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International federation of genomic medicine databases using GA4GH standards

Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla, Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume (+3 others)
2021 Cell Genomics  
We promote a shared vision and guide for how and when to federate genomic and health-related data sharing, enabling connections and insights across independent, secure databases. The GA4GH encourages a federated approach wherein data providers have the mandate and resources to share, but where data cannot move for legal or technical reasons. We recommend a federated approach to connect national genomics initiatives into a global network and precision medicine resource.
doi:10.1016/j.xgen.2021.100032 pmid:35128509 pmcid:PMC8813094 fatcat:ohdthlnmczb3fbjpunldtbvuza

GA4GH Passport standard for digital identity and access permissions

Craig Voisin, Mikael Linden, Stephanie O.M. Dyke, Sarion R. Bowers, Pinar Alper, Maxmillian P. Barkley, David Bernick, Jianpeng Chao, Mélanie Courtot, Francis Jeanson, Melissa A. Konopko, Martin Kuba (+12 others)
2021 Cell Genomics  
Highlights d The GA4GH Passport is an open standard to encode data access permissions of users d The standard enables communication of data access permissions at international scale d Passport facilitates data access and analysis across international platforms d Implementers include research initiatives, infrastructures, and national institutes
doi:10.1016/j.xgen.2021.100030 fatcat:idfx5dtwhncbtdzurl5at47t4m

International federation of genomic medicine databases using GA4GH standards

Adrian Thorogood, Heidi L Rehm, Peter Goodhand, Angela J H Page, Yann Joly, Michael Baudis, Jordi Rambla, Arcadi Navarro, Tommi H Nyronen, Mikael Linden, Edward S Dove, Marc Fiume (+3 others)
2021
We promote a shared vision and guide for how and when to federate genomic and health-related data sharing, enabling connections and insights across independent, secure databases. The GA4GH encourages a federated approach wherein data providers have the mandate and resources to share, but where data cannot move for legal or technical reasons. We recommend a federated approach to connect national genomics initiatives into a global network and precision medicine resource.
doi:10.5167/uzh-210472 fatcat:yohkhzyd7zgaro44eci33i226m

The Data Use Ontology to streamline responsible access to human biomedical datasets

Jonathan Lawson, Moran N. Cabili, Giselle Kerry, Tiffany Boughtwood, Adrian Thorogood, Pinar Alper, Sarion R. Bowers, Rebecca R. Boyles, Anthony J. Brookes, Matthew Brush, Tony Burdett, Hayley Clissold (+45 others)
2021 Cell Genomics  
Guidry Auvil, 28 Tommi H. Nyro ¨nen, 20 and Me ´lanie Courtot 2,38, *  ... 
doi:10.1016/j.xgen.2021.100028 pmid:34820659 pmcid:PMC8591903 fatcat:2eqm5raidnfvpbljfi5g3idx5e

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J.S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran (+190 others)
2021 Cell Genomics  
As nascent genomic medicine programs emerge in many countries, we believe that federated approaches (see Federated access below), in addition to centralized data sharing where Alex H.  ... 
doi:10.1016/j.xgen.2021.100029 pmid:35072136 pmcid:PMC8774288 fatcat:ho5hntolr5gdrlrfcgfzgah6s4

CINECA Report on GA4GH Researcher ID D2.2

Mikael Linden, Martin Kuba, Jorge Izquierdo, Mamana Mbiyavanga
2021 Zenodo  
Nyrönen (CSC), Dominik F.  ...  , T., Blomberg, N., Firth, H., Hurles, M., Philippakis, A., Rätsch, G., Brudno, M., Boycott, K., Rehm, H., Baudis, M., Sherry, S., Kato, K., Knoppers, B., Baker, D., Flicek  ... 
doi:10.5281/zenodo.5795408 fatcat:zwz6wmc3d5ez5popxg7vwjsqiu

