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245 results on '"Guarracino, Mario Rosario"'

7. Segmenting Dermoscopic Images

Author

Guarracino, Mario Rosario and Maddalena, Lucia

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We propose an automatic algorithm, named SDI, for the segmentation of skin lesions in dermoscopic images, articulated into three main steps: selection of the image ROI, selection of the segmentation band, and segmentation. We present extensive experimental results achieved by the SDI algorithm on the lesion segmentation dataset made available for the ISIC 2017 challenge on Skin Lesion Analysis Towards Melanoma Detection, highlighting its advantages and disadvantages., Comment: 4 pages

Published
2017

10. Network Distances for Weighted Digraphs

Author

Granata, Ilaria, Guarracino, Mario Rosario, Maddalena, Lucia, Manipur, Ichcha, Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Kochetov, Yury, editor, Bykadorov, Igor, editor, and Gruzdeva, Tatiana, editor

Published
2020
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11. HELP: A computational framework for labelling and predicting human common and context-specific essential genes.

Author

Granata, Ilaria, Maddalena, Lucia, Manzo, Mario, Guarracino, Mario Rosario, and Giordano, Maurizio

Subjects
INDIVIDUALIZED medicine, HUMAN genes, PREDICTION models, CELL growth, MULTIOMICS
Abstract

Machine learning-based approaches are particularly suitable for identifying essential genes as they allow the generation of predictive models trained on features from multi-source data. Gene essentiality is neither binary nor static but determined by the context. The databases for essential gene annotation do not permit the personalisation of the context, and their update can be slower than the publication of new experimental data. We propose HELP (Human Gene Essentiality Labelling & Prediction), a computational framework for labelling and predicting essential genes. Its double scope allows for identifying genes based on dependency or not on experimental data. The effectiveness of the labelling method was demonstrated by comparing it with other approaches in overlapping the reference sets of essential gene annotations, where HELP demonstrated the best compromise between false and true positive rates. The gene attributes, including multi-omics and network embedding features, lead to high-performance prediction of essential genes while confirming the existence of essentiality nuances. Author summary: Essential genes (EGs) are commonly defined as those required for an organism or cell's growth and survival. The essentiality is strictly dependent on both environmental and genetic conditions, determining a difference between those considered common EGs (cEGs), essential in most of the contexts considered, and those essential specifically to one or few contexts (context-specific EGs, csEGs). In this paper, we present a library of tools and methodologies to address the identification and prediction of cEGs and csEGs. Furthermore, we attempt to experimentally explore the statement that essentiality is not a binary property by identifying, predicting and analysing an intermediate class between the Essential (E) and Not Essential (NE) genes. Among the multi-source data used to predict the EGs, we found the best attributes combination to capture the essentiality. We demonstrated that the additional class of genes we defined as "almost Essential" shows differences in these attributes from the E and NE genes. We believe that investigating the context-specificity and the dynamism of essentiality is particularly relevant to unravelling crucial insights into biological mechanisms and suggesting new candidates for precision medicine. [ABSTRACT FROM AUTHOR]

Published
2024
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13. The MetaboX library: building metabolic networks from KEGG database

Author

Maiorano, Francesco, Ambrosino, Luca, and Guarracino, Mario Rosario

Subjects
Quantitative Biology - Molecular Networks
Abstract

In many key applications of metabolomics, such as toxicology or nutrigenomics, it is of interest to profile and detect changes in metabolic processes, usually represented in the form of pathways. As an alternative, a broader point of view would enable investigators to better understand the relations between entities that exist in different processes. Therefore, relating a possible perturbation to several known processes represents a new approach to this field of study. We propose to use a network representation of metabolism in terms of reactants, enzyme and metabolite. To model these systems it is possible to describe both reactions and relations among enzymes and metabolites. In this way, analysis of the impact of changes in some metabolites or enzymes on different processes are easier to understand, detect and predict. Results: We release the MetaboX library, an open source PHP framework for developing metabolic networks from a set of compounds. This library uses data stored in Kyoto Encyclopedia for Genes and Genomes (KEGG) database using its RESTful Application Programming Interfaces (APIs), and methods to enhance manipulation of the information returned from KEGG webservice. The MetaboX library includes methods to extract information about a resource of interest (e.g. metabolite, reaction and enzyme) and to build reactants networks, bipartite enzyme-metabolite and unipartite enzyme networks. These networks can be exported in different formats for data visualization with standard tools. As a case study, the networks built from a subset of the Glycolysis pathway are described and discussed. Conclusions: The advantages of using such a library imply the ability to model complex systems with few starting information represented by a collection of metabolites KEGG IDs.

