Coordinated Research Infrastructures Building Enduring Life-science services

Risultati finali

D9.3.2 Pilot courses and staff exchange provided

Pilot courses and staff exchange provided: final report of activities achieved.

D4.1 Strategy for enabling user access within pilot use cases

D4.1 Strategy for enabling user access within pilot use cases (MDC/FVB/EMBL/SZN)

D3.2.2 Assessment of animal model phenotypes against outcome measures

Assessment of animal model phenotypes against outcome measures

D5.1 Report on existing user access models and regulatory access policies identifying common elements

D5.1 Report on existing user access models and regulatory access policies identifying common elements (UOXF/ INFRAFRONTIER)

D2.3 Report on user engagement activities
D3.1.1.2 Medical infrastructure user forum reporting (M22)
D6.1 Review of identifier schemes, standards and interoperability maps and proposed harmonization strategy
D3.3.2 Report on implementation, including economic model and solutions for sustainability

Report on implementation, including economic model and solutions for sustainability for the innovation office.

D2.4 Final stakeholder meeting
D7.1 Report on ELSI support needs for BMS RIs and ethics check procedure
D8.1 Concept paper on intellectual property issues in pre-competitive research
D9.3.1 Pilot courses and staff exchange provided

D9.3.1 Pilot courses and staff exchange provided (M24)

D3.1.1.4 Medical infrastructure user forum reporting (M46)

Report summarising the outcomes of the MIUF meeting in October 2019.

D3.1.1.3 Medical infrastructure user forum reporting (M37)
D8.4 Sustainability plan for extended BMS RI Innovation Office

Sustainability plan for extended BMS RI Innovation Office

D4.2 Sustainable plan for user access to common RI services for 4 use case cross-ESFRI BMS research infrastructure pipelines

D4.2 Sustainable plan for user access to common RI services for 4 use case cross-ESFRI BMS research infrastructure pipelines. (MDC/FVB/EMBL/SZN)

D3.2.1 Core set of outcome measures for clinical trials for each disease condition
D1.1 Project handbook
D9.1 Refined organisational competency framework needed by distributed RIs at 3 development stages
D3.5.2 Report on integrated biomedical data and project proposals for biomarker validation in clinical trial monitoring
D1.3 Implementation of an equal opportunities programme
D3.4.2 Report on final assessment and generalization of integration platform

Report on final assessment and generalization of integration platform (Lygature)

D5.2 Report on common access framework concept
D3.1.1.1 Medical infrastructure user forum reporting (M10)
D8.3 Industry collaboration best practice guide
D6.2 Access to Sustainable cross infrastructure identifier service(s) through ELIXIR service registry
D5.3 Strategy for expanding application of common access model based on feedback from WP3 and WP4 pilots
D1.2 Project-wide data management plan adopted
D4.3 Report on impact of integrated access standards tested for open user access

D4.3 Report on impact of integrated access standards tested for open user access (MDC/FVB/EMBL/SZN/ECRIN): 1st and 2nd Open Call; for the 2nd Open Call this will include the experiences of the users from the medical community in addition (see WP3, Task 3.6).

D3.3.1 Report on conclusions from multi-stakeholder taskforce
D3.5.1 Report describing informational lacunes and data enrichment strategy
D6.4 Report on models and pilot designs for sustainable scalable cloud-based provision of data access and compute across infrastructures
D2.1 Communication strategy based on stakeholder analysis
D1.4 Final report common infrastructures and services

This report will summarise the outcomes of the project from a users perspective. D1.4 “Final report common infrastructures and services” will be due in month 48 and will give an overview about all the services the different BMS Research Infrastructures are offering the scientific community under the umbrella of CORBEL.

D6.6 Ocean Sampling Day a demonstrator of a cross-domain distributed data set
D8.2 Concept paper on new business models related to open innovation
D7.3 Sustainability Plan for extended BMS RI ELSI common services

Sustainability Plan for extended BMS RI ELSI common services

D4.4 Framework in place for launching transnational open user access via the common BMS cluster web-portal and RI specific user community communication channels

D4.4 Framework in place for launching transnational open user access via the common BMS cluster web-portal and RI specific user community communication channels (EMBL / MDC)

D6.5 Prototype implementation of distributed automated data access request, review and authorization and delivery systems
D9.2 New course syllabi for a modular curriculum for piloting in RIs
D7.2 ELSI guidance for new scientific, technological and cross-border developments using a “help-desk format”
D6.3 Delivery of Toolkit supporting community ontology mapping and development
D3.4.1 Robust data upload procedures for biosample data and molecular profiling data

D3.4.1 Robust data upload procedures for biosample data and molecular profiling data (EATRIS-CTMM)

Pubblicazioni

Four simple recommendations to encourage best practices in research software

Autori: Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutierrez, Neil Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla Garcia, Josep Ll. Gelpí, Simon Gladman, Carole Goble, Montserrat González Ferreiro, Alejandra Gonzalez-Beltran, Philippa C. Griffin, Björn Grüning, Jonas Hagberg, Petr Holub, Rob Hooft, Jon Ison, D
Pubblicato in: F1000Research, Numero 6, 2017, Pagina/e 876, ISSN 2046-1402
Editore: F1000 Research Ltd.
DOI: 10.12688/f1000research.11407.1

Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Autori: Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Dan
Pubblicato in: PLOS Genetics, Numero 13/6, 2017, Pagina/e e1006812, ISSN 1553-7404
Editore: PLOS
DOI: 10.1371/journal.pgen.1006812

