EATRIS is a non-profit European Research Infrastructure Consortium (ERIC), a legal status designed to facilitate the joint establishment and operation of research infrastructures of European interest. Its education and training activities focus on providing opportunities in Translational Medicine, which have high impact on researchers’ daily practice; developing curricula that support the education of the next generation of translational scientists.

EATRIS’s role in the programme is to offer both online and face-to-face training to the IMIBIC-P2Med Fellows

Translational medicine is a discipline in biomedical research that aims to turn observations in the laboratory, clinic and community into interventions that improve the health of individuals and the public. This training course introduces the key aspects of translational research and medicines development including: A general introduction to translational medicine; Different research and development phases of a new medicine; Target validation; Predictive models; Biomarkers and personalised medicine; Clinical trial design and implementation; and European regulations in this field. After the course, the participants will be able to identify the different steps that are necessary to take a new discovery from the lab to the patient’s bedside and back again, describe the characteristics of good and bad preclinical models, give a definition of personalized medicine and biomarkers, and are familiar with the process to get a new medicine on the market. This course includes approx. 12h of self-paced learning, and is available for all IMIBIC-P2Med Fellows.

For more information: The Landscape of Translation Medicine Flyer

The course consists of an introductory e-learning (~12 hours student investment time) followed by a 5-day face-to-face workshop. The course is intended for early postdocs who are involved in biomedical research. It will offer the students a holistic understanding of the medicines development process, an opportunity to meet and engage in discussion with experts from academia and pharma at eye level, and introduction to new approaches in the medicines development sciences. The course is generally organised once a year, and in different locations in Europe. The IMIBIC-P2Med Fellow applicants may solicit participation in the editions of 2020 and 2021.

TRANSMED Academy provides open access to online courses and webinars around drug development and translational research.

To access the platform, click here.

For more information, see the TRANSMED Academy Flyer

The National Institute of Health of Italy – ISS (Instituto Superiore di Sanità) is a research institute and the scientific advisory body of the National Health Service in Italy, which includes the Ministry of Health, the Regions and the Local Health Units. It has research, control and training functions aimed at promoting the Public Health and the development of programs according to the National Health Plan. The institute's activities cover a wide variety of fields, from cutting-edge molecular and genetic research to population-based studies aiming to prevent, diagnose, and treat disease and disability.

ISS is equipped with facilities and services to perform biomedical and biotechnology research (see ISS Core Facilities), Biosafety Level (BSL) 3 laboratories, and experimental animal facilities.

ISS offers research stays and training opportunities in the areas of:

• Cardiovascular, dysmetabolic and ageing-associated diseases
• Oncology and molecular medicine
• Infectious diseases
• Neurosciences
• HIV/AIDS
• Rare diseases

The Department takes care of promotion of the health and longevity of the population through etiological, translational, clinical, epidemiological, technological and prevention research in the field of cardiovascular, endocrine-metabolic and aging-related diseases, which together constitute the area with the greatest impact in terms of morbidity, disability and mortality for the population. It has multidisciplinary expertise on: longitudinal studies of the general population supported by banks of biological samples; pathology and pharmacovigilance registers; research on the role of new biomarkers; research of new instrumental techniques for the early diagnosis and treatment of chronic degenerative diseases; and identification of new therapeutic principles.

Groups offering hosting/training:

• Group 1: Adult general population cohorts followed longitudinally and large databases: (PI: Luigi Palmieri, luigi.palmieri@iss.it; +39 06 4990 4226). Assessment of cardiovascular risk and favourable risk profile; development of new technologies for data collection and analysis and for international cooperation in prevention.
• Group 2: Improvement of medical clinical devices for cardiovascular diseases : (PI: Giovanni Calcagnini, giovanni.calcagnini@iss.it; +38 06 4990 2862). Technical-scientific activities for the definition and evaluation of the professional figures of product specialists for medical devices, in particular pacemaker devices and implantable defibrillators; realization of experimental set-up for the acquisition of cardiovascular and neurovegetative signals in magnetic resonance.
• Group 3: Study of the physiopathological mechanisms underlying inflammatory and thrombotic events in subjects at cardio-cerebrovascular risk. :
  - PI: Rachele Riganò, rachele.rigano@iss.it; +39 06 4990 2760. Evaluation of the oxidative stress in the activation of pro-inflammatory autoimmune reactions directed to the endothelium and responsible for the progression of atherosclerotic plaque.
  - PI: Raffaella Guerriero, raffaella.guerriero@iss.it; +39 06 4990 2987. In vivo and in vitro studies of platelet factors involved in inflammatory and thrombotic processes.
• Group 4: Prevention and etiopathogenesis of diabetes, thyroid diseases and their complications with a high social-health impact.
  - PI: Flavia Pricci, flavia.pricci@iss.it; +39 06 4990 6149. Search for new interfering substances, metabolic control markers and progression of diabetes.
  - PI: Claudia Giacomozzi, claudia.giacomozzi@iss.it; +39 06 4990 2864. In vivo studies relating to diagnosis, prevention and treatment of diabetes complications related to alterations of the neuro-musculo-skeletal system, by means of innovative instrumental methods.
  - PI: Antonella Olivieri, antonella.olivieri@iss.it; +39 06 4990 6150. Research of genetic and environmental risk factors of congenital hypothyroidism (IC), optimization of neonatal screening procedures for IC and definition of the reference limits of neonatal TSH as a biomarker; studies on the thyroid effects of the interaction between iodic nutrition and exposure to pesticides with thyrostatic action.
• Group 5: Healthy-Active Ageing. Epidemiological aspects and assessment tools for recovery and functional maintenance of the elderly : (PI: Lucia Galluzzo, lucia.galluzzo@iss.it; +39 06 4990 4198). Follow-up and analysis of epidemiological data of two cohorts of elderly (ILSA and IPREA) for the study of the main age-related risk factors, including those associated with cognitive impairment and dementia; The frailty of the elderly: creation of a shared model for the prevention and management of frailty.

