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167 results on '"Sengstag, Thierry"'

1. Reintegration Into the Workforce After Kidney Transplantation Based on Urbanization Status in Switzerland

Author

Amico, Patrizia, Bachofner, Adrian, Banz, Vanessa, Beckmann, Sonja, Beldi, Guido, Berger, Christoph, Berishvili, Ekaterine, Berzigotti, Annalisa, Bochud, Pierre-Yves, Branca, Sanda, Bucher, Heiner, Cairoli, Anne, Catana, Emmanuelle, Chalandon, Yves, De Geest, Sabina, De Seigneux, Sophie, Dickenmann, Michael, Dreifuss, Joëlle Lynn, Duchosal, Michel, Fehr, Thomas, Ferrari-Lacraz, Sylvie, Frossard, Jaromil, Garzoni, Christian, Golshayan, Déla, Goossens, Nicolas, Haidar, Fadi, Halter, Jörg, Heim, Dominik, Hess, Christoph, Hillinger, Sven, Hirsch, Hans, Hirt, Patricia, Hoessly, Linard, Hofbauer, Günther, Huynh-Do, Uyen, Immer, Franz, Koller, Michael, Kremer, Andreas, Krueger, Thorsten, Kuhn, Christian, Laesser, Bettina, Lamoth, Frédéric, Lehmann, Roger, Leichtle, Alexander, Manuel, Oriol, Marti, Hans-Peter, Martinelli, Michele, McLin, Valérie, Mellac, Katell, Merçay, Aurélia, Mettler, Karin, Müller, Nicolas, Müller-Arndt, Ulrike, Müllhaupt, Beat, Nägeli, Mirjam, Oldani, Graziano, Pascual, Manuel, Passweg, Jakob, Pazeller, Rosemarie, Posfay-Barbe, Klara, Reineke, David, Rick, Juliane, Rosselet, Anne, Rossi, Simona, Rössler, Rothlin, Silvia, Ruschitzka, Frank, Schachtner, Thomas, Schaub, Stefan, Scherrer, Alexandra, Schneidawind, Dominik, Schnyder, Aurelia, Schuurmans, Macé, Schwab, Simon, Sengstag, Thierry, Simonetta, Federico, Steiger, Jürg, Stirniman, Guido, Stürzinger, Ueli, Van Delden, Christian, Venetz, Jean-Pierre, Villard, Jean, Vionnet, Julien, Wick, Madeleine, Wilhlem, Markus, Yerly, Patrick, Bocchi, Federica, Müller, Selina, Binet, Isabelle, Golshayan, Dela, Müller, Thomas, Sidler, Daniel, and Storni, Federico

Published
2025
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2. Outcome of Patients Transplanted for C3 Glomerulopathy and Primary Immune Complex-Mediated Membranoproliferative Glomerulonephritis

Author

Amico, Patrizia, Aubert, John-David, Banz, Vanessa, Beckmann, Sonia, Beldi, Guido, Berger, Christoph, Berishvili, Ekaterine, Binet, Isabelle, Bochud, Pierre-Yves, Branca, Sanda, Bucher, Heiner, Catana, Emmanuelle, Chalandon, Yves, De Geest, Sabina, De Seigneux Michael Dickenmann, Sophie, Dreifuss, Joëlle Lynn, Duchosal, Michel, Fehr, Thomas, Ferrari-Lacraz, Sylvie, Garzoni, Christian, Gaudet, Christophe, Golshayan, Déla, Goossens, Nicolas, Halter, Jörg, Heim, Dominik, Hess, Christoph, Hillinger, Sven, Hirsch, Hans H., Hirt, Patricia, Hofbauer, Günther, Huynh-Do, Uyen, Immer, Franz, Koller, Michael, Laager, Mirjam, Laesser, Bettina, Lamoth, Frédéric, Lehmann, Roger, Leichtle, Alexander, Manuel, Oriol, Marti, Hans-Peter, Martinelli, Michele, McLin, Valérie, Mellac, Katell, Mercay, Aurelia, Mettler, Karin, Mueller, Nicolas J., Müller, Antonia, Müller-Arndt, Ulrike, Müllhaupt, Beat, Nägeli, Mirjam, Oldani, Graziano, Pascual, Manuel, Passweg, Jakob, Posfay-Barbe, Klara, Rick, Juliane, Rosselet, Anne, Rossi, Simona, Rothlin, Silvia, Ruschitzka, Frank, Schachtner, Thomas, Schanz, Urs, Schaub, Stefan, Schwab, Simon, Schnyder, Aurelia, Schuurmans, Macé, Sengstag, Thierry, Simonetta, Federico, Steiger, Jürg, Stirniman, Guido, Stürzinger, Ueli, Van Delden, Christian, Venetz, Jean-Pierre, Villard, Jean, Vionnet, Julien, Wick, Madeleine, Wilhlem, Markus, Yerly, Patrick, Halfon, Matthieu, Taffé, Patrick, Bucher, Christian, Haidar, Fadi, Huynh-do, Uyen, Mani, Laila-Yasmin, Wehmeier, Caroline, Fakhouri, Fadi, and Golshayan, Dela

