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151. Large-scale annotation of proteins with labelling methods

Author

Casadio, R., Martelli, P. L., Savojardo, C., Fariselli, P., R. Casadio, P. L. Martelli, C. Savojardo, and P. Fariselli

Subjects
Proteomic, Structure of biomolecule, fuzzy logic, artificial intelligence, Neural network
Abstract

We revise a major important problem in bioinformatics: how to annotate protein sequences in the genomic era and all the solutions that have been described by implementing tools based on labelling methods. In this paper we mainly focus on our own work and the theoretical methods that are popular in the field of biosequence analysis in modern molecular biology. We will also review a recent application from our group that largely improves on the topology prediction of disulfide bonds in proteins from Eukaryotic organisms.

Published
2012

152. The LIBI Grid Platform an International Laboratory for Bioinformatics

Author

Mirto, M., Epicoco, I., Fiore, S., Cafaro, M., Ferramosca, A., Zara, V., Scioscia, ALOISIO G SCIOSCIA G. ALOISIO G., Leo, P., Donvito, G., Cuscela, G., Maggi, G., Pierro, A., Falciano, F., Rossi, E., Castrignano', T., Fariselli, P., Fronza, R., Margara, L., Montanucci, L., Martelli, P. L., Rossi, I., Vassura, M., DI LENA, P., Casadio, R., Anselmo, A., Grillo, G., Horner, D., Licciulli, F., Liuni, S., Gisel, A., Mignone, F., Pavesi, G., Pesole, G., Picardi, E., Piccolo, V., Re, M., Saccone, C., Santamaria, M., Vicario, S., Zambelli, F., M. Mirto, I. Epicoco, S. Fiore, M. Cafaro, A. Ferramosca, V. Zara, G. Aloisio G. Scioscia, P. Leo, G. Donvito, G. Cuscela, G. Maggi, A. Pierro, F. Falciano, E. Rossi, T. Castrignanò, P. Fariselli, R. Fronza, L. Margara, L. Montanucci, P. L. Martelli, I. Rossi, M. Vassura, P. Di Lena, R. Casadio, A. Anselmo, G. Grillo, D. Horner, F. Licciulli, S. Liuni, A. Gisel, F. Mignone, G. Pavesi, G. Pesole, E. Picardi, V. Piccolo, M. Re, C. Saccone, M. Santamaria, S. Vicario, and F. Zambelli

Abstract

The International Laboratory of BioInformatics (LIBI - www.libi.it) aims at setting up of an advanced Bioinformatics and Computational Biology Laboratory, focusing on the central activities of basic and applied research in modern Biology and Biotechnologies. The main activities include the construction and the maintenance of general genomic, proteomic and transcriptomic databases (e.g. ENSEMBL) as well as specialized databases developed by LIBI partners (e.g. MitoRes, UTRdb, UTRSite, ASPicDB, CSTdb, etc.); the design and implementation of new algorithms and software for the analysis of genomes and their expression products and for the prediction of the structure of proteins; the development of a Grid Problem Solving Environment in order to exploit the distributed computational infrastructure.

Published
2008

153. The Graph Theory and the Protein Universe: selecting the close-to-the-native structures within a model decoy set

Author

Casadio, R., Margara, L., Fariselli, P., Vassura, M., CASTELLANI ET AL, R. Casadio, L. Margara, P. Fariselli, and M. Vassura

Abstract

Proteins are complex systems as the Anfinsen’s thermodynamic hypothesis highlights. Their complexity hampers an analytical solution to the protein folding problem, so to say how to predict the tertiary structure of the proteins from the residue sequence or primary structure. However nature presently provides us with over 40000 protein structures known with atomic resolution suggesting that possibly heuristic methods may help us in unraveling protein folding. Indeed several methods have been described to address this point: how to generalize from known examples of folding predictive methods suited to compute the three-dimensional protein structure. This is stressed to the point the automatic servers nowadays may generate 3D structures as soon as genomes are sequenced contributing several millions of putative structures that however need to be validated in most of the cases. The question then arises: how to select good structures among many different models generated by different methods starting from the same protein sequence? In protein structure prediction potential energy functions are adopted both to compute “ab initio” models and to score threading candidates. It is however known that small intrinsic errors in these models can lead to a high number of erroneous structures endowed with values of conformational energy lower than the native one (Filkenstein 1997). Decreasing the number of false candidates among the best scoring structures is therefore a major goal in protein structure prediction, and several types of energy functions and decoy sets have been described in order to address this issue (Park et al., 1997; Felts et al., 2002; Hardin et al., 2002; Tsai et al., 2003). The notion that the protein native structure is endowed with the lowest free energy with respect to all the other conformations may help us to develop a filter procedure. A very stringent test for reliability is when the adopted energy function is able to compute lower conformational energies for native and near native conformations with respect to non-native ones. To test the capabilities of new scoring functions, sets of “good decoys” were developed (Tsai et al. (2003)). These sets routinely contain protein-like structures for a wide variety of different structural domains to avoid over-fitting; including conformations close to the native structure (RMSD

