokozy-Korenblat ,  F. Ciocchetta,  C. Priami.

    Formalization of a Biological Domain with Beta-binders ,


    International Conference of Computational Methods in Sciences and Engineering, ICSME 2005.,

    2005



  • Journal Papers M. Cavaliere,  D. Sburlan.

    Time and Synchronization in Membrane Systems,


    2005



  • proceeding Papers M. Curti,  P. Degano,  D. Prandi,  C. Priami,  P. Quaglia,  L. Brodo.

    Formal Executable Descriptions of Biological Systems,


    2005



  • Book Chapter F. Jordan.

    Topological constraints on the dynamics of wasp-waist ecosystems. In: Velikova, V. and Chipev, N. (Eds.): Large-scale disturbances (regime shifts) and recovery in aquatic ecosystems: challenges for management towards sustainability,


    2005



  • Journal Papers T. Pfeiffer,  O. Soyer,  S. Bonhoeffer.

    Evolution of connectivity in metabolic networks,


    2005


    abstract | pdf pdf


  • proceeding Papers M. Cavaliere,  D. Sburlan.

    Time-Independent P Systems,


    2005



  • proceeding Papers M. Cannataro,  P. Guzzi,  T. Mazza,  G. Tradigo,  P. Veltri.

    Algorithms and Databases in Bioinformatics: Towards a Proteomic Ontology,


    2005


    pdf pdf


  • proceeding Papers F. Baudi,  M. Cannataro,  R. Casadonte,  F. Costanzo,  G. Cuda,  M. Faniello,  M. Gaspari,  P. Guzzi,  T. Mazza,  B. Quaresima,  P. Tagliaferri,  G. Tradigo,  P. Veltri,  S. Venuta.

    Mass Spectrometry Data Analysis for Early Detection of Inherited Breast Cancer,


    2005


    pdf pdf


  • Journal Papers R. Mardare,  C. Priami.

    Logical analysis of biological systems,


    2005



  • Journal Papers C. Bodei,  P. Degano,  R. Focardi,  C. Priami.

    Authentication Primitives for Secure Protocol Specification,


    2005



  • Journal Papers A. Csikasz-Nagy,  D. Battogtokh,  B. Novák,  J. Tyson.

    A generic model of eukaryotic cell cycle regulation,


    2005



  • proceeding Papers F. de Santis,  G. Iaccarino.

    Logical Design with Molecular Components,


    Proceedings of Intelligent Information Systems, Gdansk, Poland, June 13-16, 2005 (IIS05). Advances in Soft Computing,

    31/2005:476-480, Springer-Verlag Heidelberg, 2005


    pdf pdf


  • proceeding Papers N. Barker,  C. Myers,  H. Kuwahara.

    Learning genetic regulatory network connectivity from time series data,


    2005



  • proceeding Papers C. Priami,  P. Quaglia.

    Beta binders for biological interactions,


    2005



  • Journal Papers I. Ardelean,  M. Cavaliere,  D. Sburlan.

    Computing Using Signals: From Cells to P Systems,


    2005



  • proceeding Papers C. Bodei,  M. Buchholtz,  M. Curti,  P. Degano,  F. Nielson,  H. Nielson,  C. Priami.

    On Evaluating the Performance of Security Protocols,


    2005



  • Book Chapter F. Jordan.

    Topological key players in communities: the network perspective,


    2005



  • proceeding Papers M. Cavaliere,  M. Ionescu,  T. Ishdorj.

    Inhibiting/De-Inhibiting Rules in P Systems,


    2005



  • Journal Papers C. Bodei,  M. Curti,  P. Degano,  C. Priami.

    A quantitative study of two attacks1,


    2005



  • proceeding Papers R. Mardare,  C. Priami,  P. Quaglia,  O. Vagin.

    Model checking biological systems described using ambient calculus,


    2005



  • proceeding Papers H. Kuwahara,  C. Myers,  N. Barker,  M. Samoilov,  A. Arkin.

    Asynchronous abstraction methodology for genetic regulatory networks,


    2005



  • Journal Papers D. Prandi,  C. Priami,  P. Quaglia.

    Shape Spaces in Formal Interactions,


    2005



  • proceeding Papers M. Cavaliere,  N. Jonoska,  S. Yogev,  R. Piran,  E. Keinan,  N. Seeman.

    Biomolecular Implementation of Computing Devices with Unbounded Memory,


    2005



  • proceeding Papers M. Cannataro,  P. Guzzi,  T. Mazza,  G. Tradigo,  P. Veltri.

    Preprocessing of Mass Spectrometry Proteomics Data on the Grid,


    2005


    pdf pdf


  • Journal Papers F. Jordan,  B. Jávor,  J. Török.

    A comparative sink web analysis of two birds in two habitats: trophic structure, functionality, aggregation and system-level indication,


    2005



  • proceeding Papers O. Kahramanogullari.

    Towards Planning as Concurrency,


    Artificial Intelligence and Applications (AIA 2005),

    Acta Press - Innsbruck, Austria, 2005



  • Journal Papers R. Carletti,  M. Corsi,  S. Melotto,  L. Caberlotto.

