Marzio Pennisi - Profile on Academia.edu (original) (raw)

Papers by Marzio Pennisi

Searching of optimal vaccination schedules: Application of genetic algorithms to approach the problem in cancer immunoprevention

Genetic algorithms (GAs) are a particular class of evolutionary algorithms that use techniques in... more Genetic algorithms (GAs) are a particular class of evolutionary algorithms that use techniques inspired by evolutionary biology. These are widely used in different areas of bioinformatics. In immunoinformatics, a common optimization problem is the search of optimal vaccination schedules. The problem of defining optimal schedules is particularly acute in cancer immunopreventive approaches, which requires a sequence of vaccine administrations to

Computational modeling of the expansion of human cord blood CD133+ hematopoietic stem/progenitor cells with different cytokine combinations

Bioinformatics (Oxford, England), Jan 25, 2015

Many important problems in cell biology require dense nonlinear interactions between functional m... more Many important problems in cell biology require dense nonlinear interactions between functional modules to be considered. The importance of computer simulation in understanding cellular processes is now widely accepted, and a variety of simulation algorithms useful for studying certain subsystems have been designed. Expansion of hematopoietic stem and progenitor cells (HSC/HPC) in ex vivo culture with cytokines and small molecules is a method to increase the restricted numbers of stem cells found in umbilical cord blood while also enhancing the content of early engrafting neutrophil and platelet precursors. The efficacy of the expanded product depends on the composition of the cocktail of cytokines and small molecules used for culture. Testing the influence of a cytokine or small molecule on the expansion of HSC/HPC is a laborious and expensive process. We therefore developed a computational model based on cellular signaling interactions that predict the influence of a cytokine on t...

A Model of Cytotoxic T Antitumor Activation Stimulated by Pulsed Dendritic Cells

We present a preliminary ODE model to sketch the immune response of cytotoxic T cells against can... more We present a preliminary ODE model to sketch the immune response of cytotoxic T cells against cancer through the use of pulsed autologous dendritic cells. The model is partially based on data coming from experiments that are presently in progress in the wet lab of our collaborators, but it can be applied in principle to different tumors. To this end,

Computational modelling approaches to vaccinology

Pharmacological Research, 2015

Excepting the Peripheral and Central Nervous Systems, the Immune System is the most complex of so... more Excepting the Peripheral and Central Nervous Systems, the Immune System is the most complex of somatic systems in higher animals. This complexity manifests itself at many levels from the molecular to that of the whole organism. Much insight into this confounding complexity can be gained through computational simulation. Such simulations range in application from epitope prediction through to the modelling of vaccination strategies. In this review, we evaluate selectively various key applications relevant to computational vaccinology: these include technique that operates at different scale that is, from molecular to organisms and even to population level.

Tumor Associated Antigen Variation In silico experiments using the Sicilian Grid

AGENT BASED MODELING OF HUMORAL IMMUNE RESPONSE TO ATHEROGENESIS

Abstract. Atherosclerosis is a pathology where the immune system control plays a relevant role. W... more Abstract. Atherosclerosis is a pathology where the immune system control plays a relevant role. We present studies on the increased atherosclerosis risk using an agent based model of atherogenesis. It is well known that the major risk in atherosclerosis is the persistent ...

Grid-based Atherosclerosis Simulations

Agent based modeling of melanoma immune system competition

The immunogrid simulator: how to use it

1 Department of Mathematics and Computer Science, University of Catania 2 Faculty of Pharmacy, Un... more 1 Department of Mathematics and Computer Science, University of Catania 2 Faculty of Pharmacy, University of Catania 3 Istituto per le applicazioni del calcolo Mauro Picone, CNR, Roma 4 Department of Biological Sciences and Institute of Structural and Molecular ...

Cancer Immunoprevention: What Can We Learn from in Silico Models?

Cancer Immunoprevention: What Can We Learn from in Silico Models? Francesco Pappalardo1, Marzio P... more Cancer Immunoprevention: What Can We Learn from in Silico Models? Francesco Pappalardo1, Marzio Pennisi1, Alessandro Cincotti2, Ferdinando Chiacchio1, Santo Motta1, and Pier-Luigi Lollini3 1 University of Catania, Dept. of Mathematics and Computer ...