Mitochondrial Targeting of Normal and Mutant Protoporphyrinogen Oxidase

Mikael von und zu Fraunberg, Tommi Nyrönen, Raili Kauppinen
2003 Journal of Biological Chemistry  
For mitochondrial staining, 40 nM MitoTracker Red CMXRos (Molecular Probes, Eugene, OR) was added to medium for 45 min at 48 h posttransfection.  ...  GFP Fluorescence, Mitochondrial Staining, and Confocal Laser Scanning Microscopy-For GFP fluorescence studies, COS-1 cells were trypsinized and replated on glass coverslips 24 h after transfection.  ... 
doi:10.1074/jbc.m300151200 pmid:12556518 fatcat:rdgo7r3jpjf2nmvmt5gvdpk3zu

EOSC-Life Access and user management system for life science – the blueprint

Mikael Linden, Dominik Frantisek Bucik, Philipp Gormanns, Natalie Haley, Jani Heikkinen, Petr Holub, Pasi Kankaanpää, Daniel Kouril, Martin Kuba, Slavek Licehammer, Ludek Matyska, Tommi Nyrönen (+7 others)
2019 Zenodo  
., Nyrönen, T., Paetow, S., Paglione, L., Parlati, S., Phillips, C., Prochazka, M., Rees, N., Short, H., Stevanovic, U., Tartakovsky, M., Venekamp, G., Vitez, T., Wartel, R., Whalen, C., White, J., Zwölf  ...  May, 2019. http://doi.org/10.5281/zenodo.2662134 CORB19b Linden, M., Boiten, J., Courtot, M., Holub, P., van de Geijn, G., ; van Enckevort, D., Lappalainen, I., Nyrönen, T., Parkinson, H., Reihs, R., Senf  ... 
doi:10.5281/zenodo.3386306 fatcat:4tuobkxpzbfvfpttdq4pfwa2xe

Three-dimensional Models of α2A-Adrenergic Receptor Complexes Provide a Structural Explanation for Ligand Binding

Tiina Salminen, Minna Varis, Tommi Nyrönen, Marjo Pihlavisto, Anna-Marja Hoffrén, Tuomas Lönnberg, Anne Marjamäki, Heini Frang, Juha-Matti Savola, Mika Scheinin, Mark S. Johnson
1999 Journal of Biological Chemistry  
Hygromycin B (Roche Molecular Biochemicals)resistant (550 g/ml) cell cultures were examined for their ability to bind the ␣a 2 -AR antagonist [ 3 H]RX821002.  ...  Other Ligands Ligand Binding-The results from the competition of [ 3 H]RX821002 binding to the wild type ␣ 2A -AR and mutant receptors using clonidine, para-aminoclonidine, oxymetazoline, UK14,304, and  ... 
doi:10.1074/jbc.274.33.23405 pmid:10438518 fatcat:rh34zbiwzzfohdhmdkzphq65uu

EOSC-Life Access and User Management System for Life Science – the blueprint update

Mikael Linden, Dominik Frantisek Bucik, Philipp Gormanns, Natalie Haley, Jani Heikkinen, Petr Holub, Pasi Kankaanpää, Daniel Kouril, Martin Kuba, Slavek Licehammer, Ludek Matyska, Tommi Nyrönen (+7 others)
2021 Zenodo  
http://doi.org/10.5281/zenodo.2662134 CORB19b Linden, M., Boiten, J., Courtot, M., Holub, P., van de Geijn, G., ; van Enckevort, D., Lappalainen, I., Nyrönen, T., Parkinson, H., Reihs, R., Senf, A.  ...  ., Nyrönen, T., Paetow, S., Paglione, L., Parlati, S., Phillips, C., Prochazka, M., Rees, N., Short, H., Stevanovic, U., Tartakovsky, M., Venekamp, G., Vitez, T., Wartel, R., Whalen, C., White, J., Zwölf  ... 
doi:10.5281/zenodo.4633190 fatcat:adhth5mwf5hqlf4ah7ud5ecxgm