    Down-regulation of amygdala preprotachykinin A mRNA but not 3H-SP receptor binding sites in subjects affected by mood disorders and schizophrenia. ,


    Eur J Neurosci.,

    21:1712-8, 2005


    abstract


  • Journal Papers G. Karetsos,  S. Kyriazakos,  E. Gkroustiotis,  F. Di Giandomenico,  I. Mura.

    A Hierarchical Radio Resource Management Framework for Integrating WLANs in Cellular Networking Environments,


    2005



  • Journal Papers C. Bodei,  P. Degano,  C. Priami.

    Checking Security Policies through an Enhanced Control Flow Analysis,


    2005



  • proceeding Papers H. Kuwahara,  C. Myers,  N. Barker,  M. Samoilov,  A. Arkin.

    Automatic abstraction methodology for genetic regulatory networks,


    2005



  • proceeding Papers P. Nguyen,  T. Ho,  N. Nguyen.

    Discovering Reliable Protein Interactions Using Bayesian Networks,


    2005



  • proceeding Papers A. Uhrmacher,  C. Priami.

    Discrete Event Systems Specification in Systems Biology - A Discussion of Sthocastic pi-Calculus and DEVS,


    2005



  • Journal Papers F. Ciocchetta,  C. Priami,  P. Quaglia.

    Modeling Kohn interaction maps with Beta-binders: an example,


    2005



  • Journal Papers A. Ihekwaba,  D. Broomhead,  R. Grimley,  N. Benson,  M. White,  D. Kell.

    Synergistic control of oscillations in the NF-kB signalling pathway,


    2005



  • proceeding Papers A. Alhazov,  M. Cavaliere.

    Computing By Observing Bio-Systems: the Case of Sticker Systems.,


    2005



  • proceeding Papers M. Cavaliere,  P. Leupold.

    Evolution and Observation, a Non-Standard Way to Accept Formal Languages,


    2005



  • Journal Papers F. Jordan,  W. Liu,  T. Wyatt.

    Topological constraints on the dynamics of wasp-waist ecosystems,


    2005



  • Journal Papers C. Eccher,  P. Lecca.

    Translating SBML models to stochastic pi-calculus for stochastic simulation in 'Transactions on Computational Systems Biology',


    2005



  • 2004

  • Journal Papers M. Curti,  P. Degano,  C. Priami,  C. Baldari.

    Modelling biochemical pathways through enhanced pi-calculus,


    2004



  • Journal Papers D. Errampalli,  C. Priami,  P. Quaglia.

    A formal language for computational systems biology,


    2004



  • proceeding Papers C. Priami.

    Informatica e Biologia dei Sistemi,


    2004



  • proceeding Papers K. Pokozy-Koremblat,  C. Priami,  P. Quaglia.

    Performance Analysis of a UML Micro-business Case Study,


    2004



  • Journal Papers F. Jordan,  I. Scheuring.

    Network Ecology: topological constraints on ecosystems dynamics,


    2004



  • Journal Papers S. Kyriazakos,  G. Karetsos,  I. Mura,  E. Gkroustiotis,  N. Papaoulakis,  C. Kechagias,  K. Vlahodimitropoulos.

    A Real-Time Monitoring and Intelligent Decisions-Making Platform for Enhanced Radio Resource Management in Wireless Cellular Systems,


    2004



  • proceeding Papers P. Ballarini,  M. Fisher,  M. Wooldridge.

    Uncertain Agents Verification through Probabilistic Model-Checking,


    2004



  • Journal Papers K. Pokozy-Koremblat,  C. Priami.

    Toward extracting pi-calculus from UML sequence and state diagrams,


    2004



  • Journal Papers C. Priami,  P. Quaglia.

    Modeling the dynamics of bio-systems,


    2004



  • Journal Papers K. Chen,  L. Calzone,  A. Csikasz-Nagy,  F. Cross,  B. Novák,  J. Tyson.

    Integrative Analysis of Cell Cycle Control in Budding Yeast,


    2004



  • proceeding Papers D. D'Ambrosio,  P. Lecca,  C. Priami,  C. Laudanna.

    Concurrency in Leukocyte Vascular Recognition: Developing the Tools for a Predictive Computer Model,


    2004



  • Journal Papers A. Ihekwaba,  D. Broomhead,  R. Grimley,  N. Benson,  D. Kell.

    Sensitivity analysis of parameters controlling oscillatory signalling in the NF-kB pathway: the roles of IKK and IkBa,


    2004



  • Editor C. Priami.

    Guest editor of the special issue on Computational Methods in Systems Biology,


    2004



  • proceeding Papers A. Alhazov,  M. Cavaliere.

    Proton Pumping P Systems,


    2004



  • Journal Papers O. Soyer,  R. Goldstein.

    Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters,


    2004


    abstract | pdf pdf


  • Journal Papers L. Caberlotto,  R. Rimondini,  A. Hansson,  S. Eriksson,  M. Heilig.

    Corticotropin-releasing hormone (CRH) mRNA expression in rat central amygdala in cannabinoid tolerance and withdrawal: evidence for an allostatic shift? ,


    Neuropsychopharmacology.,

    29:15-22, 2004


    abstract


  • Journal Papers A. Bondavalli,  S. Chiaradonna,  F. Di Giandomenico,  I. Mura.