Published
2025
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3. Surgical site infections after kidney transplantation are independently associated with graft loss

Author

Amico, Patrizia, Aubert, John-David, Banz, Vanessa, Beckmann, Sonja, Beldi, Guido, Berger, Christoph, Berishvili, Ekaterine, Berzigotti, Annalisa, Binet, Isabelle, Bochud, Pierre-Yves, Branca, Sanda, Bucher, Heiner, Catana, Emmanuelle, Cairoli, Anne, Chalandon, Yves, De Geest, Sabina, De Rougemont, Olivier, De Seigneux, Sophie, Dickenmann, Michael, Dreifuss, Joëlle Lynn, Duchosal, Michel, Fehr, Thomas, Ferrari-Lacraz, Sylvie, Garzoni, Christian, Golshayan, Déla, Goossens, Nicolas, Haidar, Fadi, Halter, Jörg, Heim, Dominik, Hess, Christoph, Hillinger, Sven, Hirsch, Hans H., Hirt, Patricia, Hoessly, Linard, Hofbauer, Günther, Huynh-Do, Uyen, Immer, Franz, Koller, Michael, Laesser, Bettina, Lamoth, Frédéric, Lehmann, Roger, Leichtle, Alexander, Manuel, Oriol, Marti, Hans-Peter, Martinelli, Michele, McLin, Valérie, Mellac, Katell, Merçay, Aurélia, Mettler, Karin, Mueller, Nicolas J., Müller-Arndt, Ulrike, Müllhaupt, Beat, Nägeli, Mirjam, Oldani, Graziano, Pascual, Manuel, Passweg, Jakob, Pazeller, Rosemarie, Posfay-Barbe, Klara, Rick, Juliane, Rosselet, Anne, Rossi, Simona, Rothlin, Silvia, Ruschitzka, Frank, Schachtner, Thomas, Schaub, Stefan, Scherrer, Alexandra, Schnyder, Aurelia, Schuurmans, Macé, Schwab, Simon, Sengstag, Thierry, Simonetta, Federico, Stampf, Susanne, Steiger, Jürg, Stirnimann, Guido, Stürzinger, Ueli, Van Delden, Christian, Venetz, Jean-Pierre, Villard, Jean, Vionnet, Julien, Wick, Madeleine, Wilhelm, Markus, Yerly, Patrick, Schreiber, Peter W., Hoessly, Linard D., Boggian, Katia, Neofytos, Dionysios, van Delden, Christian, Egli, Adrian, Hirzel, Cédric, Schmied, Bruno, Guerke, Lorenz, Matter, Maurice, de Rougemont, Olivier, Bonani, Marco, Sidler, Daniel, and Kuster, Stefan P.

Published
2024
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4. BK polyomavirus serotype-specific antibody responses in blood donors and kidney transplant recipients with and without new-onset BK polyomavirus-DNAemia: A Swiss Transplant Cohort Study

Author

Amico, Patrizia, Bachofner, Adrian, Banz, Vanessa, Beckmann, Sonja, Beldi, Guido, Berger, Christoph, Berishvili, Ekaterine, Berzigotti, Annalisa, Binet, Françoise-Isabelle, Bochud, Pierre-Yves, Borner, Petra, Branca, Sanda, Cairoli, Anne, Catana, Emmanuelle, Chalandon, Yves, Compagnon, Philippe, De Geest, Sabina, De Seigneux, Sophie, Dickenmann, Michael, Dreifuss, Joëlle Lynn, Duchosal, Michel, Fehr, Thomas, Ferrari-Lacraz, Sylvie, Flammer, Andreas, Frossard, Jaromil, Golshayan, Dela, Goossens, Nicolas, Haidar, Fadi, Halter, Jürg, Hess, Christoph, Hillinger, Sven, Hirsch, Hans H., Hirt, Patricia, Hoessly, Linard, Hofbauer, Günther, Huynh-Do, Uyen, Immer, Franz, Khanna, Nina, Koller, Michael, Kremer, Andreas, Krueger, Thorsten, Kuhn, Christian, Laesser, Bettina, Lamoth, Frédéric, Lehmann, Roger, Leichtle, Alexander, L'Huillier, Arnaud, Manuel, Oriol, Marti, Hans-Peter, Martinelli, Michele, McLin, Valérie, Mellac, Katell, Merçay, Aurélia, Mettler, Karin, Müller, Nicolas, Müller, Jelena, Müller-Arndt, Ulrike, Nägeli, Mirjam, Neofytos, Dionysios, Nilsson, Jakob, Pascual, Manuel, Pazeller, Rosmarie, Reineke, David, Rick, Juliane, Rössler, Fabian, Rothlin, Silvia, Schachtner, Thomas, Schaub, Stefan, Schneidawind, Dominik, Schuurmans, Macé, Schwab, Simon, Sengstag, Thierry, Sidler, Daniel, Simonetta, Federico, Steiger, Jürg, Stirnimann, Guido, Stürzinger, Ueli, Van Delden, Christian, Venetz, Jean-Pierre, Villard, Jean, Vionnet, Julien, Wehmeier, Caroline, Wilhelm, Markus, Yerly, Patrick, Hillenbrand, Caroline A., Akbari Bani, Dorssa, Follonier, Océane, Kaur, Amandeep, Weissbach, Fabian H., Wernli, Marion, Wilhelm, Maud, Leuzinger, Karoline, Binet, Isabelle, Hirzel, Cédric, and Mueller, Nicolas J.

