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2. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, N., Almouzni, G., Gorski, S., Aerts, S., Amit, I., Bertero, M., Bock, C., Bredenoord, A., Cavalli, G., Chiocca, S., Clevers, H., Strooper, B., Eggert, A., Ellenberg, J., Fernández, X., Figlerowicz, M., Gasser, S., Hubner, N., Kjems, J., Knoblich, J., Krabbe, G., Lichter, P., Linnarsson, S., Marine, J., Marioni, J., Marti-Renom, M., Netea, M., Nickel, D., Nollmann, M., Novak, H., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F., Torres-Padilla, M., Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M., Voet, T., Alberi, L., Alexander, S., Alexandrov, T., Arenas, E., Bagni, C., Balderas, R., Bandelli, A., Becher, B., Becker, M., Beerenwinkel, N., Benkirame, M., Beyer, M., Bickmore, W., Biessen, E., Blomberg, N., Blumcke, I., Bodenmiller, B., Borroni, B., Boumpas, D., Bourgeron, T., Bowers, S., Braeken, D., Brooksbank, C., Brose, N., Bruining, H., Bury, J., Caporale, N., Cattoretti, G., Chabane, N., Chneiweiss, H., Cook, S., Curatolo, P., de Jonge, M., Deplancke, B., de Witte, P., Dimmeler, S., Draganski, B., Drews, A., Dumbrava, C., Engelhardt, S., Gasser, T., Giamarellos-Bourboulis, E., Graff, C., Grün, D., Gut, I., Hansson, O., Henshall, D., Herland, A., Heutink, P., Heymans, S., Heyn, H., Huch, M., Huitinga, I., Jackowiak, P., Jongsma, K., Journot, L., Junker, J., Katz, S., Kehren, J., Kempa, S., Kirchhof, P., Klein, C., Koralewska, N., Korbel, J., Kühnemund, M., Lamond, A., Lauwers, E., Le Ber, I., Leinonen, V., Tobon, A., Lundberg, E., Lunkes, A., Maatz, H., Mann, M., Marelli, L., Matser, V., Matthews, P., Mechta-Grigoriou, F., Menon, R., Nielsen, A., Pagani, M., Pasterkamp, R., Pitkänen, A., Popescu, V., Pottier, C., Puisieux, A., Rademakers, R., Reiling, D., Reiner, O., Remondini, D., Ritchie, C., Rohrer, J., Saliba, A., Sanchez-Valle, R., Santosuosso, A., Sauter, A., Scheltema, R., Scheltens, P., Schiller, H., Schneider, A., Seibler, P., Sheehan-Rooney, K., Shields, D., Sleegers, K., Smit, A., Smith, K., Smolders, I., Synofzik, M., Tam, W., Teichmann, S., Thom, M., Turco, M., van Beusekom, H., Vandenberghe, R., den Hoecke, S., de Poel, I., van der Ven, A., van der Zee, J., van Lunzen, J., van Minnebruggen, G., Paesschen, W., van Swieten, J., van Vught, R., Verhage, M., Verstreken, P., Villa, C., Vogel, J., von Kalle, C., Walter, J., Weckhuysen, S., Weichert, W., Wood, L., Ziegler, A., Zipp, F., HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., Medical Research Council (MRC), UK DRI Ltd, TWINCORE, Zentrum für experimentelle und klinische Infektionsforschung GmbH,Feodor-Lynen Str. 7, 30625 Hannover, Germany., Barcelona Supercomputing Center, LifeTime Community Working Groups, Cardiology, Neurology, Institut de génétique humaine (IGH), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Human genetics, Rajewsky N., Almouzni G., Gorski S.A., Aerts S., Amit I., Bertero M.G., Bock C., Bredenoord A.L., Cavalli G., Chiocca S., Clevers H., De Strooper B., Eggert A., Ellenberg J., Fernandez X.M., Figlerowicz M., Gasser S.M., Hubner N., Kjems J., Knoblich J.A., Krabbe G., Lichter P., Linnarsson S., Marine J.-C., Marioni J.C., Marti-Renom M.A., Netea M.G., Nickel D., Nollmann M., Novak H.R., Parkinson H., Piccolo S., Pinheiro I., Pombo A., Popp C., Reik W., Roman-Roman S., Rosenstiel P., Schultze J.L., Stegle O., Tanay A., Testa G., Thanos D., Theis F.J., Torres-Padilla M.-E., Valencia A., Vallot C., van Oudenaarden A., Vidal M., Voet T., Alberi L., Alexander S., Alexandrov T., Arenas E., Bagni C., Balderas R., Bandelli A., Becher B., Becker M., Beerenwinkel N., Benkirame M., Beyer M., Bickmore W., Biessen E.E.A.L., Blomberg N., Blumcke I., Bodenmiller B., Borroni B., Boumpas D.T., Bourgeron T., Bowers S., Braeken D., Brooksbank C., Brose N., Bruining H., Bury J., Caporale N., Cattoretti G., Chabane N., Chneiweiss H., Cook S.A., Curatolo P., de Jonge M.I., Deplancke B., de Witte P., Dimmeler S., Draganski B., Drews A., Dumbrava C., Engelhardt S., Gasser T., Giamarellos-Bourboulis E.J., Graff C., Grun D., Gut I., Hansson O., Henshall D.C., Herland A., Heutink P., Heymans S.R.B., Heyn H., Huch M., Huitinga I., Jackowiak P., Jongsma K.R., Journot L., Junker J.P., Katz S., Kehren J., Kempa S., Kirchhof P., Klein C., Koralewska N., Korbel J.O., Kuhnemund M., Lamond A.I., Lauwers E., Le Ber I., Leinonen V., Tobon A.L., Lundberg E., Lunkes A., Maatz H., Mann M., Marelli L., Matser V., Matthews P.M., Mechta-Grigoriou F., Menon R., Nielsen A.F., Pagani M., Pasterkamp R.J., Pitkanen A., Popescu V., Pottier C., Puisieux A., Rademakers R., Reiling D., Reiner O., Remondini D., Ritchie C., Rohrer J.D., Saliba A.-E., Sanchez-Valle R., Santosuosso A., Sauter A., Scheltema R.A., Scheltens P., Schiller H.B., Schneider A., Seibler P., Sheehan-Rooney K., Shields D., Sleegers K., Smit A.B., Smith K.G.C., Smolders I., Synofzik M., Tam W.L., Teichmann S., Thom M., Turco M.Y., van Beusekom H.M.M., Vandenberghe R., Van den Hoecke S., Van de Poel I., van der Ven A., van der Zee J., van Lunzen J., van Minnebruggen G., Van Paesschen W., van Swieten J., van Vught R., Verhage M., Verstreken P., Villa C.E., Vogel J., von Kalle C., Walter J., Weckhuysen S., Weichert W., Wood L., Ziegler A.-G., Zipp F., Center for Neurogenomics and Cognitive Research, Functional Genomics, Rajewsky, N, Almouzni, G, Gorski, S, Aerts, S, Amit, I, Bertero, M, Bock, C, Bredenoord, A, Cavalli, G, Chiocca, S, Clevers, H, De Strooper, B, Eggert, A, Ellenberg, J, Fernández, X, Figlerowicz, M, Gasser, S, Hubner, N, Kjems, J, Knoblich, J, Krabbe, G, Lichter, P, Linnarsson, S, Marine, J, Marioni, J, Marti-Renom, M, Netea, M, Nickel, D, Nollmann, M, Novak, H, Parkinson, H, Piccolo, S, Pinheiro, I, Pombo, A, Popp, C, Reik, W, Roman-Roman, S, Rosenstiel, P, Schultze, J, Stegle, O, Tanay, A, Testa, G, Thanos, D, Theis, F, Torres-Padilla, M, Valencia, A, Vallot, C, van Oudenaarden, A, Vidal, M, Voet, T, Cattoretti, G, Alliance for Modulation in Epilepsy, Pharmaceutical and Pharmacological Sciences, Experimental Pharmacology, RS: Carim - H02 Cardiomyopathy, MUMC+: MA Med Staf Spec Cardiologie (9), and Cardiologie