    Dependability Modeling & Evaluation of Multiple-Phased Systems using DEEM,


    2004



  • Journal Papers P. Lecca,  C. Priami,  P. Quaglia,  B. Rossi,  C. Laudanna,  G. Constantin.

    A Stochastic Process Algebra Approach to Simulation of Autoreactive Lymphocyte Recruitment,


    2004



  • proceeding Papers N. Nguyen,  P. Nguyen.

    A Specification for Underground Tank Monitoring System (UTMS) Using Real-Time Process Algebra (RTPA),


    RIVF04,

    Editions Suger , Paris, 2004



  • proceeding Papers F. de Santis,  G. Iaccarino.

    A DNA Arithmetic Logic Unit,


    WSEAS Transactions on Biology and Biomedicine,

    1:436-440, 2004



  • proceeding Papers P. Lecca,  C. Priami,  C. Laudanna,  G. Constantin.

    A BioSpi model of lymphocyte-endothelial interactions in inflamed brain venules,


    2004



  • Journal Papers M. Cavaliere,  P. Leupold.

    Evolution and Observation – A Non-Standard Way to Generate Formal Languages,


    2004



  • Editor C. Priami.

    Guest editor of the special issue on Computational Methods in Systems Biology,


    2004



  • Journal Papers D. Nelson,  A. Ihekwaba,  M. Elliott,  J. Johnson,  C. Gibney,  B. Foreman,  G. Nelson,  V. See,  C. Horton,  D. Spiller,  S. Edwards,  H. McDowell,  J. Unitt,  E. Sullivan,  R. Grimley,  N. Benson,  D. Broomhead,  D. Kell,  M. White.

    Oscillations in NF-kB Signaling Control the Dynamics of Gene Expression,


    2004



  • proceeding Papers M. Cavaliere,  P. Leupold.

    Evolution and Observation – A New Way to Look at Membrane Systems,


    2004



  • proceeding Papers N. Nguyen,  V. Than,  P. Nguyen,  T. Ho.

    A Mixed Similarity Measure for Data with Numeric, Symbolic and Ordinal Attributes,


    Japan-Vietnam Joint Workshop on Active Mining,

    2004



  • proceeding Papers P. Ballarini,  L. Capra,  G. Franceschinis.

    Performance and Dependability analysis of fault-tolerant memory mechanisms. using Stochastic Well-formed Nets,


    2004


    abstract


  • Journal Papers R. Mardare,  C. Priami.

    A logical approach to security in the context of Ambient Calculus,


    2004



  • Editor C. Priami,  P. Quaglia.

    Preface,


    2004



  • Journal Papers P. Lecca,  C. Priami,  C. Laudanna,  G. Constantin.

    Computer modeling of lymphocyte behavior in inflamed brain venules by using stochastic Pi-calculus ,


    JOURNAL OF NEUROIMMUNOLOGY ,

    154:230, 2004



  • proceeding Papers P. Lecca,  C. Priami,  C. Laudanna,  G. Constantin.

    Predicting cell adhesion probability via the biochemical stochastic pi-calculus,


    2004



  • Journal Papers M. Cavaliere,  D. Genova.

    P Systems with Symport/Antiport of Rules,


    2004



  • Editor C. Priami.

    Guest editor for the special issue on Security in Global Computing,


    2004



  • proceeding Papers O. Kahramanogullari.

    System BV without the Equalities for Unit,


    Proceedings of the 19th International Symposium on Computer and Information Sciences (ISCIS 2004), LNCS 3280,

    Springer - Kemer, Turkey, 2004



  • 2003

  • proceeding Papers P. Ballarini,  L. Capra,  M. De Pierro,  G. Franceschinis.

    Memory Fault Tolerance Software mechanisms: design and configuration support through SWN models,


    2003


    abstract


  • Editor C. Priami.

    Preface,


    2003



  • proceeding Papers C. Bodei,  P. Degano,  C. Priami,  N. Zannone.

    An Enhanced CFA for Security Policies,


    2003



  • proceeding Papers L. Brodo,  P. Degano,  S. Gilmore,  J. Hillston,  C. Priami.

    Performance evaluation for global computation,


    2003



  • Journal Papers I. Ardelean,  M. Cavaliere.

    Modelling Biological Processes by Using a Probabilistic P System Software,


    2003



  • Journal Papers F. Jordan,  W. Liu,  F. van Veen.

    Quantifying the importance of species and their interactions in a host-parasitoid community,


    2003



  • proceeding Papers M. Cavaliere.

    Evolution-Communication P Systems,


    2003



  • Journal Papers B. Qian,  O. Soyer,  R. Goldstein.

    Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMS,


    2003


    abstract | pdf pdf


  • proceeding Papers O. Kahramanogullari,  M. Thielscher.

    A Formal Assessment Result for Fluent Calculus Using the Action Description Language Ak,


    Proceedings of the 26th Annual German Conference on Artificial Intelligence (KI 2003), LNAI 2821,

    Springer - Hamburg, Germany, 2003



  • Journal Papers L. Caberlotto,  Y. Hurd,  P. Murdock,  J. Wahlin ,  S. Melotto,  M. Corsi,  R. Carletti.