Improved imputation accuracy of rare and low-frequency variants using population-specific high-coverage WGS-based imputation reference panel

Autori: Mario Mitt, Mart Kals, Kalle Pärn, Stacey B Gabriel, Eric S Lander, Aarno Palotie, Samuli Ripatti, Andrew P Morris, Andres Metspalu, Tõnu Esko, Reedik Mägi, Priit Palta
Pubblicato in: European Journal of Human Genetics, Numero 25/7, 2017, Pagina/e 869-876, ISSN 1018-4813
Editore: Natue Publishing Group
DOI: 10.1038/ejhg.2017.51

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect

Autori: Chiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans Victor Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina
Pubblicato in: PLOS Computational Biology, Numero 13/9, 2017, Pagina/e e1005758, ISSN 1553-7358
Editore: PLOS
DOI: 10.1371/journal.pcbi.1005758

Sharing and reuse of individual participant data from clinical trials: principles and recommendations

Autori: Christian Ohmann, Rita Banzi, Steve Canham, Serena Battaglia, Mihaela Matei, Christopher Ariyo, Lauren Becnel, Barbara Bierer, Sarion Bowers, Luca Clivio, Monica Dias, Christiane Druml, Hélène Faure, Martin Fenner, Jose Galvez, Davina Ghersi, Christian Gluud, Trish Groves, Paul Houston, Ghassan Karam, Dipak Kalra, Rachel L Knowles, Karmela Krleža-Jerić, Christine Kubiak, Wolfgang Kuchinke, Reb
Pubblicato in: BMJ Open, Numero 7/12, 2017, Pagina/e e018647, ISSN 2044-6055
Editore: BMJ Publishing Group
DOI: 10.1136/bmjopen-2017-018647

SCORE-IT (Selecting Core Outcomes for Randomised Effectiveness trials In Type 2 diabetes): a systematic review of registered trials

Autori: Nicola L. Harman, Rebecca James, John Wilding, Paula R. Williamson
Pubblicato in: Trials, Numero 18/1, 2017, ISSN 1745-6215
Editore: BioMed Central
DOI: 10.1186/s13063-017-2317-5

Trans-ethnic meta-regression of genome-wide association studies accounting for ancestry increases power for discovery and improves fine-mapping resolution

Autori: Reedik Mägi, Momoko Horikoshi, Tamar Sofer, Anubha Mahajan, Hidetoshi Kitajima, Nora Franceschini, Mark I. McCarthy, Andrew P. Morris
Pubblicato in: Human Molecular Genetics, Numero 26/18, 2017, Pagina/e 3639-3650, ISSN 0964-6906
Editore: Oxford University Press
DOI: 10.1093/hmg/ddx280

BiobankUniverse: automatic matchmaking between datasets for biobank data discovery and integration

Autori: Chao Pang, Fleur Kelpin, David van Enckevort, Niina Eklund, Kaisa Silander, Dennis Hendriksen, Mark de Haan, Jonathan Jetten, Tommy de Boer, Bart Charbon, Petr Holub, Hans Hillege, Morris A Swertz
Pubblicato in: Bioinformatics, Numero 33/22, 2017, Pagina/e 3627-3634, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btx478

Classification of processes involved in sharing individual participant data from clinical trials

Autori: Christian Ohmann, Steve Canham, Rita Banzi, Wolfgang Kuchinke, Serena Battaglia
Pubblicato in: F1000Research, Numero 7, 2018, Pagina/e 138, ISSN 2046-1402
Editore: F1000 Research Ltd.
DOI: 10.12688/f1000research.13789.1

Comprehensive population-based genome sequencing provides insight into hematopoietic regulatory mechanisms

Autori: Michael H. Guo, Satish K. Nandakumar, Jacob C. Ulirsch, Seyedeh M. Zekavat, Jason D. Buenrostro, Pradeep Natarajan, Rany M. Salem, Roberto Chiarle, Mario Mitt, Mart Kals, Kalle Pärn, Krista Fischer, Lili Milani, Reedik Mägi, Priit Palta, Stacey B. Gabriel, Andres Metspalu, Eric S. Lander, Sekar Kathiresan, Joel N. Hirschhorn, Tõnu Esko, Vijay G. Sankaran
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 114/3, 2017, Pagina/e E327-E336, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.1619052114

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures

Autori: Joan Segura, Ruben Sanchez-Garcia, Marta Martinez, Jesus Cuenca-Alba, Daniel Tabas-Madrid, C O S Sorzano, J M Carazo
Pubblicato in: Bioinformatics, Numero 33/22, 2017, Pagina/e 3655-3657, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btx483

Selecting Core Outcomes for Randomised Effectiveness trials In Type 2 Diabetes (SCORE-IT): study protocol for the development of a core outcome set

Autori: Nicola L. Harman, John Wilding, Dave Curry, James Harris, Jennifer Logue, R. John Pemberton, Leigh Perreault, Gareth Thompson, Sean Tunis, Paula R. Williamson
Pubblicato in: Trials, Numero 19/1, 2018, ISSN 1745-6215
Editore: BioMed Central
DOI: 10.1186/s13063-018-2805-2

Significant Locus and Metabolic Genetic Correlations Revealed in Genome-Wide Association Study of Anorexia Nervosa