The research activity at the Department of Oncology and Molecular Medicine is mostly preclinical and encompasses different aspects of cancer biology. We have broad experience in cellular models with cells of different origin for the study of the molecular alterations at the basis of cancer and the identification of potential targets of therapy. Several models of cancers are also available in vivo in syngeneic or xenogeneic settings to follow up in vitro findings. The interaction of host immune system with cancer cells in vitro and in vivo is also a focus of our research as well as the genetics of tumors and the epidemiology of cancer.

Groups offering hosting/training:

• Tumour Immunology (PI: Dr. Lucia GABRIELE, lucia.gabriele@iss.it; +39 06 4990 6025). The Section of Tumour Immunology is fully committed to fostering innovative research in basic science and translational studies aimed at discovering the fine mechanisms underlying the crosstalk between cancer and immune system as well as at developing novel immunotherapeutic strategies for cancer treatment. In particular, the research topics are immunotherapy-based anticancer strategies, cancer vaccines, combination anticancer therapies, immuno-oriented drug repurposing, immunomodulation and immunomonitoring, immune biomarkers, and immune system-cancer-based organs-on-chip. Both human and mouse in vitro and vivo models are used (e.g. cell line cultures, tumour-derived primary cell cultures, primary immune cell cultures, syngeneic tumour mouse models, immune genes-deficient mouse models, human xenograft tumour models). Likewise, multiple techniques are employed (e.g. in vitro immune cell functional assays, multiparametric flow cytometry, RNA-sequences, qRT-PCR, microfluidic devices).
• Epidemiology of tumors and genetic diseases (PI: Dr. Emilia STELLACCI, emilia.stellacci@iss.it tel. +39 06 4990 3197 /2569). The research activity carried out by our group is aimed at studying the molecular basis of genetic diseases and cancer. Furthermore, functional genomic studies are directed to understanding the pathogenetic mechanisms underlying genetic diseases by using in vitro (biochemical studies and cellular models) and in vivo (C. elegans) approaches. In the field of oncological genetics and oncogenomics, our activity is focused at understanding the molecular basis of Mendelian diseases characterized by susceptibility to the onset of neoplasms, including RASopathies, and the role played by these new oncogenes / tumor suppressors in neoplastic transformation. Techniques used: The group offers access to different technologies (sequencing, bioinformatics, imaging, cellular and molecular biology methods, C. elegans model for developmental biology and neurobiology and for modelling genetic diseases by using CRISPR-Cas9 genome editing).
• Cellular and molecular biology of tumors (PI: Dr. Lucia RICCI VITIANI, lucia.riccivitiani@iss.it; +39 06 4990 3673). The topic of the research activity is the isolation and characterization of Cancer Stem Cells (CSCs) from colorectal cancer (CRC) and glioblastoma (GBM). Particularly, this group contributed to demonstrate the existence of hierarchical organization in CRC cancer according to the "Cancer Stem Cell" hypothesis (PMID:17122771). Moreover, in the field of GBM this group highlighted the correlation between GSC generation and poor prognosis, reinforcing a role for this subpopulation in tumor development and progression, and also contributed to provide further evidence of chemotherapy resistance of this subpopulation of tumor cells (PMID:28204560), as well as, their contribution to tumor vascularization (PMID:21102434). More recently the research activity has been focused on the molecular characterization of GSCs by gene expression profiling, NMR spectroscopy, phosphoproteomic analysis of signal transduction pathway and nonconding-RNAs expression profiles with the aim of finding correlation with clinical behavior.
• Cellular and molecular biology of tumors (PI: Dr. Nadia FELLI, nadia.felli@iss.it; +39 06 49902716). Emerging data support the rationale of combined therapies in advanced melanoma. The association of drugs with different mechanisms of action can reduce the frequency of resistant clone selection. Accumulating evidences suggested that non-coding RNAs (ncRNAs) (e.g. microRNAs and long ncRNAs) play important roles in all the key cellular processes. Our group demonstrated that microRNA126 (miR126) is a tumour suppressor in metastatic melanoma (Felli N. et al 2013; Felli N. et al 2016). By screening a library of 349 anticancer compounds, we then selected PIK-75, an inhibitor of the PI3K/AKT pathway, as top active drug. This drug was utilized alone or in combination with Vemurafenib, the first BRAF inhibitor approved for patients with melanoma harboring BRAFV600E mutation. In our hands, the presence of miR126 significantly increased PIK-75. The effectiveness of miR126 to boost up PIK-75 action was demonstrated in patient-derived cells, in resistant cell lines and in in vivo models (Pedini F. et al, 2019). The topic of our research activity is to develop a system able to deliver this miR into metastatic melanoma cells in combination with PIK-75 and/or Vemurafenib. For this purpose, we intend to produce different types of nanoparticles containing miR126, possibly conjugated with antibodies specific for metastatic melanoma cells. As second approach, we propose to use miR126 enriched exosomes (EXO) as vectors for delivery system. Nano- and EXO-miR126 will be tested both in vitro and in vivo. Moreover, we will study the tumour micro-environment cross-talk between resistant and sensitive metastatic melanoma cells, with particular attention to exosome-mediated transfer of ncRNAs.
• Preclinical models of tumors (PI: Dr. Ugo TESTA, ugo.testa@iss.it; +39 06 49902422). The topic of the research activity is the induction of the differentiation of leukemic cells from Acute Myeloid Leukemia (AMLs) and Myelodysplastic Syndrome (MDSs). Our group historically contributed to demonstrate the key role of retinoic acid and arsenic trioxide in the induction of differentiation of Acute Promyelocytic Leukemias (APLs). Taking advantage on this background, the actual research is devoted to explore the role of drugs that act as epigenetic modifiers, such as histone demethylase inhibitors, as inducers of leukemic cell differentiation by the study of morphological, cellular, biochemical and molecular markers of cell differentiation. This research involves the study of leukemic stem cell populations.

