showing 10 related works from this author
Reactome diagram viewer: data structures and strategies to boost performance
2017
Abstract Motivation Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. Results The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partit…
PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.
2019
Background Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data. Results In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTfu…
VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy
2017
The possibility of integrating viral vectors to become a persistent part of the host genome makes them a crucial element of clinical gene therapy. However, viral integration has associated risks, such as the unintentional activation of oncogenes that can result in cancer. Therefore, the analysis of integration sites of retroviral vectors is a crucial step in developing safer vectors for therapeutic use. Here we present VISMapper, a vector integration site analysis web server, to analyze next-generation sequencing data for retroviral vector integration sites. VISMapper can be found at: http://vismapper.babelomics.org . Because it uses novel mapping algorithms VISMapper is remarkably faster t…
Reactome graph database: Efficient access to complex pathway data
2018
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its qu…
Mutational analysis ofBRCA1andBRCA2in Mediterranean Spanish women with early-onset breast cancer: Identification of three novel pathogenic mutations
2003
In Spain, the contribution of BRCA mutations to the population incidence of early-onset breast cancer was unknown. We carried out a mutational analysis of the BRCA1 and BRCA2 genes in 124 Spanish women diagnosed with breast cancer before the age 41 and who were not selected for a family history of this disease. The genetic study was performed by PCR-SSCP analysis and DNA sequencing. We identified 6 pathogenic BRCA mutations in 7 unrelated probands (5.6%; 95% CI=2.3% to 11.3%): 1 BRCA1 (c.2080delA) and 5 BRCA2 (p.Y3006X, p.Q1994X, c.9204_9217del14, c.9254_9258del5 and c.295+2T>C). Three out of 6 mutations were novel (BRCA2 p.Y3006X, c.9204_9217del14, and c.295+2T>C), and two further mutation…
mRNA expression profiles obtained from microdissected pancreatic cancer cells can predict patient survival
2017
// Ana-Barbara Garcia-Garcia 1, 2, * , M. Carmen Gomez-Mateo 3, 7, * , Rebeca Hilario 2 , Pilar Rentero-Garrido 2 , Alvaro Martinez-Domenech 4 , Veronica Gonzalez-Albert 2 , Andres Cervantes 5 , Pablo Marin-Garcia 6 , Felipe Javier Chaves 1, 2 , Antonio Ferrandez-Izquierdo 3 and Luis Sabater 4 1 CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain 2 Unidad de Genomica y Diagnostico Genetico. Fundacion Investigacion Clinico de Valencia, Instituto de Investigacion Sanitaria Clinico de Valencia (INCLIVA), Valencia, Spain 3 Department of Pathology, Faculty of Medicine and Odontology, University of Valencia and Clinical Hospital of Valencia, and Instituto de Investigacio…
Polymorphisms of the renin-angiotensin system influence height in normotensive women in a Spanish population.
2004
The objective of this study was to analyze the influence of the polymorphisms G-6A of the angiotensinogen gene, insertion/deletion (I/D) of the angiotensin-converting enzyme, and C573T of the angiotensin II AT1 receptor gene on a healthy, middle-age population. A total of 370 (194 women) healthy normotensive Caucasian subjects, aged 25-50 yr old, were selected from the general population. A significant association was found between height and the C573T polymorphism in women (P0.001). After adjustment for age, this association remained significant (P0.002). Thus, the lowest height values were from subjects carrying TT genotype (CC, 1.627 +/- 0.008 m; CT, 1.595 +/- 0.006 m; TT, 1.586 +/- 0.01…
Molecular genetics of familial hypercholesterolemia in Spain: Ten novel LDLR mutations and population analysis
2001
Mutations underlying FH in Spain are largely unknown because only a few and limited surveys have been carried out on Spanish FH patients up to now. To gain information on this issue, we have analysed a group of 113 unrelated Spanish FH patients from an eastern area of Spain (Valencian Community). We have screened the LDLR gene by Southern blot and PCR-SSCP analysis to detect large rearrangements and small mutations, respectively. In addition, we have screened the Apo B gene for mutations known to cause FDB by PCR-SSCP analysis. We have identified a total of 47 different mutations in the LDLR gene (5 large rearrangements, and 42 small mutations, which were characterized by DNA sequencing), 1…
Reactome pathway analysis: a high-performance in-memory approach
2016
Reactome aims to provide bioinformatics tools for visualisation, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modelling, systems biology and education. Pathway analysis methods have a broad range of applications in physiological and biomedical research; one of the main problems, from the analysis methods performance point of view, is the constantly increasing size of the data samples. Here, we present a new high-performance in-memory implementation of the well-established over-representation analysis method. To achieve the target, the over-representation analysis method is divided in four different steps and, for each of them, specific data st…
Additional file 1: of PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources
2019
PyCellBase use case. Example of usage of the PyCellBase REST client library. (IPYNB 15 kb)