Autori: Laramie Duncan, Zeynep Yilmaz, Helena Gaspar, Raymond Walters, Jackie Goldstein, Verneri Anttila, Brendan Bulik-Sullivan, Stephan Ripke, Laura Thornton, Anke Hinney, Mark Daly, Patrick F. Sullivan, Eleftheria Zeggini, Gerome Breen, Cynthia M. Bulik, Laramie Duncan, Zeynep Yilmaz, Héléna Gaspar, Raymond Walters, Jackie Goldstein, Verneri Anttila, Brendan Bulik-Sullivan, Stephan Ripke, Roger Adan,
Pubblicato in: American Journal of Psychiatry, Numero 174/9, 2017, Pagina/e 850-858, ISSN 0002-953X
Editore: American Psychiatric Publishing, Inc.
DOI: 10.1176/appi.ajp.2017.16121402

Predictable Irreversible Switching Between Acute and Chronic Inflammation

Autori: Abulikemu Abudukelimu, Matteo Barberis, Frank A. Redegeld, Nilgun Sahin, Hans V. Westerhoff
Pubblicato in: Frontiers in Immunology, Numero 9, 2018, ISSN 1664-3224
Editore: Frontier
DOI: 10.3389/fimmu.2018.01596

Mind the Gap: From Tool to Knowledge Base

Autori: Michaela Th. Mayrhofer, Irene Schlünder
Pubblicato in: Biopreservation and Biobanking, 2018, ISSN 1947-5535
Editore: Mary Ann Liebert Inc.
DOI: 10.1089/bio.2018.0018

A metadata schema for data objects in clinical research

Autori: Canham, Steve; Ohmann, Christian
Pubblicato in: Trials, Numero 1, 2016, ISSN 1745-6215
Editore: BioMed Central
DOI: 10.1186/s13063-016-1686-5

Assessment of the genetic and clinical determinants of fracture risk: genome wide association and mendelian randomisation study

Autori: Katerina Trajanoska, John A Morris, Ling Oei, Hou-Feng Zheng, David M Evans, Douglas P Kiel, Claes Ohlsson, J Brent Richards, Fernando Rivadeneira
Pubblicato in: BMJ, 2018, Pagina/e k3225, ISSN 0959-8138
Editore: British Medical Association
DOI: 10.1136/bmj.k3225

3DBIONOTES: A unified, enriched and interactive view of macromolecular information

Autori: D. Tabas-Madrid, J. Segura, R. Sanchez-Garcia, J. Cuenca-Alba, C.O.S. Sorzano, J.M. Carazo
Pubblicato in: Journal of Structural Biology, Numero 194/2, 2016, Pagina/e 231-234, ISSN 1047-8477
Editore: Academic Press
DOI: 10.1016/j.jsb.2016.02.007

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling

Autori: Joan Segura, Ruben Sanchez-Garcia, Daniel Tabas-Madrid, Jesus Cuenca-Alba, Carlos Oscar S. Sorzano, Jose Maria Carazo
Pubblicato in: Biophysical Journal, Numero 110/4, 2016, Pagina/e 766-775, ISSN 0006-3495
Editore: Biophysical Society
DOI: 10.1016/j.bpj.2015.11.3519

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Autori: C. O. S. Sorzano, A. Jiménez, J. Mota, J. L. Vilas, D. Maluenda, M. Martínez, E. Ramírez-Aportela, T. Majtner, J. Segura, R. Sánchez-García, Y. Rancel, L. del Caño, P. Conesa, R. Melero, S. Jonic, J. Vargas, F. Cazals, Z. Freyberg, J. Krieger, I. Bahar, R. Marabini, J. M. Carazo
Pubblicato in: Acta Crystallographica Section F Structural Biology Communications, Numero 75/1, 2019, Pagina/e 19-32, ISSN 2053-230X
Editore: John Wiley and Sons Ltd
DOI: 10.1107/S2053230X18015108

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Autori: Julie A. McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K. Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C. Ison, Rafael C. Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Joh
Pubblicato in: PLOS Biology, Numero 15/6, 2017, Pagina/e e2001414, ISSN 1545-7885
Editore: PLOS Biology
DOI: 10.1371/journal.pbio.2001414

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

Autori: Simon Jupp, Tony Burdett, Danielle Welter, Sirarat Sarntivijai, Helen Parkinson, James Malone
Pubblicato in: Journal of Biomedical Semantics, Numero 7/1, 2016, ISSN 2041-1480
Editore: Springer Nature
DOI: 10.1186/s13326-016-0055-3

Multi-omic profiles of human non-alcoholic fatty liver disease tissue highlight heterogenic phenotypes

Autori: Wasco Wruck, Karl Kashofer, Samrina Rehman, Andriani Daskalaki, Daniela Berg, Ewa Gralka, Justyna Jozefczuk, Katharina Drews, Vikash Pandey, Christian Regenbrecht, Christoph Wierling, Paola Turano, Ulrike Korf, Kurt Zatloukal, Hans Lehrach, Hans V. Westerhoff, James Adjaye
Pubblicato in: Scientific Data, Numero 2, 2015, Pagina/e 150068, ISSN 2052-4463
Editore: Nature Publishing Group
DOI: 10.1038/sdata.2015.68

The Peculiar Glycolytic Pathway in Hyperthermophylic Archaea: Understanding Its Whims by Experimentation In Silico

Autori: Yanfei Zhang, Theresa Kouril, Jacky Snoep, Bettina Siebers, Matteo Barberis, Hans Westerhoff
Pubblicato in: International Journal of Molecular Sciences, Numero 18/4, 2017, Pagina/e 876, ISSN 1422-0067
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms18040876