Published
2008

156. Equipment, staffing, and provision of radiotherapy in Lombardy, Italy: Results of three surveys performed between 2012 and 2016

Author

Palazzi, Mauro F., Soatti, Carlo, Jereczek-Fossa, Barbara A., Cazzaniga, Luigi F., Antognoni, Paolo, Gardani, Gianstefano, Amadori, Marcello, Baio, Ambrogia, Beltramo, Giancarlo, Bignardi, Mario, Bracelli, Stefano, Buffoli, Alberto, Castiglioni, Simona, Catalano, Gianpiero, Di Muzio, Nadia, Fallai, Carlo, Fariselli, Laura, Frata, Paolo, Gramaglia, Alberto, Italia, Corrado, Ivaldi, Giovanni, Lombardi, Fabrizio, Magrini, Stefano M., Nava, Simonetta, Sarti, Enrico, Scandolaro, Luciano, Scorsetti, Marta, Stiglich, Francesco, Tortini, Roberto, Valdagni, Riccardo, Valvo, Francesca, Vavassori, Vittorio, Sbicego, Elena L., Tonoli, Sandro, and Orecchia, Roberto

Abstract

Introduction: Several efforts are being implemented at the European level to measure provision of up-to-date radiation treatments across the continent.Methods: A snapshot survey involving all radiation oncology centers within Lombardy, Italy, was performed in 2012 and repeated in 2014 and 2016, in cooperation with regional governmental officers. Centers were asked to provide detailed information concerning all individual patients being treated on the index day, and to report data on available local resources.Results: We observed an increase in the number of centers and of megavoltage units (MVU) (from 76 to 87, i.e., 8.7 MVU per million inhabitants in 2016). Mean number of MVU per center was 2.5. Average age of MVU increased from 5.3 to 7.5 years and patients on the waiting list also increased. Conformal 3D radiotherapy (RT) treatments decreased from 56% to 42% and were progressively replaced by intensity-modulated RT treatments (from 39% to 49%). Waiting times were overall satisfactory. Radiation oncologists treated on average 152 and radiation therapists 100 RT courses per year. Average reimbursement per course was €4,879 (range €2,476–€8,014).Conclusions: The methodology of snapshot survey proved feasible and provided valuable information about radiation oncology provision and accessibility in Lombardy.

Published
2018
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160. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

Author

Martelli, P, D'Antonio, M, Bonizzoni, P, Castrignanò, T, D'Erchia, A, D'Onorio De Meo, P, Fariselli, P, Finelli, M, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Rizzi, R, Rossi, I, Valletti, A, Zauli, A, Zambelli, F, Casadio, R, Pesole, G, Martelli, PL, D'Erchia, AM, Pesole, G., BONIZZONI, PAOLA, RIZZI, RAFFAELLA, Martelli, P, D'Antonio, M, Bonizzoni, P, Castrignanò, T, D'Erchia, A, D'Onorio De Meo, P, Fariselli, P, Finelli, M, Licciulli, F, Mangiulli, M, Mignone, F, Pavesi, G, Picardi, E, Rizzi, R, Rossi, I, Valletti, A, Zauli, A, Zambelli, F, Casadio, R, Pesole, G, Martelli, PL, D'Erchia, AM, Pesole, G., BONIZZONI, PAOLA, and RIZZI, RAFFAELLA

Abstract

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 256939 protein variants from 17191 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, GPI-anchor propeptides, transmembrane and coiled-coil 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/.

