Bioinformatics Unit
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Bioinformatics Unit
Overview
The Bioinformatics Unit provides researchers at CRG-CNAG/PRBB and external organizations with services of consultation, planning NGS and other genomic experiments, NGS data processing, analysis and management, software and database development, bioinformatics training, and access to high-performance computing resources at CRG.
The Unit works in synergy with the Genomics Unit and the Biomolecular Screening & Protein Technologies Unit (BMS-PT) to support users using high-throughput sequencing technologies from an experiment planning to delivery of timely and reliable results.
For more information please access the Unit website at http://biocore.crg.eu
Latest Updates
CRG researchers publish the databases of alternative splicing (30/08/2017)
The Vertebrate Alternative Splicing and Transcription Database (VastDB) is the largest resource of genome-wide, quantitative profiles of AS events assembled to date. VastDB provides readily accessible quantitative information on the inclusion levels and functional associations of AS events detected in RNA-seq data from diverse vertebrate cell and tissue types, as well as developmental stages.
The Centre for Genomic Regulation (CRG) hosts the Women for Africa Foundation awardee of 2017 (July 2017)
Dr. Elizabeth Balyejusa Kizito, Head of the Department of Agricultural Sciences, Uganda Christian University, is working together with the CRG Genomics and Bioinformatics units on the development of a robust set of genomic tools for more efficient breeding in Solanum aethiopicum.
The Women for Africa Foundation is a Spanish private, non-profit entity created in February 2012 by María Teresa Fernández de la Vega, the former Vice President of the Government of Spain, with the aim of promoting African women’s leadership in scientific research and technology transfer.
Bioinformatics Unit hosted for 6 months two PhD interns from the Cape Town University, South Africa on the Africa-Novartis-CRG program (June 2017)
Jason Limberis’ project concerned the in vivo transcriptional profiling of Mycobacterium tuberculosis from highly infectious TB patients. Melissa Nel, MD, has worked on WES and variant identification in treatment-resistant juvenile-onset ophthalmoplegic complicated Myasthenia Gravis patients.
The CRG at the Science Fair (May 2017)
Members of the CRG Core Facilities presented to the public the Saca La Lengua project and talked about mouth microbiome.
LncATLAS database for subcellular localization of long noncoding RNAs has been published in RNA journal (April 2017)
The comprehensive resource of lncRNA localization in human cells, the LncATLAS database, is based on RNA-sequencing data sets and contains 6768 GENCODE-annotated lncRNAs represented across various compartments of 15 cell lines.
Researchers find a gene that causes Opitz C syndrome in the only patient with this rare disorder in Catalonia (10/03/2017)
The study, published in the journal Scientific Reports, identifies the gene that causes Opitz C syndrome in the only patient diagnosed with this ultra-rare disorder in Catalonia, which affects only sixty people in the world. The identified mutation in the gene MAGEL2 coincides with the one seen in some patients with another minority disease, the Schaaf-Yang syndrome.
Genome Editing: Pressing the 'Delete' Button on DNA (02/10/2017)
Until recently, genomics was a «read-only» science. But scientists led by Rory Johnson at the University of Bern and the Centre for Genomic Regulation in Barcelona, have now developed a tool for quick and easy deletion of DNA in living cells.
Julia Ponomarenko CV
2002 PhD in Biology at the Institute of Cytology and Genetics, Novosibirsk, Russia.
2002 - 2004 Project Scientist, San Diego Supercomputer Center, University of California San Diego, USA.
2004 - 2008 Senior Research Scientist San Diego Supercomputer Center, University of California San Diego, USA.
2008 - 2015 Project Investigator (NIH/ NHGMS, NIAID), San Diego Supercomputer Center, University of California San Diego, USA.
2015 - Head of the Bioinformatics Unit, Centre for Genomic Regulation, Barcelona, Spain.
Service Prices
Services
- Consultation on bioinformatics methods and resources, experimental design and budgeting, grant proposal development, bioinformatics and statistical data analysis, usage of high-performance computing resources at CRG.
- Bioinformatics training (in person and via internal and external courses).
Genomics
- Reference-based and de novo assembly of eukaryotic and prokaryotic genomes.
- Genome re-sequencing and quality assessment of genome assemblies.
- ChIP-seq (TFs, histone modifications): peak calling, differential binding analysis among sample groups, peak annotation.
