
Federica CiocchettaBanca d'Italia · Financial Stability
Federica Ciocchetta
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Publications (45)
One source of complexity in ecological systems is the hierarchical organization of parallel biological processes. Our 'horizontal' knowledge describing different levels is quite massive, but the understand-ing of their vertical interactions is very poor. We present a toy model linking social networks, food webs and a landscape graph. Horizontal pro...
Several important ecological problems are related to the hierarchical organization of ecosystems. In order to better understand the ecology of a population, its internal social structure and its interspecific interactions can be equally important, but it may also matter how it is embedded in a larger-scale metacommunity system. While we know a lot...
Semantic equivalences are used in process algebra to capture the notion of
similar behaviour, and this paper proposes a semi-quantitative equivalence for
a stochastic process algebra developed for biological modelling. We consider
abstracting away from fast reactions as suggested by the Quasi-Steady-State
Assumption. We define a fast-slow bisimilar...
Compositionality is a key feature of process algebras which is often cited as
one of their advantages as a modelling technique. It is certainly true that in
biochemical systems, as in many other systems, model construction is made
easier in a formalism which allows the problem to be tackled compositionally.
In this paper we consider the extent to w...
Many models have been defined in order to describe the evolution of a disease in a population. The modelling of diseases is helpful to understand the mechanisms for their spread and to predict their future evolution. Most of the models in the literature are defined in terms of systems of differential equations and only a few of them propose stochas...
In this work we present a Bio-PEPA model describing the Nuclear Factor κB (NF-κB) signalling pathway. In particular our model focuses on the dynamic response of NF-κB to an external stimulus. Each biochemical species in the pathway is represented by a specific Bio-PEPA component and the external stimulus is abstracted by time-dependent Bio-PEPA eve...
The vast majority of biochemical systems involve the exchange of information between different compartments, either in the form of transportation or via the intervention of membrane proteins which are able to transmit stimuli between bordering compartments. The correct quantitative handling of compartments is, therefore, extremely important when mo...
Bio-PEPA is a timed process algebra designed specifically for the description of biological phenomena and their analysis through quantitative methods such as stochastic simulation and probabilistic model-checking. Two software tools are available for modelling with Bio-PEPA, the Bio-PEPA Workbench and the Bio-PEPA Eclipse Plugin. The Bio-PEPA Workb...
Circadian clocks are biochemical networks, present in nearly all living organisms, whose function is to regulate the expression of specific mRNAs and proteins to synchronise rhythms of metabolism, physiology and behaviour to the 24 hour day/night cycle. Because of their experimental tractability and biological significance, circadian clocks have be...
In this work we present Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA, originally defined for the performance analysis of computer systems, in order to handle some features of biological models, such as stoichiometry and the use of general kinetic laws. Bio-PEPA may be seen as a...
Model-checking can provide valuable insight into the behaviour of biochemical systems, answering quantitative queries which are more difficult to answer using stochastic simulation alone. However, model-checking is a computationally intensive technique which can become infeasible if the system under consideration is too large. Moreover, the finite...
Bio-PEPA is a recently defined language for the modelling and analysis of biochemical networks. It supports an abstract style of modelling, in which discrete levels of concentration within a species are considered instead of individual molecules. A finer granularity for the system corresponds to a smaller concentration step size and therefore to a...
Compartments and membranes play an important role in cell biology. Therefore it is highly desirable to be able to represent them in modelling languages for biology. Bio-PEPA is a language for the modelling and analysis of biochemical networks; in its present version compartments can be defined but they are only used as labels to express the locatio...
In this work we present an extension of Bio-PEPA, a language recently defined for the modelling and analysis of biochemical
systems, to handle events. Events are constructs that represent changes in the system due to some trigger conditions. The events considered here are
simple, but nevertheless able to describe most of the discontinuous changes i...
In this paper we present a quantified model of the synthesis of pre-rRNAs in yeast. The chemical kinetics simulation software Dizzy has been used as both the modelling and simulation framework of our study. The simulations have been used to investigate the mechanism of co-transcriptional cleavage which can occur during the synthesis of pre-rRNAs.Th...
Bio-PEPA is a novel stochastic process algebra which has been recently developed for modelling biochemical pathways [5,6].
In Bio-PEPA a reagent-centric style of modelling is adopted, and a variety of analysis techniques can be applied to a single
model expression. Such an approach facilitates easy validation of analysis results when the analyses a...