Published
2011

163. The cavernous sinus meningiomas’ dilemma: Surgery or stereotactic radiosurgery?

Author

Fariselli, Laura, Biroli, Antonio, Signorelli, Antonio, Broggi, Morgan, Marchetti, Marcello, and Biroli, Francesco

Abstract

Despite the advances in techniques and technologies, the management of cavernous sinus (CS) meningiomas still remains a challenge for both neurosurgeons and radiation oncologists. On the other hand, the improvement of the anatomical knowledge and the microsurgical techniques together with diffusion of radiosurgery are currently changing the treatment strategy, opening new perspectives to the patients which are suffering from such lesions. The authors reviewed here the literature data. A multidisciplinary treatment algorithm is also proposed. [ABSTRACT FROM AUTHOR]

Published
2016
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165. PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

Author

Amico, M., Finelli, M., Rossi, I., Zauli, A., Elofsson, A., Viklund, H., Heijne, G. von, Joes, D., Krogh, A., Fariselli, P., Luigi, Martelli P., Casadio, R., Amico, M., Finelli, M., Rossi, I., Zauli, A., Elofsson, A., Viklund, H., Heijne, G. von, Joes, D., Krogh, A., Fariselli, P., Luigi, Martelli P., and Casadio, R.

Abstract

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://pongo.biocomp.unibo.it/pongo.

Published
2006

167. Short Course Radiotherapy Concomitant with Temozolomide in GBM Patients: A Phase II Study

Author

Fariselli, Laura, Cuppini, Lucia, Gaviani, Paola, Marchetti, Marcello, Pinzi, Valentina, Milanesi, Ida, Simonetti, Giorgia, Tramacere, Irene, DiMeco, Francesco, Salmaggi, Andrea, and Silvani, Antonio

Abstract

Purpose Despite recent advances, the prognosis of glioblastoma (GBM) remains poor. The aim of this study was to assess the efficacy and tolerability of multiple daily fraction radiotherapy performed with multiple temozolomide (TMZ) administrations in newly diagnosed patients with GBM.Methods This trial was a prospective, open-label, monocentric, nonrandomized, single arm, phase II study. The primary endpoint was the proportion of progression-free patients at 12 months, and the secondary endpoints were overall survival (OS) and toxicity. Thirty-five patients underwent two radiotherapy courses concomitant with TMZ after surgery. At each course, radiation was delivered 3 times daily, 2 Gy/fraction, for 5 consecutive days, and the total dose was 60 Gy; concurrent TMZ was administered in a total dose of 150-200 mg/m2/day.Results The primary endpoint failed to be applied; Macdonald criteria could be used in 16 (46%) patients with local or intracerebral recurrence (group A). In 12 patients, due to suspicion of radiation necrosis vs recurrence, Macdonald criteria were not applied (group B). The OS was 22 months, and OS probabilities at 12, 18, and 24 months were 82%, 59%, and 44%, respectively. Hematologic toxicities generally did not exceed grade 2. The quality of life and cognitive functioning did not significantly change between baseline and the first follow-up. In the multivariate analysis, necrosis and pseudoprogression were significant prognostic factors of OS.Conclusions To improve local control and OS, a more aggressive treatment schedule should be explored. The related higher necrosis risk and its implications regarding local control deserve further investigation.

Published
2017
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171. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

Author

Martelli, P. L., primary, D'Antonio, M., additional, Bonizzoni, P., additional, Castrignano, T., additional, D'Erchia, A. M., additional, D'Onorio De Meo, P., additional, Fariselli, P., additional, Finelli, M., additional, Licciulli, F., additional, Mangiulli, M., additional, Mignone, F., additional, Pavesi, G., additional, Picardi, E., additional, Rizzi, R., additional, Rossi, I., additional, Valletti, A., additional, Zauli, A., additional, Zambelli, F., additional, Casadio, R., additional, and Pesole, G., additional

Published
2010
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184. The Pros and Cons of Predicting Protein Contact Maps.

Author

Walker, John M., Zaki, Mohammed J., Bystroff, Christopher, Bartoli, Lisa, Capriotti, Emidio, Fariselli, Piero, Martelli, Pier Luigi, and Casadio, Rita

Abstract

Is there any reason why we should predict contact maps (CMs)? The question is one of the several ‘NP-hard' questions that arise when striving for feasible solutions of the protein folding problem. At some point, theoreticians started thinking that a possible alternative to an unsolvable problem was to predict a simplified version of the protein structure: a CM. In this chapter, we will clarify that whenever problems are difficult they remain at least as difficult in the process of finding approximate solutions or heuristic approaches. However, humans rarely give up, as it is stimulating to find solutions in the face of difficulties. CMs of proteins are an interesting and useful representation of protein structures. These two-dimensional representations capture all the important features of a protein fold. We will review the general characteristics of CMs and the methods developed to study and predict them, and we will highlight some new ideas on how to improve CM predictions. [ABSTRACT FROM AUTHOR]

Published
2008
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185. Thinking the Impossible.