Published
2024
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5. Use of induction therapy in pediatric heart transplant recipients in Switzerland – Analysis of the Swiss national database

Author

Amico, Patrizia, Axel, Andres, Aubert, John-David, Banz, Vanessa, Sonja, Beckmann, Beldi, Guido, Berger, Christoph, Berishvili, Ekaterine, Binet, Isabelle, Bochud, Pierre-Yves, Branca, Sanda, Bucher, Heiner, Carrel, Thierry, Catana, Emmanuelle, Chalandon, Yves, De Geest, Sabina, De Rougemont, Olivier, Dickenmann, Michael, Dreifuss, Joëlle Lynn, Duchosal, Michel, Fehr, Thomas, Ferrari-Lacraz, Sylvie, Garzoni, Christian, Soccal, Paola Gasche, Gaudet, Christophe, Golshayan, Déla, Goossens, Nicolas, Hadaya, Karine, Halter, Jörg, Heim, Dominik, Hess, Christoph, Hillinger, Sven, Hirsch, Hans, Hirt, Patricia, Hofbauer, Günther, Huynh-Do, Uyen, Immer, Franz, Koller, Michael, Laager, Mirjam, Laesser, Bettina, Lehmann, Roger, Leichtle, Alexander, Lovis, Christian, Manuel, Oriol, Marti, Hans-Peter, Martin, Pierre Yves, Martinelli, Michele, McLin, Valérie, Mellac, Katell, Merçay, Aurélia, Mettler, Karin, Mueller, Nicolas, Müller, Antonia, Müller, Thomas, Müller-Arndt, Ulrike, Müllhaupt, Beat, Nägeli, Mirjam, Oldani, Graziano, Pascual, Manuel, Posfay-Barbe, Klara, Rick, Juliane, Rosselet, Anne, Rossi, Simona, Rothlin, Silvia, Ruschitzka, Frank, Schanz, Urs, Schaub, Stefan, Schnyder, Aurelia, Schuurmans, Macé, Sengstag, Thierry, Simonetta, Federico, Staufer, Katharina, Stampf, Susanne, Steiger, Jürg, Stirniman, Guido, Stürzinger, Ueli, Van Delden, Christian, Venetz, Jean-Pierre, Villard, Jean, Vionnet, Julien, Wick, Madeleine, Wilhlem, Markus, Yerly, Patrick, Schweiger, M., Erdil, T., Di Bernardo, S., Balmer, C., Yildiz, M., and Kadner, A.

Published
2021
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6. The FAIR Guiding Principles for scientific data management and stewardship.

Author

Wilkinson, Mark D, Dumontier, Michel, Aalbersberg, I Jsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan-Willem, da Silva Santos, Luiz Bonino, Bourne, Philip E, Bouwman, Jildau, Brookes, Anthony J, Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scott, Evelo, Chris T, Finkers, Richard, Gonzalez-Beltran, Alejandra, Gray, Alasdair JG, Groth, Paul, Goble, Carole, Grethe, Jeffrey S, Heringa, Jaap, 't Hoen, Peter AC, Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J, Martone, Maryann E, Mons, Albert, Packer, Abel L, Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, van Schaik, Rene, Sansone, Susanna-Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A, Thompson, Mark, van der Lei, Johan, van Mulligen, Erik, Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, and Mons, Barend

Subjects
Data Collection, Reproducibility of Results, Research Design, Database Management Systems, Guidelines as Topic, Data Curation
Abstract

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Published
2016

8. Addendum: The FAIR Guiding Principles for scientific data management and stewardship

Author

Wilkinson, Mark D., Dumontier, Michel, Jan Aalbersberg, Ijsbrand, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan-Willem, da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scott, Evelo, Chris T., Finkers, Richard, Gonzalez-Beltran, Alejandra, Gray, Alasdair J. G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, Hoen, Peter A. C. ’t, Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, van Schaik, Rene, Sansone, Susanna-Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, van der Lei, Johan, van Mulligen, Erik, Jan Velterop, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, and Mons, Barend

Published
2019
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9. Supplementary Table 1 from CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma

Author

Monnier, Yan, primary, Farmer, Pierre, primary, Bieler, Gregory, primary, Imaizumi, Natsuko, primary, Sengstag, Thierry, primary, Alghisi, Gian Carlo, primary, Stehle, Jean-Christophe, primary, Ciarloni, Laura, primary, Andrejevic-Blant, Snezana, primary, Moeckli, Raphael, primary, Mirimanoff, René-Olivier, primary, Goodman, Simon L., primary, Delorenzi, Mauro, primary, and Rüegg, Curzio, primary

Published
2023
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10. Data from CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma

Author

Monnier, Yan, primary, Farmer, Pierre, primary, Bieler, Gregory, primary, Imaizumi, Natsuko, primary, Sengstag, Thierry, primary, Alghisi, Gian Carlo, primary, Stehle, Jean-Christophe, primary, Ciarloni, Laura, primary, Andrejevic-Blant, Snezana, primary, Moeckli, Raphael, primary, Mirimanoff, René-Olivier, primary, Goodman, Simon L., primary, Delorenzi, Mauro, primary, and Rüegg, Curzio, primary

Published
2023
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11. Supplementary Figure 1 from CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma

Author

Monnier, Yan, primary, Farmer, Pierre, primary, Bieler, Gregory, primary, Imaizumi, Natsuko, primary, Sengstag, Thierry, primary, Alghisi, Gian Carlo, primary, Stehle, Jean-Christophe, primary, Ciarloni, Laura, primary, Andrejevic-Blant, Snezana, primary, Moeckli, Raphael, primary, Mirimanoff, René-Olivier, primary, Goodman, Simon L., primary, Delorenzi, Mauro, primary, and Rüegg, Curzio, primary

Published
2023
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12. Supplementary Figure 2 from CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma

Author

Monnier, Yan, primary, Farmer, Pierre, primary, Bieler, Gregory, primary, Imaizumi, Natsuko, primary, Sengstag, Thierry, primary, Alghisi, Gian Carlo, primary, Stehle, Jean-Christophe, primary, Ciarloni, Laura, primary, Andrejevic-Blant, Snezana, primary, Moeckli, Raphael, primary, Mirimanoff, René-Olivier, primary, Goodman, Simon L., primary, Delorenzi, Mauro, primary, and Rüegg, Curzio, primary

Published
2023
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13. Supplementary Methods and Materials from CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma

Author

Monnier, Yan, primary, Farmer, Pierre, primary, Bieler, Gregory, primary, Imaizumi, Natsuko, primary, Sengstag, Thierry, primary, Alghisi, Gian Carlo, primary, Stehle, Jean-Christophe, primary, Ciarloni, Laura, primary, Andrejevic-Blant, Snezana, primary, Moeckli, Raphael, primary, Mirimanoff, René-Olivier, primary, Goodman, Simon L., primary, Delorenzi, Mauro, primary, and Rüegg, Curzio, primary

Published
2023
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14. Supplementary Figure 3 from CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma

Author

Monnier, Yan, primary, Farmer, Pierre, primary, Bieler, Gregory, primary, Imaizumi, Natsuko, primary, Sengstag, Thierry, primary, Alghisi, Gian Carlo, primary, Stehle, Jean-Christophe, primary, Ciarloni, Laura, primary, Andrejevic-Blant, Snezana, primary, Moeckli, Raphael, primary, Mirimanoff, René-Olivier, primary, Goodman, Simon L., primary, Delorenzi, Mauro, primary, and Rüegg, Curzio, primary

Published
2023
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15. Sensing the (digital) pulse. Future steps for improving the secondary use of data for research in Switzerland

Author

Martani, Andrea, primary, Geneviève, Lester Darryl, additional, Wangmo, Tenzin, additional, Maurer, Julia, additional, Crameri, Katrin, additional, Erard, Frédéric, additional, Spoendlin, Julia, additional, Pauli-Magnus, Christiane, additional, Pittet, Valerie, additional, Sengstag, Thierry, additional, Soldini, Emiliano, additional, Hirschel, Bernard, additional, Borisch, Bettina, additional, Kruschel Weber, Cornelia, additional, Zwahlen, Marcel, additional, and Elger, Bernice Simone, additional

Published
2023
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16. Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD

Author

Heck, Angela, Milnik, Annette, Vukojevic, Vanja, Petrovska, Jana, Egli, Tobias, Singer, Jochen, Escobar, Pablo, Sengstag, Thierry, Coynel, David, Freytag, Virginie, Fastenrath, Matthias, Demougin, Philippe, Loos, Eva, Hartmann, Francina, Schicktanz, Nathalie, Delarue Bizzini, Bernardo, Vogler, Christian, Kolassa, Iris-Tatjana, Wilker, Sarah, Elbert, Thomas, Schwede, Torsten, Beisel, Christian, Beerenwinkel, Niko, de Quervain, Dominique J.-F., and Papassotiropoulos, Andreas

