The INB is organized as a distributed institute that currently consists of 19 nodes, including a total of 30+ staff and internationally renowned scientists, plus a central node that directs and coordinates the activities.
The nodes cover complementary areas of expertise, and were selected after an international evaluation of proposals: genomics, proteomics, functional genomics, structural biology, population genomics and genome diversity, biomedical informatics, algorithm development and high performance computing. The computational effort of the INB is localized in the computational node by a special agreement with the Barcelona Supercomputing Centre.
Universitat Pompeu Fabra participates on this platform through the Research Programme on Biomedical Informatics (GRIB) (http://grib.upf.edu/), which is a joint programme of the UPF and the IMIM. The GRIB mission is to develop and apply computational methods and information technologies for a better understanding and prediction of biological phenomena, giving especial emphasis to those related to the human diseases, their prevention, diagnosis and pharmacological treatment. GRIB has a long record of leadership and participation in EU-funded projects and collaboration with pharmaceutical industry in knowledge management, translational bioinformatics and predictive modelling. GRIB has a long tradition of collaboration with the pharmaceutical and biotechnological industry in the framework of R&D projects and also providing services, especially in the development of computational methods for drug discovery. GRIB staff is involved in pre and postgraduate teaching at the UPF and we are coordinators of the Master in Bioinformatics for Health Sciences. GRIB is the node for Biomedical Informatics of the INB and jointly with Farmaindustria, coordinates the Plataforma Tecnológica Española de Medicamentos Innovadores (PTEMI). GRIB participates also in the Bioinformatics Barcelona Association (BIB), which aims to promote training, research, and technology transfer in bioinformatics.
Research in the Structural Bioinformatics & Network Biology lab mainly focuses on understanding the molecular bases of how macromolecular complexes and cell networks operate, in health and disease states, by analyzing protein-protein interaction networks with the help of high-resolution 3D structures. Modern molecular and cell biology no longer focus on single macromolecules but now look into complexes, pathways or even entire organism interactomes. Accordingly, the group has been developing tools to systematically annotate disease-related networks with quasi-atomic details, to provide the fine details necessary to understand their function.
The Bioinformatics Unit at the Spanish National Cancer Research Institute (CNIO) aims to provide the framework and expertise for the systematic analysis and interpretation of cancer genomes. We have collaborations with hospitals from National Health System and CNIO Clinical Units that provide an initial framework to promote the application of Bioinformatics resources into the clinic. Our goal is to provide expertise in cancer genomics research, share best practices and working experiences, organize training activities and foster cooperation between bioinformatics nodes and other organizations in oncology research.
The Biocomputing Unit of the National Center for Biotechnology, led by Prof Carazo, is an interdisciplinary team of researchers working on Computational and Structural Biology and Bioinformatics, specially focused in the area of image processing in three-dimensional electron microscopy and structural bioinformatics. The unit is member of Instruct-ERIC, a pan-european research infrastructure in structural biology and a partner of the research environment WestLife.
The group works on new computational and experimental methodologies for solving key problems in biology focusing on structural biology by 3D electron microscopy and Soft X-rays cellular tomography, integrating structural information with biological annotations, machine learning and scientific computing.
The BBGLab, led by Nuria Lopez-Bigas, is focused on the study of cancer genomics. Specifically, the group is interested in the development of computational approaches to analyse cancer genomes to identify mutations, genes and pathways driving tumorigenesis and the identification of their therapeutic targeting opportunities. The group also analyzes the mutations detected across thousands of tumors to study the interplay between the DNA damage and repair and normal cellular processes.
Among the most important achievements obtained by BBGLab are the development of pioneering methods to identify cancer driver genes (Oncodrive methods)(NAR 2012, Bioinformatics 2013, Genome Biology 2016), the development of IntOGen, a discovery tool for cancer research (Nature Methods 2013), the description of a landscape of driver events and their therapeutic opportunities across around 7000 tumours of 28 different cancer types (Cancer Cell 2015), the discovery that DNA-bound proteins interfere with the nucleotide excision repair machinery, leading to increased rate of DNA mutations at the protein binding sites (Nature 2016).
The Molecular Modeling and Bioinformatics (MMB) research group is located in the Barcelona Science Park (PCB), and is part of the Institute for Research in Biomedicine (IRB Barcelona). Its research is mainly focused in two major topics:
- The study of protein dynamics and flexibility.
- The analysis of unusual or stressed DNAs of biological importance, with particular emphasis in chromatin-stressed DNAs.