    Neurokinin 1 receptor and relative abundance of the short and long isoforms in the human brain. ,


    Eur J Neurosci. ,

    17:1736-46, 2003


    abstract


  • proceeding Papers E. Gkroustiotis,  I. Mura,  S. Kyriazakos.

    Real-Time Management of Radio Resources for Congestion Control in Wireless Telecommunications Networks,


    2003



  • Editor C. Priami.

    Preface,


    2003



  • proceeding Papers C. Priami.

    Design environments for complex systems,


    2003



  • proceeding Papers P. Degano,  C. Priami.

    Enhanced Operational Semantics in Systems Biology,


    2003



  • proceeding Papers F. Ciocchetta,  R. Dell'Anna,  F. Demichelis,  A. Dhillon,  A. Quaglia,  A. Sboner,  Et al..

    Knowledge Discovery to Support Hepatocellular Carcinoma Early Diagnosis,


    Proc. of the IEEE International Joint Conference on Neural Networks, IJCNN 2003.,

    2003



  • Journal Papers M. Cavaliere,  N. Jonoska.

    Forbidding and Enforcing in Membrane Computing,


    2003



  • proceeding Papers F. Jordan.

    Quantifying landscape connectivity: key patches and key corridors,


    2003



  • Editor C. Priami.

    Preface,


    2003



  • proceeding Papers A. Sveiczer,  A. Csikasz-Nagy,  J. Tyson,  B. Novák.

    A deterministic molecular model of the fission yeast cell cycle,


    2003



  • proceeding Papers C. Bodei,  P. Degano,  R. Focardi,  C. Priami.

    Authentication Primitives for Protocol Specifications,


    2003



  • proceeding Papers F. Ciocchetta,  F. Demichelis,  A. Sboner.

    Machine Learning methods to understand hepatocellular carcinoma pathology ,


    Proc.of IDAMAP KBIM-AIC 2003.,

    2003



  • Journal Papers F. Jordan.

    Comparability: the key to the applicability of food web research,


    2003



  • Journal Papers F. Jordan,  I. Scheuring,  I. Molnár.

    Persistence and flow reliability in simple food webs,


    2003



  • Journal Papers O. Soyer,  M. Dimmic,  R. Neubig,  R. Goldstein.

    Dimerization in aminergic G-protein coupled receptors: application of a hidden-site class model of protein evolution,


    2003


    abstract | pdf pdf


  • Journal Papers S. Porcarelli,  F. Di Giandomenico,  A. Bondavalli,  M. Barbera,  I. Mura.

    Service Level Availability Estimation of GPRS,


    2003



  • proceeding Papers P. Degano,  F. Gadducci,  C. Priami.

    Causality and Replication in Concurrent Processes,


    2003



  • proceeding Papers L. Brodo,  P. Degano,  C. Priami.

    Reflecting Mobile Ambients into the pi-calculus,


    2003



  • proceeding Papers F. Ciocchetta,  R. Dell'Anna,  F. Demichelis,  A. Dhillon,  A. Quaglia,  A. Sboner.

    Combining Supervised and Unsupervised Methods to Support Early Diagnosis of Hepatocellular Carcinoma,


    Proc. of AIME, LNCS,

    2003



  • proceeding Papers G. Bel-Enguix,  M. Cavaliere,  R. Ceterchi,  R. Gramatovici,  C. Martin-Vide.

    An Application of Dynamic P Systems: Generating Context-Free Languages,


    2003



  • Journal Papers F. Jordan.

    On the functional trophic height of whiting,


    2003



  • Journal Papers F. Jordan,  A. Báldi,  K. Orci,  I. Rácz,  Z. Varga.

    Characterizing the importance of habitat patches and corridors in maintaining the landscape connectivity of a Pholidoptera transsylvanica (Orthoptera) metapopulation,


    2003



  • Journal Papers N. Goldberg,  T. Beuming,  O. Soyer,  R. Goldstein,  H. Weinstein,  J. Javitch.

    Probing conformational changes in neurotransmitter transporters in a structural context,


    2003



  • 2002

  • proceeding Papers M. Barbera,  C. Barbero,  P. Dal Zovo,  F. Farinaccio,  E. Gkroustiotis,  S. Kyriazakos,  I. Mura,  G. Previti,  S. Pestrin.

    An Application of Case-Based Reasoning to the Adaptive Management of Wireless Networks,


    2002



  • Journal Papers P. Degano,  F. Gadducci,  C. Priami.

    A causal semantics for CCS via rewriting logics,


    2002



  • Journal Papers F. Jordan,  I. Scheuring,  G. Vida.

    Species positions and extinction dynamics in simple food webs,


    2002



  • proceeding Papers P. Ballarini,  S. Bernardi,  S. Donatelli.

    Validation and evaluation of a software solution for fault tolerant distributed synchronization,


    2002


    abstract


  • Journal Papers C. Priami.

    Language-based performance prediction of ditributed and mobile systems,


    2002



  • Journal Papers F. Jordan,  I. Scheuring.

    Searching for keystones in ecological networks,


    2002



  • proceeding Papers O. Soyer,  M. Dimmic,  R. Neubig,  R. Goldstein.

    Using evolutionary methods to study G-protein coupled receptors,


    2002


    abstract | pdf pdf


  • Journal Papers J. Tyson,  A. Csikasz-Nagy,  B. Novák.