- Whole exome and whole genome analysis: variant calling, CNVs.
- Identification and annotation of DNA structural variants for common and rare human diseases: individual and family analysis, cancer driver gene mutations.
- Genomes comparison.
- Genome functional annotation: ab initio gene prediction, annotation of genes, transcripts, DNA motifs, promoters, and other DNA regulatory elements.
- Analysis of 5C, Hi-C, ATAC-seq, and other high-throughput data.
Transcriptomics
- Reference-based and de novo assembly of eukaryotic and prokaryotic transcriptomes.
- Transcriptome functional annotation: ab initio gene prediction, annotation of genes, transcripts, DNA motifs, promoters, and other regulatory elements.
- Variant calling from transcriptome sequencing data.
- Analysis of commercial and custom microarrays: differentially expressed genes, group comparison.
- RNA-seq for mRNA: discovery of new transcripts, differentially expressed genes/transcripts.
- Functional analysis of differentially expressed genes/transcripts: Gene Ontology terms, DNA motifs, and pathways enrichment analysis.
- RNA-seq for small and non-coding RNA: differential expression, discovery of new microRNAs, microRNA target prediction.
- Analysis of OpenArray real-time PCR, and other high-throughput experimental data.
- Identification of batch effects and visualization of data and results: hierarchical clustering, heatmaps, dendrograms, volcano plots, principal components analysis for the overall (dis)similarity among experiments.
- RNA-target-based sequencing: RIP-seq, iCLIP, CLIP-seq, and other.
- Data submission to GEO, ArrayExpress and other public data repositories.
Metagenomics
- Analysis of amplicon (16S rRNA genes), whole genome and transcriptome shotgun sequencing data.
- Identification of microbial communities, taxonomic diversity and abundances at the levels of genus, family, order, class, phylum.
- Conservation and abundance of bacterial gene functional modules and biochemical pathways.
- Estimation of microbial diversity and sequence coverage.
- ORF prediction and functional annotation.
- Comparative analysis of samples: microbial profiles, Gene Ontology terms, metabolic and pathway analyses.
Proteomics
- Protein functional annotation and prediction.
- Analysis of SNPs and other variations effects on protein structure and function.
- Multiple sequence alignment.
- Orthologs and paralogs assignment.
- Phylogenetic analysis and tree construction.
- Protein structure comparison and 3D homology modeling.
- Protein-protein and protein-ligand 3D docking.
- B- and T-cell epitope prediction.
Databases, Websites and Software
- Databases: Relational and NoSQL.
- Websites for data submission, search, and analysis.
- Web-tools.
- LIMSs (Laboratory Information Management System) for management of the laboratory's operations, data flow, and communication with users and external collaborators.
- External software evaluation and benchmarking.
- Software development: bioinformatics scripts; data processing and analysis pipelines; integrative bioinformatics web applications; customized genome browsers.
- External and internal data integration solutions.
In addition to services provided for fee, we support fully collaborative grant-funded investigations. This includes preliminary data analysis, planning the grant budget and experiments provided by the CRG Core facility, writing the grant, data analysis and biological inference, custom software development, and co-authored dissemination of the grant results.
For more information and service fees please access the Unit website at http://biocore.crg.eu
For specifics on procedures and deliverables please contact the Unit at BioinformaticsUnit@crg.eu
To request a service or to propose a collaborative project please contact the Unit head at julia.ponomarenko@crg.eu
Equipment
- Linux cluster with 3020 cores for computing and more than 200 compute nodes and servers.
- Univa Grid Engine batch queuing system
- 87 compute nodes with 2 Intel Xeon E5-2680 20M Cache 8 core at 2.70 Ghz, 128 GB memory
- 56 compute nodes with 2 Intel Xeon E5530 4 core at 2.40GHz, 48 GB memory
- High memory compute node with 2 processor Intel Xeon E5-2699 v4 22 core at 2.20GHz, 1 TB memory
- High memory compute node: with 8 processor Intel Xeon E7450 6 core at 2.40 GHz, 512GB memory
- High memory compute node with 4 processors Intel Xeon E7540 6 core at 2.00 GHz, 256 GB memory
- 60 heterogeneous compute nodes with different hardware specifications
- 4.5 PB of storage EMC-Isilon, DDN and Nexsan
