Computational & Mathematical Biology
Most phenomena studied by the Natural Sciences, from Material Sciences to Astrophysics, are multi-scale processes, i.e. they involve the coupling of multiple different processes characterised by widely-ranging time and length scales, with the macroscopic behaviour emerging from the complex interactions between them. Whilst considerable progress has been done in dealing with such problems in the Physical Sciences, the success achieved so far in the Biological Sciences is rather more limited. This is partly due to the fact that the individual components of biological systems (e.g. cells) are much more complex than their counterparts in physical systems and, therefore, new methods and models are needed to analyse multi-scale processes in Biology. Such is the remit of the Computational & Mathematical Biology group at CRM: To propose new models relevant to experimental biologists and clinicians and develop the analytical and computational tools necessary for their analysis. We pay special attention to problems with clinical relevance, in particular those related to cancer.
The research activity of our group is developed along the following lines:
- Multiscale modelling of tumour growth and tumour-induced angiogenesis
- Evolutionary dynamics of populations with complex structure, in particular cell populations with hierarchical structure and genotype-phenotype map
- Mathematical modelling of the cell-cycle
- Stochastic modelling of receptor tyrosine kinases
- Tumour dormancy
Main projects
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1.
Multiscale modelling of tumour growth
Cancer is (a set of) disease(s) which is characterised by disrupting the normal, homeostatic mechanisms at all levels of biological organisation, from abherrant structure of the vasculature all the way down to abnormalities in regulation of gene expression, with complex interactions between them. In this context, it is very clear that verbal models and traditional, lineal thinking are unlikely to produce a thorough understanding of tumour growth and its treatment. Instead, an integrative approach that includes within a unified framework phenomena occurring at different scales is needed. Together with some of my collaborators listed below, such framework has been developed to integrate processes as disparate, but at the same strongly interelated, as angiogenesis and delay of cell-cycle progression under oxygen starvation
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2.
Hybrid methods for multiscale models
Multiscale models of tumour growth and angiogenesis provide a wealth of detail on the state of the system which is not always needed. It often occurs that we only need such detailed information regarding a restricted part of the system (e.g. a limited spatial domain, a particular cell type, etc.) while a more coarse-grained description provides an accurate enough description of the rest of the system. We are working on developing methods for hybridisation of mean-field and stochastic descriptions of multiscale models of tumour growth. To this end, we are
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3.
Stochastic modelling of somatic cell reprogramming
The seminal work of Yamanaka and Gurdon on reprogramming somatic cells into induced pluripotent stem cells (IPSCs) was followed by a wealth of interesting results, applications and improvements of their initial technique. Yet, a lot needs to be learnt about mechanisms for improving the efficiency of the reprogramming process so it can become a viable biomedical technology. Our work within this area involves the stochastic modelling of the gene regulatory network involved in reprogramming and how it is affected by metabolic factors. We are also investigating the potential connections tof reprogramming to cancer stem cells
Institutions
Bioinformatics expertise:
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Algorithmics (26)
- AIZON (Aizon)
- Algorithms, Computational Biology, Complexity and Formal Methods (UPC)
- Amalfi Analytics (Amalfi)
- Artificial Intelligence Research Institute (CSIC)
- Biomedical Signal Processing and Interpretation (IBEC)
- Chemometrics for Environmental Omics (CSIC)
- Comparative Bioinformatics (CRG)
- Computational & Mathematical Biology (CRM)
- Computational Biology and Complex Systems Group (UPC)
- Computational continuum mechanics (UPC)
- Computational RNA Biology group of GRIB (UPF, IMIM)
- Computational Science group of GRIB (UPF, IMIM)
- Computer Vision and Robotics Group (UdG)
- Control Engineering and Intelligent Systems (UdG)
- Data and Signal Processing Research Group (UVic-UCC)
- Distributed Computation Group (UdL)