Published
2017
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18. SwissPK$^{cdw}$ - A clinical data warehouse for the optimization of pediatric dosing regimens

Author

Goers, Roland, Coman Schmid, Diana, Jäggi, Vera F, Paioni, Paolo, Okoniewski, Michal J, Parker, Althea, Bangerter, Beat, Georgakopoulou, Sofia, Sengstag, Thierry, Bielicki, Julia A, Tilen, Romy, Vermeul, Swen, Krämer, Stefanie D, Berger, Christoph, Rinn, Bernd, Meyer Zu Schwabedissen, Henriette E, University of Zurich, Krämer, Stefanie D, Berger, Christoph, Rinn, Bernd, and Meyer Zu Schwabedissen, Henriette E

Subjects
10036 Medical Clinic, 2736 Pharmacology (medical), 610 Medicine & health, 2611 Modeling and Simulation
Abstract

Clinical trials have been performed mainly in adults and accordingly the necessary information is lacking for pediatric patients, especially regarding dosage recommendation for approved drugs. This gap in information could be filled with results from pharmacokinetic (PK) modeling, based on data collected in daily clinical routine. In order to make this data accessible and usable for research, the Swiss Pharmacokinetics Clinical Data Warehouse (SwissPK(cdw)) project has been set up, including a clinical data warehouse (CDW) and the regulatory framework for data transfer and use within. Embedded into the secure BioMedIT network, the CDW can connect to various data providers and researchers in order to collaborate on the data securely. Due to its modularity, partially containerized deployment and open-source software, each of the components can be extended, modified, and re-used for similar projects that require integrated data management, data analysis, and web tools in a secure scientific data and information technology (IT) environment. Here, we describe a collaborative and interprofessional effort to implement the aforementioned infrastructure between several partners from medical health care and academia. Furthermore, we describe a real-world use case where blood samples from pediatric patients were analyzed for the presence of genetic polymorphisms and the results were aggregated and further analyzed together with the health-related patient data in the SwissPK(cdw)., CPT: Pharmacometrics and Systems Pharmacology, 10 (12), ISSN:2163-8306

Published
2021

20. SwissPK cdw – A clinical data warehouse for the optimization of pediatric dosing regimens

Author

Goers, Roland, primary, Coman Schmid, Diana, additional, Jäggi, Vera F., additional, Paioni, Paolo, additional, Okoniewski, Michal J., additional, Parker, Althea, additional, Bangerter, Beat, additional, Georgakopoulou, Sofia, additional, Sengstag, Thierry, additional, Bielicki, Julia, additional, Tilen, Romy, additional, Vermeul, Swen, additional, Krämer, Stefanie D., additional, Berger, Christoph, additional, Rinn, Bernd, additional, and Meyer zu Schwabedissen, Henriette E., additional

Published
2021
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21. Use of induction therapy in pediatric heart transplant recipients in Switzerland – Analysis of the Swiss national database

Author

Schweiger, M., primary, Erdil, T., additional, Di Bernardo, S., additional, Balmer, C., additional, Yildiz, M., additional, Kadner, A., additional, Amico, Patrizia, additional, Axel, Andres, additional, Aubert, John-David, additional, Banz, Vanessa, additional, Sonja, Beckmann, additional, Beldi, Guido, additional, Berger, Christoph, additional, Berishvili, Ekaterine, additional, Binet, Isabelle, additional, Bochud, Pierre-Yves, additional, Branca, Sanda, additional, Bucher, Heiner, additional, Carrel, Thierry, additional, Catana, Emmanuelle, additional, Chalandon, Yves, additional, De Geest, Sabina, additional, De Rougemont, Olivier, additional, Dickenmann, Michael, additional, Dreifuss, Joëlle Lynn, additional, Duchosal, Michel, additional, Fehr, Thomas, additional, Ferrari-Lacraz, Sylvie, additional, Garzoni, Christian, additional, Soccal, Paola Gasche, additional, Gaudet, Christophe, additional, Golshayan, Déla, additional, Goossens, Nicolas, additional, Hadaya, Karine, additional, Halter, Jörg, additional, Heim, Dominik, additional, Hess, Christoph, additional, Hillinger, Sven, additional, Hirsch, Hans, additional, Hirt, Patricia, additional, Hofbauer, Günther, additional, Huynh-Do, Uyen, additional, Immer, Franz, additional, Koller, Michael, additional, Laager, Mirjam, additional, Laesser, Bettina, additional, Lehmann, Roger, additional, Leichtle, Alexander, additional, Lovis, Christian, additional, Manuel, Oriol, additional, Marti, Hans-Peter, additional, Martin, Pierre Yves, additional, Martinelli, Michele, additional, McLin, Valérie, additional, Mellac, Katell, additional, Merçay, Aurélia, additional, Mettler, Karin, additional, Mueller, Nicolas, additional, Müller, Antonia, additional, Müller, Thomas, additional, Müller-Arndt, Ulrike, additional, Müllhaupt, Beat, additional, Nägeli, Mirjam, additional, Oldani, Graziano, additional, Pascual, Manuel, additional, Posfay-Barbe, Klara, additional, Rick, Juliane, additional, Rosselet, Anne, additional, Rossi, Simona, additional, Rothlin, Silvia, additional, Ruschitzka, Frank, additional, Schanz, Urs, additional, Schaub, Stefan, additional, Schnyder, Aurelia, additional, Schuurmans, Macé, additional, Sengstag, Thierry, additional, Simonetta, Federico, additional, Staufer, Katharina, additional, Stampf, Susanne, additional, Steiger, Jürg, additional, Stirniman, Guido, additional, Stürzinger, Ueli, additional, Van Delden, Christian, additional, Venetz, Jean-Pierre, additional, Villard, Jean, additional, Vionnet, Julien, additional, Wick, Madeleine, additional, Wilhlem, Markus, additional, and Yerly, Patrick, additional