Fighting against infectious diseases, by promoting and coordinating public health and research activities. Surveillance and control of bacterial, viral, fungal and parasitic diseases. Research on mechanisms underlying both protective and harmful immune responses against pathogens, antimicrobial treatment and vaccines.

Groups offering hosting/training:

• Immunology Section (PI: Eliana Marina Coccia, Eliana.coccia@iss.it; +39 06 4990 3638): understanding how the immune response against pathogens contributes to the induction of autoimmunity or chronic inflammation; host-pathogen interaction; set-up alternative method to animal testing to evaluate vaccine potency and pyrogenicity. Research line/topic in which the group offers secondment/training. Techniques used: RNA and protein analysis, cytometry, cell isolation and characterization, cytokine analysis.
• Immunology Section (PI: Martina Severa, martina.severa@iss.it; 06 4990 3638): investigating cell mechanisms behind the metabolic reprogramme associated to lymphocyte response and control of inflammation in health status and in autoimmune disorders. Techniques used: multiparametric flow cytometry, isolation of lymphocytes and in vitro characterization, quantitative real time PCR and western blotting, cytokine analysis.

The scientific programs for neurodegenerative and neuroinflammatory diseases aim at clarifying the aetiology, the pathogenic pathways and the genetic modifiers responsible for disease onset and clinical phenotype, at improving patient care, and at identifying new therapeutic targets. Moreover, the identification of new biomarkers and strategies for early diagnosis is a pivotal aspect of our research activities.

Groups offering hosting/training:

Unit ‘Clinical studies, diagnosis and therapy of central nervous system degenerative diseases’

• Prion diseases (PI: Dr. Anna Poleggi, anna.poleggi@iss.it; +39 0649903088). Identification of genetic modifiers of disease age at onset/phenotype and functional validation in genetic and sporadic human prion diseases. Techniques: Gene expression studies, Sanger and NGS genotyping, gene silencing by CRISPR-Cas9.
• Biochemistry of misfolded proteins (PI: Dr. Franco Cardone, franco.cardone@iss.it; +390649903313). In vivo amplification of protein aggregates for the diagnosis of prion diseases and other human amyloidoses; study of basic mechanisms of amyloid formation Techniques: Real-Time Quaking Induced Conversion (RT-QuIC) assay.