    The Dynamics of Cell Cycle Regulation,


    2002



  • Journal Papers C. Bodei,  P. Degano,  R. Focardi,  C. Priami.

    Primitives for authentication in process algebras,


    2002



  • Journal Papers D. Chung,  E. Zuiderweg,  C. Fowler,  O. Soyer,  H. Mosberg,  R. Neubig.

    NMR structure of the second intracellular loop of the alpha2a adrenergic receptor: evidence for a novel cytoplasmic helix,


    2002



  • Journal Papers A. Sveiczer,  A. Csikasz-Nagy,  B. Novák.

    Morphogenetic checkpoint in fission yeast? Yes!,


    2002



  • Journal Papers A. Thorsell,  L. Caberlotto,  R. Rimondini,  M. Heilig.

    Leptin suppression of hypothalamic NPY expression and feeding, but not amygdala NPY expression and experimental anxiety.,


    Pharmacol Biochem Behav.,

    71:425-30, 2002


    abstract


  • 2001

  • Journal Papers F. Jordan.

    Adding function to structure - comments on Palmarola landscape connectivity,


    2001



  • Journal Papers W. Sommer,  L. Caberlotto,  C. Arlinde,  A. Thorsell,  P. Hyyttia,  M. Heilig.

    Mol Psychiatry. 2001 Jan;6(1):103-8; 5. Differential expression of diacylglycerol kinase iota and L18A mRNAs in the brains of alcohol-preferring AA and alcohol-avoiding ANA rats.,


    Mol Psychiatry.,

    6:103-8, 2001


    abstract


  • Book Chapter J. Arlat,  A. Bondavalli,  F. Di Giandomenico,  M. Jarboui,  E. Jenn,  K. Kanoun,  I. Mura,  D. Powell.

    Dependability Evaluation” in “A Generic Fault-Tolerant Architecture for Real-Time Dependable Systems,


    2001



  • Journal Papers P. Quaglia.

    Explicit substitutions for pi-congruences,


    Theoretical Computer Science,

    269:83--134, Elsevier, 2001



  • Journal Papers C. Nottegar,  C. Priami,  P. Degano.

    Performance Evaluation of Mobile Processes via Abstract Machines,


    2001



  • Journal Papers F. Jordan.

    Seasonal changes in the positional importance of components in the trophic flow network of the Chesapeake Bay,


    2001



  • Book Chapter F. Jordan.

    Ecosystem flow networks and community control,


    2001



  • Journal Papers L. Caberlotto,  Y. Hurd.

    Neuropeptide Y Y(1) and Y(2) receptor mRNA expression in the prefrontal cortex of psychiatric subjects. Relationship of Y(2) subtype to suicidal behavior.,


    Neuropsychopharmacology,

    25:91-7, 2001


    abstract


  • proceeding Papers B. Battaglino,  R. Cicci,  I. Mura,  G. Previti.

    Effective Radio Interface Resource Management in GPRS,


    2001



  • Journal Papers P. Degano,  C. Priami.

    Enhanced Operational Semantics: A Tool for Describing and Analysing Concurrent Systems,


    2001



  • Journal Papers F. Jordan,  E. Szathmáry,  C. Pál.

    Can genes explain biological complexity?,


    2001



  • Journal Papers F. Jordan.

    Trophic fields,


    2001



  • Journal Papers L. Caberlotto,  A. Thorsell,  R. Rimondini,  W. Sommer,  P. Hyyttia,  M. Heilig.

    Differential expression of NPY and its receptors in alcohol-preferring AA and alcohol-avoiding ANA rats. ,


    Alcohol Clin Exp Res. 2001 Nov;25(11):1564-9.,

    25:1564-9, 2001


    abstract


  • Journal Papers I. Mura,  A. Bondavalli.

    Markov Regenerative Stochastic Petri Nets to Model and Evaluate Phased Mission Systems,


    2001



  • Journal Papers C. Priami,  A. Regev,  E. Shapiro,  W. Silverman.

    Application of a stochastic name-passing calculus to representation and simulation of molecular processes,


    2001



  • Journal Papers F. Jordan.

    Strong threads and weak chains? - a graph theoretical estimation of the power of indirect effects,


    2001



  • proceeding Papers F. Jordan,  M. Ribera d'Alcala,  T. Wyatt.

    Topology and dynamics of plankton networks: are pelagic ecosystems robust? ,


    2001



  • 2000

  • proceeding Papers I. Mura,  A. Bondavalli,  F. Sandrini.

    DEEM: a Tool for the Dependability Modeling and Evaluation of Multiple Phased Systems,


    2000



  • Journal Papers A. Sveiczer,  B. Győrffy,  A. Csikasz-Nagy,  J. Mitchison,  B. Novák.

    Quantised cycles in the fission yeast wee1-50 cdc25D double mutant,


    2000



  • Journal Papers A. Sveiczer,  A. Csikasz-Nagy,  B. Győrffy,  J. Tyson,  B. Novák.

    Modeling the fission yeast cell cycle: quantized cycle times in wee1 - cdc25D mutant cells,


    2000



  • Journal Papers F. Jordan.

