Vincenzo Manca
Università di Verona, Computer Science, Faculty Member
This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
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Lecture Notes in Computer Science, Invited Lectur
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An equational calculus dealing with empty carrier sets in many-sorted algebras is presented
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Representation of metabolic processes by MP systems
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An equational calculus dealing with empty carrier sets in many-sorted algebras is presented
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Representation of metabolic processes by MP systems
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Oncogenes are known drivers of cancer phenotypes and targets of molecular therapies; however, the complex and diverse signaling mechanisms regulated by oncogenes and potential routes to targeted therapy resistance remain to be fully... more
Oncogenes are known drivers of cancer phenotypes and targets of molecular therapies; however, the complex and diverse signaling mechanisms regulated by oncogenes and potential routes to targeted therapy resistance remain to be fully understood. To this end, we present an approach to infer regulatory mechanisms downstream of the HER2 driver oncogene in SUM-225 metastatic breast cancer cells from dynamic gene expression patterns using a succession of analytical techniques, including a novel MP grammars method to mathematically model putative regulatory interactions among sets of clustered genes. Our method highlighted regulatory interactions previously identified in the cell line and a novel finding that the HER2 oncogene, as opposed to the proto-oncogene, upregulates expression of the E2F2 transcription factor. By targeted gene knockdown we show the significance of this, demonstrating that cancer cell-matrix adhesion and outgrowth were markedly inhibited when E2F2 levels were reduced...
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Introduction to and recent research in discrete biomathematics ▶ Presents new approaches in discrete biomathematics at borders between biology, discrete mathematics, and computer science ▶ Presents an integrated way to make the subject... more
Introduction to and recent research in discrete biomathematics ▶ Presents new approaches in discrete biomathematics at borders between biology, discrete mathematics, and computer science ▶ Presents an integrated way to make the subject accessible to a number of audiences The book presents topics in discrete biomathematics. Mathematics has been widely used in modeling biological phenomena. However, the molecular and discrete nature of basic life processes suggests that their logic follow principles that are intrinsically based on discrete and informational mechanisms. The ultimate reason of polymers, as key element of life, is directly based on the computational power of strings, and the intrinsic necessity of metabolism is related to the mathematical notion of multiset. The switch of the two roots of bioinformatics suggests a change of perspective. In bioinformatics, the biologists ask computer scientists to assist them in processing biological data. Conversely, in infobiotics mathe...
Genomes follow laws resembling celestial orbits. In a recent publication on Nature Scientific Reports[1] two computer scientists (V. Manca and V. Bonnici) discovered strong mathematical regularities in the structure of genomes. These... more
Genomes follow laws resembling celestial orbits. In a recent publication on Nature Scientific Reports[1] two computer scientists (V. Manca and V. Bonnici) discovered strong mathematical regularities in the structure of genomes. These regularities can be expressed in terms of simple laws based on ellipses, hyperbolas and parabolas. But the geometrical forms do not cope with spatial movements, rather they refer to genomic indexes defined by means of information theory[2]. The research started in 2009 at Center of Biomedical Computing of the University of Verona (Italy) directed by one of two authors, with the aim of finding rigorous proofs supporting the intuition that genomes are texts, with a complex internal organization, written during the evolutionary process of living organisms. Along a line of thought, called Infogenomics[3-7], it was argued that these texts contain the deepest secrets that rule the universal mechanisms of life, in all the various and complex phenomena of biolo...
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Background In the post-genomic era several methods of computational genomics are emerging to understand how the whole information is structured within genomes. Literature of last five years accounts for several alignment-free methods,... more
Background In the post-genomic era several methods of computational genomics are emerging to understand how the whole information is structured within genomes. Literature of last five years accounts for several alignment-free methods, arisen as alternative metrics for dissimilarity of biological sequences. Among the others, recent approaches are based on empirical frequencies of DNA k-mers in whole genomes. Results Any set of words (factors) occurring in a genome provides a genomic dictionary. About sixty genomes were analyzed by means of informational indexes based on genomic dictionaries, where a systemic view replaces a local sequence analysis. A software prototype applying a methodology here outlined carried out some computations on genomic data. We computed informational indexes, built the genomic dictionaries with different sizes, along with frequency distributions. The software performed three main tasks: computation of informational indexes, storage of these in a database, i...
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Some recent types of membrane systems have shown their potential in the modelling of specific processes governing biological cell behavior. These models represent the cell as a huge and complex dynamical system in which quantitative... more
Some recent types of membrane systems have shown their potential in the modelling of specific processes governing biological cell behavior. These models represent the cell as a huge and complex dynamical system in which quantitative aspects, such as biochemical ...