Subjects
0301 basic medicine, Male, Artificial intelligence, Legislation, Medical, [SDV]Life Sciences [q-bio], Molecular datasets, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Cell- and Tissue-Based Therapy, Diseases, LifeTime Community Working Groups, Disease, Biomarkers, Systems biology, Health data, Pharmacology, Toxicology and Pharmaceutics(all), 0302 clinical medicine, Conjunts de dades, ethics [Delivery of Health Care], Health care, Pathology, Medicine, European healthcare, BRAIN, Single-cell multi-omics, GENE-EXPRESSION, Multidisciplinary, methods [Medicine], Education, Medical, Settore BIO/13, Intel.ligència artificial, 3. Good health, ALZHEIMERS-DISEASE, Europe, Health, Management system, Perspective, Female, ddc:500, Single-Cell Analysis, Biomarkers, Diseases, Systems biology, Complex diseases, Informàtica::Aplicacions de la informàtica::Bioinformàtica [Àrees temàtiques de la UPC], medicine.medical_specialty, General Science & Technology, Cells, MEDLINE, cell-based interceptive medicine, LifeTime Initiative, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Clinical datasets, Artificial Intelligence, REVEALS, LifeTime Community, standards [Medicine], Humans, OMICS, RECONSTRUCTION, Intensive care medicine, trends [Medicine], trends [Delivery of Health Care], business.industry, Disease progression, standards [Delivery of Health Care], methods [Delivery of Health Care], 030104 developmental biology, lnfectious Diseases and Global Health Radboud Institute for Health Sciences [Radboudumc 4], single cell, personalized therapy, machine learning, bioinformatics, systems biology, disease, cell-based interceptive medicine, Early Diagnosis, Cardiovascular and Metabolic Diseases, Human medicine, business, Delivery of Health Care, 030217 neurology & neurosurgery, Cell based
Abstract

Here we describe the LifeTime Initiative, which aims to track, understand and target human cells during the onset and progression of complex diseases, and to analyse their response to therapy at single-cell resolution. This mission will be implemented through the development, integration and application of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during the progression from health to disease. The analysis of large molecular and clinical datasets will identify molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. The timely detection and interception of disease embedded in an ethical and patient-centred vision will be achieved through interactions across academia, hospitals, patient associations, health data management systems and industry. The application of this strategy to key medical challenges in cancer, neurological and neuropsychiatric disorders, and infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade., The LifeTime initiative is an ambitious, multidisciplinary programme that aims to improve healthcare by tracking individual human cells during disease processes and responses to treatment in order to develop and implement cell-based interceptive medicine in Europe.

Published
2020
Full Text
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3. Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine (Nature, (2020), 587, 7834, (377-386), 10.1038/s41586-020-2715-9)

Author

Rajewsky, N. Almouzni, G. Gorski, S.A. Aerts, S. Amit, I. Bertero, M.G. Bock, C. Bredenoord, A.L. Cavalli, G. Chiocca, S. Clevers, H. De Strooper, B. Eggert, A. Ellenberg, J. Fernández, X.M. Figlerowicz, M. Gasser, S.M. Hubner, N. Kjems, J. Knoblich, J.A. Krabbe, G. Lichter, P. Linnarsson, S. Marine, J.-C. Marioni, J.C. Marti-Renom, M.A. Netea, M.G. Nickel, D. Nollmann, M. Novak, H.R. Parkinson, H. Piccolo, S. Pinheiro, I. Pombo, A. Popp, C. Reik, W. Roman-Roman, S. Rosenstiel, P. Schultze, J.L. Stegle, O. Tanay, A. Testa, G. Thanos, D. Theis, F.J. Torres-Padilla, M.-E. Valencia, A. Vallot, C. van Oudenaarden, A. Vidal, M. Voet, T. Alberi, L. Alexander, S. Alexandrov, T. Arenas, E. Bagni, C. Balderas, R. Bandelli, A. Becher, B. Becker, M. Beerenwinkel, N. Benkirane, M. Beyer, M. Bickmore, W.A. Biessen, E.E.A.L. Blomberg, N. Blumcke, I. Bodenmiller, B. Borroni, B. Boumpas, D.T. Bourgeron, T. Bowers, S. Braeken, D. Brooksbank, C. Brose, N. Bruining, H. Bury, J. Caporale, N. Cattoretti, G. Chabane, N. Chneiweiss, H. Cook, S.A. Curatolo, P. de Jonge, M.I. Deplancke, B. de Witte, P. Dimmeler, S. Draganski, B. Drews, A. Dumbrava, C. Engelhardt, S. Gasser, T. Giamarellos-Bourboulis, E.J. Graff, C. Grün, D. Gut, I.G. Hansson, O. Henshall, D.C. Herland, A. Heutink, P. Heymans, S.R.B. Heyn, H. Huch, M. Huitinga, I. Jackowiak, P. Jongsma, K.R. Journot, L. Junker, J.P. Katz, S. Kehren, J. Kempa, S. Kirchhof, P. Klein, C. Koralewska, N. Korbel, J.O. Kühnemund, M. Lamond, A.I. Lauwers, E. Le Ber, I. Leinonen, V. López-Tobón, A. Lundberg, E. Lunkes, A. Maatz, H. Mann, M. Marelli, L. Matser, V. Matthews, P.M. Mechta-Grigoriou, F. Menon, R. Nielsen, A.F. Pagani, M. Pasterkamp, R.J. Pitkänen, A. Popescu, V. Pottier, C. Puisieux, A. Rademakers, R. Reiling, D. Reiner, O. Remondini, D. Ritchie, C. Rohrer, J.D. Saliba, A.-E. Sanchez-Valle, R. Santosuosso, A. Sauter, A. Scheltema, R.A. Scheltens, P. Schiller, H.B. Schneider, A. Seibler, P. Sheehan-Rooney, K. Shields, D.J. Sleegers, K. Smit, A.B. Smith, K.G.C. Smolders, I. Synofzik, M. Tam, W.L. Teichmann, S.A. Thom, M. Turco, M.Y. van Beusekom, H.M.M. Vandenberghe, R. Van den Hoecke, S. van de Poel, I. van der Ven, A. van der Zee, J. van Lunzen, J. van Minnebruggen, G. van Oudenaarden, A. Van Paesschen, W. van Swieten, J.C. van Vught, R. Verhage, M. Verstreken, P. Villa, C.E. Vogel, J. von Kalle, C. Walter, J. Weckhuysen, S. Weichert, W. Wood, L. Ziegler, A.-G. Zipp, F. LifeTime Community Working Groups

Subjects
ComputingMethodologies_DOCUMENTANDTEXTPROCESSING
Abstract

In this Perspective, owing to an error in the HTML, the surname of author Alejandro López-Tobón of the LifeTime Community Working Groups consortium was indexed as ‘Tobon’ rather than ‘López-Tobón’ and the accents were missing. The HTML version of the original Perspective has been corrected; the PDF and print versions were always correct. © 2021, The Author(s).