Author

Walker, John M., Bai, Yawen, Nussinov, Ruth, Casadio, Rita, Fariselli, Piero, Martelli, Pier Luigi, and Tasco, Gianluca

Abstract

Structure prediction of proteins is a difficult task as well as prediction of protein-protein interaction. When no homologous sequence with known structure is available for the target protein, search of distantly related proteins to the target may be done automatically (fold recognition/threading). However, there are difficult proteins for which still modeling on the basis of a putative scaffold is nearly impossible. In the following, we describe that for some specific examples, human expertise was able to derive alignments to proteins of similar function with the aid of machine learning-based methods specifically suited for predicting structural features. The manually curate search of putative templates was successful in generating low-resolution threedimensional (3D) models in at least two cases: the human tissue transglutaminase and the alcohol dehydrogenase from Sulfolobus solfataricus. This is based on the structural comparison of the model with the 3D protein structure that became available after prediction. For protein-protein interaction, a knowledge-based method can give predictions of putative interaction patches on the protein surface; this feature may help in adding additional weight to specific nodes in nets of interacting proteins. [ABSTRACT FROM AUTHOR]

Published
2006
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193. Protein Sequence Annotation by Means of Community Detection

Author

Profiti, Giuseppe, Piovesan, Damiano, Martelli, Pier Luigi, Fariselli, Piero, and Casadio, Rita

Abstract

In the postgenomic era different electronic procedures are available for protein sequence annotation, the process of enriching, with structural and functional features, any protein after electronic translation from its correspondent gene or mRNA. The demand of reliable annotation systems is particularly urgent given the volume of genomic data that are daily produced by next generation sequencing machines. In this paper we present a procedure that enhances the annotation performance of the previously described Bologna Annotation Resource (BAR+). BAR is based on clustering of the graphs representing the similarity between a large number of protein sequences and here we apply community detection algorithms to detect subclusters within any graph. When the cluster is endowed with specific Gene Ontology terms associated both to Biological Process and Molecular Function, the application of our procedure allows a fine tuning of the annotation process and generates subclusters where proteins sharing strictly related GO terms are grouped.

Published
2015

195. A European Organisation for Research and Treatment of Cancer Phase III Trial of Adjuvant Whole-Brain Radiotherapy Versus Observation in Patients With One to Three Brain Metastases From Solid Tumors After Surgical Resection or Radiosurgery:...

Author

Soffietti, Riccardo, Kocher, Martin, Abacioglu, Ufuk M., Villa, Salvador, Fauchon, François, Baumert, Brigitta G., Fariselli, Laura, Tzuk-Shina, Tzahala, Kortmann, Rolf-Dieter, Carrie, Christian, Hassel, Mohamed Ben, Kouri, Mauri, Valeinis, Egils, den Berge, Dirk van, Mueller, Rolf-Peter, Tridello, Gloria, Collette, Laurence, and Bottomley, Andrew

Published
2013
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197. The Secret Life of Jewelming Damselflies Calopteryx splendens.

Author

Fariselli, Piero

Abstract

The article features Calopteryx splendens, Europen jewelming damselflies which fly like butterflies and are distinguished for their striking colors, and non-transparent wings. The author discusses aspects of the life cycle of the beautiful insect species, highlighting its feeding, mating, and reproduction behavior. Included are photographs of male and female jewelming damselfies in various mating and ovipositing activities.

Published
2011

199. DOMINICAN REPUBLIC PARADISE PARQUE NACIONAL del ESTE.

Author

Fariselli, Piero

Abstract

The article provides information on the Parque Nacional de Este in the Dominican Republic, considered a paradise teeming with marine habitat and endemic fauna. Details related to the many species of reptilia and amphibians such as the Bufo marinus, anoles, 300 species of insects with spiders like the Haitaian brown tarantula and crustaceans like red rock crabs (Grapsus grapsus ) and whip scorpions are included. The Dominican Republic has reportedly kept a big part of the park intact and the author encourages tourists to see its natural wonders.

Published
2009

200. SPINY ORB-WEAVER SPIDERS.

Author

FARISELLI, PIERO

Abstract

The article focuses on spiny orb-weaver spiders. The two most common genera of this spider are Gasteracantha, which are common in sub-Saharan Africa and southern Asia, and Micrathena, which is found in the New World. These spiders have spines and a general hypothesis by Dr. Herbert W. Levi is that the spines serve as protection against predators. It also helps the spider camouflage in its surroundings. The species construct circular webs for trapping prey. The webs' shape vary in shape and orientation. They are also carnivorous and when it senses vibration on its web, it runs immediately to capture the prey.

Published
2009

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