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Abstract. In this paper we propose a new formal operation on words and languages, called superposition. By this operation, based on a Watson-Crick-like complementarity, we can generate a set of words, starting from a pair of words, in... more
Abstract. In this paper we propose a new formal operation on words and languages, called superposition. By this operation, based on a Watson-Crick-like complementarity, we can generate a set of words, starting from a pair of words, in which the contribution of a word to the result need not be one subword only, as happens in classical bio-operations of DNA computing. Specifically, starting from two single stranded molecules x and y such that a suffix of x is complementary to a prefix of y, a prefix of x is complementary to a suffix of y, or x is complementary to a subword of y, a new word z, which is a prolongation of x to the right, to the left, or to both, respectively, is obtained by annealing. If y is complementary to a subword of x, then the result is x. This operation is considered here as an abstract operation on formal languages. We relate it to other operations in formal language theory and we settle the closure properties under this operation of classes in the Chomsky hiera...
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The metabolic P algorithm is a procedure which determines, in a biochemically realistic way, the evolution of P systems representing biological phenomena. A new formulation of this algorithm is given and a graphical formalism is... more
The metabolic P algorithm is a procedure which determines, in a biochemically realistic way, the evolution of P systems representing biological phenomena. A new formulation of this algorithm is given and a graphical formalism is introduced which seems to be very natural in expressing biological networks by means of a two level representation: a basic biochemical level and a second one which regulates the dynamical interaction among the reactions of the first level. After some basic examples, the mitotic oscillator in amphibian embryos is considered as an important case study. Three formulations of this biological network are developed. The first two are directly derived by Goldbeter's differential equations representation. The last one, entirely deduced by translating the biological description of the phenomenon in our diagrams, exhibits an analogous pattern, but it is conceptually simpler and avoids many details on the kinetic aspects of the reactions.
Research Interests: Engineering, Mathematics, Computer Science, Algorithms, Kinetics, and 15 moreMedicine, Signal Transduction, Biological Sciences, Software, Computer Simulation, Case Study, Oscillations, Biological Network, Differential equation, Biosystems, Embryos, Proteome, Gene Expression Regulation, Gene expression profiling, and discrete model
Abstract. The extraction of DNA strands including a given sequence of bases is a crucial step in the Adleman-Lipton extract model of DNA computing. In this paper, a special type of PCR is presented with a related algorithm which performs... more
Abstract. The extraction of DNA strands including a given sequence of bases is a crucial step in the Adleman-Lipton extract model of DNA computing. In this paper, a special type of PCR is presented with a related algorithm which performs a specified extraction from a given pool of DNA double stranded (shortly dsDNA) molecules. This kind of PCR, called Cross Pairing PCR (shortly XPCR) was tested in several situations, and used in a biotechnological procedure which implements the extraction algorithm.
P systems have clear structural analogies with the cell. However, certain difficulties arise when one attempts to represent a biomolecular process using these systems. This chapter suggests some ways to overcome such difficulties and to... more
P systems have clear structural analogies with the cell. However, certain difficulties arise when one attempts to represent a biomolecular process using these systems. This chapter suggests some ways to overcome such difficulties and to provide P systems with further functionalities aimed at increasing their versatility in the modeling of biomolecular processes. Concepts from state transition dynamics are taken to put P systems in a general analysis framework for dynamical discrete systems. An explicit notion of environment is proposed to provide P systems with a regulatory and constraining agent, as real biomolecular processes must deal with. The chapter focuses on a new rewriting strategy inspired by biochemistry, in which reactivities play a central role in driving the rules as it happens during biochemical reactions. Tests on an algorithm implementing rewriting with reactivities, realized on a simulator called Psim, show the capability of this algorithm to express several proces...
The study of P systems as a mathematical model for biological systems is an important research topic in the area of membrane computing. In this respect, the detection of periodicity and almost periodicity as aspects of the system dynamics... more
The study of P systems as a mathematical model for biological systems is an important research topic in the area of membrane computing. In this respect, the detection of periodicity and almost periodicity as aspects of the system dynamics seems to be of particular relevance for understanding many biological processes and their related phenomena. This paper introduces specific notions of periodicity and almost periodicity for (infinite) sequences of multisets, which are used to describe the dynamics of P systems. Specifically, a variant of P systems, called P systems with resources, is considered where the rules always consume a certain amount of resources, which are provided in the form of a periodic input sequence of multisets. It is then shown that P systems with resources are computationally complete (when halting computations are considered) and that, in general, they can generate sequences of multisets that are not even almost periodic (once the constraint of having halting com...