Andalusian Platform for Computational Medicine
The Andalusian Platform for Computational Medicine, one of the research platforms of the Fundación Progreso y Salud (FPS), has been conceived as a fundamental piece of the Personalized Medicine plan of the Andalusian community, with the mission of facilitating and providing the tools for the inclusion of the genomic data of the patient in the electronical health record. This platform has the dual aim of developing innovative algorithms and methods for the analysis of genomic data of patients, combined with the production of high quality software specifically designed to be used by clinician end users, all this with a strong translational orientation. The ultimate objective of the platform is to bring complex algorithms to the clinician for the management of complex genomics data in a transparent way for them, which ultimately foster the adoption of innovative technologies in the current clinical practice.
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Biocomputing unit
The Biocomputing Unit (BCU) of the National Center for Biotechnology / Instruct Image Processing Center (I2PC), led by Jose Maria Carazo and Carlos Oscar Sanchez Sorzano, works in the area of cryo electron microscopy. The group develops new ways to extract information from very noisy electron microscopy images obtained under cryogenic conditions, and integrates these new tools into advanced image processing software packages such as XMIPP and Scipion, together with integrative biological environments such as 3DBIONOTES and the COVID-19 Structural Hub. The research team works in new computational and experimental methodologies to solve key problems in biology and their first application to a number of key specimens. The approach is focused on Structural Biology by cryo Electron Microscopy, Biomedical Information Integration and Scientific Computing.
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Bioinformatics and Functional Genomics group
The Bioinformatics and Functional Genomics Group at the Cancer Research Center (CiC-IBMCC, USAL/CSIC) in Salamanca, led by Javier De Las Rivas, works on two main research areas: 1) Development and application of bioinformatics and computational biology methods for "omics data integration and analysis" in Cancer Research, focusing on human genomic, transcriptomic and proteomic data (now including "single-cell" data) combined with clinical data, with the aim of discovering gene signatures, gene markers of response or resistance, gene markers of survival, master regulators and causal genes (in all cases using sample cohorts derived from studies on patients). 2) Research on protein-protein interactions (PPIs), interactomes and networks, focusing on the human interactome and the construction of gene and protein networks to study different pathological subtypes in cancer and in neurodegenerative diseases. We also use bioinformatics strategies to build networks of drugs and their protein targets, as a way to identify the molecular landscape of anti-cancer drugs action.
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Bioinformatics unit
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. The unit collaborates with hospitals from the National Health System and the CNIO Clinical Units that provide an initial framework to promote the application of Bioinformatics resources into the clinic. HTe group's goal is to provide expertise in cancer genomics research, share best practices and working experiences, organise training activities and foster cooperation between bioinformatics nodes and other organisations in oncology research.
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Bioinformatics unit
The Bioinformatics Unit led by Julia Ponomeranko at Centre for Genomic Research (CRG) provides researchers with services of analyses of high-throughput sequencing (NGS, Nanopore, droplet-based) and other biomedical data, software/pipelines and database development, and bioinformatics training. The group focuses on delivering reproducible results using modern computational solutions (NextFlow, Cloud deployments, Linux containers).
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Bioinformatics Unit (BU-ISCIII)
BU-ISCIII is established as a core facility for genomic analysis, primarily providing bioinformatics support in genomic surveillance, outbreak studies, and diagnostic genetic studies of rare diseases. Additionally, BU-ISCIII is involved in national and international research projects, focusing on the development of analytical tools for high-throughput sequencing (HTS) data and conducting ring trials and quality assurance studies for HTS on microbiology. It is also actively involved in developing interoperable repositories for clinical and genomic data in order to support pathogen genomic surveillance and personalized medicine.
Bioinformatics unit - GENCODE
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. The unit collaborates with hospitals from the National Health System and the CNIO Clinical Units that provide an initial framework to promote the application of Bioinformatics resources into the clinic. The group's goal is to provide expertise in cancer genomics research, share best practices and working experiences, organise training activities and foster cooperation between bioinformatics nodes and other organisations in oncology research.
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Biomedical Genomics Group (BBGLAB)
The BBGLab, led by Nuria Lopez-Bigas, is focused on the study of cancer genomics. 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 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, the development of IntOGen, a discovery tool for cancer research, the description of a landscape of driver events and their therapeutic opportunities across around 33000 tumours of 73 different cancer types.
