Papers by Michele Finelli
Nucleic Acids Research, 2011
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and ... more Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256 939 protein variants from 17 191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPIanchor propeptides, transmembrane and coiledcoil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www .caspur.it/ASPicDB/.
We apply the two di erent deÿnitions of chaos given by Devaney and by Knudsen for general discret... more We apply the two di erent deÿnitions of chaos given by Devaney and by Knudsen for general discrete time dynamical systems (DTDS) to the case of elementary cellular automata, i.e., 1-dimensional binary cellular automata with radius 1. A DTDS is chaotic according to the Devaney's deÿnition of chaos i it is topologically transitive, has dense periodic orbits, and it is sensitive to initial conditions. A DTDS is chaotic according to the Knudsen's deÿnition of chaos i it has a dense orbit and it is sensitive to initial conditions. We enucleate an easy-to-check property (left or rightmost permutivity) of the local rule associated with a cellular automaton which is a su cient condition for D-chaotic behavior. It turns out that this property is also necessary for the class of elementary cellular automata. Finally, we prove that the above mentioned property does not remain a necessary condition for chaoticity in the case of non elementary cellular automata.
This paper is a full and more detailed presentation of the work of Finelli and Marchignoli [8]. T... more This paper is a full and more detailed presentation of the work of Finelli and Marchignoli [8]. The reason why we started investigating game semantics is whether it is possible to use the game model of Abramsky, Jagadeesan and Malacaria (AJM games, for short), which has been shown suitable to model Classical Linear Logic [6] and a functional language like PCF [1], to model a concurrent language. The answer that we gave in the previous work is that the native AJM game model is not suited to model the message passing paradigm of concurrency, but it is possible to modify their definitions in a conservative way so that it is possible to build a categorical model of a CCS-like process algebra whose games are an extension of AJM games. The main novelty with respect to the existing game categories [1, 6, 14], is the relaxation of the constraint that players should alternate: the constraint we impose is that the players should alternate only in a round of the game, that is, every sequence of an odd and of an even move can not be played by the same player, but we are free to choose if the first should be the Player or the Opponent (the Player / Opponent terminology is standard in game semantics to denote the two players of the game). Next, in our model, each move is associated with two new attributes: its value and its name. The value intuitively captures what it is carried by a channel, where the name is the semantic analogue of the channel: players alternate only with respect to the names of the moves (i.e. you are not allowed to play moves with different names within the same round), this means that the communication between two processes on a given channel is issued by two moves with same name, taken by different players. We proceed as follows. In Section 1 the basic definitions about games are introduced and some basic property is stated. Section 2 introduces the category of games we work with and a particular construction-the exponential game-which is responsible for the modeling of a-calculus like replication operator. The application of the category as a denotational semantics framework for a process algebra is achieved in Section 3 where a simple process algebra is introduced. Conclusions, work in progress and future developments are in Section 4.
Lecture Notes in Computer Science, 1997
We apply the definition of chaos given by Devaney for discrete time dynamical systems to the case... more We apply the definition of chaos given by Devaney for discrete time dynamical systems to the case of elementary cellular automata, i.e., 1-dimensional binary cellular automata with radius 1. A discrete time dynamical system is chaotic according to the Devaney's definition of chaos if it is topologically transitive, is sensitive to initial conditions, and has dense periodic orbits. We enucleate an easy-to-check property of the local rule on which a cellular automaton is based which is a necessary condition for chaotic behavior. We prove that this property is also sufficient for a large class of elementary cellular automata. The main contribution of this paper is the formal proof of chaoticity for many non additive elementary cellular automata. Finally, we prove that the above mentioned property does not remain a necessary condition for chaoticity in the case of non elementary cellular automata.
Theoretical Computer Science, 2000
We apply the two di erent deÿnitions of chaos given by Devaney and by Knudsen for general discret... more We apply the two di erent deÿnitions of chaos given by Devaney and by Knudsen for general discrete time dynamical systems (DTDS) to the case of elementary cellular automata, i.e., 1-dimensional binary cellular automata with radius 1. A DTDS is chaotic according to the Devaney's deÿnition of chaos i it is topologically transitive, has dense periodic orbits, and it is sensitive to initial conditions. A DTDS is chaotic according to the Knudsen's deÿnition of chaos i it has a dense orbit and it is sensitive to initial conditions. We enucleate an easy-to-check property (left or rightmost permutivity) of the local rule associated with a cellular automaton which is a su cient condition for D-chaotic behavior. It turns out that this property is also necessary for the class of elementary cellular automata. Finally, we prove that the above mentioned property does not remain a necessary condition for chaoticity in the case of non elementary cellular automata.