Unit ‘Demyelinating and inflammatory diseases of the nervous system’

• Neuropathology of multiple sclerosis (PI: Dr. Barbara Serafini, Barbara.serafini@iss.it; +390649903542). Characterization of the immunopathological mechanisms leading to brain/spinal cord damage. Techniques: histopathology, immunohistochemistry, immunofluorescence, in situ hybridization, laser capture microdissection for gene expression analysis in human tissue samples, microscopy and image analysis.
• Molecular pathogenesis of genetic leukodystrophies (PI: Dr. Elena Ambrosini, elena.ambrosini@iss.it; +390649902037). Identification of disease mechanisms in relevant patient-derived cellular models. Techniques: Molecular/cellular biology, biochemistry, human iPSC-derived glial cell cultures, immunofluorescence and confocal microscopy, cell transfections, qPCR, site-specific mutagenesis, cloning, western-blot analysis, pull-down, immunoprecipitation, protein interaction assays.
• Remyelination and neuroprotection strategies (PI: Dr. Cristina Agresti, cristina.agresti@iss.it; +390649902037). Identification of small molecules capable of promoting myelin regeneration in multiple sclerosis. Techniques: Cellular and molecular biology techniques, murine oligodendrocyte progenitor and organotypic brain slice cultures, drug screening, drug-target identification.
• Biomarkers in multiple sclerosis (PI: Dr. Paola Margutti: paola.margutti@iss.it; +390649902424). Identification of microvescicle-associated molecules potentially useful for disease diagnosis and prognosis and assessment of therapy response. Techniques: Purification and characterization of microvesicles and exosomes, flow cytometry, cellular and molecular biology techniques, immunochemical techniques, western blot and gene expression analysis of exosomes.

The National Center for HIV/AIDS Research (CNAIDS) has been established in 2005. Mission of CNAIDS is the fighting to HIV/AIDS and associated diseases through the development of innovative vaccines and therapeutic approaches based on studies on HIV immune-pathogenesis and epidemiology. The Center carries out translational research programs, from basic research to clinical studies in order to develop preventive and therapeutic products. Most advanced products are a therapeutic vaccine against HIV/AIDS, based on the viral Tat protein and e new therapy for Kaposi’s sarcoma, both ready for phase III clinical studies.

The Centers also conducts studies targeted at evaluating presence and prevalence of HIV and the co-infecting HBV and HCV genetic forms and of HIV ART-resistance variants in both the general and fragile populations, such as migrants, inmates, drug users, homosexuals and sex workers.

CNAIDS has established collaborations with other public and private institutions, as well as industries, through the coordination (or the collaboration in) of many national and international research programs. This has assured implementation and transfer of new preventative and therapeutic products to citizens and ownership of intellectual properties.

Due to its scientific and technological knowledge, its leadership in national and international networks and its multiple cooperation programs with the Developing Countries and with Humanitarian Agencies, the National Center for HIV/AIDS Research is a national and international reference subject for the fight against HIV/AIDS.

Groups offering hosting/training:

• Unit of Surveillance and pathogenesis of HIV variants and associated co-infections (PI: Stefano Buttò, stefano.butto@iss.it, tel: +39 06 4990 3249). The Group carries out molecular epidemiological studies on HIV, HBV and HCV in Italy, Europe and Developing countries. Techniques: PCR, Sanger and NGS sequencing, phylogenetic trees.
• Research & Development Section (PI: Paolo Monini, paolo.monini@iss.it, tel: +39 06 4990 3217). The groups conducts studies on HIV reservoirs and models of HIV latency/reactivation. Techniques: cell biology and cell culture models; cell transfection, transduction, infection; multicolour flow cytometry, molecular biology, molecular virology and cloning; qPCR, DNA sequencing, biostatistics.

The NCRD, directed by Domenica Taruscio, is the National and International reference point for rare diseases (RD): scientific research, technical-scientific coordination, public health, surveillance as well as monitoring of the national rare diseases network through the national register. Priority topics include: translational research, promoting high-quality diagnosis and care, training of national health services staff, providing information on relevant services, legislation and regulations, promoting the social inclusion of patients, and participating in the development of European and international programmes and networks on RD. Specific activity areas are: epidemiological surveillance of RD: National Registry and rare disease specific registries; Primary and secondary prevention of rare diseases; National external quality assurance of genetic tests; Undiagnosed rare diseases.

Groups offering hosting/training:

• Epidemiologic surveillance of rare diseases: (PI: Paola Torreri; paola.torreri@iss.it, +39064990 4408). The Group coordinates the National Registry for Rare Diseases and disease specific registries (http://www.registrare.org/). Epidemiologic and statistics methods. Interoperability and data sharing strategies at international level.
• Primary and secondary prevention of rare diseases: (PI: Paolo Salerno, paolo.salerno@iss.it, +39 06 4990 4405; Yllka Kodra, Yllka.kodra@iss.it, +39 06 4990 4365). Primary prevention of congenital anomalies: research on risk factors, risk communication, health education and empowerment of professionals and citizens, and surveillance at National Level. Secondary prevention: coordination of activities of the National programme of newborn screening of 40 rare metabolic diseases. This activity extends from monitoring performances of screening centers to the National surveillance.
• National External Quality Assessment programme for genetic testing (PI: Federica Censi; fedirica.censi01@iss.it; +39 06 4990 2805): assessing and reviewing the control quality programme of national laboratories (> 120) performing diagnostic genetic test for rare diseases. The assessment programme includes: genotyping, banding quality, karyotype reconstructions, completeness/accuracy of the analysis, appropriate use of International System for Human Cytogenetic Nomenclature (ISCN), description and interpretation of the results, completeness/accuracy and timeliness of the reports.
• Undiagnosed Rare Diseases (PI: Dr. Marco Salvatore, marco.salvatore@iss.it; +39 064 9904363): Rare diseases lacking of a diagnosis are a complex ensemble including: groups of unnamed disorders with common characteristics, phenotypically well described diseases with an unknown molecular basis, and/or whose pathogenesis involves unknown, non-genetic factors. Use of international database to collect and analyze phenotypic information of patients with genetic disorders; WES; NGS; functional studies on identified variants.

