ProjectsBlocks

Saca La Lengua

‘Stick Out Your Tongue’ (‘Saca la Lengua’) is a citizen’s science project that aims to study the mouth’s microbiome of a large population of healthy young Spaniards and the microbiome profiles relationship with environmental characteristics and lifestyle. The Bioinformatics Core is involved in processing of the 16S rRNA sequencing data, obtaining microbiome abundance profiles for each individual, setting up a website for the data analysis competition, and teaching students and public about bioinformatics and microbiome analysis. For more information, visit www.sacalalengua.org.

Whole Genome Analysis of an Opitz-C Syndrome Patient

The C syndrome, also known as the Opitz trigonocephaly syndrome, is a malformation syndrome characterized by trigonocephaly, severe mental retardation, hypotonia, variable cardiac defects, redundant skin, and dysmorphic facial features, including upslanted palpebral fissures, epicanthal folds, depressed nasal bridge, and low-set, posteriorly rotated ears (summary by Kaname et al., 2007). The Bioinformatics Core collaborates with the University of Barcelona analyzing the whole genomes of a patient and her parents to detect the putative causative mutations.

Lung Microbiome of COPD Patients

CRG collaborates with the Hospital San Pau, Hospital Clinic, Hospital del Mar and other institutions in Barcelona on studies of the lung micro biomes of patients affected by chronic obstructive pulmonary disease (COPD). The Bioinformatics Core is part contributes to the project by processing and analyzing of the sequencing data.

AnnoWiki

AnnoWiki is a Semantic MediaWiki based platform aimed to host, display and manage big data on genome annotations in a collaborative manner. This advanced Content Management System (CMS) is currently under development in the Bioinformatics Core. For more information, see a poster illustrating the application at http://www.slideshare.net/lucacozzuto/annowiki.

Wiki-based CMS for Core Facilities

The Bioinformatics Core developed a number of Semantic MediaWiki LIMSs (Laboratory Information Management System) to manage the laboratory's operations, data flow, and communication with users. One of such LIMS is used by the CRG Proteomics Core and can be accessed at http://proteowiki.crg.eu.

De novo genome assembly of three different flies

The Bioinformatics Core collaborates with the group of Yogi Jaegher to the genome assembly of three non-drosophilid diptera: Clogmia albipunctata, Megaselia abdita and Episyrphus balteatus. We previously published the de novo transcriptome of those flies [1].

Mycoplasma DB

MyMpn is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. M. pneumoniae is also an interesting model organisms for the development of systems biology for unicellular organisms. The Bioinformatics Core designed and developed this database to host a wealth of omics-scale datasets generated by hundreds of experimental and computational analyses generated in the context of the mycoplasma project, an international collaboration between the The Design of Biological Systems Group at the CRG Barcelona and different research groups at the EMBL Heidelberg. For more information visit http://mympn.crg.eu/ or read the paper [2].

Melon genome project

Melon (Cucumis melo L.) is a cucurbit with high economic impact and a well-known and appreciated product in Europe. Spain is the fifth world producer and the main exporter. Genoma España, a Governmental Foundation that promotes the development of research in Genomics and Proteomics, funded in 2008 the Project: "Development of genomic tools in Cucurbits, including the sequencing of the melon genome and its application for breeding these crop species", "MELONOMICS". The Bioinformatics Core contributed to this study by predicting small non coding RNAs and detecting resistant genes predicted from the genomic sequence. Visit https://melonomics.net/ for more information or read the paper [3].

Common Bean genome project

The Bioinformatics Core collaborated with an international consortium to decode the Mesoamerican common bean (Phaseolus vulgaris). The findings are reported in the journal Genome Biology [4]. The contribution of the core was to identify small ncRNAs and to assign functions to genes predicted from the genomic sequence.

SuperFly database

SuperFly is a database for the comparative analysis of segmentation gene expression and regulation in dipteran species (flies, midges, and mosquitoes). Currently, it hosts semi-quantitative, spatio-temporal expression data for maternal co-ordinate, and gap genes in three species: the vinegar fly Drosophila melanogaster (Drosophilidae), the scuttle fly Megaselia abdita (Phoridae), and the moth midge Clogmia albipunctata (Psychodidae). The Bionformatics Core developed both the database and the website to collect and display the data. The website can be visited here: http://superfly.crg.eu/. Here the publication: [5]

PRGdb 2.0

The Plant Resistance Genes database (PRGdb; http://prgdb.crg.eu/wiki/Main_Page) is a comprehensive resource on resistance genes (R-genes), a major class of genes in plant genomes that convey disease resistance against pathogens. Initiated in 2009, the database has grown more than 6-fold to recently include annotation derived from recent plant genome sequencing projects. Release 2.0 currently hosts useful biological information on a set of 112 known and 104 310 putative R-genes present in 233 plant species and conferring resistance to 122 different pathogens. Moreover, the website has been completely redesigned with the implementation of Semantic MediaWiki technologies, which makes this repository freely accessed and easily edited by any scientists. The Bionformatics Core participated to this project by providing the wiki infrastructure and redesigning the interface. The databased was published in NAR:[6]

Iberian Lynx genome project

A total of six research Spanish centers and more than thirty researchers are involved in Lynxgenomics, which aims is the generation of a first map of the Iberian lynx genome (an annotated draft) and of a comprehensive set of markers for genomic analyses in the species. Specialists in genomic and biology have joined forces and knowledge to reach these two aims under EBD's coordination in this project, framed in the Project Zero program FGCSIC 2010 in Endangered Species, and financed by Banco Santander and Fundación General CSIC. More info at http://www.lynxgenomics.eu/