Identification of Three Early Phases of Cell-Fate Determination during Osteogenic and Adipogenic Differentiation by Transcription Factor Dynamics

Autori: Jeroen van de Peppel, Tanja Strini, Julia Tilburg, Hans Westerhoff, Andre J. van Wijnen, Johannes P. van Leeuwen
Pubblicato in: Stem Cell Reports, Numero 8/4, 2017, Pagina/e 947-960, ISSN 2213-6711
Editore: Cell Press
DOI: 10.1016/j.stemcr.2017.02.018

Targeting pathogen metabolism without collateral damage to the host

Autori: Jurgen R. Haanstra, Albert Gerding, Amalia M. Dolga, Freek J. H. Sorgdrager, Manon Buist-Homan, François du Toit, Klaas Nico Faber, Hermann-Georg Holzhütter, Balázs Szöör, Keith R. Matthews, Jacky L. Snoep, Hans V. Westerhoff, Barbara M. Bakker
Pubblicato in: Scientific Reports, Numero 7, 2017, Pagina/e 40406, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/srep40406

Assessment of a demonstrator repository for individual clinical trial data built upon DSpace

Autori: Birol Tilki, Thomas Schulenberg, Steve Canham, Rita Banzi, Wolfgang Kuchinke, Christian Ohmann
Pubblicato in: F1000Research, Numero 9, 2020, Pagina/e 311, ISSN 2046-1402
Editore: F1000 Research Ltd.
DOI: 10.12688/f1000research.23468.2

Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity

Autori: Abulikemu Abudukelimu, Matteo Barberis, Frank Redegeld, Nilgun Sahin, Raju P. Sharma, Hans V. Westerhoff
Pubblicato in: Frontiers in Immunology, Numero 10, 2020, ISSN 1664-3224
Editore: Frontiers Media SA
DOI: 10.3389/fimmu.2019.03091

Reply to “Missed opportunities in large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery”

Autori: Nicolas Bosc, Francis Atkinson, Eloy Félix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Pubblicato in: Journal of Cheminformatics, Numero 11/1, 2019, ISSN 1758-2946
Editore: Chemistry Central
DOI: 10.1186/s13321-019-0388-x

Parents of early‐maturing girls die younger

Autori: Peeter Hõrak, Markus Valge, Krista Fischer, Reedik Mägi, Tanel Kaart
Pubblicato in: Evolutionary Applications, Numero 12/5, 2019, Pagina/e 1050-1061, ISSN 1752-4571
Editore: John Wiley & Sons
DOI: 10.1111/eva.12780

Using Scipion for stream image processing at Cryo-EM facilities

Autori: J. Gómez-Blanco, J.M. de la Rosa-Trevín, R. Marabini, L. del Cano, A. Jiménez, M. Martínez, R. Melero, T. Majtner, D. Maluenda, J. Mota, Y. Rancel, E Ramírez-Aportela, J.L. Vilas, M. Carroni, S. Fleischmann, E. Lindahl, A.W. Ashton, M. Basham, D.K. Clare, K. Savage, C.A. Siebert, G.G. Sharov, C.O.S. Sorzano, P. Conesa, J.M. Carazo
Pubblicato in: Journal of Structural Biology, Numero 204/3, 2018, Pagina/e 457-463, ISSN 1047-8477
Editore: Academic Press
DOI: 10.1016/j.jsb.2018.10.001

3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures

Autori: Ruben Sanchez-Garcia, Carlos Sorzano, Jose Carazo, Joan Segura
Pubblicato in: Molecules, Numero 22/12, 2017, Pagina/e 2230, ISSN 1420-3049
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules22122230

Large scale comparison of QSAR and conformal prediction methods and their applications in drug discovery

Autori: Nicolas Bosc, Francis Atkinson, Eloy Felix, Anna Gaulton, Anne Hersey, Andrew R. Leach
Pubblicato in: Journal of Cheminformatics, Numero 11/1, 2019, ISSN 1758-2946
Editore: Chemistry Central
DOI: 10.1186/s13321-018-0325-4

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

Autori: Kent A Shefchek, Nomi L Harris, Michael Gargano, Nicolas Matentzoglu, Deepak Unni, Matthew Brush, Daniel Keith, Tom Conlin, Nicole Vasilevsky, Xingmin Aaron Zhang, James P Balhoff, Larry Babb, Susan M Bello, Hannah Blau, Yvonne Bradford, Seth Carbon, Leigh Carmody, Lauren E Chan, Valentina Cipriani, Alayne Cuzick, Maria Della Rocca, Nathan Dunn, Shahim Essaid, Petra Fey, Chris Grove, Jean-Phillip
Pubblicato in: Nucleic Acids Research, Numero 48/D1, 2019, Pagina/e D704-D715, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz997

PiGx: reproducible genomics analysis pipelines with GNU Guix

Autori: Ricardo Wurmus, Bora Uyar, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin
Pubblicato in: GigaScience, Numero 7/12, 2018, ISSN 2047-217X
Editore: Oxford University Press
DOI: 10.1093/gigascience/giy123

Sharing individual participant data from clinical studies: a cross-sectional online survey among Italian patient and citizen groups

Autori: Cinzia Colombo, Anna Roberto, Karmela Krleza-Jeric, Elena Parmelli, Rita Banzi
Pubblicato in: BMJ Open, Numero 9/2, 2019, Pagina/e e024863, ISSN 2044-6055
Editore: BMJ Publishing Group
DOI: 10.1136/bmjopen-2018-024863

