108 research outputs found
Integration and analysis of protein-protein and signalling networks to create graph dynamical systems
No full textUnderstanding networks of biological interactions is essential to all life sciences. Nowadays, a large amount of biological information is archived in diverse resources that often contain complementary information. Scientists have to search various data repositories in order to reconstruct, understand and speculate on the steps that lead to specific phenomena. The amount of digitalised interaction data has grown to such an extent that it is now advisable to integrate different kinds of data through computational means. Bioinformatics can offer tools and strategies to manipulate such information automatically. In order to address the need of integrating and retrieving structured protein interaction data, I implemented a new resource called mentha, which merges the data archived in different repositories in order to assemble large networks of protein interactions. This resource has low data redundancy and it assigns a reliability score to each interaction. mentha can be seen as a workbench to assemble custom protein-protein interaction networks. Furthermore, I contributed to the development of a new resource that archives manually curated signalling information. I investigated the possibility of exploiting the information contained in mentha to assemble signalling networks. I analysed strategies to automatically link proteins of interest with other relevant proteins in order to create a backbone to build graph dynamical systems that can represent biological signalling networks. I conclude that manually curated signalling information can be integrated with information inferred from interactomes where signal direction can be predicted using orientation algorithms, while signal effect can be derived from RNA interference screenings. Finally, I analysed the resulting biological models as graph dynamical systems. I transformed the topology of a signed oriented biological network into transition boolean functions and, using boolean formalism, I analysed dynamical networks to simulate biological behaviours
A Wikipedia Based Map of Science
No full text15th January 2020 - A Map of Science. v. 1.0 Description:A network which shows the similarities among different branches of science. It's based on Wikipedia pages in outline of natural, formal, social and applied sciences plus Data Science, which is not yet included (18 Jan. 2020). All pages called "Outline of X" were ignored. Pages are pre processed to get the main content with regular expressions. Stop words removal, lemmatization with WordNetLemmatizer in NLTK. Edges represent cosine similarity and filtered calculating zscore leaving only edges with a zscore > 1.959964 . Isolated nodes were removed.Materials:R, python, igraph, nltk, d3, javascript, html, wikipedia Contact:Alberto Calderone - [email protected]:http://www.sinnefa.com/wikipediasciencemap/</div
mentha: a resource for browsing integrated protein-interaction networks
No full textAbout mentha
mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome".
mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global netowrk that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users
Suplemento Especial La Corte Suprema: 160 años de Jurisprudencia (número completo)
No full textContenido: La Corte Suprema: 160 años de jurisprudencia / Bautista Cañón ; Sofía Calderone.-- “De primera mano”: una conversación con Rodolfo C. Barra / Bautista Cañón ; Sofía Calderone.-- La Corte Suprema desde la mirada de una jurista: un diálogo con María Angélica Gelli / Bautista Cañón ;Sofía Calderone.-- En los pasillos del cuarto piso: una conversación con Pablo G. Hirschmann / Bautista Cañón ;Sofía Calderone.-- De la Corte Suprema a las aulas: una conversación con Santiago Legarre / Bautista Cañón ;Sofía Calderone.-- En los detalles: la Corte Suprema bajo la lupa de Estela B. Sacristán / Bautista Cañón ;Sofía Calderone.-- De cara a la historia: una entrevista con Alfonso Santiago en los 160 años de la Corte Suprema / Bautista Cañón ;Sofía Calderone.-- Semblanza de los primeros jueces de la Corte Suprema /Alberto B. Bianchi.-- La primera sentencia de nuestra Corte Suprema y sus protagonistas / Enrique del Carril.-- El origen del control judicial de constitucionalidad en la Argentina / Manuel José García-Mansilla.-- Nacimiento de la competencia originaria por la materia, /Alberto F. Garay.-- Un legado en tomos: la publicidad de sentencias de la Corte
Suprema de Justicia de la Nación ayer y hoy / Florencia Ratti Mendaña ; Sofía Calderone.-- En disidencia. Historia del voto en soledad en la Corte Suprema / Jerónimo Lau Alberdi.-
The cell-autonomous mechanisms underlying the activity of metformin as an anticancer drug.
No full textThe biguanide drug metformin profoundly affects cell metabolism, causing an impairment of the cell energy balance and triggering a plethora of pleiotropic effects that vary depending on the cellular or environmental context. Interestingly, a decade ago, it was observed that metformin-treated diabetic patients have a significantly lower cancer risk. Although a variety of in vivo and in vitro observations emphasising the role of metformin as anticancer drug have been reported, the underlying mechanisms are still poorly understood. Here, we discuss our current understanding of the molecular mechanisms that are perturbed by metformin treatment and that might be relevant to understand its antitumour activities. We focus on the cell-autonomous mechanisms modulating growth and death of cancer cells
DBATE: database of alternative transcripts expression
No full textThe use of high-throughput RNA sequencing technology (RNA-seq) allows whole transcriptome analysis, providing an unbiased and unabridged view of alternative transcript expression. Coupling splicing variant-specific expression with its functional inference is still an open and difficult issue for which we created the DataBase of Alternative Transcripts Expression (DBATE), a web-based repository storing expression values and functional annotation of alternative splicing variants. We processed 13 large RNA-seq panels from human healthy tissues and in disease conditions, reporting expression levels and functional annotations gathered and integrated from different sources for each splicing variant, using a variant-specific annotation transfer pipeline. The possibility to perform complex queries by cross-referencing different functional annotations permits the retrieval of desired subsets of splicing variant expression values that can be visualized in several ways, from simple to more informative. DBATE is intended as a novel tool to help appreciate how, and possibly why, the transcriptome expression is shaped. DATABASE URL: http://bioinformatica.uniroma2.it/DBATE/
Comparing Alzheimer’s and Parkinson’s diseases networks using graph communities structure
No full textDatasets: communities, networks, enrichments (ZIP available at https://dx.doi.org/10.6084/m9.figshare.2070124 )
SIGNOR: A Database of Causal Relationships Between Biological Entities—A Short Guide to Searching and Browsing
No full textEl caso Dobbs: reflexiones sobre un fallo de fuerte impacto
No full textContenido: A modo de presentación: ¿Nos importa el caso Dobbs? /
Eugenio Luis Palazzo.-- Apuntes al paso sobre el caso Dobbs / Luis María Bandieri.-- "FAL” también está terriblemente equivocado / Pedro J. M.
Andereggen y Rodolfo C. Barra.-- Las fisuras del nuevo derecho antidiscriminatorio: las inquietantes sugerencias del fallo Dobbs para el jurista de hoy / Ursula C. Basset.-- La Corte Suprema de los Estados Unidos devuelve a los estados la facultad de legislar sobre el aborto /Alberto B. Bianchi.-- Un análisis del fallo Dobbs. Activismo judicial, política y federalismo / Ignacio Colombo Murúa.-- Por qué Dobbs no es una decisión “originalista” / Manuel José García Mansilla.-- Una sentencia que renueva el debate / Florencia Ratti Mendaña y Sofía Calderone.-- Back to Blackstone: sentido y límites del stare decisis en Dobbs v. Jackson / Eduardo R. Sodero.-- Entendiendo Dobbs / Alfredo M. Vítolo
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