Published
2021
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22. A promoter-level mammalian expression atlas

Author

Forrest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A. C., Arner, Peter, Babina, Magda, Rennie, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan-Bhatt, Swati, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S. B., Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gibson, Andrew P., Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Huminiecki, Lukasz, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori-Katayama, Mutsumi, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F. J., Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay-sim, Alan, Manabe, Ri-ichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G. D., Rackham, Owen J. L., Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., ’t Hoen, Peter A. C., Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Susan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin, Hume, David A., Carninci, Piero, and Hayashizaki, Yoshihide

Published
2014
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23. SPHN – The BioMedIT Network: A Secure IT Platform for Research with Sensitive Human Data

Author

Coman Schmid, Diana, Crameri, Katrin, Oesterle, Sabine, Rinn, Bernd, Sengstag, Thierry, Stockinger, Heinz, Pape-Haugaard, Louise B., Lovis, Christian, Cort Madsen, Inge, Weber, Patrick, Hostrup Nielsen, Per, and Scott, Philip

Subjects
Scientific IT services, Health-related data, Research infrastructure, Interoperability, Private-cloud, Service virtualization, Federated computation, SPHN, Confidential data, Sensitive data, Personalized health, Data privacy, Data security
Abstract

The BioMedIT project is funded by the Swiss government as an integral part of the Swiss Personalized Health Network (SPHN), aiming to provide researchers with access to a secure, powerful and versatile IT infrastructure for doing data-driven research on sensitive biomedical data while ensuring data privacy protection. The BioMedIT network gives researchers the ability to securely transfer, store, manage and process sensitive research data. The underlying BioMedIT nodes provide compute and storage capacity that can be used locally or through a federated environment. The network operates under a common Information Security Policy using state-of-the-art security techniques. It utilizes cloud computing, virtualization, compute accelerators (GPUs), big data storage as well as federation technologies to lower computational boundaries for researchers and to guarantee that sensitive data can be processed in a secure and lawful way. Building on existing expertise and research infrastructure at the partnering Swiss institutions, the BioMedIT network establishes a competitive Swiss private-cloud – a secure national infrastructure resource that can be used by researchers of Swiss universities, hospitals and other research institutions., Studies in Health Technology and Informatics, 270, ISSN:0926-9630, ISSN:1879-8365, Digital Personalized Health and Medicine, ISBN:978-1-64368-082-8, ISBN:978-1-64368-083-5

Published
2020

24. Epidemiology and outcomes of bone and joint infections in solid organ transplant recipients

Author

Pham, Truong‐Thanh, Andrey, Diego O., Stampf, Susanne, Burkhard, Sara H., Hirzel, Cédric, Tschopp, Johnathan, Ullrich, Kathrin, Strahm, Carol, Schreiber, Peter W., Boillat‐Blanco, Noémie, Garzoni, Christian, Khanna, Nina, Manuel, Oriol, Mueller, Nicolas J., Suva, Domizio, Delden, Christian, Uçkay, Ilker, Neofytos, Dionysios, Amico, Patrizia, Axel, Andres, Aubert, John‐David, Banz, Vanessa, Beckmann, Sonja, Beldi, Guido, Berger, Christoph, Berishvili, Ekaterine, Berzigotti, Annalisa, Binet, Isabelle, Bochud, Pierre‐Yves, Branca, Sanda, Bucher, Heiner, Catana, Emmanuelle, Cairoli, Anne, Chalandon, Yves, De Geest, Sabina, De Rougemont, Olivier, De Seigneux, Sophie, Dickenmann, Michael, Dreifuss, Joëlle Lynn, Duchosal, Michel, Fehr, Thomas, Ferrari‐Lacraz, Sylvie, Golshayan, Déla, Goossens, Nicolas, Halter, Jörg, Heim, Dominik, Hess, Christoph, Hillinger, Sven, Hirsch, Hans H., Hirt, Patricia, Hofbauer, Günther, Huynh‐Do, Uyen, Immer, Franz, Koller, Michael, Laager, Mirjam, Laesser, Bettina, Lamoth, Frédéric, Lehmann, Roger, Leichtle, Alexander, Marti, Hans‐Peter, Martinelli, Michele, McLin, Valérie, Mellac, Katell, Merçay, Aurélia, Mettler, Karin, Müller, Antonia, Müller‐Arndt, Ulrike, Müllhaupt, Beat, Nägeli, Mirjam, Oldani, Graziano, Pascual, Manuel, Passweg, Jakob, Pazeller, Rosemarie, Posfay‐Barbe, Klara, Rick, Juliane, Rosselet, Anne, Rossi, Simona, Rothlin, Silvia, Ruschitzka, Frank, Schachtner, Thomas, Schanz, Urs, Schaub, Stefan, Scherrer, Alexandra, Schnyder, Aurelia, Schuurmans, Macé, Schwab, Simon, Sengstag, Thierry, Simonetta, Federico, Steiger, Jürg, Stirnimann, Guido, Stürzinger, Ueli, Venetz, Jean‐Pierre, Villard, Jean, Vionnet, Julien, Wick, Madeleine, Wilhelm, Markus, and Yerly, Patrick