Published
2021

7. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, N. (Nikolaus), Almouzni, G. (Geneviève), Gorski, S.A. (Stanislaw A.), Aerts, S. (Stein), Amit, I. (Ido), Bertero, M.G. (Michela G.), Bock, C. (Christoph), Bredenoord, A.L. (Annelien L.), Cavalli, G. (Giacomo), Chiocca, S. (Susanna), Clevers, H.C. (Hans), Strooper, B. (Bart) de, Eggert, A. (Angelika), Ellenberg, J. (Jan), Fernández, X.M. (Xosé M.), Figlerowicz, M. (Marek), Gasser, S.M. (Susan M.), Hübner, N. (Norbert), Kjems, J. (Jørgen), Knoblich, J.A. (Jürgen A.), Krabbe, G. (Grietje), Lichter, P. (Peter), Linnarsson, S. (Sten), Marine, J.-C. (J.), Marioni, J. (John), Marti-Renom, M.A. (Marc A.), Netea, M.G. (Mihai), Nickel, D. (Dörthe), Nollmann, M. (Marcelo), Novak, H.R. (Halina R.), Parkinson, H. (Helen), Piccolo, S. (Stefano), Pinheiro, I. (Inês), Pombo, A. (Ana), Popp, C. (Christian), Reik, W. (Wolf), Roman-Roman, S. (Sergio), Rosenstiel, P. (Philip), Schultze, J.L. (Joachim), Stegle, O. (Oliver), Tanay, A. (Amos), Testa, G. (Giuseppe), Thanos, D. (Dimitris), Theis, F. (Fabian), Torres-Padilla, M.-E. (Maria-Elena), Valencia, A. (Alfonso), Vallot, C. (Céline), van Oudenaarden, A. (Alexander), Vidal, M. (Marie), Voet, T. (Thierry), Alberi, L. (Lavinia), Alexander, S. (Stephanie), Alexandrov, T. (Theodore), Arenas, E. (Ernest), Bagni, C. (Claudia), Balderas, R. (Robert), Bandelli, A. (Andrea), Becher, B. (Burkhard), Becker, M. (Matthias), Beerenwinkel, N. (Niko), Benkirame, M. (Monsef), Beyer, M. (Marc), Bickmore, W. (Wendy), Biessen, E.E.A.L. (Erik E.A.L.), Blomberg, N. (Niklas), Blumcke, I. (Ingmar), Bodenmiller, B. (Bernd), Borroni, B. (Barbara), Boumpas, D.T. (Dimitrios T.), Bourgeron, T. (Thomas), Bowers, S. (Sarion), Braeken, D. (Dries), Brooksbank, C. (Catherine), Brose, N. (Nils), Bruining, J. (Hans), Bury, J. (Jo), Caporale, N. (Nicolo), Cattoretti, G. (Giorgio), Chabane, N. (Nadia), Chneiweiss, H. (Hervé), Cook, S.A. (Stuart A.), Curatolo, P. (Paolo), Jonge, M.I. (Marien) de, Deplancke, B. (Bart), De Strooper, B. (Bart), de Witte, P. (Peter), Dimmeler, S. (Stefanie), Draganski, B. (Bogdan), Drews, A.-D. (Anna-Dorothee), Dumbrava, C. (Costica), Engelhardt, S. (Stefan), Gasser, T. (Thomas), Giamarellos-Bourboulis, E. (Evangelos), Graff, C. (Caroline), Grün, D. (Dominic), Gut, I. (Ivo), Hansson, O. (Oskar), Henshall, D.C. (David C.), Herland, A. (Anna), Heutink, P. (Peter), Heymans, S. (Stephane), Heyn, H. (Holger), Huch, M. (Meritxell), Huitinga, I. (Inge), Jackowiak, P. (Paulina), Jongsma, K.R. (Karin), Journot, L. (Laurent), Junker, J.P. (Jan Philipp), Katz, S. (Shauna), Kehren, J. (Jeanne), Kempa, S. (Stefan), Kirchhof, P. (Paulus), Klein, C. (Christoph), Koralewska, N. (Natalia), Korbel, J.O. (Jan), Kühnemund, M. (Malte), Lamond, A.I. (Angus I.), Lauwers, E. (Elsa), Le Ber, I. (Isabelle), Leinonen, V. (Ville), Tobon, A.L. (Alejandro Lopez), Lundberg, E. (Emma), Lunkes, A. (Astrid), Maatz, H. (Henrike), Mann, M. (Mathias), Marelli, L. (Luca), Matser, V. (Vera), Matthews, P.M. (P.), Mechta-Grigoriou, F. (Fatima), Menon, R. (Radhika), Nielsen, A.F. (Anne F.), Pagani, M. (Massimiliano), Pasterkamp, R.J. (Jeroen), Pitkanen, A. (Asla), Popescu, V. (Valentin), Pottier, C. (Cyril), Puisieux, A. (Alain), Rademakers, R. (Rosa), Reiling, D. (Dory), Reiner, O. (Orly), Remondini, D. (Daniel), Ritchie, C. (Craig), Rohrer, J.D. (Jonathan D.), Saliba, A.-E. (Antione-Emmanuel), Sánchez-Valle, R. (Raquel), Santosuosso, A. (Amedeo), Sauter, A. (Arnold), Scheltema, R.A. (Richard A.), Scheltens, P. (Philip), Schiller, H.B. (Herbert B.), Schneider, A. (Anja), Seibler, P. (Philip), Sheehan-Rooney, K. (Kelly), Shields, D. (David), Sleegers, K. (Kristel), Smit, G. (Guus), Smith, K.G.C. (Kenneth G. C.), Smolders, I. (Ilse), Synofzik, M. (Matthis), Tam, W.L. (Wai Long), Teichmann, S. (Sarah), Thom, M. (Maria), Turco, M.Y. (Margherita Y.), Beusekom, H.M.M. (Heleen) van, Vandenberghe, R. (Rik), den Hoecke, S.V. (Silvie Van), Van de Poel, E. (Ellen), der Ven, A. (Andre van), van der Zee, J. (Julie), van Lunzen, J. (Jan), van Minnebruggen, G. (Geert), Van Paesschen, W. (Wim), Swieten, J.C. (John) van, van Vught, R. (Remko), Verhage, M. (Matthijs), Verstreken, P. (Patrik), Villa, C.E. (Carlo Emanuele), Vogel, J. (Jörg), Kalle, C. (Christof) von, Walter, J. (Jörn), Weckhuysen, S. (Sarah), Weichert, W. (Wilko), Wood, L. (Louisa), Ziegler, A.