Besozzi, Daniela, Cazzaniga, Paolo, Dugo, Matteo, Pescini, Dario, Mauri, Giancarlo
The chemotactic pathway allows bacteria to respond and adapt to environmental changes, by tuning the tumbling and running motions that are due to clockwise and counterclockwise rotations of their...
Daniela Besozzi, Supervisore Prof, Giancarlo Mauri, Coordinatore Prof, Giovanni Degli Antoni, ...
Computational and modelling power of P systems Tesi di Dottorato di
Ontological Modeling for Neurovascular Disease Studies: Issues in the Adoption of DL (2009)
Gianluca Colombo, Marco Antoniotti, Daniele Merico, Flavio De Paoli, Giancarlo Mauri
We describe the ontological modeling issues encountered in the EU-funded NEU-ROWEB project. The aim of the project is to support association studies in the field of neurovascular medicine,...
Abstract Approximation Algorithms for Protein Folding Prediction (2009)
Giancarlo Mauri, Giulio Pavesit, Antonio Piccolbonif
We present a new polynomial-time algorithm for the pro-tein folding problem in the two-dimensional HP model in-troduced by Dill [l], which has been recently proved to be NP-hard [2]. Our algorithm...
Weeder Web: a Web-Based Tool for the Discovery of Transcription Factor Binding Sites (2008)
Giulio Pavesi, Giancarlo Mauri, Graziano Pesole
Understanding the complex mechanisms governing basic biological processes requires the characterization of regulatory motifs modulating gene expression at transcriptional and post-transcriptional...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2008)
Bmc Bioinformatics, Manuela Helmer-citterich, Rita Casadio, Ro Guffanti, Giancarlo Mauri, Luciano Milanesi, ...
Scuola Di, Dottorato Di, Ricerca In Scienze, Coordinatore Prof, Giancarlo Mauri, Federico Cabitza, ...
To my parents,
Using Subtree Crossover Distance to Investigate Genetic Programming Dynamics (2008)
Leonardo Vanneschi, Steven Gustafson, Giancarlo Mauri
Abstract. To analyse various properties of the search process of genetic programming it is useful to quantify the distance between two individuals. Using operator-based distance measures can make...
Giulio Pavesi is assistant professor of Computer Science at the (2008)
Giancarlo Mauri, Graziano Pesole
research interests are mainly focused on bioinformatics in general, and regulatory motif discovery in particular. He also works on discrete models of complex systems.
Andrea Splendiani, Rue Auguste Blanqui, Viale Della Vittoria, Skype Sergentpeng, Supervisor Prof, Giancarlo Mauri
www.ea3888.univ-rennes1.fr
Frequency Membrane Systems (2008)
Davide Molteni, Claudio Ferretti, Giancarlo Mauri
Summary. We define a model of membrane system where each membrane is clocked independently from the others, in the sense that every derivation step is applied without a global synchronization. The...
Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri
Communicated by The Maximum Isomorphic Agreement Subtree (MIT) problem is one of the simplest versions of the Maximum Interval Weight Agreement Subtree method (MIWT) which is used to compare...
Approximation of Optimization Problems and Learnability (2007)
Bruno Apolloni, Claudio Ferretti, Giancarlo Mauri
We study optimization problems in a context derived from the studies about computational learnability. While an optimization problem can be hard to solve, it could be easy to approximate. But when...
Identifying Regular Languages over Partially-Commutative Monoids (2007)
Partially-commutative Monoids, Claudio Ferretti, Giancarlo Mauri
. We define a new technique useful in identifying a subclass of regular languages defined on a free partially commutative monoid (regular trace languages), using equivalence and membership queries....
Identifying Regular Languages over Partially-Commutative Monoids (2007)
Partially-commutative Monoids, Claudio Ferretti, Giancarlo Mauri
We define a new technique useful in identifying a subclass of regular languages defined on a free partially commutative monoid (regular trace languages), using equivalence and membership queries. Our...
Labels Transformations and New Distance Measures (2007)
Note Trasformazioni, Bruno Apolloni, Claudio Ferretti, Giancarlo Mauri
In this note we use a formalism recently presented, which extends the PAC protocol to real valued functions, in order to obtain new bounds on the number of examples needed to learn functions,...
Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri
Communicated by The Maximum Isomorphic Agreement Subtree (MIT) problem is one of the simplest versions of the Maximum Interval Weight Agreement Subtree method (MIWT) which is used to compare...
Shunsuke Inenaga, Hiromasa Hoshino, Ayumi Shinohara, Setsuo Arikawa, Giancarlo Mauri, Giulio Pavesi
2 1
Grammars Working on Layered Strings (2007)
Paolo Bottoni, Giancarlo Mauri, Piero Mussio, Gheorghe Paun, Turku Centre, Computer Science
We consider first an operation with strings and languages suggested by superposed windows on the computer screen (as well as by cryptographic systems of Richelieu type): we assume that the strings...
Paolo Bottoni, Giancarlo Mauri, Piero Mussio, Gheorghe Paun, Turku Centre, Computer Science
We introduce a computability model-- called shape grammar-- based on adjoining polyominoes. A computation in a shape grammar is correct when: (1) it starts by using a specified polyomino; (2) it ends...
Pandini, Alessandro, Mauri, Giancarlo, Bordogna, Annalisa, Bonati, Laura
Aim of this work is to assess the informativeness of protein dynamics in the detection of similarities among distant homologous proteins. To this end, an approach to perform large-scale comparisons...
The Genopolis Microarray Database (2007)
Splendiani, Andrea, Brandizi, Marco, Even, Gael, Beretta, Ottavio, Pavelka, Norman, Pelizzola, Mattia, ...
