PathExpand: Extending biological pathways using molecular interaction networks

We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes. Finally, these extended pathways and processes are used to analyze their enrichment in cancer mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes

Modernidad, Diseño Urbano y Utopía: Notas sobre el fundamento político de las acciones de Remodelación Urbana en Santiago. El caso de CORMU 1966-1973. Primera parte / Modernity, Urban Design and Utopia: Notes on the political basis of the shares of Urban Renewal in Santiago. CORMU 1966-1973. (Part One)

Se intenta responder sobre lo que se instala en Chile, con la Corporación de Mejoramiento Urbano CORMU, en el período 1965 –1976, y sobre las formalizaciones conceptuales y prácticas técnicas que se desarrollan, constituidas bajo el designio de “mejoramiento urbano”, al interior del aparato político-administrativo del Estado chileno? Los autores suponen que, en virtud de una coyuntura histórica, emerge en el marco de la cultura urbanística y prácticas técnicas del Estado, una nueva modalidad de trato con el desarrollo urbano. Se incorporan con primacía, por sobre los planes urbanísticos, los proyectos de arquitectura urbana y con ello se reinstala como principio el concepto de proyecto urbano. En este contexto emerge una cultura profesional que había tenido hasta entonces escaso protagonismo en las prácticas institucionales del dominio público nacional: el "Diseño Urbano"./This is a response to the Corporación de Mejoramiento Urbano CORMU and what this corporation accomplished from 1965 to 1976, and the conceptual formalizations and the technical practices that are developed as "urban upgrade" within the political and administrative spheres of the State of Chile. The authors conclude that because of the historical moment, within the urban cultural ambit and the technical practices of the State a new way of dealing with urban development is developed. Urban Architectural Projects become more important than Urban Plans thus the concept of Urban Projects becomes a principle. This is when Urban Design becomes important as a profession within public institutions in Chile

Deep and cognitive learning applied to Precision Medicine: the initial experiments linking (epi)genome to phenotypes-disease characteristics

Present-day era of Big Data provides the unique opportunity to develop innovative approaches for data analysis to find new insights into specialized fields of biomedical research such as Precision Medicine [1]. Precision Medicine is defined as the integration of molecular research with clinical data in order to deliver better diagnoses and treatments tailored to the individual characteristics of each patient. Advanced analysis of health related data that is specific to a given individual must focus on both clinical information (e.g. clinical reports, medical images, patient histories) and biological data (e.g. gene and protein sequences, functions and pathways). This wealth of information has the potential to inspire systematic ways of making sense from the massive and heterogeneous stream of data and providing a unified view. In the regards, Deep Learning (DL) [2] and Cognitive Computing (CC) [3] are two branches of Artificial Intelligence (AI) representing convenient choices to tackle the problem of Big Data integration for Precision Medicine. DL comprises several machine learning techniques modeling multiple representations of data through many layers of nonlinear processing units. CC is a cross-disciplinary technology for adaptive and contextual knowledge representation and reasoning through sophisticated analytics aiming to mimic human learning mechanisms

The success (or not) of HUGO nomenclature

Current usage of gene nomenclature is ambiguous and impairs the efficient handling of scientific information. Therefore it is important to propose guidelines to deal with this problem. This study attempts to evaluate the success of HUGO nomenclature for human genes. The results indicate that HUGO guidelines are not supported by the scientific community

Text-mining and information-retrieval services for molecular biology

Text-mining in molecular biology - defined as the automatic extraction of information about genes, proteins and their functional relationships from text documents - has emerged as a hybrid discipline on the edges of the fields of information science, bioinformatics and computational linguistics. A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators

Patient dossier: healthcare queries over distributed resources

As with many other aspects of the modern world, in healthcare, the explosion of data and resources opens new opportunities for the development of added-value services. Still, a number of specific conditions on this domain greatly hinders these developments, including ethical and legal issues, fragmentation of the relevant data in different locations, and a level of (meta)data complexity that requires great expertise across technical, clinical, and biological domains. We propose the Patient Dossier paradigm as a way to organize new innovative healthcare services that sorts the current limitations. The Patient Dossier conceptual framework identifies the different issues and suggests how they can be tackled in a safe, efficient, and responsible way while opening options for independent development for different players in the healthcare sector. An initial implementation of the Patient Dossier concepts in the Rbbt framework is available as open-source at https://github.com/mikisvaz and https://github.com/Rbbt-Workflows.This work has received funding from the Elixir-Excelerate project, from the European Union's Horizon 2020 Research and Innovation Programme, under grant agreement N. 676559, and from Plataforma de Recursos Biomoleculares y Bioinformáticos PT13/0001/0030. Additional support came from the Lenovo - BSC Master Collaboration Agreement (2015) and from the IBM-BSC Deep Learning Centre (2016). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer ReviewedPostprint (published version