Ten quick tips for biocuration

Autori: Y. Amy Tang, Klemens Pichler, Anja Füllgrabe, Jane Lomax, James Malone, Monica C. Munoz-Torres, Drashtti V. Vasant, Eleanor Williams, Melissa Haendel
Pubblicato in: PLOS Computational Biology, Numero 15/5, 2019, Pagina/e e1006906, ISSN 1553-7358
Editore: PLOS
DOI: 10.1371/journal.pcbi.1006906

Neural plasticity and adult neurogenesis: the deep biology perspective

Autori: AnnaMaria Colangelo, HansV Westerhoff, Giovanni Cirillo, Lilia Alberghina, Michele Papa
Pubblicato in: Neural Regeneration Research, Numero 14/2, 2019, Pagina/e 201, ISSN 1673-5374
Editore: Neural Regeneration Research
DOI: 10.4103/1673-5374.244775

Light sheet microscopy with acoustic sample confinement

Autori: Zhengyi Yang, Katy L. H. Cole, Yongqiang Qiu, Ildikó M. L. Somorjai, Philip Wijesinghe, Jonathan Nylk, Sandy Cochran, Gabriel C. Spalding, David A. Lyons, Kishan Dholakia
Pubblicato in: Nature Communications, Numero 10/1, 2019, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-019-08514-5

BIPSPI: a method for the prediction of partner-specific protein–protein interfaces

Autori: Ruben Sanchez-Garcia, C O S Sorzano, J M Carazo, Joan Segura
Pubblicato in: Bioinformatics, Numero 35/3, 2018, Pagina/e 470-477, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/bty647

Ensembl Genomes 2020—enabling non-vertebrate genomic research

Autori: Kevin L Howe, Bruno Contreras-Moreira, Nishadi De Silva, Gareth Maslen, Wasiu Akanni, James Allen, Jorge Alvarez-Jarreta, Matthieu Barba, Dan M Bolser, Lahcen Cambell, Manuel Carbajo, Marc Chakiachvili, Mikkel Christensen, Carla Cummins, Alayne Cuzick, Paul Davis, Silvie Fexova, Astrid Gall, Nancy George, Laurent Gil, Parul Gupta, Kim E Hammond-Kosack, Erin Haskell, Sarah E Hunt, Pankaj Jaiswal,
Pubblicato in: Nucleic Acids Research, Numero 48/D1, 2019, Pagina/e D689-D695, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkz890

Search for Early Pancreatic Cancer Blood Biomarkers in Five European Prospective Population Biobanks Using Metabolomics

Autori: Jesse Fest, Lisanne S Vijfhuizen, Jelle J Goeman, Olga Veth, Anni Joensuu, Markus Perola, Satu Männistö, Eivind Ness-Jensen, Kristian Hveem, Toomas Haller, Neeme Tonisson, Kairit Mikkel, Andres Metspalu, Cornelia M van Duijn, Arfan Ikram, Bruno H Stricker, Rikje Ruiter, Casper H J van Eijck, Gert-Jan B van Ommen, Peter A C ʼt Hoen
Pubblicato in: Endocrinology, Numero 160/7, 2019, Pagina/e 1731-1742, ISSN 1945-7170
Editore: Endocrine Society
DOI: 10.1210/en.2019-00165

Ample Arsenite Bio-Oxidation Activity in Bangladesh Drinking Water Wells: A Bonanza for Bioremediation?

Autori: Zahid Hassan, Munawar Sultana, Sirajul I. Khan, Martin Braster, Wilfred F.M. Röling, Hans V. Westerhoff
Pubblicato in: Microorganisms, Numero 7/8, 2019, Pagina/e 246, ISSN 2076-2607
Editore: MDPI
DOI: 10.3390/microorganisms7080246

Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Autori: D. Maluenda, T. Majtner, P. Horvath, J. L. Vilas, A. Jiménez-Moreno, J. Mota, E. Ramírez-Aportela, R. Sánchez-García, P. Conesa, L. del Caño, Y. Rancel, Y. Fonseca, M. Martínez, G. Sharov, C.A. García, D. Strelak, R. Melero, R. Marabini, J. M. Carazo, C. O. S. Sorzano
Pubblicato in: Acta Crystallographica Section D Structural Biology, Numero 75/10, 2019, Pagina/e 882-894, ISSN 2059-7983
Editore: International Union of Crystallography
DOI: 10.1107/s2059798319011860

A Simple and Fast Assay Based on Carboxyfluorescein-Loaded Liposome for Quantitative DNA Detection

Autori: Jacopo Sforzi, Giuseppe Ferrauto, Silvio Aime, Simonetta Geninatti Crich
Pubblicato in: ACS Omega, Numero 5/4, 2020, Pagina/e 1764-1772, ISSN 2470-1343
Editore: ACS Publications
DOI: 10.1021/acsomega.9b01457

Evaluation of repositories for sharing individual-participant data from clinical studies

Autori: Rita Banzi, Steve Canham, Wolfgang Kuchinke, Karmela Krleza-Jeric, Jacques Demotes-Mainard, Christian Ohmann
Pubblicato in: Trials, Numero 20/1, 2019, ISSN 1745-6215
Editore: BioMed Central
DOI: 10.1186/s13063-019-3253-3

Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars

Autori: Denise Carvalho-Silva, Leyla Garcia, Sarah L. Morgan, Cath Brooksbank, Ian Dunham
Pubblicato in: PLOS Computational Biology, Numero 14/11, 2018, Pagina/e e1006419, ISSN 1553-7358
Editore: PLOS
DOI: 10.1371/journal.pcbi.1006419