Abstract Background Gene expression databases are key resources for microarray data management and analysis and the importance of a proper annotation of their content is well understood. Public...
Biowep: a workflow enactment portal for bioinformatics applications (2007)
Romano, Paolo, Bartocci, Ezio, Bertolini, Guglielmo, De Paoli, Flavio, Marra, Domenico, Mauri, Giancarlo, ...
Abstract Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and...
BioMed Central Open Access (2007)
Bmc Bioinformatics, Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Flavio De Paoli, Domenico Marra, ...
Biowep: a workflow enactment portal for bioinformatics applications
Mauri: Solving numerical NP-complete problems with spiking neural P systems (2007)
Alberto Leporati, Claudio Z, Claudio Ferretti, Giancarlo Mauri
Summary. Starting from an extended nondeterministic spiking neural P system that solves the Subset Sum problem in a constant number of steps, recently proposed in a previous paper, we investigate how...
BioMed Central Research The Genopolis Microarray Database (2007)
Bmc Bioinformatics, Andrea Splendiani, Marco Br, Gael Even, Ottavio Beretta, Norman Pavelka, ...
© 2007 Splendiani et al; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License
Pavesi, Giulio, Mereghetti, Paolo, Zambelli, Federico, Stefani, Marco, Mauri, Giancarlo, Pesole, Graziano
Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
Abstract The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005,...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....
Circular splicing and regularity (2004)
Bonizzoni, Paola, Felice, Clelia De, Mauri, Giancarlo, Zizza, Rosalba
Giulio Pavesi, Paolo Mereghetti, Giancarlo Mauri, Graziano Pesole
One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the...
Pavesi, Giulio, Mauri, Giancarlo, Stefani, Marco, Pesole, Graziano
The recent interest sparked due to the discovery of a variety of functions for non-coding RNA molecules has highlighted the need for suitable tools for the analysis and the comparison of RNA...
Pavesi, Giulio, Mereghetti, Paolo, Mauri, Giancarlo, Pesole, Graziano
One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the...
In silico representation and discovery of transcription factor binding sites (2004)
Pavesi, Giulio, Mauri, Giancarlo, Pesole, Graziano
Understanding the complex mechanisms governing basic biological processes requires the characterisation of regulatory motifs modulating gene expression at transcriptional and posttranscriptional...
On-Line Construction of Compact Directed Acyclic Word Graphs (2001)
Shunsuke Inenaga, Hiromasa Hoshino, Ayumi Shinohara, Masayuki Takeda, Setsuo Arikawa, Giancarlo Mauri, ...
A Compact Directed Acyclic Word Graph (CDAWG) is a space--e#cient text indexing structure, that can be used in several di#erent string algorithms, especially in the analysis of biological sequences.
An algorithm for finding signals of unknown length in DNA sequences (2001)
Pavesi, Giulio, Mauri, Giancarlo, Pesole, Graziano
Pattern discovery in unaligned DNA sequences is a challenging problem in both computer science and molecular biology. Several different methods and techniques have been proposed so far, but in most...
Approximation Algorithms For Protein Folding Prediction (1999)
Giancarlo Mauri, Antonio Piccolboni, Giulio PAVESI
We present a new polynomial-time algorithm for the protein folding problem in the two-dimensional HP model introduced by Dill [1], which has been recently proved to be NP-hard [2]. The model...
Experimenting an approximation algorithm for the LCS (1998)
Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri
The problem of finding the longest common subsequence (lcs) of a given set of sequences over an alphabet # occurs in many interesting contexts, such as data compression and molecular biology, in...
Bottoni, Paolo, Mauri, Giancarlo, Mussio, Piero, Pãun, Gheorghe
http://www.tucs.fi/Publications/techreports/TR136.php
Grammars Working on Layered Strings (1997)
Bottoni, Paolo, Mauri, Giancarlo, Mussio, Piero, Pãun, Gheorghe
http://www.tucs.fi/Publications/techreports/TR135.php
Identifying Unrecognizable Regular Languages by Queries (1994)
Claudio Ferretti, Giancarlo Mauri
. We describe a new technique useful in identifying a subclass of regular trace languages (defined on a free partially commutative monoid). We extend an algorithm defined by Dana Angluin in 1987 for...
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
Pavesi, Giulio, Mauri, Giancarlo, Stefani, Marco, Pesole, Graziano
The recent interest sparked due to the discovery of a variety of functions for non-coding RNA molecules has highlighted the need for suitable tools for the analysis and the comparison of RNA...
Pavesi, Giulio, Mereghetti, Paolo, Mauri, Giancarlo, Pesole, Graziano
One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the...
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
Pavesi, Giulio, Mereghetti, Paolo, Zambelli, Federico, Stefani, Marco, Mauri, Giancarlo, Pesole, Graziano
Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif...
RNAProfile: an algorithm for finding conserved secondary structure motifs in unaligned RNA sequences
Pavesi, Giulio, Mauri, Giancarlo, Stefani, Marco, Pesole, Graziano
The recent interest sparked due to the discovery of a variety of functions for non-coding RNA molecules has highlighted the need for suitable tools for the analysis and the comparison of RNA...
Pavesi, Giulio, Mereghetti, Paolo, Mauri, Giancarlo, Pesole, Graziano
One of the greatest challenges that modern molecular biology is facing is the understanding of the complex mechanisms regulating gene expression. A fundamental step in this process requires the...
MoD Tools: regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes
Pavesi, Giulio, Mereghetti, Paolo, Zambelli, Federico, Stefani, Marco, Mauri, Giancarlo, Pesole, Graziano
Understanding the complex mechanisms regulating gene expression at the transcriptional and post-transcriptional levels is one of the greatest challenges of the post-genomic era. The MoD (MOtif...
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society
Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...
The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....