The group devotes a large effort in development of new methodologies, but also in the study of especially relevant biological systems, with the experimental support from the IRB-BSC Experimental Bioinformatics Laboratory, where experimental validations are performed. MMB research group is part of the Joint BSC-CRG-IRB program in Computational Biology. This program between the Barcelona Supercomputing Center (BSC), the Institute for Research in Biomedicine (IRB-Barcelona) and the Center for Genomic Regulation (CRG) joins around 200 scientists working in the wide field of Computational Biology. Our long-term objective is to understand the behavior of living organisms from the basic rules of physics, in other words, to represent life by means of theoretical calculations.
The Bioinformatics Area from the Fundación Progreso y Salud (FPS) is a central stakeholder in the Personalized Medicine plan of the Andalusian community, with the mission of facilitating and providing the tools for the use of patient’s genomic data in the current clinical practice. This Area has the dual aim of developing innovative algorithms and methods for the analysis of genomic data, combined with the production of high quality software specifically designed to be used by clinician end users, to make precision medicine a reality within the public health system. Particularly, the Area main research interests focus on the development of innovative translational and clinical bioinformatics solutions for diagnosis, prognosis and therapeutic recommendation in human diseases by integrating molecular and clinical data using a systems medicine perspective. Ongoing pilot programs include diagnostic of rare diseases and cancer treatment recommendation but applications to other areas, such as infectious diseases, complex diseases and pharmacogenomics are currently under development.
The Population Genomics group at the Universitat Pompeu Fabra (UPF) works on the evolutionary and population aspects of genome-phenome relationships, specializing on the handling and analysis of Biomedical BigData. The groups interrogates patterns of variability in our genomes and those of other species to advance our understanding of such diverse issues as the dynamics of recombination, virus-host interactions, human disease or senescence and patterns of ageing.
The BITLAB group is a multi-disciplinary research group belonging to the Computer Architecture Department of the University of Malaga, led by Oswaldo Trelles, that focuses on developing solutions using advanced computing for data processing and data analysis problems in the bioinformatics (in particular, in Comparative Genomics) and biomedicine fields. The group is mainly interested in the application of High Performance and Cloud Computing to Machine Learning and Deep Learning in the fields of medicine and biology. BITLAB has delivered user-friendly platforms that bridge the gap between research and applied science. The group is also member of the Instituto de Investigación Biomédica de Málaga (IBIMA) and the Fundación Pública Andaluza para la Investigación de Málaga en Biomedicina y Salud (FIMABIS).
The research interest of the Comparative Genomics group at Centre for Genomic Regulation (CRG) are focused around the use of comparative genomics and phylogenomics to study the origin, evolution and function of complex biological systems, ranging from metabolic pathways to microbial communities. A particular focus is to understand how genomes and phenotypes evolve within and between species and how we can use this information to gain insight into the function and roles of biological systems.
The group has expertise in comparative genomics, phylogenomics, genome assembly and annotation, comparative transcritomics, as well as metagenomics and microbiome-analyses.
The CNAG-CRG, directed by Dr Ivo Gut, is one of the reference sequencing centers in Europe that operates as an open-access facility (http://www.cnag.crg.cat/contact-us). It carries out large scale projects in DNA/RNA sequencing and analysis in areas as diverse as cancer genetics, rare disorders, evolutionary studies and the improvement of species of agricultural interest. Operations are supported by an extensive informatics infrastructure (7.6 petabyte of data storage and 3,472 cores of computing). Researchers at the CNAG-CRG participate in several genome sequencing and analysis consortia (http://www.cnag.crg.cat/research/projects), with a solid publishing record (http://www.cnag.crg.cat/research/publications).
Dr Sergi Beltran leads the CNAG-CRG Bioinformatics Analysis Unit that implements and operates standardised analysis pipelines besides doing research and software/infrastructure development on biomedical and applied genomics. The CNAG-CRG leads the development of the RD-Connect platform (https://platform.rd-connect.eu/) for rare disease research, co-leads with ELIXIR-NL the Rare Disease Use Case, and participates in three national pilot initiatives for personalized medicine.
The Bioinformatics and Functional Genomics Group at the Cancer Research Center (CiC-IBMCC, USAL/CSIC) in Salamanca, led by Dr. Javier De Las Rivas, works on two main research areas: 1) Development and application of bioinformatics and computational biology methods for "omics data analysis", focusing on the integration of genomic, transcriptomic and proteomic data, and aiming to the discovery of gene signatures, master regulators and causal genes on cancer sample cohorts derived from clinical studies. 2) Research on protein-protein interactions (PPIs), interactomes and networks, with main focus on the human interactome and the construction of gene and protein networks to study different pathological subtypes in cancer and in neurodegenerative diseases. The group participates in several EU Horizon 2020 projects.