Selecting Core Outcomes for Randomised Effectiveness trials In Type 2 diabetes (SCORE-IT): a patient and healthcare professional consensus on a core outcome set for type 2 diabetes

Autori: Nicola L Harman, John P H Wilding, Dave Curry, James Harris, Jennifer Logue, R John Pemberton, Leigh Perreault, Gareth Thompson, Sean Tunis, Paula R Williamson
Pubblicato in: BMJ Open Diabetes Research & Care, Numero 7/1, 2019, Pagina/e e000700, ISSN 2052-4897
Editore: BMJ Publishing Group Ltd.
DOI: 10.1136/bmjdrc-2019-000700

Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network

Autori: Kazuhiro Maeda, Hans V. Westerhoff, Hiroyuki Kurata, Fred C. Boogerd
Pubblicato in: npj Systems Biology and Applications, Numero 5/1, 2019, ISSN 2056-7189
Editore: Springer Nature
DOI: 10.1038/s41540-019-0091-6

CORBEL Pilot courses and staff exchange provided

Autori: Matser, Vera; Battaglia, Serena; Amaral, Ana Margarida
Pubblicato in: 2017
Editore: zenodo
DOI: 10.5281/zenodo.1044176

3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures

Autori: Segura, Joan; Sanchez-Garcia, Ruben; Martinez, Marta; Cuenca-Alba, Jesus; Tabas-Madrid, Daniel; Sorzano, C.O.S; Carazo, JM
Pubblicato in: 2017
Editore: Zenodo

CORBEL Briefing document: Evidence of shared services provided through Instruct structural biology infrastructure to other Biomedical Sciences Research Infrastructures in the CORBEL partnership

Autori: Carazo, J M
Pubblicato in: 2017
Editore: Zenodo
DOI: 10.5281/zenodo.1026294

Intellectual Property Issues in Open Science, pre-competitive Research and Open Innovation

Autori: Zacherl, Nikolaus; Zatloukal, Kurt
Pubblicato in: 2017
Editore: Zenodo
DOI: 10.5281/zenodo.1109265

CORBEL Concept paper on new business models related to Open Innovation

Autori: Abuja, Peter M., Zatloukal, Kurt
Pubblicato in: 2018
Editore: Zenodo
DOI: 10.5281/zenodo.1408808

"CORBEL ELSI guidance for new scientific, technological and cross-border developments using a ""help-desk format"""

Autori: Mayrhofer, Michaela Th., Schlünder, Irene
Pubblicato in: 2018
Editore: Zenodo
DOI: 10.5281/zenodo.1408804

CORBEL Report on conclusions from multi-stakeholder taskforce

Autori: Serena Battaglia
Pubblicato in: 2017
Editore: Zenodo
DOI: 10.5281/zenodo.1409571

Report about a workshop on sensitive data: Repositories for sharing individual participant data from clinical trials and existing tools/services for storing clinical trial data

Autori: Rita Banzi, Steve Canham, Christian Ohmann, Wolfgang Kuchinke, Karmela Krleza-Jeric, Birol Tilki, Serena Battaglia, Jacques Demotes-Mainard
Pubblicato in: 2018
Editore: Zenodo
DOI: 10.5281/zenodo.1438261

CORBEL Equal Opportunities Survey and Recommendations

Autori: Asrar Ali Khan, Michael Raess
Pubblicato in: 2018
Editore: Zenodo
DOI: 10.5281/zenodo.1441066

CORBEL Access to Sustainable cross infrastructure identifier service(s) through ELIXIR service registry

Autori: Nick Juty, Carole Goble, Helen Parkinson, Simon Jupp
Pubblicato in: 2018
Editore: Zenodo
DOI: 10.5281/zenodo.1441303

Federated Identity Management for Research Collaborations

Autori: Christopher John Atherton, Thomas Barton, Jim Basney, Daan Broeder, Alessandro Costa, Mirjam van Daalen, Stephanie Dyke, Willem Elbers, Carl-Fredrik Enell, Enrico Maria Vincenzo Fasanelli, João Fernandes, Licia Florio, Peter Gietz, David L. Groep, Matthias Bernhard Junker, Christos Kanellopoulos, David Kelsey, Philip Kershaw, Cristina Knapic, Thorsten Kollegger, Scott Koranda, Mikael Linden, Fili
Pubblicato in: 2018
Editore: Zenodo
DOI: 10.5281/zenodo.1307551

CORBEL Sustainable plan for user access to common RI services for 4 use case cross-ESFRI BMS research infrastructure pipelines

Autori: Leitner, Frauke; Popp, Christian; Vidal, Marie
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.2222358

CORBEL Delivery of Toolkit supporting community ontology mapping and development

Autori: Jupp, Simon; Parkinson, Helen; Goble, Carol; Juty, Nick; Boiten, Jan-Willem; Swertz, Morris
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.2559160

CORBEL 3rd Medical Infrastructure user forum reporting

Autori: Battaglia, Serena
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.2025791

CORBEL Strategy for enabling user access within pilot use cases

Autori: Leither, Frauke; Vanmaele, Sofie; Stechmann, Bahne; Vidal, Marie
Pubblicato in: 2016
Editore: zenodo
DOI: 10.5281/zenodo.154081

CORBEL Refined organisational competency framework needed by distributed RIs at 3 development stages