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Biomedical genomics group and Bioinformatics unit
The Biomedical Genomics group's in the Centro Nacional de Análisis Genómico (CNAG) is led by Ivo G. Gut, and its main line of research is mining, analysis and re-analysis of genomic data from biomedical studies. The group’s objective is to answer questions that go beyond the initial hypotheses that underlay the studies to shed light on how genome sequence, structure and usage relates to disease, disease initiation, disease progression and disease mechanisms. The group also studies genomic features related to disease at different cellular levels. The group analyses data generated within the Spanish and EU-funded projects IMMUcan, BCLLatlas, EasiGenomics, EUCANCan, Screen4Care, B1MG and 3TR.
The Bioinformatics Unit in the CNAG is led by Sergi Beltrán, and provides a link between Project Management, the Sequencing Unit and the CNAG collaborators. It develops and operates tools and pipelines for data management, quality control, analysis and interpretation.
Comparative Bioinformatics
The Comparative Bionformatics Group (aka Notredame's lab) is a research group of the Center for Genomic Regulation (CRG) in Barcelona led by Cedric Notredame. The main focus of the group is the development of novel algorithms for the comparison of multiple biological sequences. Multiple comparisons have the advantage of precisely revealing evolutionary traces, thus allowing the identification of functional constraints imposed on the evolution of biological entities. Most comparisons are currently carried out on the basis of sequence similarity. The group’s goal is to extend this scope by allowing comparisons based on any relevant biological signal such as sequence homology, structural similarity, genomic structure, functional similarity and more generally any signal that may be identified within biological sequences.
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Comparative Genomics
The Comparative Genomics's group is jointly affiliated to the Biomedical Research Institute (IRB Barcelona) and the Barcelona Supercomputing Center (BSC). The main research interest of the group is to understand the complex relationships between genome sequences and phenotypes and how these two features evolve within and across species. The group generally use large-scale phylogenetics and molecular evolution approaches that allow looking at the evolution of genomes from the perspective of all of their genes, and we apply these analyses to a variety of biological questions related the evolution and function of biological systems, ranging from individual molecules to entire biological communities.
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Comparative Genomics and Metagenomics
The Comparative Genomics and Metagenomics Laboratory develops computational methods and genomic resources to characterize microbial communities (microbiomes) from a functional and phylogenetic perspective, with a particular interest in understanding the evolution and ecological roles of novel microbial gene functions and rare organisms. To this end, they combine evolutionary biology, ecology, comparative genomics, massive sequencing data, and high-performance computing resources.
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Computational and Structural Biology
The Computational and Structural Biology group at Estación Experimental Aula Dei (EEAD-CSIC), which is led by Bruno Contreras Moreira has interest in the following research topics: (Pan)genomics and transcriptional regulation of grasses and Evolutionary and structural analysis of ductile proteins (IDPs) and flavoenzymes.
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Computational Biology Group
The Life Sciences Department at the BSC integrates the independent research of senior scientists that work on various aspects of Computer Science applied to Life Sciences, ranging from healthcare applications of machine learning and AI to the use of High Performance Computing (HPC) for biomedical research. The Computational Biology group (http://life.bsc.es/compbio) is involved in multiple projects covering a wide range of topics including computational systems biology, network science, digital medicine, structural biology.
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Computational Biology of RNA Processing
The overarching theme of the research in the Computational Biology of RNA Processing, led by Roderic Guigó, is the understanding of the information encoded in genomic sequences, and how this information is processed in the pathway leading from DNA to protein sequences. The group is intrigued by the parallelism between computation and the processing of information encoded in biological sequences. The bulk of their research currently focuses on the mechanisms underlying RNA production (transcription) and post-processing (splicing), and it is increasingly incorporating high throughput and experimental approaches.
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Computational Health Informatics Group
The Computational Health Informatics Group is an R&D&I group focused on the development of computational methods and tools for healthcare and human health research, led by Carlos Luis Parra Calderón, head of the Department of Technological Innovation at the Virgen del Rocío University Hospital. This multidisciplinary group comprises researchers in informatics and medicine in the field of semantic interoperability in the Electronic Health Record environment, Clinical Decision Support Systems, Informatics for clinical and translational research, Learning Health Systems, and AI in Health and Biomedicine. With an intense scientific activity of participation in projects funded in regional, national, and European competitive calls. Also noteworthy is its contribution to technology transfer, with the development of seven patents and three intellectual property registrations and the management of the innovation cycle of technology for healthcare digital transformation.