Abstract

Bone and joint infection (BJI) epidemiology and outcomes in solid organ transplant recipients (SOTr) remain largely unknown. We aim to describe BJI in a multi‐center cohort of SOTr (Swiss Transplant Cohort Study). All consecutive SOTr with BJI (01.05.2008–31.12.2019) were included. A nested case–control study to identify risk factors for BJI was performed. Among 4482 patients, 61 SOTr with 82 BJI were included, at an incidence of 1.4% (95% CI 1.1–1.7), higher in heart and kidney‐pancreas SOTr (Gray's test p< .01). Although BJI were predominately late events (median of 18.5 months post‐SOT), most infections occurred during the first year post‐transplant in thoracic SOTr. Diabetic foot osteomyelitis was the most frequent infection (38/82, 46.3%), followed by non‐vertebral osteomyelitis (26/82, 31.7%). Pathogens included Gram‐positive cocci (70/131, 53.4%), Gram‐negative bacilli (34/131, 26.0%), and fungi (9/131, 6.9%). BJI predictors included male gender (OR 2.94, 95% CI 1.26–6.89) and diabetes (OR 2.97, 95% CI 1.34–6.56). Treatment failure was observed in 25.9% (21/81) patients and 1‐year mortality post‐BJI diagnosis was 14.8% (9/61). BJI remain a rare event in SOTr, associated with subtle clinical presentations, high morbidity and relapses, requiring additional studies in the future. In solid organ transplant recipients, bone and joint infections, rare complications with subtle clinical presentation, high morbidity and frequent relapse, require special attention from treating physicians.

Published
2022
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26. Mutant huntingtinʼs effects on striatal gene expression in mice recapitulate changes observed in human Huntingtonʼs disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage

Author

Kuhn, Alexandre, Goldstein, Darlene R., Hodges, Angela, Strand, Andrew D., Sengstag, Thierry, Kooperberg, Charles, Becanovic, Kristina, Pouladi, Mahmoud A., Sathasivam, Kirupa, Cha, Jang-Ho J., Hannan, Anthony J., Hayden, Michael R., Leavitt, Blair R., Dunnett, Stephen B., Ferrante, Robert J., Albin, Roger, Shelbourne, Peggy, Delorenzi, Mauro, Augood, Sarah J., Faull, Richard L.M., Olson, James M., Bates, Gillian P., Jones, Lesley, and Luthi-Carter, Ruth

Published
2007

28. Regional and cellular gene expression changes in human Huntingtonʼs disease brain

Author

Hodges, Angela, Strand, Andrew D., Aragaki, Aaron K., Kuhn, Alexandre, Sengstag, Thierry, Hughes, Gareth, Elliston, Lyn A., Hartog, Cathy, Goldstein, Darlene R., Thu, Doris, Hollingsworth, Zane R., Collin, Francois, Synek, Beth, Holmans, Peter A., Young, Anne B., Wexler, Nancy S., Delorenzi, Mauro, Kooperberg, Charles, Augood, Sarah J., Faull, Richard L.M., Olson, James M., Jones, Lesley, and Luthi-Carter, Ruth

Published
2006

29. SwissPKcdw – A clinical data warehouse for the optimization of pediatric dosing regimens.

Author

Goers, Roland, Coman Schmid, Diana, Jäggi, Vera F., Paioni, Paolo, Okoniewski, Michal J., Parker, Althea, Bangerter, Beat, Georgakopoulou, Sofia, Sengstag, Thierry, Bielicki, Julia, Tilen, Romy, Vermeul, Swen, Krämer, Stefanie D., Berger, Christoph, Rinn, Bernd, and Meyer zu Schwabedissen, Henriette E.