Published
2014

14. Rigidity and flexibility in protein-protein interaction networks: a case study on neuromuscular disorders

Author

Sharma, Ankush, Ferraro, Maria Brigida, Maiorano, Francesco, Blanco, Francesca Del Vecchio, and Guarracino, Mario Rosario

Subjects
Quantitative Biology - Molecular Networks
Abstract

Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing weakness in muscles and disability to perform muscular functions progressively. Different types of mutations in the gene coding translates into defunct proteins cause different neuro-muscular diseases. Defunct protein interactions in human proteome may cause a stress to its neighboring proteins and its modules. We therefore aimed to understand the effects of mutated proteins on interacting partners in different muscular dystrophies utilizing network biology to understand system properties of these MDs subnetworks .We investigated rigidity and flexibility of protein-protein interaction subnetworks associated with causative mutated genes showing high mean interference values in muscular dystrophy. Rigid component related to EEF1A1 subnetwork and members of 14.3.3 protein family formed the core of network showed involvement in molecular function related to protein domain specific binding. CACNA1S and CALM1 showing functionality related to Voltage-dependent calcium channel demonstrated highest flexibility. The interconnected subnets of proteins corresponding to known causative genes having large genetic variants are shared in different muscular dystrophies inferred towards comorbidity in diseases. The studies demonstrates core network of MDs as highly rigid, constituting of large intermodular edges and interconnected hub nodes suggesting high information transfer flow. The core skeleton of the network is organized in protein specific domain binding. This suggests neuro-muscular disorders may initiate due to interruption in molecular function related with the core and its aggression may depend on the tolerance level of the networks.

Published
2014

16. The sbv IMPROVER Systems Toxicology computational challenge: Identification of human and species-independent blood response markers as predictors of smoking exposure and cessation status

Author

Belcastro, Vincenzo, Poussin, Carine, Xiang, Yang, Giordano, Maurizio, Tripathi, Kumar Parijat, Boda, Akash, Balci, Ali Tugrul, Bilgen, Ismail, Dhanda, Sandeep Kumar, Duan, Zhongqu, Gong, Xiaofeng, Kumar, Rahul, Romero, Roberto, Sarac, Omer Sinan, Tarca, Adi L., Wang, Peixuan, Yang, Hao, Yang, Wenxin, Zhang, Chenfang, Boué, Stéphanie, Guarracino, Mario Rosario, Martin, Florian, Peitsch, Manuel C., and Hoeng, Julia

Published
2018
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20. Comparison of Gene Expression Signature Using Rank Based Statistical Inference

Author

Tripathi, Kumar Parijat, Chavan, Sonali Gopichand, Parashuraman, Seetharaman, Piccirillo, Marina, Magliocca, Sara, Guarracino, Mario Rosario, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Angelini, Claudia, editor, Rancoita, Paola MV, editor, and Rovetta, Stefano, editor

Published
2016
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21. A Web Resource on Skeletal Muscle Transcriptome of Primates

Author

Evangelista, Daniela, Avino, Mariano, Tripathi, Kumar Parijat, Guarracino, Mario Rosario, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Angelini, Claudia, editor, Rancoita, Paola MV, editor, and Rovetta, Stefano, editor

Published
2016
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23. The MetaboX Library: Building Metabolic Networks from KEGG Database

Author

Maiorano, Francesco, Ambrosino, Luca, Guarracino, Mario Rosario, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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24. HvDBase: A Web Resource on Hydra Vulgaris Transcriptome

Author

Evangelista, Daniela, Tripathi, Kumar Parijat, Scuotto, Valentina, Guarracino, Mario Rosario, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, Series editor, Pevzner, Pavel, Series editor, Waterman, Michael S., Series editor, Ortuño, Francisco, editor, and Rojas, Ignacio, editor

Published
2015
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36. Supervised Classification Methods for Mining Cell Differences as Depicted by Raman Spectroscopy

Author

Xanthopoulos, Petros, De Asmundis, Roberta, Guarracino, Mario Rosario, Pyrgiotakis, Georgios, Pardalos, Panos M., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Rizzo, Riccardo, editor, and Lisboa, Paulo J. G., editor

Published
2011
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37. Prior Knowledge in the Classification of Biomedical Data

Author

Abbate, Danilo, De Asmundis, Roberta, Guarracino, Mario Rosario, Kacprzyk, Janusz, editor, Borgelt, Christian, editor, González-Rodríguez, Gil, editor, Trutschnig, Wolfgang, editor, Lubiano, María Asunción, editor, Gil, María Ángeles, editor, Grzegorzewski, Przemysław, editor, and Hryniewicz, Olgierd, editor

Published
2010
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41. Application Oriented Brokering in Medical Imaging: Algorithms and Software Architecture

Author

Guarracino, Mario Rosario, Laccetti, Giuliano, Murli, Almerico, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Sloot, Peter M. A., editor, Hoekstra, Alfons G., editor, Priol, Thierry, editor, Reinefeld, Alexander, editor, and Bubak, Marian, editor

Published
2005
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45. Adversarial attacks on graph-level embedding methods: a case study

Author

Maurizio, Giordano, Lucia, Maddalena, Mario, Manzo, and Guarracino, Mario Rosario

Subjects
Graph embedding, Adversarial attacks, Adversarial machine learning, Graph classification, Adversarial attacks, Adversarial machine learning, Graph embedding, Graph neural networks, Graph classification, Graph neural networks
Published
2022

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