In this chapter we introduce process algebras, a class of formal mod- elling techniques developed in theoretical computer science, and discuss their use within systems biology. These formalisms have a number of attractive features which make them ideal candidates to be intermediate, formal, compositional rep- resentations of biological systems. As...
In this work we introduce Bio-PEPA, a process algebra for the modelling and the analysis of biochemical networks. It is a modification of PEPA to deal with some features of biological models, such as stoichiometry and the use of generic kinetic laws. Bio-PEPA may be seen as an intermediate, formal, compositional representation of biological systems...
An extension of the BlenX language with biological transactions, called TBlenX, is presented. The aim of this extension is to model a sequence of elementary actions as if it were atomic. This extension
is useful when we need to specify multi-reactant multi-product reactions or when we use a sequence of actions to represent
a biological interaction....
In this work we present an extension of Bio-PEPA, a language re- cently defined for the modelling and analysis of biological systems, to handle events. Broadly speaking, events are constructs that represent changes in the sys- tem due to some,trigger conditions. Some mappings,from Bio-PEPA with events to analysis tools are reported. in order to tes...
A translation of Systems Biology Markup Language (SBML) into a process algebra is proposed in order to allow the formal specification, the simulation and the formal analysis of biological models. Beta-binders, a language with a quantitative stochastic extension, is chosen for the translation. The proposed translation focuses on the main components...
In this paper we present a quantified model concerning the synthesis of pre-rRNAs. The chemical kinetics simulation software Dizzy has been chosen as both the modelling and simulation framework of our study. We discuss the validation of the model against the available ex- perimental data and we show some preliminary results obtained from the study...
In this work an extension of stochastic π-calculus with biological transactions is presented. This permits to model multi-reactant multi-product reactions as atomic actions when quantitative information are given. First, the syntax and the semantics are defined, then some transaction properties are discussed. Finally, some examples are described.
Given a set of gene expression time series obtained by a microarray experiment, this work proposes a novel quality control
procedure that exploits six analytical methods, each of which allows for the identification in an automated way of genes that
have expression spikes within narrow time-windows and over a chosen amplitude threshold. The output o...
PEPA has been recently applied for the modelling and the analysis of some biological pathways. PEPA is useful in this field, but unfortunately not all the fea- tures of biological systems can be considered. In this work we show a first version of Bio-PEPA, a new language that extends PEPA in order to model biochemical networks.
We represent a subset of the mammalian cell cycle Kohn interaction map using Beta-binders, a formalism inspired to the pi-calculus
and enriched with binders that allow the description of enclosing surfaces equipped with interaction sites. Specifically,
the interactions between the p53 protein and its main regulator Mdm2 is analyzed.
Beta-binders c...
9600 Background: We investigated the prognostic significance of Her2/neu expression using FDA approved Herceptest® and the tissue microarray (TMA) technique. We used our in-house developed WATMAS, and investigated the most appropriate scoring system to be applied to the analysis of multiple replica samples from the same tumors. Methods: WATMAS incl...
The early diagnosis of Hepatocellular Carcinoma (HCC) is extremely important for effective treatment and improvements in diagnosis
are indispensable, particularly concerning the differentiation between “early” HCC and non neoplastic nodules. In this paper,
we reconsidered the results obtained previously and compared them with the results of an unsu...
Hepatocellular carcinoma (HCC) is one of the commonest fatal tumors, and it is usually diagnosed at a late stage, when effective treatment is very difficult. Unfortunately early diagnosis of HCC is almost mandatory in terms of patient survival, but is represents a very difficult task. Detailed histological characteristics of small HCC and precursor...
Hepatocellular carcinoma (HCC) is one of the commonest fatal tumors, and it is usu-ally diagnosed at a late stage, when effective treatment is very difficult. Unfortunately early diagnosis of HCC is almost mandatory in terms of patient survival, but it represents a very difficult task. Detailed histological characteristics of small HCC and precurso...
Living systems are hierarchically organised. A number of components are linked by the multiplicity of interactions at each
level (from organisms to species to ecosystems). This kind of compositional and hierarchical complexity is a computational
and conceptual challenge. We need new approaches to determine the key components of large interaction ne...
In this work we extend the -calculus with a simple class of trans-actions, suitable to model multi-reactant, multiproduct chemical re-actions. Some examples are reported to validate our extension.
In this work we propose an extension of Beta-binders with biological transactions, called TBeta-binders, in order to model a sequence of elementary actions atomically. This extension is useful when we need to specify multi-reactant multi-product reactions or when we use a sequence of actions to represent a single biological interaction. Some proper...