    Is the role of trophic control larger in a stressed ecosystem?,


    2000



  • proceeding Papers P. Quaglia,  D. Walker.

    On Synchronous and Asynchronous Mobile Processes,


    Proc. 3rd International Conference on Foundations of Software Science and Computation Structures, FOSSACS 2000, LNCS 1784,

    Springer, 2000



  • Journal Papers K. Chen,  A. Csikasz-Nagy,  B. Győrffy,  J. Val,  B. Novák,  J. Tyson.

    Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle,


    2000



  • proceeding Papers P. Ballarini,  S. Donatelli,  G. Franceschinis.

    Parametric Stochastic Well-formed Nets and compositional modeling,


    2000


    abstract


  • proceeding Papers L. Brodo,  P. Degano,  C. Priami.

    A tool for quantitative analysis of pi-calculus processes,


    2000



  • Journal Papers A. Thorsell,  M. Michalkiewicz,  Y. Dumont ,  R. Quirion,  L. Caberlotto,  R. Rimondini,  A. Mathè,  M. Heilig.

    Behavioral insensitivity to restraint stress, absent fear suppression of behavior and impaired spatial learning in transgenic rats with hippocampal neuropeptide Y overexpression.,


    Proc Natl Acad Sci ,

    97:12852-7, 2000


    abstract


  • Journal Papers C. Bodei,  P. Degano,  C. Priami.

    Handling Names of pi-Calculus Agents locally,


    2000



  • Journal Papers A. Csikasz-Nagy.

    A Mathematical models of the budding yeast cell cycle,


    2000



  • Journal Papers F. Jordan.

    A reliability-theory approach to corridor design,


    2000



  • Journal Papers L. Caberlotto,  K. Fuxe,  Y. Hurd.

    Characterization of NPY mRNA-expressing cells in the human brain: co-localization with Y2 but not Y1 mRNA in the cerebral cortex, hippocampus, amygdala, and striatum.,


    J Chem Neuroanat.,

    20:327-37, 2000


    abstract


  • 1999

  • proceeding Papers I. Mura,  S. Berio.

    Operational Deployment of Business Models for Wireless Systems Resources Management,


    1999



  • Journal Papers C. Priami.

    Operational Methods in Theoretical Computer Science,


    1999



  • proceeding Papers C. Nottegar,  C. Priami,  P. Degano.

    Semantic-driven Performance Evaluation,


    1999



  • Journal Papers L. Caberlotto,  P. Jimenez,  D. Overstreet,  Y. Hurd,  A. Mathè,  K. Fuxe.

    Alterations in neuropeptide Y levels and Y1 binding sites in the Flinders Sensitive Line rats, a genetic animal model of depression.,


    Neurosci Lett.,

    265:191-4, 1999


    abstract


  • proceeding Papers A. Bondavalli,  I. Mura,  K. Trivedi.

    Dependability Modeling and Sensitivity Analysis of Scheduled Maintenance Systems,


    1999



  • proceeding Papers I. Mura,  A. Bondavalli,  X. Zang,  K. Trivedi.

    Dependability Modeling and Evaluation of Phased Mission Systems: a DSPN Approach,


    1999



  • Journal Papers A. Sveiczer,  B. Novák,  A. Csikasz-Nagy,  B. Győrffy,  J. Mitchison,  J. Tyson.

    Quantised cell cycles in fission yeast,


    1999



  • proceeding Papers C. Bodei,  P. Degano,  R. Focardi,  C. Priami.

    Authentication via localized names,


    1999



  • Journal Papers F. Jordan,  I. Molnár.

    Reliable flows and preferred patterns in food webs,


    1999



  • Journal Papers L. Caberlotto,  Y. Hurd.

    Reduced neuropeptide Y mRNA expression in the prefrontal cortex of subjects with bipolar disorder. ,


    Neuroreport. 1999,

    10:1747-50, 1999


    abstract


  • proceeding Papers A. Bondavalli,  I. Majzik,  I. Mura.

    Automatic Dependability Analysis for Supporting Design Decisions in UML,


    1999



  • proceeding Papers A. Bondavalli,  I. Majzik,  I. Mura.

    Automated Dependability Analysis of UML Designs,


    1999



  • proceeding Papers I. Mura,  G. Previti,  G. Recchia,  L. Torasso,  J. Urbina.

    Location Aided Mobility Management in Heterogeneous Networks,


    1999



  • Journal Papers P. Quaglia.

    The Pi-Calculus: Notes on Labelled Semantics,


    Bulletin of the EATCS,

    68:104--115, 1999



  • Journal Papers B. Novák,  A. Tóth,  A. Csikasz-Nagy,  B. Győrffy,  J. Tyson,  K. Nasmyth.

    Finishing the Cell Cycle,


    1999



  • Journal Papers P. Degano,  C. Priami.

    Non-Interleaving Semantics of Mobile Processes,


    1999



  • Journal Papers F. Jordan,  A. Takács-Sánta,  I. Molnár.

    A reliability theoretical quest for keystones,


    1999



  • Journal Papers I. Mura,  A. Bondavalli.

    Hierarchical Modeling and Evaluation of Phased-Mission Systems,


    1999



  • proceeding Papers A. Bondavalli,  I. Mura.