GRIDUISS–A Grid Based Universal Immune System Simulator Framework

D.-S. Huang et al. (Eds.): ICIC 2010, LNCS 6215, pp. 285290, 2010. © Springer-Verlag Berlin Heid... more D.-S. Huang et al. (Eds.): ICIC 2010, LNCS 6215, pp. 285290, 2010. © Springer-Verlag Berlin Heidelberg 2010 ... GRIDUISS A Grid Based Universal Immune System ... Francesco Pappalardo1,*, Marzio Pennisi1, Ferdinando Chiacchio1, Alessandro Cincotti2, and ...

The MWF method for kinetic models: An overview and research perspective

THE STABILIZATION EFFECT OF THE TRIPLEX VACCINE This work was supported in part by IMMUNOGRID project, under EC contract FP6-2004-IST-4, No. 028069. FP and SM acknowledge partial support from University of Catania research grant and MIUR (PRIN 2004: Problemi matematici delle teorie cinetiche). Th...

iAtheroSim: atherosclerosis process simulator on smart devices

Modeling artificial immunity against mammary carcinoma

Abstract A typical, and unfortunately very spread, endogenous cancer is represented by the mammar... more Abstract A typical, and unfortunately very spread, endogenous cancer is represented by the mammary carcinoma. Lollini et al.[1] prevented mammary carcinogenesis in HER-2/neu transgenic mice using the Triplex cellular vaccine under a Chronic schedule (vaccine ...

Similarity is a vague concept which can be treated in a quantitative manner only using appropriat... more Similarity is a vague concept which can be treated in a quantitative manner only using appropriate mathematical representation of the objects to compare and a metric on the space representation. In biology the mathematical representation of structure relies on strings taken from an alphabet of m symbols. Very often binary strings, m = 2, are used. The size of the binary string depends on the complexity of the structure to represent, so the string can be quite long. The Hamming distance is the most used metric with binary strings. The computational effort required to compute the Hamming distance linearly depends on the size of the string. However even a linear effort case may be computational heavy if many computations are required. One of the fastest computational approach to evaluate Hamming distances relies on look-up tables. The computational performance, however, rapidly deteriorates with the size of binary string length, due to cache misses. We present a computational strategy and implementation which can handle huge number of Hamming distance evaluation between binary strings of arbitrary length keeping computational performance competitive.

The Triplex vaccine is a cell vaccine developed as an immunopreventive approach to breast cancer.... more The Triplex vaccine is a cell vaccine developed as an immunopreventive approach to breast cancer. Recent studies showed that the same vaccine has a considerable therapeutic effect against lung metastases derived by mammary carcinoma[1].

Atherosclerosis, a pathology affecting arterial blood vessels, is one of most common diseases of ... more Atherosclerosis, a pathology affecting arterial blood vessels, is one of most common diseases of the developed countries. We present studies on the increased atherosclerosis risk using an agent based model of atherogenesis that has been previously validated using clinical data. It is well known that the major risk in atherosclerosis is the persistent high level of low density lipoprotein (LDL) concentration. However, it is not known if short period of high LDL concentration can cause irreversible damage and if reduction of the LDL concentration (either by life style or drug) can drastically or partially reduce the already acquired risk. We simulated four different clinical situations in a large set of virtual patients (200 per clinical scenario). In the first one the patients lifestyle maintains the concentration of LDL in a no risk range. This is the control case simulation. The second case is represented by patients having high level of LDL with a delay to apply appropriate treatments; The third scenario is characterized by patients with high LDL levels treated with specific drugs like statins. Finally we simulated patients that are characterized by several oxidative events (smoke, sedentary life style, assumption of alcoholic drinks and so on so forth) that effective increase the risk of LDL oxidation. Those preliminary results obviously need to be clinically investigated. It is clear, however, that SimAthero has the power to concretely help medical doctors and clinicians in choosing personalized treatments for the prevention of the atherosclerosis damages.

In this paper, the Universal Immune System Simulator (UISS) framework is sketched, showing some o... more In this paper, the Universal Immune System Simulator (UISS) framework is sketched, showing some of its applications for successfully modeling and simulating multiple immune system related pathologies.