Nucleic Acids Research, 2005
TRAMPLE (http://gpcr.biocomp.unibo.it/biodec/) is a web application server dedicated to the detec... more TRAMPLE (http://gpcr.biocomp.unibo.it/biodec/) is a web application server dedicated to the detection and the annotation of transmembrane protein sequences. TRAMPLE includes different state-ofthe-art algorithms for the prediction of signal peptides, transmembrane segments (both beta-strands and alpha-helices), secondary structure and fast fold recognition. TRAMPLE also includes a complete content management system to manage the results of the predictions. Each user of the server has his/ her own workplace, where the data can be stored, organized, accessed and annotated with documents through a simple web-based interface. In this manner, TRAMPLE significantly improves usability with respect to other more traditional web servers.
Nucleic Acids Research, 2006
The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several di... more The annotation efforts of the BIOSAPIENS European Network of Excellence have generated several distributed annotation systems (DAS) with the aim of integrating Bioinformatics resources and annotating metazoan genomes (http://www.biosapiens. info). In this context, the PONGO DAS server (http:// pongo.biocomp.unibo.it) provides the annotation on predictive basis for the all-alpha membrane proteins in the human genome, not only through DAS queries, but also directly using a simple web interface. In order to produce a more comprehensive analysis of the sequence at hand, this annotation is carried out with four selected and high scoring predictors: TMHMM2.0, MEMSAT, PRODIV and ENSEMBLE1.0. The stored and pre-computed predictions for the human proteins can be searched and displayed in a graphical view. However the web service allows the prediction of the topology of any kind of putative membrane proteins, regardless of the organism and more importantly with the same sequence profile for a given sequence when required. Here we present a new web server that incorporates the state-of-the-art topology predictors in a single framework, so that putative users can interactively compare and evaluate four predictions simultaneously for a given sequence. Together with the predicted topology, the server also displays a signal peptide prediction determined with SPEP. The PONGO web server is available at http://pongo. biocomp.unibo.it/pongo.
Nucleic Acids Research, 2011
Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and ... more Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256 939 protein variants from 17 191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPIanchor propeptides, transmembrane and coiledcoil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www .caspur.it/ASPicDB/.
Computing Research Repository - CORR, 2005
Many computer-basedauthentication schemata are based on pass- words. Logging on a computer, readi... more Many computer-basedauthentication schemata are based on pass- words. Logging on a computer, reading email, accessing content on a web server are all examples of applications where the identification of the user is usually accomplished matching the data provided by the user with data known by the application. Such a widespread approach relies on some assumptions, whose satisfaction is of foremost importance to guarantee the robustness of the solution. Some of these assumptions, like having a "secure" chan- nel to transmit data, or having sound algorithms to check the correct- ness of the data, are not addressed by this paper. We will focus on two simple issues: the problem of using adequate passwords and the problem of managing passwords. The proposed solution, the pathword, is a method that guarantees: • that the passwords generated with the help of a pathword are adequate (i.e. that they are not easy to guess), • that managing pathwords is more user friendly than managing...
Journal of Complexity, 1998
Bioinformatics, 2003
Motivation: A problem in predicting the topography of transmembrane proteins is the optimal local... more Motivation: A problem in predicting the topography of transmembrane proteins is the optimal localization of the transmembrane segments along the protein sequences, provided that each residue is associated with a propensity of being or not being included in the transmembrane protein region. From previous work it is known that postprocessing of propensity signals with suited algorithms can greatly improve the quality and the accuracy of the predictions. In this paper we describe a general dynamic programming-like algorithm (MaxSubSeq, Maximal Sub-Sequence) specifically designed to optimize the number and length of segments with constrained length in a given protein sequence. Previous application of our algorithm, has proved its effectiveness in the optimization task of both neural network and hidden Markov models output, and in this paper we present the detailed description of MaxSubSeq. Results: We describe the application of MaxSubSeq to the location of both helical and beta strand transmembrane segments, optimizing the outputs derived with different predictive algorithms. For all-alpha transmembrane proteins we use both the standard Kyte-Doolittle (KD) hydropathy scale and the TMHMM predictor (http://www.cbs.dtu.dk/). Using a set of 188 well characterized membrane proteins, MaxSubSeq nearly doubles the correct location of transmembrane segments as compared to the standard KD hydrophobicity plot, reaching 51% accuracy. If MaxSubSeq is used to optimize the TMHMM method the accuracy increases from 68 to 72%. When used to regularize the prediction of beta transmembrane strands, obtained using both a neural network and a HMM based predictors, MaxSubSeq increases the accuracy per protein up to 72 and 73% respectively.
A problem in predicting the topography of transmembrane proteins is the optimal localisation of t... more A problem in predicting the topography of transmembrane proteins is the optimal localisation of the transmembrane segments along the protein sequences, provided that each residue is associated with a propensity of being or not included in the transmembrane protein region. From previous work it is known that post-processing of propensity signals with suited algorithms can greatly improve the quality and the accuracy of the predictions. In this paper we describe a general dynamic programming-like algorithm (MaxSubSeq, Maximal SubSequence) specifically designed to optimise the number and length of segments with constrained length in a given protein sequence. Our algorithm is devised to be used independently of the predictive method
Uploads
Papers by Michele Finelli