-G. (Anette-Gabriele), Zipp, F. (Frauke), Rajewsky, N. (Nikolaus), Almouzni, G. (Geneviève), Gorski, S.A. (Stanislaw A.), Aerts, S. (Stein), Amit, I. (Ido), Bertero, M.G. (Michela G.), Bock, C. (Christoph), Bredenoord, A.L. (Annelien L.), Cavalli, G. (Giacomo), Chiocca, S. (Susanna), Clevers, H.C. (Hans), Strooper, B. (Bart) de, Eggert, A. (Angelika), Ellenberg, J. (Jan), Fernández, X.M. (Xosé M.), Figlerowicz, M. (Marek), Gasser, S.M. (Susan M.), Hübner, N. (Norbert), Kjems, J. (Jørgen), Knoblich, J.A. (Jürgen A.), Krabbe, G. (Grietje), Lichter, P. (Peter), Linnarsson, S. (Sten), Marine, J.-C. (J.), Marioni, J. (John), Marti-Renom, M.A. (Marc A.), Netea, M.G. (Mihai), Nickel, D. (Dörthe), Nollmann, M. (Marcelo), Novak, H.R. (Halina R.), Parkinson, H. (Helen), Piccolo, S. (Stefano), Pinheiro, I. (Inês), Pombo, A. (Ana), Popp, C. (Christian), Reik, W. (Wolf), Roman-Roman, S. (Sergio), Rosenstiel, P. (Philip), Schultze, J.L. (Joachim), Stegle, O. (Oliver), Tanay, A. (Amos), Testa, G. (Giuseppe), Thanos, D. (Dimitris), Theis, F. (Fabian), Torres-Padilla, M.-E. (Maria-Elena), Valencia, A. (Alfonso), Vallot, C. (Céline), van Oudenaarden, A. (Alexander), Vidal, M. (Marie), Voet, T. (Thierry), Alberi, L. (Lavinia), Alexander, S. (Stephanie), Alexandrov, T. (Theodore), Arenas, E. (Ernest), Bagni, C. (Claudia), Balderas, R. (Robert), Bandelli, A. (Andrea), Becher, B. (Burkhard), Becker, M. (Matthias), Beerenwinkel, N. (Niko), Benkirame, M. (Monsef), Beyer, M. (Marc), Bickmore, W. (Wendy), Biessen, E.E.A.L. (Erik E.A.L.), Blomberg, N. (Niklas), Blumcke, I. (Ingmar), Bodenmiller, B. (Bernd), Borroni, B. (Barbara), Boumpas, D.T. (Dimitrios T.), Bourgeron, T. (Thomas), Bowers, S. (Sarion), Braeken, D. (Dries), Brooksbank, C. (Catherine), Brose, N. (Nils), Bruining, J. (Hans), Bury, J. (Jo), Caporale, N. (Nicolo), Cattoretti, G. (Giorgio), Chabane, N. (Nadia), Chneiweiss, H. (Hervé), Cook, S.A. (Stuart A.), Curatolo, P. (Paolo), Jonge, M.I. (Marien) de, Deplancke, B. (Bart), De Strooper, B. (Bart), de Witte, P. (Peter), Dimmeler, S. (Stefanie), Draganski, B. (Bogdan), Drews, A.-D. (Anna-Dorothee), Dumbrava, C. (Costica), Engelhardt, S. (Stefan), Gasser, T. (Thomas), Giamarellos-Bourboulis, E. (Evangelos), Graff, C. (Caroline), Grün, D. (Dominic), Gut, I. (Ivo), Hansson, O. (Oskar), Henshall, D.C. (David C.), Herland, A. (Anna), Heutink, P. (Peter), Heymans, S. (Stephane), Heyn, H. (Holger), Huch, M. (Meritxell), Huitinga, I. (Inge), Jackowiak, P. (Paulina), Jongsma, K.R. (Karin), Journot, L. (Laurent), Junker, J.P. (Jan Philipp), Katz, S. (Shauna), Kehren, J. (Jeanne), Kempa, S. (Stefan), Kirchhof, P. (Paulus), Klein, C. (Christoph), Koralewska, N. (Natalia), Korbel, J.O. (Jan), Kühnemund, M. (Malte), Lamond, A.I. (Angus I.), Lauwers, E. (Elsa), Le Ber, I. (Isabelle), Leinonen, V. (Ville), Tobon, A.L. (Alejandro Lopez), Lundberg, E. (Emma), Lunkes, A. (Astrid), Maatz, H. (Henrike), Mann, M. (Mathias), Marelli, L. (Luca), Matser, V. (Vera), Matthews, P.M. (P.), Mechta-Grigoriou, F. (Fatima), Menon, R. (Radhika), Nielsen, A.F. (Anne F.), Pagani, M. (Massimiliano), Pasterkamp, R.J. (Jeroen), Pitkanen, A. (Asla), Popescu, V. (Valentin), Pottier, C. (Cyril), Puisieux, A. (Alain), Rademakers, R. (Rosa), Reiling, D. (Dory), Reiner, O. (Orly), Remondini, D. (Daniel), Ritchie, C. (Craig), Rohrer, J.D. (Jonathan D.), Saliba, A.-E. (Antione-Emmanuel), Sánchez-Valle, R. (Raquel), Santosuosso, A. (Amedeo), Sauter, A. (Arnold), Scheltema, R.A. (Richard A.), Scheltens, P. (Philip), Schiller, H.B. (Herbert B.), Schneider, A. (Anja), Seibler, P. (Philip), Sheehan-Rooney, K. (Kelly), Shields, D. (David), Sleegers, K. (Kristel), Smit, G. (Guus), Smith, K.G.C. (Kenneth G. C.), Smolders, I. (Ilse), Synofzik, M. (Matthis), Tam, W.L. (Wai Long), Teichmann, S. (Sarah), Thom, M. (Maria), Turco, M.Y. (Margherita Y.), Beusekom, H.M.M. (Heleen) van, Vandenberghe, R. (Rik), den Hoecke, S.V. (Silvie Van), Van de Poel, E. (Ellen), der Ven, A. (Andre van), van der Zee, J. (Julie), van Lunzen, J. (Jan), van Minnebruggen, G. (Geert), Van Paesschen, W. (Wim), Swieten, J.C. (John) van, van Vught, R. (Remko), Verhage, M. (Matthijs), Verstreken, P. (Patrik), Villa, C.E. (Carlo Emanuele), Vogel, J. (Jörg), Kalle, C. (Christof) von, Walter, J. (Jörn), Weckhuysen, S. (Sarah), Weichert, W. (Wilko), Wood, L. (Louisa), Ziegler, A.-G. (Anette-Gabriele), and Zipp, F. (Frauke)