Bioinformatics Barcelona Association – BIB, is a non-profit association for the provision of education and training, the promotion of advanced research, knowledge and technology transfer, the stimulation of competitiveness and innovation within the industrial sector, and the provision of greater visibility as an international node in the field of Bioinformatics. BIB will facilitate the Fellows' access to its 55 member organisations both for research stays and training opportunities. The Fellows will enjoy the same benefits as BIB members in all training activities organised by BIB.

If you are interested in carrying out a research stay in one of the BIB member organisations, please contact coordination@bioinformaticsbarcelona.eu and imibic.p2med@imibic.org.

The University of Vic - Universitat Central de Catalunya (UVic-UCC) is a young and dynamic institution located in Vic, Barcelona, devoted to deliver teaching and innovative research to the highest level of quality. The hosting group is embedded within the group of Bioinformatics and Statistical medicine (https://mon.uvic.cat/bms/), a consolidated group recognized by Catalan government (2014SGR-596) which in turn is part of the Faculty of Science and Technology (https://www.uvic.cat/en/faculties-and-colleges). The Bioinformatics and Medical Statistics is an interdisciplinary group that includes life sciences, statistics and bioinformatics in a Systems Biology framework.

Groups offering hosting:

• PI: Narcis Fernandez, narcis.fernandez@uvic.cat (ORCID ID: 0000-0002-6421-1080) RyC Fellow. Our research is eminently technology-oriented and involves the development of novel computational tools and resources tailored to tackle relevant questions in different aspects of biomedical science and biotechnology. It also includes collaborative projects with experimental groups whereby computational-driven hypotheses are used to guide and complement experimental research and data. Such examples include a range of multidisciplinary projects, ranging from molecular immunology, virology, pharmacology, protein design, genomics, data mining, and drug discovery. Over the last five years we have addressed computational studies of protein-protein interactions (PPI) at different levels: genome wide interactomes, structural modelling of protein complexes, characterization of protein interfaces, and the exploitation of the druggability of PPIs using de novo designed peptides. Our research also includes the study of genetic changes linked to diseases, the modelling of their impact at functional level and developing technologies to harness the power of ‘omic technologies or the so-called big data. More information at http://www.bioinsilico.org and http://interactomix.com

The Universitat Internacional de Catalunya shares with UVIC-UCC the youth and ambition to become a reference institution in research within the Catalan University system. The area of Health and Life Sciences, located in the premises of the Hospital General de Catalunya, in Sant Cugat del Vallès (15 minutes drive from central Barcelona), aims at becoming a pole of attracting for research talent around a comprehensive teaching structure including Medicine, Odontology, Nursery, Psychology, Physiotherapy, Biomedicine and Bioengineering. To provide support for this variety of studies, the Department of Basic Sciences incorporates lecturers and researchers in fields that range from basic molecular biology through materials engineering. The department is located in the premises of the Hospital and is about to open a new plant devoted to bioengineering research. The team participating in the project (the Computational Biochemistry and Biophysics lab) is led by Jordi Villà, also member of the Bioinformatics and Medical Statistics research group, in collaboration with the colleagues in Vic.

Groups offering hosting:

• PI: Jordi Villà-Freixa, jvilla@uic.cat (ORCID ID: 0000-0002-6359-3929) Full professor. The research of the Computational Biochemistry and Biophysics lab, currently split between the Universitat de Vic - Universitat Central de Catalunya (located in Vic) and the Universitat Internacional de Catalunya (located in Sant Cugat), deals with the use of simulation tools to explore the energy landscapes of biomolecules, in order to assess structure-function relationships in a variety of issues, including protein-ligand interactions, PPIs, and, most importantly, enzyme reactivity. The tools that we use include Molecular Dynamics, Monte Carlo simulations, free energy calculations, docking and structure modelling. In addition, we are active developers of new tools related to our fields of expertise, and we are currently working on improvements in OpenMM Python libraries to cope with structure based potentials and advanced features like empirical valence bond (EVB) calculations to assess enzymatic free energy profiles.