EGA (European Genome-phenome Archive) joined the INB in 2013. The EGA (https://ega-archive.org) is a service co-managed between the European Bioinformatics Institute (EBI) and the CRG. In consequence, it is part of both the EGA Strategic Committee and the EGA Operations Committee. The Strategic Committee is responsible for developing the strategic plans, overseeing its implementation and providing guidance to the Operations Committee. The latter is responsible for the planning, definition and progress of all matters relevant for the operation of the Project and for management of new development decisions such as archiving pipelines, data transfer software, backend microservices, end-user portals, etc.
The EGA is an ELIXIR core resource and central to the ELIXIR Human Data strategy (https://www.elixir-europe.org/use-cases/human-data).
The EGA is archiving just human data under controlled access, and it is being used by hundreds of projects related to human health and is contributing to development of tools like the EGA Beacon (in service since 2015), the ELIXIR Beacon reference implementation, and the GA4GH Beacon projects.
The Bioinformatics and Genomics Group, led by Dr. Roderic Guigó, has historically been involved in genome annotation projects, either by developing matrices/profiles for our gene finding programs geneid, SGP2 and SelenoProfiles and, since 2012, by generating high-quality structural genome and functional reference annotations using two complex pipelines. We are also involved in the development of resources for the analysis of biomedical and genomics data, including sQTLseekerR (pipeline to identify genetic variants affecting the splicing phenotype) and GRAPE (provides an extensive pipeline for RNA-Seq analyses).
The Genomics of Gene Expression group is formed by researchers from the Centro de Investigación Príncipe Felipe (Valencia, Spain) and from the University of Florida (Gainesville, USA). The team at the University of Florida is led by Dr. Ana Conesa and the team at the Centro de Investigación Príncipe Felipe is led by Dr. Sonia Tarazona. We are interested in understanding functional aspects of gene expression at the genome-wide level and across different organisms and its relationship with diseases and traits. For that, we develop statistical methods and software tools that analyze the dynamic aspects of transcriptomes, integrate these with other types of molecular data and annotate them functionally, with a special focus on Next Generation Sequencing (NGS) data. Functional genomics research is complemented with the development of bioinformatics software for the analysis of genomics data.
The INB Computational Platform, hosted by the BSC, provides computing services to the INB, TransBioNet and the bioinformatics community. Services would include cloud computing systems, data storage and mobilization, virtual research environments, and support to access HPC resources. Initial available resources consists in a 500-core cluster, associated to the StarLife project (https://www.bsc.es/marenostrum/star-life), with a hybrid configuration (HPC and Cloud).
Directed by Prof. Alfonso Valencia, the group is dedicated to the application of machine learning and artificial intelligence to Personalized Medicine, and exhibits ample experience in the development of software platforms for the extraction, integration and representation of big data for large-scale genome projects. The group participates in different international consortia such as the ENCODE project, the ICGC cancer genome effort (including the Spanish subproject on CLL), the BLUEPRINT project and Rare Diseases (RD)-Connect part of the International Rare Diseases Research Consortium (IRDiRC).
The UB group performs a multidisciplinary research, combining techniques for an integrated analysis of biological samples within a Systems Biology and Systems Medicine approach. Our team is partner in international projects aimed at precision medicine (EC FP7 and H2020 programs). As UB node of INB, we develop and maintain software tools in the field of metabolomics and fluxomics and to establish Europe-wide standards in these fields. We have pioneered the development and application of software tools supporting the workflow of 13C-based fluxomics, starting from curation of raw mass spectra of metabolites of interests to computer simulations of the curated data with mathematical models of metabolism. To provide a set of fluxes consistent with the data, we develop a new generation of genome scale metabolic models to characterize metabolic alterations underlying human diseases. Our tools help to reveal the role of metabolic reprogramming in two key players of tumorigenesis: metastasis and resistance to chemotherapy, to identify vulnerabilities exploitable as therapeutic metabolic targets efficient for both processes.
The Coordination team of the Spanish National Bioinformatics Institute (INB) at BSC looks after the activities of the INB groups across Spain as well as their participation in the ELIXIR projects, activities and communities. The team has also established and led TransBioNet, a network of bioinformatics groups at Health Research Institutions of Spain. In the context of TransBioNet, the Coordination team works to increase the translational impact of the INB in the Spanish National Health System by articulating interactions and collaborations between groups at clinical settings with others at research environments, fostering the adoption of best-practices and protocols, and the adoption of the latest analytical technologies. The Coordination team also leads technological works around security solutions and the use of software containers for diverse purposes.
In the context of European Projects, the INB Coordination team at BSC leads the ELIXIR benchmarking platform which aims to establish a knowledge hub where ends-users, software developers, scientific communities and funding agencies can gather information about the technical and scientific performance of bioinformatics resources including analytical workflows. Moreover, this team participates actively at the RD-Connect project leading the security developments of the genomics platform as well as the activitires regarding the RNASeq analysis pipelines and how to integrate those results with genomics data for a better understanding of the genetic bases of rare-diseases.