Abstract

LifeTime aims to track, understand and target human cells during the onset and progression of complex diseases and their response to therapy at single-cell resolution. This mission will be implemented through the development and integration of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during progression from health to disease. Analysis of such large molecular and clinical datasets will discover molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. Timely detection and interception of disease embedded in an ethical and patient-centered vision will be achieved through interactions across academia, hospitals, patient-associations, health data management systems and industry. Applying this strategy to key medical challenges in cancer, neurological, infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.

Published
2020
Full Text
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8. Data access: Toward unrestricted use of public genomic data

Author

Amann, RI, Baichoo, S, Blencowe, BJ, Bork, P, Borodovsky, M, Brooksbank, C, Chain, PSG, Colwell, RR, Daffonchio, DG, Danchin, A, De Lorenzo, V, Dorrestein, PC, Finn, RD, Fraser, CM, Gilbert, JA, Hallam, SJ, Hugenholtz, P, Ioannidis, JPA, Jansson, JK, Kim, JF, Klenk, HP, Klotz, MG, Knight, R, Konstantinidis, KT, Kyrpides, NC, Mason, CE, McHardy, AC, Meyer, F, Ouzounis, CA, Patrinos, AAN, Podar, M, Pollard, KS, Ravel, J, Muñoz, AR, Roberts, RJ, Rosselló-Móra, R, Sansone, SA, Schloss, PD, Schriml, LM, Setubal, JC, Sorek, R, Stevens, RL, Tiedje, JM, Turjanski, A, Tyson, GW, Ussery, DW, Weinstock, GM, White, O, Whitman, WB, and Xenarios, I

Subjects
General Science & Technology, MD Multidisciplinary
Published
2019
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9. Microbiology Managers: Managerial Training in the RItrain Project

Author

Paterson, R, Lima, N, Brooksbank, C, Guarini, E, Pasterk, M, Lavitrano, M, GUARINI, ENRICO, LAVITRANO, MARIALUISA, Paterson, R, Lima, N, Brooksbank, C, Guarini, E, Pasterk, M, Lavitrano, M, GUARINI, ENRICO, and LAVITRANO, MARIALUISA

Abstract

Leaders of research infrastructures (RIs) in Europe who are scientists require competencies in management. RItrain has addressed this issue by identifying skills required, locating relevant courses and finding gaps, whilst establishing a Master of Management programme. We describe how one contributing microbiology RI determined the most relevant skills.

Published
2017

10. GOBLET: the Global Organisation for Bioinformatics Learning, Education and Training

Author

Atwood T.K., Bongcam-Rudloff E., Brazas M.E., Corpas M., Gaudet P., Lewitter F., Mulder N., Palagi P.M., Schneider M.V., van Gelder C.W.G., Attwood T.K., Banag C., Blackford S., Blatter M.C., Brazas M.D., Brooksbank C., Budd A., Charleston M., Christoffels A., Conesa A., Crowe M., Davies A., de Crecy-Lagard V., De Las Rivas J., Doyle M., Edwards R., Facchiano A., Fernandes P., Gaeta B., Heger A., Herringa J., Hughes D., Jimenez R.C., Kille P., Korpelainen E., Kumuthini J., MacLean D., Martinez S.A.R., McGrath A., Michalopoulos I., Ouellette B.F., Pearson W.R., Qi W., Romano P., Rother K., Sansone S-A., Schonbach C., Tastan-Bishop O., Trelles O., Twells R., Via A., Vriend G., Warnow T., Watson M., Westervelt N., and Zanzoni A.

Subjects
Bioinformatics, learning, education, training, QH301-705.5, Computer science, International scale, Big data, Globe, Other Research Radboud Institute for Molecular Life Sciences [Radboudumc 0], ddc:616.07, Training (civil), Cellular and Molecular Neuroscience, Genetics, medicine, Biology (General), Molecular Biology, Curriculum, Ecology, Evolution, Behavior and Systematics, Ecology, business.industry, 4. Education, Outreach, March of Progress, medicine.anatomical_structure, Computational Theory and Mathematics, Modeling and Simulation, Perspective, Stewardship, business
Abstract

Contains fulltext : 155330.pdf (Publisher’s version ) (Open Access) In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy--paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.

Published
2015
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12. iAnn: an event sharing platform for the life sciences

Author

Jimenez, R.C., Albar, J.P., Bhak, J., Blatter, M.C., Blicher, T., Brazas, M.D., Brooksbank, C., Budd, A., Rivas, J. De Las, Dreyer, J., Driel, M.A. van, Dunn, M.J., Fernandes, P.L., Gelder, C.W.G. van, Hermjakob, H., Ioannidis, V., Judge, D.P., Kahlem, P., Korpelainen, E., Kraus, H.J., Loveland, J., Mayer, C., McDowall, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Salazar, G.A., Schneider, R., Via, A., Villaveces, J.M., Yu, P., Schneider, M.V., Attwood, T.K., Corpas, M., Jimenez, R.C., Albar, J.P., Bhak, J., Blatter, M.C., Blicher, T., Brazas, M.D., Brooksbank, C., Budd, A., Rivas, J. De Las, Dreyer, J., Driel, M.A. van, Dunn, M.J., Fernandes, P.L., Gelder, C.W.G. van, Hermjakob, H., Ioannidis, V., Judge, D.P., Kahlem, P., Korpelainen, E., Kraus, H.J., Loveland, J., Mayer, C., McDowall, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Salazar, G.A., Schneider, R., Via, A., Villaveces, J.M., Yu, P., Schneider, M.V., Attwood, T.K., and Corpas, M.

Abstract

Item does not contain fulltext, SUMMARY: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. AVAILABILITY: http://iann.pro/iannviewer CONTACT: manuel.corpas@tgac.ac.uk.

Published
2013

13. Best practices in bioinformatics training for life scientists

Author

Via, A., Blicher, T., Bongcam-Rudloff, E., Brazas, M.D., Brooksbank, C., Budd, A., Rivas, J. De Las, Dreyer, J., Fernandes, P.L., Gelder, C.W. van, Jacob, J., Jimenez, R.C., Loveland, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Schneider, M.V., Attwood, T.K., Via, A., Blicher, T., Bongcam-Rudloff, E., Brazas, M.D., Brooksbank, C., Budd, A., Rivas, J. De Las, Dreyer, J., Fernandes, P.L., Gelder, C.W. van, Jacob, J., Jimenez, R.C., Loveland, J., Moran, F., Mulder, N., Nyronen, T., Rother, K., Schneider, M.V., and Attwood, T.K.

Abstract

Item does not contain fulltext, The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

Published
2013

14. Best practices in bioinformatics training for life scientists

Author

Via, A, Blicher, T, Bongcam-Rudloff, E, Brazas, MD, Brooksbank, C, Budd, A, De Las Rivas, J, Dreyer, J, Fernandes, PL, van Gelder, C, Jacob, J, Jimenez, RC, Loveland, J, Moran, F, Mulder, N, Nyroenen, T, Rother, K, Schneider, MV, Attwood, TK, Via, A, Blicher, T, Bongcam-Rudloff, E, Brazas, MD, Brooksbank, C, Budd, A, De Las Rivas, J, Dreyer, J, Fernandes, PL, van Gelder, C, Jacob, J, Jimenez, RC, Loveland, J, Moran, F, Mulder, N, Nyroenen, T, Rother, K, Schneider, MV, and Attwood, TK

Abstract

The mountains of data thrusting from the new landscape of modern high-throughput biology are irrevocably changing biomedical research and creating a near-insatiable demand for training in data management and manipulation and data mining and analysis. Among life scientists, from clinicians to environmental researchers, a common theme is the need not just to use, and gain familiarity with, bioinformatics tools and resources but also to understand their underlying fundamental theoretical and practical concepts. Providing bioinformatics training to empower life scientists to handle and analyse their data efficiently, and progress their research, is a challenge across the globe. Delivering good training goes beyond traditional lectures and resource-centric demos, using interactivity, problem-solving exercises and cooperative learning to substantially enhance training quality and learning outcomes. In this context, this article discusses various pragmatic criteria for identifying training needs and learning objectives, for selecting suitable trainees and trainers, for developing and maintaining training skills and evaluating training quality. Adherence to these criteria may help not only to guide course organizers and trainers on the path towards bioinformatics training excellence but, importantly, also to improve the training experience for life scientists.