Groups offering hosting:

• PI: Toni Gabaldón, toni.gabaldon@bsc.es (www.cgenomics.org) ICREA Research Professor. The research of the Comparative Genomics group is performed at both the Barcelona Supercomputing Centre (BSC, www.bsc.es) and the Institute for Research in Biomedicine (IRB, www.irb.org). Our group is generally interested in how organisms evolve and interact with their environments, including host-pathogen interactions. We use genomics, meta-genomics and population genomics approaches to address host-pathogen interactions and have long-term expertise in genome sequencing and comparison, and in microbiome analysis. We would be happy to host postdocs interested in learning how to deal with large-scale genomic or meta-genomics sequencing data and properly interpreting it in the context of a project related to human disease, including infectious diseases.

• PI: Marta Mele, marta.mele@bsc.es, +34 934137728. The Transcriptomics and Functional Genomics Lab is interested in understanding how the information encoded in our genome determines gene expression variation across individuals and tissues. To address this, we use a combination of cutting-edge computational analyses, next generation sequencing, and high-throughput functional assays. Our goal is to perform integrative analyses of “-omics” data to ultimately understand how expression changes in both coding and non-coding genes are associated with disease. Research areas: transcriptomics, functional genomics, personalized medicine, long non-coding RNAs. Web: https://www.bsc.es/discover-bsc/organisation/scientific-structure/transcriptomics-and-functional-genomics-lab-tfgl

Program of Predictive and Personalized Medicine of Cancer (PMPPC)

Groups offering hosting:

• Cancer genetics and epigenetics PI: Sergio Alonso, salonsou@igtp.cat, +34 93 554 3050 extn: 3063, (ORCID: 0000-0001-6497-892X). Our group studies tumours from the intestinal tract (i.e. colon, and stomach) that develop when the cell machinery preserving the integrity of the genome is not working properly. Genome integrity is tightly controlled by a complex multi-layer machinery that can be disrupted by genetic and epigenetic alterations. Computational modeling of these layers using systems biology has become an essential tool to explore this complexity, elicit novel mechanisms driving tumorogenesis, identify novel therapeutic targets and cancer biomarkers. The research lines of our group include: Molecular mechanisms for gastrointestinal cancer pathogenesis; Epigenetic biomarkers for cancer susceptibility and metastatic spread; DNA demethylation, predictive for the development of multiple colon cancers; Genomics and epigenomics of colorectal cancer prediction.

The University of Barcelona founded in 1450, attracts over 60,000 students a year. It is positioned at Ranking 69th in the world in the Reuters Top 100: The World’s Most Innovative Universities, and 19th in the 2018 edition of the Europe Teaching Rankings and the highest-ranked public university in Spain (Times Higher Education). The “Computer Vision and Machine Learning at the University of Barcelona” (CVUB) is a consolidated research group involving highly experienced Computer Vision and Machine Learning researchers from the University of Barcelona. Its main goal is to explore novel Computer Vision and Machine Learning algorithms to address problems from the real world, with special focus on healthcare among others. CVUB has special interest in:
a) Predictive Analytics using machine learning, especially deep learning, data mining, predictive modeling and artificial intelligence to interpret big data and make predictions about future;
b) Computer Vision by designing deep learning methodologies to solve problems like: visual representation and scene understanding, object recognition, motion analysis, egocentric vision, medical imaging and human behaviour analysis.
CVUB believes that Computer Vision technology should stay very close to the society. It collaborates with and completed many international patents and technological transfers to companies like Boston Sci. (USA), GivenImaging Medtronics (USA), and hospitals like Hospital "Vall d'Hebron" (Spain), Consorci Sanitari de Terrassa (Spain), University Hospital "Germans Trias i Pujol" (Spain), Hospital Clinic (Spain), etc.

Projects in Medical imaging and Healthcare offering hosting:

• Computer Vision and Deep Learning for Food intake monitoring (PI: “Petia Radeva“, radevap@gmail.com). The group is developing novel algorithms for food recognition from images taken by a smartphone, camera or downloaded from the internet. The group applies novel Transfer learning (Multi-task learning, Domain adaptation, etc.) to construct a Food ontology and integrates it in an end-to-end framework. The group applies this innovation results in 3 European and 3 national projects related to nutrition monitoring of elderly, kidney transplant, diabetic and cardiac patients.
• Advanced breast image analysis (PI: Oliver Díaz, o.diaz.montesdeoca@gmail.com) focusing on X-ray mammography, tomosynthesis or MRI technologies in collaboration with local hospitals. The group research lines are aimed to overcome several challenges for breast cancer diagnosis: the development of automated (i.e. deep learning based) pipelines for lesion detection, segmentation or/and tissue classification. In addition, the group has interested in the study of the physics behind imaging through Monte Carlo simulations of particles and the use of depth and pressure sensors to monitor the breast compression during mammography. Furthermore finite element analysis has been used to develop compressible biomechanical breast models.
• IntraVascular UltraSound (IVUS) analysis (PI: Simone Balocco, balocco.simone@gmail.com). Atherosclerosis is a leading cause of cardiovascular diseases often leading to myocardial infarction. IVUS is a catheter based technique used for the diagnosis and treatment of coronary arteries. The research of the group focuses on creating Computer Vision and Deep Learning tools for the IVUS image analysis. The main applications include the analysis ofaterosclerotic plaque development and rupture, the early detection of cardiovascular diseases and the Computed-assisted treatment planning. The research is developed in collaboration with clinicians belonging to a major clinical center in Barcelona.
• Computer Vision and Deep Learning for Active Aging (PI: Petia Radeva, radevap@gmail.com). The group applies last advances in Deep learning and Computer vision to analyse and recognize the Activities of Daily Living of elderly from images acquired by a wearable camera. The final purpose is to early detect changes in behaviour of elderly and promote physical activities of elderly for well-being and long-life. This project is developed in close collaboration with a company for social services that works with 30 centers in Catalunya (Spain).
• Multi-centre data sharing and multi-study personalised medicine research in cardiology (PI: Karim Lekadir, karim.lekadir@upf.edu). This project is part of the euCanSHare EU project (2018-2022) coordinated by our group and in which participate 16 institutions across Europe and Canada. With this project, the group has access to an unprecedented amount of cardiac imaging datasets, specifically 35,000 cardiac MRI datasets, for developing new machine and deep learning techniques with much higher statistical power than ever before. Furthermore, we have access to genomic, lifestyle and clinical information for building integrative predictive models of cardiac diseases and events, such as diabetic cardiomyopathy and myocardial infarction. This work will be developed in collaboration with Bart Hospital London, McGill University in Canada, and Hamburg Clinical University in Germany. Concretely, we work on three themes:
  1) Multi-centre deep learning based segmentation of cardiac MRI datasets
  2) Multi-centre cardiovascular radiomics for advanced disease phenotyping.
  3) Multi-factorial integrative methods to build predictive models integrating imaging, genomics and lifestyle data.
• Personalised disease monitoring and predictive modelling based on longitudinal exposome, wearable and sensor data (PI: Karim Lekadir, karim.lekadir@upf.edu). This work is part of a new EU project called LONGITOOLS (2020-2024), in which our group leads a WP that aims to build an app for person-specific disease monitoring integrating wearable and sensor data such as air pollution, noise, humidity, temperature, exercise and other lifestyle data such as diet. From a methodological point of view, this will include the development of deep learning based predictive models integrating such exposome data on a longitudinal scale, as well as error and uncertainty estimation. This work will be developed in collaboration with the University of Oulu in Finland, Erasmus Medical Centre Rotterdam and an Italian SME Ab.Acus.
• Brain image analysis (PI: Laura Igual, ligual@ub.edu): The group works in developing new techniques for brain image analysis. In particular, the interest is to define new explainable Deep Learning models to solve the problem of brain segmentation and classification combining different datasets of MRI images. Explainable models will allow to understand the neural network results as well as to validate that the method is based on proper medical imaging features.
• Modelling movement control and decision-making (PI: Ignasi Cos, ignasi.cos@ub.edu). The group applies cutting edge expertise in computational models of human motor control to explain the neural mechanisms driving the selection of specific parameters of movement and the criteria for decisions between actions. The ultimate goal is to reach a formal, unified model of motor control capable of describing the relationship between physiological aspects such as motivation, onto the principles of motor control, both under healthy and pathological states. This is performed in collaboration with the Department of Kinesiology at the University of Montreal, Canada.
• Characterization of mental states of motivation and music (PI: Ignasi Cos, ignasi.cos@ub.edu): the group applied cutting edge machine learning and connectomics’ techniques that characterize task-related mental states, with specific emphasis on motivation, from EEG recordings. In particular, we are developing algorithms that provide a formal network characterization of the brain as a function of mental states related to motivation, music, and movement related disorders, such as Parkinson’s disease, and controlled from a behavioural perspective. This is developed in collaboration with the Hospital Clinic at the University of Barcelona, and the University of Aarhus, Denmark.

Groups offering hosting:

• Comparative and Functional Genomics Group, PI: Mario Cáceres, mcaceres@icrea.cat, +34935868726. Inversions are one type of structural variants linked to phenotypic differences and adaptation in multiple organisms. However, there is still very little information about the functional and evolutionary impact of polymorphic inversions in the human genome due to the difficulty of their detection. In particular, an important part of the genetic variation of phenotypic traits is still unexplained. Therefore, our group is focused in combining all the inversion genotyping data that we have generated and the available information from genome-wide association studies to determine for the first time the contribution of these variants to complex disorders, such as neurodegenerative diseases, diabetes, inflammatory diseases or cancer, helping to fulfill precision medicine promises.

• Protein Folding and Conformational Diseases, PI: Salvador Ventura, salvador.ventura@uab.es, +34935868956. Our lab uses a multidisciplinary approach to address fundamental aspects of protein folding, misfolding and aggregation. In addition to define the basic mechanistic principles underlying these processes, we aim to understand how their deregulation leads to the onset of human neurodegenerative diseases and to develop innovative therapeutics to target these pathologies. Moreover, this knowledge should allow us to design and produce novel and better protein-based biopharmaceuticals as well as the development of new self-assembled materials for nanotechnology applications.