Autori: Brooksbank, Cath; Pasterk, Markus
Pubblicato in: 2016
Editore: zenodo
DOI: 10.5281/zenodo.154085

CORBEL Report describing informational lacunes and data enrichment strategy: Expanding the consortium and selecting samples for CORBEL Use case

Autori: Toernwall, Outi; van Ommen, Gertjan
Pubblicato in: 2016
Editore: zenodo
DOI: 10.5281/zenodo.154076

CORBEL Communication Strategy based on stakeholder analysis

Autori: Schuengel, Manuela
Pubblicato in: 2016
Editore: zenodo
DOI: 10.5281/zenodo.154033

CORBEL Project-wide data management plan adopted

Autori: Jenkinson, Andrew M.
Pubblicato in: 2016
Editore: zenodo
DOI: 10.5281/zenodo.154022

CORBEL 1st Medical Infrastructure/Users Forum (MIUF) Report

Autori: Battaglia, Serena
Pubblicato in: 2016
Editore: zenodo
DOI: 10.5281/zenodo.154035

CORBEL Report on ELSI support needs for BMS RIs and towards a joint Ethical Governance Framework

Autori: Schluender, Irene; Cambon-Thomsen, Anne; Suhr, Stephanie (editor); Chassang, Gauthier; Mayrhofer, Michaela Th.
Pubblicato in: 2016
Editore: zenodo
DOI: 10.5281/zenodo.154084

CORBEL Report on Common Access Framework Concept

Autori: Haley, Natalie
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.2662134

CORBEL Prototype implementation of distributed automated data access request, review and authorization and delivery systems

Autori: Linden, Mikael; Boiten, Jan-Willem; Courtot, Melanie; Holub, Petr; van de Geijn, Gert-Jan; van Enckevort, David; Lappalainen, Ilkka; Nyrönen, Tommi; Parkinson, Helen; Reihs, Robert; Senf, Alexander; Spalding, Dylan; Swedlow, Jason; Swertz, Morris; Törnroos, Juha; Kankaanpää, Pasi; van Iperen, Erik
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.3238496

CORBEL Industry Collaboration Best Practice Guide

Autori: Abuja, Peter M.; Carapina, Tamara; de Kort, Martin; Raess, Michael; Tieken, Chris; Wagstaff, Nigel
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.2615364

CORBEL Report on integrated biomedical data and project proposals for biomarker validation in clinical trial monitoring

Autori: van Ommen, Gertjan
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.3238313

CORBEL Report on models and pilot designs for sustainable scalable cloud-based provision of data access and compute across infrastructures

Autori: Morris Swertz, Fleur Kelpin, David van Enckevort, Ilkka Lappalainen, Mikael Linden, Tommi Nyrönen, Petr Holub, Jan-Willem Boiten, Anna Leida Molder, Helen Parkinson
Pubblicato in: 2017
Editore: Zenodo
DOI: 10.5281/zenodo.376279

CORBEL Review of identifier schemes, standards and interoperability maps and proposed harmonization strategy

Autori: Carole Goble, Helen Parkinson, Simon Jupp, Renzo Kottmann, Jan-Willem Boiten, Frank Oliver Glöckner, Eleanor Williams, Jason Swedlow, Morris Swertz, David van Enckevort, Nick Juty, Anna Gaulton
Pubblicato in: 2017
Editore: Zenodo
DOI: 10.5281/zenodo.376236

CORBEL Report on existing user access models and regulatory access policies identifying common elements

Autori: Susan Daenke, Narayanan Krishnan
Pubblicato in: 2017
Editore: Zenodo
DOI: 10.5281/zenodo.376187

CORBEL Report on final assessment and generalization of integration platform

Autori: Boiten, Jan-Willem; Aime, Silvio; Bierkens, Mariska; Dastrù, Walter; Hansson, Mattias; Klein, Stefan; Longo, Dario; Peelen, Sjaak; Zullino, Sara; Sangiorgi, Luca; Mordenti, Marina; Boarini, Manila; Welsing, Paco
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3628369

CORBEL Assessment of animal model phenotypes against outcome measures

Autori: Nicola Harman; Adrian Sanz-Moreno; Patricia da Silva-Buttkus; Serena Battaglia
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3685932

CORBEL Report on user engagement activities

Autori: Hauk, Christiane; Schmidt-Tremmel, Friederike; Battaglia, Serena; Leitner, Frauke; Hansen, Sonja; Haley, Natalie; Raess, Michael; Parkinson, Helen; Jupp, Simon; Mayrhofer, Michaela Th.; Wagstaff, Nigel; Matser, Vera
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3678774

CORBEL Sustainability plan for extended BMS RI Innovation Office

Autori: Abuja, Peter M.; Carapina, Tamara; de Kort, Martin; Fauvel, Anne-Charlotte; Tieken, Chris; Ussi, Anton; Wagstaff, Nigel
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3663759

CORBEL Pilot courses and staff exchange provided (Summary)

Autori: Lloret Llinares, Marta; Matser, Vera; Raess, Michael; Herzog, Katja; Haley, Natalie; Alen Amaro, Claudia; Battaglia, Serena; Brooksbank, Cath; Vidal, Marie; Ludwig, Rebecca; Hauk, Christiane; Leitner, Frauke; Popp, Christian; Hansen, Sonja; Kalinowska, Gosia; Mayrhofer, Michaela Th.
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3738191

CORBEL 4th Medical Infrastructure user forum reporting

Autori: Battaglia, Serena
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3726777