Published
2013

15. iAnn: an event sharing platform for the life sciences

Author

Jimenez, RC, Albar, JP, Bhak, J, Blatter, M-C, Blicher, T, Brazas, MD, Brooksbank, C, Budd, A, De Las Rivas, J, Dreyer, J, van Driel, MA, Dunn, MJ, Fernandes, PL, van Gelder, CWG, Hermjakob, H, Ioannidis, V, Judge, DP, Kahlem, P, Korpelainen, E, Kraus, H-J, Loveland, J, Mayer, C, McDowall, J, Moran, F, Mulder, N, Nyronen, T, Rother, K, Salazar, GA, Schneider, R, Via, A, Villaveces, JM, Yu, P, Schneider, MV, Attwood, TK, Corpas, M, Jimenez, RC, Albar, JP, Bhak, J, Blatter, M-C, Blicher, T, Brazas, MD, Brooksbank, C, Budd, A, De Las Rivas, J, Dreyer, J, van Driel, MA, Dunn, MJ, Fernandes, PL, van Gelder, CWG, Hermjakob, H, Ioannidis, V, Judge, DP, Kahlem, P, Korpelainen, E, Kraus, H-J, Loveland, J, Mayer, C, McDowall, J, Moran, F, Mulder, N, Nyronen, T, Rother, K, Salazar, GA, Schneider, R, Via, A, Villaveces, JM, Yu, P, Schneider, MV, Attwood, TK, and Corpas, M

Abstract

SUMMARY: We present iAnn, an open source community-driven platform for dissemination of life science events, such as courses, conferences and workshops. iAnn allows automatic visualisation and integration of customised event reports. A central repository lies at the core of the platform: curators add submitted events, and these are subsequently accessed via web services. Thus, once an iAnn widget is incorporated into a website, it permanently shows timely relevant information as if it were native to the remote site. At the same time, announcements submitted to the repository are automatically disseminated to all portals that query the system. To facilitate the visualization of announcements, iAnn provides powerful filtering options and views, integrated in Google Maps and Google Calendar. All iAnn widgets are freely available. AVAILABILITY: http://iann.pro/iannviewer CONTACT: manuel.corpas@tgac.ac.uk.

Published
2013

16. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers.

Author

Schneider, M.V., Walter, P., Blatter, M.C., Watson, J., Brazas, M.D., Rother, K., Budd, A., Via, A., Gelder, C.W.G. van, Jacob, J., Fernandes, P., Nyronen, T.H., Rivas, J. De Las, Blicher, T., Jimenez, R.C., Loveland, J., McDowall, J., Jones, P., Vaughan, B.W., Lopez, R., Attwood, T.K., Brooksbank, C., Schneider, M.V., Walter, P., Blatter, M.C., Watson, J., Brazas, M.D., Rother, K., Budd, A., Via, A., Gelder, C.W.G. van, Jacob, J., Fernandes, P., Nyronen, T.H., Rivas, J. De Las, Blicher, T., Jimenez, R.C., Loveland, J., McDowall, J., Jones, P., Vaughan, B.W., Lopez, R., Attwood, T.K., and Brooksbank, C.

Abstract

1 mei 2012, Item does not contain fulltext, Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.

Published
2012

17. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Author

Schneider, MV, Walter, P, Blatter, M-C, Watson, J, Brazas, MD, Rother, K, Budd, A, Via, A, van Gelder, CG, Jacob, J, Fernandes, P, Nyroenen, TH, De Las Rivas, J, Blicher, T, Jimenez, RC, Loveland, J, McDowall, J, Jones, P, Vaughan, B, Lopez, R, Attwood, TK, Brooksbank, C, Schneider, MV, Walter, P, Blatter, M-C, Watson, J, Brazas, MD, Rother, K, Budd, A, Via, A, van Gelder, CG, Jacob, J, Fernandes, P, Nyroenen, TH, De Las Rivas, J, Blicher, T, Jimenez, RC, Loveland, J, McDowall, J, Jones, P, Vaughan, B, Lopez, R, Attwood, TK, and Brooksbank, C

Abstract

Funding bodies are increasingly recognizing the need to provide graduates and researchers with access to short intensive courses in a variety of disciplines, in order both to improve the general skills base and to provide solid foundations on which researchers may build their careers. In response to the development of 'high-throughput biology', the need for training in the field of bioinformatics, in particular, is seeing a resurgence: it has been defined as a key priority by many Institutions and research programmes and is now an important component of many grant proposals. Nevertheless, when it comes to planning and preparing to meet such training needs, tension arises between the reward structures that predominate in the scientific community which compel individuals to publish or perish, and the time that must be devoted to the design, delivery and maintenance of high-quality training materials. Conversely, there is much relevant teaching material and training expertise available worldwide that, were it properly organized, could be exploited by anyone who needs to provide training or needs to set up a new course. To do this, however, the materials would have to be centralized in a database and clearly tagged in relation to target audiences, learning objectives, etc. Ideally, they would also be peer reviewed, and easily and efficiently accessible for downloading. Here, we present the Bioinformatics Training Network (BTN), a new enterprise that has been initiated to address these needs and review it, respectively, to similar initiatives and collections.

Published
2012

18. Best practices in bioinformatics training for life scientists

Author

Via, A., primary, Blicher, T., additional, Bongcam-Rudloff, E., additional, Brazas, M. D., additional, Brooksbank, C., additional, Budd, A., additional, De Las Rivas, J., additional, Dreyer, J., additional, Fernandes, P. L., additional, van Gelder, C., additional, Jacob, J., additional, Jimenez, R. C., additional, Loveland, J., additional, Moran, F., additional, Mulder, N., additional, Nyronen, T., additional, Rother, K., additional, Schneider, M. V., additional, and Attwood, T. K., additional

Published
2013
Full Text
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19. Bioinformatics Training Network (BTN): a community resource for bioinformatics trainers

Author

Schneider, M. V., primary, Walter, P., additional, Blatter, M.-C., additional, Watson, J., additional, Brazas, M. D., additional, Rother, K., additional, Budd, A., additional, Via, A., additional, van Gelder, C. W. G., additional, Jacob, J., additional, Fernandes, P., additional, Nyronen, T. H., additional, De Las Rivas, J., additional, Blicher, T., additional, Jimenez, R. C., additional, Loveland, J., additional, McDowall, J., additional, Jones, P., additional, Vaughan, B. W., additional, Lopez, R., additional, Attwood, T. K., additional, and Brooksbank, C., additional

Published
2011
Full Text
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21. Bioinformatics training: a review of challenges, actions and support requirements

Author

Schneider, M. V., primary, Watson, J., additional, Attwood, T., additional, Rother, K., additional, Budd, A., additional, McDowall, J., additional, Via, A., additional, Fernandes, P., additional, Nyronen, T., additional, Blicher, T., additional, Jones, P., additional, Blatter, M.-C., additional, De Las Rivas, J., additional, Judge, D. P., additional, van der Gool, W., additional, and Brooksbank, C., additional

Published
2010
Full Text
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30. iAnn: an event sharing platform for the life sciences

Author

Rc, Jimenez, Jp, Albar, Bhak J, Mc, Blatter, Blicher T, Md, Brazas, Brooksbank C, Aidan Budd, De Las Rivas J, Dreyer J, Ma, Driel, Mj, Dunn, Pl, Fernandes, Cw, Gelder, Hermjakob H, Ioannidis V, Dp, Judge, Kahlem P, Korpelainen E, and Hj, Kraus

32. Standards for microarray data [1]

Author

Ball, C. A., Sherlock, G., Parkinson, H., Rocca-Sera, P., Brooksbank, C., Causton, H. C., DUCCIO CAVALIERI, Gaasterland, T., Hingamp, P., Holstege, F., Ringwald, M., Spellman, P., Stoeckert Jr, C. J., Stewart, J. E., Taylor, R., Brazma, A., and Quackenbush, J.