    High-Level Petri Net Modeling of Phased Mission Systems,


    1999



  • Journal Papers P. Degano,  C. Priami,  L. Leth,  B. Thomsen.

    Causality for Debugging Mobile Agents,


    1999



  • proceeding Papers C. Priami,  M. Lonardi,  S. Martini.

    Searching the Web via Mobile Agents,


    1999



  • proceeding Papers F. Di Giandomenico,  F. Grandoni,  A. Bondavalli,  I. Mura.

    Scheduling Solutions for a Unified Approach to the Tolerance of Value and Timing Faults,


    1999



  • Journal Papers A. Bondavalli,  F. Di Giandomenico,  I. Mura.

    An Optimal Value-Based Admission Policy and its Reflective Use in Real-Time Systems,


    1999



  • 1998

  • Journal Papers B. Novák,  A. Csikasz-Nagy,  B. Győrffy,  K. Nasmyth,  J. Tyson.

    Model Scenarios for the Evolution of the Eukaryotic Cell Cycle,


    1998



  • Journal Papers G. Cologna,  P. Lecca.

    Electromagnetic fields in Schwarzschild and Reissner-Notrom geometry: quantum corrections to the black hole entropy, Physical Review,


    1998



  • Journal Papers P. Degano,  C. Priami.

    LR Techniques for Handling Syntax Errors,


    1998



  • proceeding Papers C. Bodei,  P. Degano,  C. Priami.

    Constructing Specific SOS Semantics for Concurrency via Abstract Interpretation,


    1998



  • Journal Papers L. Caberlotto,  B. Tinner,  B. Bunnemann,  L. Agnati,  K. Fuxe.

    On the relationship of neuropeptide Y Y1 receptor-immunoreactive neuronal structures to the neuropeptide Y-immunoreactive nerve terminal networks. A double immunolabelling analysis in the rat brain.,


    Neuroscience,

    86:827-46, 1998


    abstract


  • proceeding Papers P. Quaglia.

    Pi-Congruences as CCS Equivalences,


    Proc. 7th International Conference on Algebraic Methodology and Software Technology, AMAST 1998, LNCS 1548,

    Springer, 1998



  • proceeding Papers C. Priami.

    Enabling and General Distributions in Stochastic Process Algebras,


    1998



  • Journal Papers L. Caberlotto,  K. Fuxe,  J. Rimland,  G. Sedvall ,  Y. Hurd.

    Regional distribution of neuropeptide Y Y2 receptor messenger RNA in the human post mortem brain.,


    Neuroscience,

    86:167-78, 1998


    abstract


  • proceeding Papers P. Quaglia,  D. Walker.

    On Encoding ppi in mpi,


    Proc. 18th International Conference on Foundations of Software Technology and Theoretical Computer Science, FST&TCS 1998, LNCS 1530,

    Springer, 1998



  • Journal Papers B. Novák,  A. Csikasz-Nagy,  B. Győrffy,  K. Chen,  J. Tyson.

    Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions,


    1998



  • Journal Papers L. Caberlotto,  K. Fuxe,  D. Overstreet,  P. Gerrard,  Y. Hurd.

    Alterations in neuropeptide Y and Y1 receptor mRNA expression in brains from an animal model of depression: region specific adaptation after fluoxetine treatment.,


    Brain Res Mol Brain Res.,

    59:58-65, 1998


    abstract


  • 1997

  • proceeding Papers C. Bodei,  C. Priami.

    True Concurrency via Abstract Interpretation,


    1997



  • proceeding Papers D. Latella,  P. Quaglia.

    Stochastic Analysis via a Probabilistic Process Algebra,


    Proc. 5th International Workshop on Process Algebra and Performance Modelling, PAPM 1997,

    1997



  • Journal Papers L. Caberlotto,  K. Fuxe,  G. Sedvall ,  Y. Hurd.

    Localization of neuropeptide Y Y1 mRNA in the human brain: abundant expression in cerebral cortex and striatum.,


    Eur J Neurosci.,

    9:1212-1215, 1997


    abstract


  • proceeding Papers A. Bondavalli,  F. Di Giandomenico,  I. Mura.

    A Value-Based Approach to Flexible Decision Making in Real-Time Dependable Systems,


    1997



  • proceeding Papers S. Balsamo,  I. Mura.

    On Queue Length Moments in Fork and Join Queuing Networks with General Service Times,


    1997



  • Journal Papers A. Csikasz-Nagy,  B. Győrffy,  B. Novák,  J. Tyson.

    Modeling the control of DNA replication in fission yeast,


    1997



  • proceeding Papers A. Bondavalli,  I. Mura,  M. Nelli.

    Analytical Modelling and Evaluation of Phased-Mission Systems for Space Applications,


    1997



  • Journal Papers B. Novák,  A. Csikasz-Nagy,  B. Győrffy,  J. Tyson.

    Model Scenarios for Evolution of the Eukaryotic Cell Cycle,


    1997



  • Journal Papers K. Fuxe,  B. Tinner,  L. Caberlotto,  B. Bunnemann,  L. Agnati.