EOSC-Life Initial EOSC-LS Cloud Observatory Report

Steven Newhouse, Harald Wagener, Montserrat González Ferrero, Oihane Fano-Bilbao, Tony Wildish, Marius Dieckmann, Ania Niewielska, Shubham Kapoor, Tommi Nyrönen
2020 Zenodo  
-Task 7.3 h. Provide deployable platforms for e.g. Galaxy and CWL based workflows (using GA4GH Cloud-WG compatible service).  ... 
doi:10.5281/zenodo.4010420 fatcat:nf52or3nxndv5e3jioklfoq6wq

Molecular mechanisms of ligand-receptor interactions in transmembrane domain V of theα2A-adrenoceptor

Juha M Peltonen, Tommi Nyrönen, Siegfried Wurster, Marjo Pihlavisto, Anna-Marja Hoffrén, Anne Marjamäki, Henri Xhaard, Liisa Kanerva, Juha-Matti Savola, Mark S Johnson, Mika Scheinin
2003 British Journal of Pharmacology  
The docked structures were clustered into similar groups that were within 1 Å r.m.s.d. of each other. a 2A -wt a 2A Ser201 a 2A Ser201Cys200 a 2A Ser201Cys204 K i (nm) n H K i (nm) n H K i (nm) n H K i  ...  -resistant (550 mg ml À1 ) cell cultures were examined for their ability to bind the a 2 -AR antagonist [ 3 H]RX821002.  ... 
doi:10.1038/sj.bjp.0705439 pmid:12970108 pmcid:PMC1574035 fatcat:dn3emopdgra6bds2fifagomuzy

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L Rehm, Angela J H Page, Lindsay Smith, Jeremy B Adams, Gil Alterovitz, Lawrence J Babb, Maxmillian P Barkley, Michael Baudis, Michael J S Beauvais, Tim Beck, Jacques S Beckmann, Sergi Beltran (+191 others)
2022
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective,
more » ... we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
doi:10.17863/cam.81862 fatcat:akcjm6wrurbqbklnghqnuvutvi

EOSC-Life Access and User Management System for Life Science – the blueprint update

Mikael Linden, Dominik Frantisek Bucik, Philipp Gormanns, Natalie Haley, Jani Heikkinen, Petr Holub, Pasi Kankaanpää, Daniel Kouril, Martin Kuba, Slavek Licehammer, Ludek Matyska, Tommi Nyrönen (+6 others)
2022 Zenodo  
GA4GH Passports Life Science service ID A Life Science ID which is used by services which need to RASC19 The delivery is delayed: Yes Rasche, H.  ...  ., Nyrönen, T., Parkinson, H., Reihs, R., Senf, A., Spalding, D., Swedlow, J., Swertz, M., Törnroos, J., Kankaanpää, P., van Technical interfaces Federated login and attribute release The Life Science  ... 
doi:10.5281/zenodo.6782892 fatcat:7mjn3mn755d63feht7qlietkpu

"RKKH" Peptides from the Snake Venom Metalloproteinase ofBothrops jararacaBind Near the Metal Ion-dependent Adhesion Site of the Human Integrin α2I-domain

Olli Pentikäinen, Anna-Marja Hoffrén, Johanna Ivaska, Jarmo Käpylä, Tommi Nyrönen, Jyrki Heino, Mark S. Johnson
1999 Journal of Biological Chemistry  
were added at the indicated concentrations to the coated wells and incubated for 3 h at 37°C.  ...  Sulfo-NHS-biotin (Calbiochem) was added 1:2 (w/w) peptide:biotin and incubated for 2 h at room temperature. The biotinylation reaction was stopped by adding 1/10 volume 0.5 M Tris-HCl (pH 8.0).  ... 
doi:10.1074/jbc.274.44.31493 pmid:10531352 fatcat:acy3kbqgh5co5l52obg65wkhlm
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