The University of Girona (Universitat de Girona, UdG, www.udg.edu) is located in the city of Girona, Catalonia, Spain. It was reconstituted as a university in 1991, although its origins go back to the General Studio, an entity created in 1446. The UdG consists of 3 campuses and several buildings across Girona: Montilivi, Barri Vell, Centre, and the Scientific and Tecnological Park. Despite being a young and relatively small university, it has been placed within the top 4% of universities in the World University Rankings 2018.

The Image Analysis Lab (https://visio.udg.edu/) is one of the four research labs of the Computer Vision and Robotics Institute (VICOROB), which employs more than 40 people and has more than 20 years of experience in research at the Universitat de Girona (UdG). The lab works on the development and optimisation of methods for the analysis of the data, with a particular interest in the study of medical images. To this end, the IAL group develops computer vision, machine learning and image processing algorithms which include techniques such as image segmentation, image characterization, pattern recognition, object detection, statistical signal processing, and image registration. Furthermore, the capabilities of IAL include image analysis for a variety of imaging modalities including X-rays, magnetic resonance imaging (MRI), ultrasound (US), and computed tomography (CT).

The main research lines, and groups offering hosting, are:

• Neurocomputing. PI: Prof. Xavier Lladó (xavier.llado@udg.edu). Development and validation of automatic tools which allow detection, segmentation and characterization of brain MRI images, with a particular interest in multiple sclerosis lesions. These tools are very useful to diagnose and follow-up the disease by looking at the evolution of brain lesions and brain atrophy in patients. The aims of our projects in this line are to develop new automatic computerized tools to extract robust MRI biomarkers. This will enable a new paradigm that will provide the basis for improving the diagnosis and monitoring of MS and stratification of patients by introducing objectivity and simplifying the daily clinical practice.

• Computer Aided Diagnosis of cancer. PI: Dr. Robert Martí (robert.marti@udg.edu). The group is engaged in Computer-Aided Detection (CADe) and Computer-Aided Diagnosis (CADx) of breast cancer in X-ray mammograms, breast US and breast MRI. Furthermore, the group is currently developing computer application tools to combine breast images from different modalities (digital mammography, MRI and US). The aim of these tools is to help radiologists to improve breast cancer diagnosis by producing more efficient detection and prediction models.

Crosadis is a new transversal programme of the Carlos III Health Institute (Instituto de Salud Carlos III - ISCIII). Crosadis integrates a research unit in Chronic Diseases, another one in Digital Health and a research unit in Nursing and Healthcare services. This research program addresses the challenges of chronicity from an integrative perspective, combining basic and translational research with the use of new digital health technologies and the application of systemic approaches for the design, implementation and evaluation of personalized service delivery interventions. Crosadis connects different health related disciplines, technologies, healthcare services, with the aim of contributing to patient empowerment and reducing the impact that chronic diseases have on the population and healthcare systems.

Crosadis offers research stays and learning opportunities within its three research areas:

1. Digital Health
2. Research in Nursing and healthcare services
3. Physiopathology of chronic diseases

For more information about Crosadis, please contact mmoreno@isciii.es

The Nursing and Healthcare Research Unit (Investén-isciii) of the “Instituto de Salud Carlos III” was created in 1996. Its objective is to promote research in health care in nursing and other related disciplines. The main activities of the Unit are to promote and coordinate multidisciplinary research in health care, and to encourage knowledge transfer to clinical practice, so the care provided in health institutions is of high quality and based on valid and reliable research results. The Unit has collaboration agreements within the Spanish National Health System with institutions of all the regions, as well as with international institutions.

Investén-isciii actively promotes the transfer of knowledge to clinical practice for a significant number of clinical researchers, mainly nurses and physiotherapists. By participating in Investén-isciii programs, young researchers will improve their future career perspectives and employability in the field of healthcare and health services.

If you decide to carry out a research stay with us, we will provide you with opportunities for collaboration across Spain. This offers a unique opportunity to carry out a research program including the possibility to obtain patient data, implement and evaluate clinical interventions as well as full training in Evidence-Based Clinical Practice. Taking part in the Investén-isciii research activities in cooperation with various international institutions will further expand your professional experience.

Groups offering hosting/training:

• Group 1 (PI: Teresa Moreno-Casbas RN, PhD, FEAN, FAAN. mmoreno@isciii.es. +34637390052).Our research program in “Aging and Fragility” includes the prevention and treatment of dysphagia, prevention and treatment of falls, the study of chronodisruption, the prevention of delirium, dementia and depression and finally the detection and management of pain in people with cognitive impairment.
• Group 2 (PI: Esther González-María RN, PhD. esthergomaria@isciii.es. +34918222548). Our Research activities are related to knowledge transfer methodology, including implementation training as well as national projects implementing guidelines in clinical practices. The group also works in evaluation of this implementation projects  through development of nursing sensitive outcomes indicators.