CORBEL Ocean Sampling Day: a demonstrator of a cross-domain distributed data set

Autori: Glöckner, Frank Oliver; Kostadinov, Ivaylo; Cochrane, Guy
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3839957

BBMRI-ERIC ELSI Glossary

Autori: Grewal, Jasjote; Mayrhofer, Michaela Th.
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.3754254

CORBEL Final Stakeholder Meeting

Autori: Gaber, Sabrina; Battaglia, Serena; Schmidt-Tremmel, Friederike; Blomberg, Niklas
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3744802

CORBEL Strategy for expanding application of common access model based on feedback from WP3 and WP4 pilots

Autori: Haley, Natalie; Räß, Michael
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3859788

CORBEL Report on impact of integrated access standards tested for open user access

Autori: Hansen, Sonja; Leitner, Frauke
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3856121

CORBEL Framework in place for launching transnational open user access via the common LS (formerly BMS) cluster web portal and RI specific user community communication channels

Autori: Hansen, Sonja; Leitner, Frauke
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3856040

CORBEL Sustainability Plan for extended BMS RI ELSI Services

Autori: Mayrhofer, Michaela Th.; Grewal, Jasjote; Schlünder, Irene; Goisauf, Melanie; Akyüz, Kaya; Adeniran, Ayodeji
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3859796

CORBEL Report on implementation, including economic model and solutions for sustainability

Autori: Lydall, Ben
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3862715

CORBEL Final report common infrastructures and services

Autori: Schmidt-Tremmel, Friederike; Blomberg, Niklas
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3865548

CORBEL Core set of outcome measures for clinical trials for each disease condition

Autori: Battaglia, Serena; Da Silva-Buttkus, Patricia; Demotes, Jacques; Fuchs, Helmut; Gailus-Durner, Valérie; Garattini, Silvio; Harman, Nicola; Prinsen, Cecilia; Raess, Michael; Terwee, Caroline; Williamson, Paula
Pubblicato in: 2017
Editore: zenodo
DOI: 10.5281/zenodo.886494

CORBEL Robust data upload procedures for biosample data and molecular profiling data

Autori: Boiten, Jan-Willem; Bierkens, Mariska; Hansson, Matthias; Klein, Stefan; Peelen, Sjaak
Pubblicato in: 2017
Editore: zenodo
DOI: 10.5281/zenodo.886508

CORBEL 2nd Medical Infrastructure user forum reporting

Autori: Battaglia, Serena
Pubblicato in: 2017
Editore: zenodo
DOI: 10.5281/zenodo.825054

CORBEL New course syllabi for a modular curriculum for piloting in RIs

Autori: Matser, Vera; Schuengel, Manuela
Pubblicato in: 2017
Editore: zenodo
DOI: 10.5281/zenodo.841702

CORBEL Concept paper on intellectual property issues in pre-competitive research

Autori: Zatloukal, Kurt; Zacherl, Nikolaus; Schreiner, Christoph
Pubblicato in: 2017
Editore: zenodo
DOI: 10.5281/zenodo.580056

A framework for quality management in the biomedical research infrastructures (BMS RIs)

Autori: BBMRI-ERIC; EATRIS; ECRIN; ELIXIR; EMBRC; EMPHASIS; ERINHA; EU-OPENSCREEN; Euro-BioImaging; INFRAFRONTIER; Instruct; ISBE; MIRRI
Pubblicato in: 2017
Editore: zenodo
DOI: 10.5281/zenodo.834332

Informed Consent Matrix for Clinical Trials

Autori: Colombo, Cinzia; Mosconi, Paola; Mayrhofer, Michaela; Kubiak, Christine; Battaglia, Serena; Matei, Mihaela; Lavitrano, Marialuisa; Casati, Sara; Chico, Victoria; Schlünder, Irene; Boiten, Jan-Willem; Carapina, Lygature Tamara; Uzun, Oskar; Suhr, Stephanie
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.3928317

Non-repudiable provenance for clinical decision support systems

Autori: Fairweather, Elliot; Wittner, Rudolf; Chapman, Martin; Holub, Petr; Curcin, Vasa
Pubblicato in: 2020
Editore: Arxiv.org

EMPHASIS - European Infrastructure for Multi-scale Plant Phenomics and Simulation for Food Security in a Chancing Climate

Autori: Pieruschka, Roland
Pubblicato in: CORBEL User Meeting, Heidelberg, Germany, 2019-10-01 - 2019-10-02, 2019
Editore: N/A

Provenance Week 2020 Poster: ISO 23494: Biotechnology - Provenance Information Model for Biological Specimen and Data

Autori: Wittner, Rudolf; Holub, Petr; Geiger, Jörg; Müller, Heimo; Goble, Carole; Soiland-Reyes, Stian; Fairweather, Elliot; Pirredu, Luca; Frexia, Francesca; Mascia, Cecilia; Zanetti, Gianluigi; Nakae, Hiroki; Strambio, Caterina; Moore, Josh; Grunwald, David; Swedlow, Jason
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3901011

Incorporating Patients' Perspectives into the Initial Stages of Core Outcome Set Development: A Rapid Review of Qualitative Studies of Type 2 Diabetes

Autori: Sarah L. Gorst, Bridget Young, Paula R. Williamson, John PH Wilding, Nicola Harman
Pubblicato in: SSRN Electronic Journal, 2019, ISSN 1556-5068
Editore: ELSEVIER
DOI: 10.2139/ssrn.3234869

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