    NPY Y1 receptor like immunoreactivity exists in a subpopulation of beta-endorphin immunoreactive nerve cells in the arcuate nucleus: a double immunolabelling analysis in the rat.,


    Neurosci Lett. ,

    225 :49-52, 1997


    abstract


  • proceeding Papers A. Bondavalli,  F. Di Giandomenico,  I. Mura.

    Value-driven resource assignment in object-oriented real-time dependable systems,


    1997



  • 1996

  • PhD Thesis C. Priami.

    Enhanced Operational Semantics for Concurrency,




  • Journal Papers P. Degano,  C. Priami.

    Enhanced Operational Semantics,


    1996



  • proceeding Papers C. Priami.

    Integrating Behavioural and Quantitative Analysis with Topology Information,


    1996



  • PhD Thesis P. Quaglia.

    The pi-calculus with explicit substitutions,


    PhD Thesis, Pisa University, Computer Science Dept,



  • proceeding Papers G. Ferrari,  G. Modoni,  P. Quaglia.

    Towards a Semantic-Based Verification Environment for the pi-calculus,


    Proc. 5th Italian Conference on Theoretical Computer Science,

    - World Scientific, 1996



  • proceeding Papers C. Bodei,  P. Degano,  C. Priami.

    Mobile Processes with a Distributed Environment,


    1996



  • proceeding Papers P. Degano,  J. Loddo,  C. Priami.

    Mobile Processes with Local Clocks,


    1996



  • proceeding Papers S. Balsamo,  I. Mura.

    Synchronization delay in hardware fault-tolerance techniques,


    1996



  • technical report R. Borgia,  P. Degano,  C. Priami,  L. Leth,  B. Thomsen.

    Understanding mobile agents via a non interleaving semantics for facile,




  • Journal Papers P. Inverardi,  C. Priami.

    Automatic Verification of Distributed Concurrent Systems: The Process Algebra Approach,


    1996



  • proceeding Papers P. Degano,  C. Priami,  L. Leth,  B. Thomsen.

    Analysis of Facile Programs: a Case Study,


    1996



  • proceeding Papers C. Priami.

    Interleaving Based Partial Ordering Semantics,


    1996



  • Journal Papers G. Ferrari,  U. Montanari,  P. Quaglia.

    A pi-calculus with Explicit Substitutions,


    Theoretical Computer Science,

    168:53--103, Elsevier, 1996



  • 1995

  • proceeding Papers P. Degano,  C. Priami.

    Causality for Mobile Processes,


    1995



  • proceeding Papers A. Bianchi,  S. Coluccini,  P. Degano,  C. Priami.

    An Efficient Verifier of Truly Concurrent Properties,


    1995



  • proceeding Papers S. Balsamo,  I. Mura.

    Approximate response time distribution in Fork and Join systems.,


    1995



  • Journal Papers C. Priami.

    Stochastic pi-calculus,


    1995



  • proceeding Papers A. Mycroft,  P. Degano,  C. Priami.

    Complexity as a Basis for Comparing Semantic Models of Concurrency,


    1995



  • proceeding Papers G. Ferrari,  U. Montanari,  P. Quaglia.

    The Weak Late pi-calculus Semantics as Observation Equivalence,


    Proc. 6th International Conference on Concurrency Theory, CONCUR 1995, LNCS 962,

    Springer, 1995



  • Journal Papers P. Degano,  C. Priami.

    Comparison of Syntactic Error Handling in LR Parsers,


    1995



  • 1994

  • Journal Papers P. Inverardi,  C. Priami,  D. Yankelevich.

    Automatizing Parametric Reasoning on Distributed Concurrent Systems,


    1994



  • proceeding Papers C. Priami,  D. Yankelevich.

    Read-Write Causality,


    1994



  • proceeding Papers G. Ferrari,  U. Montanari,  P. Quaglia.

    A pi-calculus with Explicit Substitutions: the Late Semantics,


    Proc. 19th International Symposium on Mathematical Foundations of Computer Science, MFCS 1994, LNCS 841,

    Springer, 1994



  • 1993

  • Journal Papers U. Bianchi,  P. Degano,  S. Mannucci,  S. Martini,  B. Mojana,  C. Priami,  E. Salvatori.

    Generating the Analytic Component Parts of Syntax-Directed Editors with Efficient Error Recovery,


    1993



  • proceeding Papers D. Latella,  P. Quaglia.

    A Fully Parallel Calculus of Synchronizing Processes,


    Proc. 3rd International Joint Conference on Theory and Practice of Software Development, TAPSOFT 1993, LNCS 668,

    Springer, 1993



  • proceeding Papers P. Inverardi,  C. Priami,  D. Yankelevich.

    Extended Transition Systems for Parametric Bisimulation,


    1993



  • 1992

  • proceeding Papers P. Degano,  C. Priami.

    Proved Trees,


    1992



  • proceeding Papers P. Inverardi,  C. Priami,  D. Yankelevich.

    Verification of Concurrent Systems in SML,


    1992



  • 1991

  • technical report P. Quaglia.

    Proposta per una variante probabilistica di LOTOS,


    Laurea Thesis, Pisa University,



  • Journal Papers P. Inverardi,  C. Priami.

    Evaluation of Tools for the Analysis of Communicating Systems,


    1991



  • 1990

  • technical report C. Priami.

    Gestione degli Errori nei Parsers LR,




.