- High Performance Computing Applications for Science and Engineering - Bioinformatics (UAB)
- IN2 Ingeniería de la Información (IN2)
- Internet Computing & Systems Optimization (FUOC)
- Laboratory of Relational Algorithmics, Complexity and Learnability (UPC)
- Laboratory of Systems Pharmacology and Bioinformatics (UAB)
- Modelling, Identification and Control Engineering (UdG)
- Numerical Genomics - Statistical and population genomics (CRAG)
- Research Group on Statistics, Econometrics and Health (UdG)
- Signal and Information Processing for Sensing Systems (IBEC)
- Soft Computing (UPC)
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Biomedical Informatics (46)
- Bioinformatics and Medical Statistics (UVic-UCC)
- Bioinformatics Core Unit (CRAG)
- Biomedical Genomics (IRB Barcelona)
- Biomedical Signal Processing and Interpretation (IBEC)
- Biostatistics and Bioinformatics Research Group (UPC)
- BITAC (BITAC)
- Centre Nacional d'Anàlisi Genòmica CNAG-CRG (CRG)
- Clinical statistics and biodiversity (UB)
- Computational & Mathematical Biology (CRM)
- Computational Bioinformatics Node (National Institute of Bioinformatics - INB) (BSC)
- Computational Biology & Drug Design (UB)
- Computational Biology and Complex Systems Group (UPC)
- Computational Biology of RNA processing (CRG)
- Computational RNA Biology group of GRIB (UPF, IMIM)
- Control Engineering and Intelligent Systems (UdG)
- Costaisa (Costaisa)
- Data and Signal Processing Research Group (UVic-UCC)
- Disease Genomics (IGTP)
- Distributed Computation Group (UdL)
- Functional Genomics group of GRIB (UPF, IMIM)
- Genomics and Bioinformatics Service (UAB)
- Hereditary Cancer Group (IGTP)
- Information Modeling and Processing (UPC)
- Information System for Research in Primary Care (IDIAP Jordi Gol)
- Institute for Innovation and Knowledge Management (ESADE)
- Integrative Biomedical Informatics group of GRIB (UPF, IMIM)
- Integrative Systems Biology, Metabolomics and Cancer (UB)
- Laboratory of Relational Algorithmics, Complexity and Learnability (UPC)
- Laboratory of Systems Pharmacology and Bioinformatics (UAB)
- Mathematical Modeling of Metabolic Processes (UdL)
- Mechanics of development and disease (IBEC)
- Mechanisms of cancer and cell differentiation (IGTP)
- Mind the Byte ()
- Modeling of Biological systems & Drug Design (UB)
- Modelling, Identification and Control Engineering (UdG)
- Molecular Modelling and Bioinformatics (UB, IRB Barcelona)
- Pharmacelera ()
- Research Group on Artificial Intelligence (URV)
- Roche Diagnostics (Roche)
- Soft Computing (UPC)
- Systems Pharmacology group of GRIB (UPF, IMIM)
- The Computational Chembiological Team (UAB)
- The CRG Bioinformatics Unit (CRG)
- The Human Microbiome Lab (VHIR)
- Theoretical Chemistry, Modelling and Molecular Engineering (UdG)
- Translational Bioinformatics group (VHIR)
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Computational Genomics (39)
- Algorithms, Computational Biology, Complexity and Formal Methods (UPC)
- Bioinformatics of Genome Diversity (UAB)
- Biomedical Genomics (IRB Barcelona)
- Cancer genetics and epigenetics (IGTP)
- Cancer Genomics Group (VHIO)
- Centre Nacional d'Anàlisi Genòmica CNAG-CRG (CRG)
- Clinical Genomics Unit ()
- Comparative Bioinformatics (CRG)
- Comparative Genomics (UPF, CSIC)
- Computational & Mathematical Biology (CRM)
- Computational Biology of RNA processing (CRG)
- Computational Genomics (BSC)
- Computational Genomics Lab @ UB (UB)
- Computational RNA Biology group of GRIB (UPF, IMIM)
- Epigenetics of Endocrine Pancreatic Tumours (IGTP)
- Evolutionary and Functional Genomics Lab (UPF, CSIC)
- Evolutionary Genomics & Bioinformatics (UB)
- Evolutionary Genomics group of GRIB (UPF, IMIM)
- Evolutionary Genomics Lab (UPF, CSIC)
- Evolutionary Population Genetics Lab (UPF, CSIC)
- Evolutionary Systems Biology (UPF, CSIC)
- Gene Function and Evolution lab (CRG)
- Genome Data Science (IRB Barcelona)
- Genomic and Epigenomic Variation in Disease (CRG)
- Genomics and Bioinformatics Service (UAB)
- Genomics and Disease (CRG)
- Genomics of Individuality (UPF, CSIC)
- High Content Genomics and Bioinformatics (IGTP)
- Human Genome Diversity Group (UPF, CSIC)
- Information Modeling and Processing (UPC)
- Laboratory of Genetic Ichthyology (UdG)
- Made of Genes (MoG)
- Mathematical Modeling of Metabolic Processes (UdL)
- Molecular Modelling and Bioinformatics (UB, IRB Barcelona)
- Oncology Data Science Group (VHIO)
- Regulatory Genomics (IGTP)
- Sequentia Biotech (SeqBio)
- The CRG Bioinformatics Unit (CRG)
- Translational & Consumer Genomics Unit ()
Bioinformatics services offered
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Expertise in mathematical modelling of complex biological phenomena