33. An open letter to the scientific journals

Author

Holstege, F., Ball, C.A., Ringwald, M., Sherlock, G., Spellman, P., Parkinson, H., Stoeckert, C.J., Rocca-Sera, P., Stewart, J.E., Brooksbank, C., Taylor, R., Causton, H.C., Cavalieri, D., Brazma, A., Quackenbush, J., Gaasterland, T., and Hingamp, P.

Published
2002

34. Microbiology Managers: Managerial Training in the RItrain Project

Author

R. Russell M. Paterson, Enrico Guarini, Cath Brooksbank, Markus Pasterk, Nelson Lima, Marialuisa Lavitrano, Paterson, R, Lima, N, Brooksbank, C, Guarini, E, Pasterk, M, Lavitrano, M, and Universidade do Minho

Subjects
0301 basic medicine, Microbiology (medical), 030106 microbiology, Management programme, Biology, Masters course, Microbiology, Training (civil), 03 medical and health sciences, Surveys and Questionnaires, Virology, research infrastructure, Humans, Mental Competency, Strategic planning, Ciências Naturais::Ciências Biológicas, Science & Technology, Research, MED/04 - PATOLOGIA GENERALE, research infrastructures, Engenharia e Tecnologia::Biotecnologia Ambiental, Ciências Sociais::Ciências da Educação, Europe, Leadership, SECS-P/07 - ECONOMIA AZIENDALE, 030104 developmental biology, Infectious Diseases, Masteŕs course
Abstract

Leaders of research infrastructures (RIs) in Europe who are scientists require competencies in management. RItrain has addressed this issue by identifying skills required, locating relevant courses and finding gaps, whilst establishing a Master of Management programme. We describe how one contributing microbiology RI determined the most relevant skills., The RItrain project is funded by the European Commission, grant agreement number 654156., info:eu-repo/semantics/publishedVersion

Published
2017
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35. EMBL's European Bioinformatics Institute (EMBL-EBI) in 2024.

Author

Thakur M, Brooksbank C, Finn RD, Firth HV, Foreman J, Freeberg M, Gurwitz KT, Harrison M, Hulcoop D, Hunt SE, R Leach A, Levchenko M, Marques D, McDonagh EM, Mithani A, Parkinson H, Perez-Riverol Y, Perova Z, Sarkans U, Tirunagari S, Tzampatzopoulou E, Venkatesan A, Vizcaino JA, Wingfield B, Zdrazil B, and McEntyre J

Abstract

The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory, Europe's only intergovernmental life sciences organization. This overview summarizes the latest developments in services that EMBL-EBI data resources provide to scientific communities globally (https://www.ebi.ac.uk/services)., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2024
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36. EMBL's European Bioinformatics Institute (EMBL-EBI) in 2022.

Author

Thakur M, Bateman A, Brooksbank C, Freeberg M, Harrison M, Hartley M, Keane T, Kleywegt G, Leach A, Levchenko M, Morgan S, McDonagh EM, Orchard S, Papatheodorou I, Velankar S, Vizcaino JA, Witham R, Zdrazil B, and McEntyre J

Subjects
Data Management, Databases, Factual, Genome, Internet, Artificial Intelligence, Computational Biology
Abstract

The European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) is one of the world's leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe's only intergovernmental life sciences organisation. This overview summarises the status of services that EMBL-EBI data resources provide to scientific communities globally. The scale, openness, rich metadata and extensive curation of EMBL-EBI added-value databases makes them particularly well-suited as training sets for deep learning, machine learning and artificial intelligence applications, a selection of which are described here. The data resources at EMBL-EBI can catalyse such developments because they offer sustainable, high-quality data, collected in some cases over decades and made openly availability to any researcher, globally. Our aim is for EMBL-EBI data resources to keep providing the foundations for tools and research insights that transform fields across the life sciences., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2023
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37. The European Bioinformatics Institute (EMBL-EBI) in 2021.

Author

Cantelli G, Bateman A, Brooksbank C, Petrov AI, Malik-Sheriff RS, Ide-Smith M, Hermjakob H, Flicek P, Apweiler R, Birney E, and McEntyre J

Subjects
Academies and Institutes, Artificial Intelligence, COVID-19, Databases, Pharmaceutical, Databases, Protein, Europe, Genome, Human, Humans, Information Storage and Retrieval, RNA, Untranslated genetics, SARS-CoV-2 genetics, Computational Biology education, Computational Biology methods, Databases, Factual economics, Databases, Factual statistics & numerical data
Abstract

The European Bioinformatics Institute (EMBL-EBI) maintains a comprehensive range of freely available and up-to-date molecular data resources, which includes over 40 resources covering every major data type in the life sciences. This year's service update for EMBL-EBI includes new resources, PGS Catalog and AlphaFold DB, and updates on existing resources, including the COVID-19 Data Platform, trRosetta and RoseTTAfold models introduced in Pfam and InterPro, and the launch of Genome Integrations with Function and Sequence by UniProt and Ensembl. Furthermore, we highlight projects through which EMBL-EBI has contributed to the development of community-driven data standards and guidelines, including the Recommended Metadata for Biological Images (REMBI), and the BioModels Reproducibility Scorecard. Training is one of EMBL-EBI's core missions and a key component of the provision of bioinformatics services to users: this year's update includes many of the improvements that have been developed to EMBL-EBI's online training offering., (© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2022
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38. The European Bioinformatics Institute: empowering cooperation in response to a global health crisis.

Author

Cantelli G, Cochrane G, Brooksbank C, McDonagh E, Flicek P, McEntyre J, Birney E, and Apweiler R

Subjects
COVID-19 epidemiology, COVID-19 virology, Computational Biology methods, Computational Biology organization & administration, Databases, Nucleic Acid organization & administration, Global Health, Humans, Information Storage and Retrieval statistics & numerical data, Internet, Pandemics, SARS-CoV-2 metabolism, SARS-CoV-2 physiology, Viral Proteins metabolism, COVID-19 prevention & control, Computational Biology statistics & numerical data, Databases, Nucleic Acid statistics & numerical data, Information Storage and Retrieval methods, SARS-CoV-2 genetics, Viral Proteins genetics
Abstract

The European Bioinformatics Institute (EMBL-EBI; https://www.ebi.ac.uk/) provides freely available data and bioinformatics services to the scientific community, alongside its research activity and training provision. The 2020 COVID-19 pandemic has brought to the forefront a need for the scientific community to work even more cooperatively to effectively tackle a global health crisis. EMBL-EBI has been able to build on its position to contribute to the fight against COVID-19 in a number of ways. Firstly, EMBL-EBI has used its infrastructure, expertise and network of international collaborations to help build the European COVID-19 Data Platform (https://www.covid19dataportal.org/), which brings together COVID-19 biomolecular data and connects it to researchers, clinicians and public health professionals. By September 2020, the COVID-19 Data Platform has integrated in excess of 170 000 COVID-19 biomolecular data and literature records, collected through a number of EMBL-EBI resources. Secondly, EMBL-EBI has strived to continue its support of the life science communities through the crisis, with updated Training provision and improved service provision throughout its resources. The COVID-19 pandemic has highlighted the importance of EMBL-EBI's core principles, including international cooperation, resource sharing and central data brokering, and has further empowered scientific cooperation., (© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2021
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39. Author Correction: Leveraging European infrastructures to access 1 million human genomes by 2022.