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Computational Systems Biology Group
The Computational Systems Biology Group is led by Florencio Pazos and Monica Chagoyen and integrated in the Systems Biology Program of the National Centre for Biotechnology (CNB-CSIC). The group is interested in different aspects of Bioinformatics, Computational Biology and Systems Biology. The main goal of the group is to obtain new biological knowledge with an "in-silico" approach which complements the "in-vivo" and "in-vitro" methodologies of Biology. This mainly involves mining the massive amounts of information stored in biological databases. Besides the lines of scientific research, the group also collaborates with experimental groups providing them with bioinformatics support for their specific needs, and participate in different teaching projects.
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EGA team
The team directed by Arcadi Navarro and led by Jordi Rambla at the CRG, co-manages the European Genome-Phenome Archive (EGA) together with the EBI-EMBL in Cambridge. The EGA is a global network for permanent archiving and sharing of personally identifiable genetic, phenotypic, and clinical data generated for the purposes of biomedical research projects or in the context of research-focused healthcare systems. With expertise in data management and a proper technical infrastructure, the EGA promotes FAIR data reuse and enable researchers to share their data securely. By leveraging public funding and strategic partnerships, the EGA provides a free service for all users. The EGA is an ELIXIR core resource and central to the ELIXIR Human Data communities. The CRG team contributes to a broad variety of collaborative projects with knowledge about genomics and genomic data management. Among them, of special note, projects aimed at creating a federated network to access to human data (Federated EGA and Genomic Data Infrastructure), and at develop the Beacon discovery tool.
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GCAT (GenomesForLife-GCAT Laboratory)
The GCAT team, led by Rafael de Cid, aims to advance knowledge of common diseases to help implement more personalized and precise preventive, diagnostic, prognostic and treatment strategies. To this end it combines clinical data, biological samples and genomic data of a large cohort of the Catalan population: GCAT|Genomes for Life. The GCAT vision is collective, multidisciplinary, open and public to responsibly and ethically expand, share and re-use the information generated at a national and international level in agreement with the FAIR criteria. The GCAT|Genomes for Life has been developed and is coordinated from the Germans Trias i Pujol Research Institute, but works together with an extensive network of collaborating Institutions from the health and research catalan landscape.
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Genome Informatics
The Genome Informatics unit is hosted by the Barcelona Supercomputing Center (BSC) and led by Miguel Vazquez. The group’s main objectives are: 1) Identify available software tools, data analysis methods, or data resources for selected tasks and incorporate them into the group's toolbox, 2) Adapt tools or develop new ones to address the group research needs, 3) Compile different tools and resources into tailored analytical pipelines and 4) Generate applications around data analysis tools that support research and enhance discovery.
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Genomics of Gene Expression group
The Genomics of Gene Expression group is led by Ana Conesa and Sonia Tarazona at the Institute for Integrative Systems Biology (I2SysBio) and the Politechnical University of Valencia (UPV), respectively. The group is interested in understanding functional aspects of gene expression by combining a wide variety of high-throughput molecular techniques, including transcriptomics, epigenomics, proteomics, metabolomics, metagenomics and single-cell data, both for model and non-model species. The lab develops statistical methods and user-friendly software tools to analyze these multi-omics data. The most current interest are the application of long reads sequencing technologies for transcriptome analysis, and the integration of multi-omics data to model chromatin-metabolome regulation, infer gene regulatory programs and created systems models of disease progression.
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INB Computational node
The INB Computational node, hosted by the Barcelona Supercomputing Center (BSC), provides computing services to the INB, TransBioNet and the bioinformatics community. It also develops applications related to data management in large genomic and biomedical projects, provides support in the use and adaptation of bioinformatics applications to HPC environments, and helps in the application of ELIXIR recommendations to national bioinformatics projects.
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INB Coordination node
The INB Coordination node, led by Salvador Capella-Gutierrez and hosted at the Barcelona Supercomputing Center (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 European Projects, the INB Coordination team at BSC leads the ELIXIR benchmarking platform, OpenEBench, 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.
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Molecular Modeling and Bioinformatics (MMB)
The Molecular Modeling and Bioinformatics (MMB) research group 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, and 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. The long-term objective of the group 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.
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NLP for Biomedical Information Analysis
TBD
Research Programme on Biomedical Informatics (GRIB)
The Research Programme on Biomedical Informatics (GRIB) is a joint research programme of the Hospital del Mar Medical Research Institute (IMIM) and the Department of Medicine and Life Sciences of the Universitat Pompeu Fabra. GRIB brings together a multidisciplinary team of more than seventy scientists, as well as technical and management staff. M. Mar Albà (IMIM) and Ferran Sanz (UPF) are both Directors of GRIB. 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.
Structural Bioinformatics and Network Biology
The Structural Bioinformatics & Network Biology lab, led by Patrick Aloy and located at IRB Barcelona, 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.
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