PROJECTS: past and current activities

Here you can find information about past and current projects.

Workgroup members who have participated can be found here.


Information related to some of the current activities can be found at the Digital Biology Unit s home page.

ABOUT MISSION-T2D

SATURDAY 19 JULY 2014


In a dissemination article published on International Innovation, some of the MISSION-T2D project’s partners discuss about the project and how the consortium is trying to address and its potential to...



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ABOUT C-IMMSIM

MONDAY 14 APRIL 2014


In this article Filippo Castiglione discusses about the field of immunoinformatics and how machine learning has benefited the most recent advancement of the immune system simulator, C-ImmSim ...



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SPECIAL ISSUE ON COMPUTATIONAL STUDIES OF IMMUNE SYSTEM FUNCTION

MONDAY 23 SEPTEMBER 2013


This special issue will focus on the computational methods and models employed to study immune system functioning under health and disease conditions.

Papers discussing computational models, at any...


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SPECIAL ISSUE ON COMPUTATIONAL AND BIOINFORMATICS TECHNIQUES FOR IMMUNOLOGY

MONDAY 1 JULY 2013


Immunology has embraced data-driven computational and mathematical approaches to understand the immune system, its disorders and infections. Computational immunology covers mathematical and/or...


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MISSION-T2D PROJECT

TUESDAY 25 SEPTEMBER 2012


Type 2 Diabetes Mellitus (T2D) is a metabolic disorder characterized by high blood glucose in the context of insulin resistance and relative insulin deficiency. T2D entails severe consequences in the...


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PEPTIDE VACCINATION IN CANCER THERAPY

WEDNESDAY, OCTOBER 5, 2011


Peptide vaccination in cancer therapy is a promising alternative to conventional methods. However, the parameters for this personalized treatment are difficult to access experimentally. In this respect, in silico models can help to narrow down the parameter space or to explain certain phenomena at a systems level.


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GENE REGULATORY NETWORKS AND MODELING

WEDNESDAY, APRIL 27, 2011


Th1 and Th2 lymphocytes are thought to be counter-regulatory. A network model of genes that regulate Th1 and Th2 cells was constructed by automated mining of 18 million abstracts in Medline. Analysis of the dynamics of this model using in silico knock-outs suggested a synergistic ...


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IMMUNO-BIOINFORMATICS

WEDNESDAY, APRIL 27, 2011


We present a new approach to the study of the immune system that combines techniques of systems biology with information provided by data-driven prediction methods. To this end, we have extended an agent-based simulator of the immune response ...


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SIMULATION OF THE GENE REGULATORY NETWORK FOR TH1/2 DIFFERENTIATION

SUNDAY, NOVEMBER 14, 2010


An unbalanced differentiation of T helper cells from precursor type TH0 to the TH1 or TH2 phenotype in immune responses often leads to a pathological condition. In general, immune reactions biased toward TH1 responses may result in ...


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SIMULATION OF HIGHLY ACTIVE ANTIRETROVIRAL THERAPY

THURSDAY, JUNE 17, 2010


The optimal stage for initiating antiretroviral therapies in HIV-1 bearing patients is still a matter of debate.  We present computer simulations of HIV-1 infection aimed at identifying the pro et contra of immediate as compared to deferred Highly Active Antiretroviral Therapy (HAART) ...


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MODELING LYMPHOCYTES HOMING AND ENCOUNTERS IN LYMPH NODES

SATURDAY, OCTOBER 25, 2008


We developed an agent-based model to describe the lymph node as composed by three regions: a T cell area (i.e., the paracortex) a B cell area (i.e., inside the node cortex), plus a region (i.e., the medulla) consisting of the exits conducting to the effererent vessel ...


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ISCHEMIA-INDUCED NEUROBLAST ACTIVATION: A MATH MODEL

WEDNESDAY, AUGUST 13, 2008


We have developed a rat brain organotypic culture model, in which tissue slices contain cortex-subventricular zone-striatum regions, to model neuroblast activity in response to in vitro ischemia. Neuroblast activation has been described in terms of two main parameters ...


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SIMULATIONS OF HIV INFECTION

MONDAY, JUNE 12, 2006


We implemented a discrete (Cellular Automata or Agent-Based) simulator of the cellular and humoral immune response to the HIV-1 infection. We study the dynamics of the HIV-1 diversity and divergence from the wild-type as an adaptive walk in a bit-string space ...