Author

Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, and Scollen S

Abstract

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Published
2019
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40. Leveraging European infrastructures to access 1 million human genomes by 2022.

Author

Saunders G, Baudis M, Becker R, Beltran S, Béroud C, Birney E, Brooksbank C, Brunak S, Van den Bulcke M, Drysdale R, Capella-Gutierrez S, Flicek P, Florindi F, Goodhand P, Gut I, Heringa J, Holub P, Hooyberghs J, Juty N, Keane TM, Korbel JO, Lappalainen I, Leskosek B, Matthijs G, Mayrhofer MT, Metspalu A, Navarro A, Newhouse S, Nyrönen T, Page A, Persson B, Palotie A, Parkinson H, Rambla J, Salgado D, Steinfelder E, Swertz MA, Valencia A, Varma S, Blomberg N, and Scollen S

Subjects
Europe, Humans, Biomedical Research, Genome, Human, Human Genome Project
Abstract

Human genomics is undergoing a step change from being a predominantly research-driven activity to one driven through health care as many countries in Europe now have nascent precision medicine programmes. To maximize the value of the genomic data generated, these data will need to be shared between institutions and across countries. In recognition of this challenge, 21 European countries recently signed a declaration to transnationally share data on at least 1 million human genomes by 2022. In this Roadmap, we identify the challenges of data sharing across borders and demonstrate that European research infrastructures are well-positioned to support the rapid implementation of widespread genomic data access.

Published
2019
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41. From trainees to trainers to instructors: Sustainably building a national capacity in bioinformatics training.

Author

McGrath A, Champ K, Shang CA, van Dam E, Brooksbank C, and Morgan SL

Subjects
Australia, Humans, Capacity Building, Computational Biology education, Computational Biology organization & administration, Models, Organizational
Abstract

Demand for training life scientists in bioinformatics skills led to the development of a train-the-trainer collaboration between the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) and 2 Australian organisations, Bioplatforms Australia and Commonwealth Scientific and Industrial Research Organisation (CSIRO) in 2012. The goal of the collaboration was to establish a group of trained instructors who could develop and deliver short bioinformatics courses nationally. A train-the-trainer course introduces instructors to aspects of andragogy and evidence-based learning principles to help them better design, develop, and deliver high-quality training. Since then, both the number of trainers in the network and the course portfolio have grown. Best practises have been developed and shared between the Australian cohort and EMBL-EBI to address common challenges in bioinformatics training. The Australian trainer cohort undertook a train-the-trainer instructor course, again with EMBL-EBI, and subsequently successfully delivered train-the-trainer courses to interested bioinformatics trainers within Australia. We conclude that a train-the-trainer approach can help build national capacity and maintain a critical mass of trained instructors., Competing Interests: The authors have declared that no competing interests exist.

Published
2019
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42. Consent insufficient for data release-Response.

Author

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, and Xenarios I

Subjects
Informed Consent
Published
2019
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43. Toward unrestricted use of public genomic data.

Author

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, and Xenarios I

Subjects
Genome, Human, Humans, Access to Information, Databases, Genetic standards, Genomics, Information Dissemination
Published
2019
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44. The European Bioinformatics Institute in 2018: tools, infrastructure and training.

Author

Cook CE, Lopez R, Stroe O, Cochrane G, Brooksbank C, Birney E, and Apweiler R

Subjects
Computational Biology history, Databases, Genetic, Europe, History, 21st Century, Humans, Software, Academies and Institutes, Computational Biology organization & administration, Computational Biology trends
Abstract

The European Bioinformatics Institute (https://www.ebi.ac.uk/) archives, curates and analyses life sciences data produced by researchers throughout the world, and makes these data available for re-use globally (https://www.ebi.ac.uk/). Data volumes continue to grow exponentially: total raw storage capacity now exceeds 160 petabytes, and we manage these increasing data flows while maintaining the quality of our services. This year we have improved the efficiency of our computational infrastructure and doubled the bandwidth of our connection to the worldwide web. We report two new data resources, the Single Cell Expression Atlas (https://www.ebi.ac.uk/gxa/sc/), which is a component of the Expression Atlas; and the PDBe-Knowledgebase (https://www.ebi.ac.uk/pdbe/pdbe-kb), which collates functional annotations and predictions for structure data in the Protein Data Bank. Additionally, Europe PMC (http://europepmc.org/) has added preprint abstracts to its search results, supplementing results from peer-reviewed publications. EMBL-EBI maintains over 150 analytical bioinformatics tools that complement our data resources. We make these tools available for users through a web interface as well as programmatically using application programming interfaces, whilst ensuring the latest versions are available for our users. Our training team, with support from all of our staff, continued to provide on-site, off-site and web-based training opportunities for thousands of researchers worldwide this year.

Published
2019
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46. The development and application of bioinformatics core competencies to improve bioinformatics training and education.

Author

Mulder N, Schwartz R, Brazas MD, Brooksbank C, Gaeta B, Morgan SL, Pauley MA, Rosenwald A, Rustici G, Sierk M, Warnow T, and Welch L

Subjects
Advisory Committees, Africa, Algorithms, Genetic Predisposition to Disease, Illinois, New South Wales, Ohio, Pennsylvania, Software, Surveys and Questionnaires, United Kingdom, Universities, Computational Biology education, Curriculum, Education, Graduate, Systems Biology education
Abstract

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user personas and training programs. The initial competencies developed based on surveys of employers and training programs have since been refined through a multiyear process of community engagement. This report describes the current status of the competencies and presents a series of use cases illustrating how they are being applied in diverse training contexts. These use cases are intended to demonstrate how others can make use of the competencies and engage in the process of their continuing refinement and application. The report concludes with a consideration of remaining challenges and future plans.

Published
2018
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47. Microbiology Managers: Managerial Training in the RItrain Project.

Author

Paterson RRM, Lima N, Brooksbank C, Guarini E, Pasterk M, and Lavitrano M

Subjects
Europe, Humans, Leadership, Mental Competency, Surveys and Questionnaires, Microbiology education, Research, Strategic Planning
Abstract

Leaders of research infrastructures (RIs) in Europe who are scientists require competencies in management. RItrain has addressed this issue by identifying skills required, locating relevant courses and finding gaps, whilst establishing a Master of Management programme. We describe how one contributing microbiology RI determined the most relevant skills., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Published
2017
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48. Applying, Evaluating and Refining Bioinformatics Core Competencies (An Update from the Curriculum Task Force of ISCB's Education Committee).

Author

Welch L, Brooksbank C, Schwartz R, Morgan SL, Gaeta B, Kilpatrick AM, Mietchen D, Moore BL, Mulder N, Pauley M, Pearson W, Radivojac P, Rosenberg N, Rosenwald A, Rustici G, and Warnow T

Subjects
Advisory Committees, Curriculum, Humans, Professional Competence, Program Development, Societies, Scientific, Computational Biology education
Published
2016
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