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SIMULATION PROTEIN-PROTEIN INTERACTIONS

SUNDAY, FEBRUARY 12, 2006


Protein interactions support cell organization and mediate its response to any specific stimulus. Recent technological advances have produced large data-sets that aim at describing the cell interactome. These data are usually presented as graphs where proteins (nodes) are linked ...


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THE COMPLEXDIS PROJECT

WEDNESDAY, FEBRUARY 1, 2006


Common diseases like allergy, obesity and cancer are complex. Each of these diseases is caused by altered interactions between multiple genes. These alterations may differ between different individuals although they appear to have the same disease. The aim of ComplexDis is to identify ...


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SIMULATIONS OF EPSTEIN-BARR VIRUS INFECTIONS

MONDAY, DECEMBER 12, 2005


Epstein-Barr virus (EBV) infects more than 90% of humans benignly for life but can be associated with tumors. It is a uniquely human pathogen that is amenable to quantitative analysis;  however, there is no applicable animal model. Computer models may provide a virtual environment ...


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THE IMMUNOGRID PROJECT

SUNDAY, JANUARY 2, 2005


The European Virtual Immune System Project ...


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SIMULATING THE IMMUNE SYSTEM

SATURDAY, JUNE 12, 2004


C-ImmSim is an Agent-based simulator of the immune system response to a generic pathogen. It has been originally developed as a porting in C of the IMMSIM simulator written by Philiph E. Seiden and Franco Celada in APL (IBM) language. ...


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CANCER IMMUNOPREVENTION

FRIDAY, MARCH 12, 2004


In vivo experiments on HER-2/neu mice have shown  the effectiveness of Triplex vaccine in the protection of mice from mammary carcinoma. Full protection was conferred using chronic (prophylactic) vaccination protocol while therapeutic vaccination was less efficient. Our in silico model ...


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CANCER IMMUNOTHERAPY

WEDNESDAY, JANUARY 21, 2004


IVaccination protocols designed to elicit anti-cancer immune responses have, many times, failed in producing tumor eradication and in prolonging patient survival. Usually in cancer vaccination, epitopes from one organism are included in the genome or linked with some protein ...


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SIMULATIONS OF HYPERSENSITIVE REACTIONS

SATURDAY, MAY 25, 2002


IVaccination protocols designed to elicit anti-cancer immune responses have, many times, failed in producing tumor eradication and in prolonging patient survival. Usually in cancer vaccination, epitopes from one organism are included in the genome or linked with some protein ...


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CELL SIGNALING TRANSDUCTION

SATURDAY, MAY 25, 2002


We study a simple reaction scheme in a two-dimensional lattice of particles/molecules with a refractory state. We are interested in the dynamics of the propagating front as a function of physicochemical properties of the host medium. Anisotropy of the medium greatly ...


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ECONOPHYSICS

TUESDAY, JUNE 12, 2001


Econophysics is an interdisciplinary research field, where theories and methods originally developed by physicists are applied to solve problems in economics. ...


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MICROSIMULATION OF THE STOCK MARKET

THURSDAY, JULY 13, 2000


FINSIM is a (computational) model to simulate the dynamic  interactions between market price and the decisions of different kind of traders.  They possess spatial mobility and group together to form coalitions. Each coalition follows a strategy chosen from a  proportional voting “dominated” by a leader's decision. The interplay of the different kind of agents gives rise to complex price dynamics that is ...


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IMAGE ANALYSIS OF ULTRASOUND BIOMICROSCOPY OF HUMAN CORNEA

TWEDNESDAY, MAY 12, 1999


The keratoconus is a corneal dystrophy evidenced by a progressive asymmetric increment of the corneal curvature and by a thickness reduction in the central area. In a recent work the Keratoconus Index (KI) has been correlated to a pathology, called keratoconus, of the human eye ...


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ONLINE SIMULATION SERVER

THURSDAY 2 FEBRUARY 2017


C-ImmSim is now available online at http://150.146.2.1/C-IMMSIM




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WORKSHOP

SATURDAY 27 MAY 2017


The 1st International Workshop on Computational Methods for the Immune System Functions (CMISF 2017)




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