Subjects
DATA warehousing, CHILD patients, GENETIC polymorphisms, MEDICAL care, INFORMATION technology
Abstract

Clinical trials have been performed mainly in adults and accordingly the necessary information is lacking for pediatric patients, especially regarding dosage recommendation for approved drugs. This gap in information could be filled with results from pharmacokinetic (PK) modeling, based on data collected in daily clinical routine. In order to make this data accessible and usable for research, the Swiss Pharmacokinetics Clinical Data Warehouse (SwissPKcdw) project has been set up, including a clinical data warehouse (CDW) and the regulatory framework for data transfer and use within. Embedded into the secure BioMedIT network, the CDW can connect to various data providers and researchers in order to collaborate on the data securely. Due to its modularity, partially containerized deployment and open‐source software, each of the components can be extended, modified, and re‐used for similar projects that require integrated data management, data analysis, and web tools in a secure scientific data and information technology (IT) environment. Here, we describe a collaborative and interprofessional effort to implement the aforementioned infrastructure between several partners from medical health care and academia. Furthermore, we describe a real‐world use case where blood samples from pediatric patients were analyzed for the presence of genetic polymorphisms and the results were aggregated and further analyzed together with the health‐related patient data in the SwissPKcdw. [ABSTRACT FROM AUTHOR]

Published
2021
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30. Defining new criteria for selection of cell-based intestinal models using publicly available databases

Author

Christensen Jon, El-Gebali Sara, Natoli Manuela, Sengstag Thierry, Delorenzi Mauro, Bentz Susanne, Bouzourene Hanifa, Rumbo Martin, Felsani Armando, Siissalo Sanna, Hirvonen Jouni, Vila Maya R, Saletti Piercarlo, Aguet Michel, and Anderle Pascale

Subjects
Cell lines, Genomic profiling, Malignant traits, Epithelial-mesenchymal transition, Intestine, Colon cancer, Chemosensitivity, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, therefore, to establish objective criteria for choosing relevant cell lines to assess their appropriateness as tumor models as well as for drug absorption studies. Results We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium. We have compared a panel of intestinal cell lines with patient-derived normal and tumor epithelium and classified them according to traits relating to oncogenic pathway activity, epithelial-mesenchymal transition (EMT) and stemness, migratory properties, proliferative activity, transporter expression profiles and chemosensitivity. For example, SW480 represent an EMT-high, migratory phenotype and scored highest in terms of signatures associated to worse overall survival and higher risk of recurrence based on patient derived databases. On the other hand, differentiated HT29 and T84 cells showed gene expression patterns closest to tumor bulk derived cells. Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine. Regarding chemosensitivity we were unable to confirm a recently proposed association of chemo-resistance with EMT traits. However, a novel signature was identified through mining of NCI60 GI50 values that allowed to rank the panel of intestinal cell lines according to their drug responsiveness to commonly used chemotherapeutics. Conclusions This study presents a straightforward strategy to exploit publicly available gene expression data to guide the choice of cell-based models. While this approach does not overcome the major limitations of such models, introducing a rank order of selected features may allow selecting model cell lines that are more adapted and pertinent to the addressed biological question.

Published
2012
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31. Medical diagnoses showed low relatedness in an explorative mutual information analysis of 190,837 inpatient cases

Author

Roth, Jan A., primary, Sakoparnig, Thomas, additional, Neubauer, Simon, additional, Kuenzel-Pawlik, Eleonore, additional, Gerber, Martin, additional, Widmer, Andreas F., additional, Hug, Balthasar L., additional, Abshagen, Christian, additional, Fucile, Geoffrey, additional, Jaegle, Bernd, additional, Padiyath, Rakesh, additional, Roth, Jan A., additional, Sengstag, Thierry, additional, and Spyra, Damian, additional

Published
2019
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32. Changes in the transcriptional profile of transporters in the intestine along the anterior-posterior and crypt-villus axes

Author

Delorenzi Mauro, Mansourian Robert, Praz Viviane, Rumbo Martin, Mutch David M, Sengstag Thierry, Anderle Pascale, Williamson Gary, and Roberts Matthew-Alan

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The purpose of this work was to characterize the expression of drug and nutrient carriers along the anterior-posterior and crypt-villus axes of the intestinal epithelium and to study the validity of utilizing whole gut tissue rather than purified epithelial cells to examine regional variations in gene expression. Results We have characterized the mRNA expression profiles of 76 % of all currently known transporters along the anterior-posterior axis of the gut. This is the first study to describe the expression profiles of the majority of all known transporters in the intestine. The expression profiles of transporters, as defined according to the Gene Ontology consortium, were measured in whole tissue of the murine duodenum, jejunum, ileum and colon using high-density microarrays. For nine transporters (Abca1, Abcc1, Abcc3, Abcg8, Slc10a2, Slc28a2, Slc2a1, Slc34a2 and Slc5a8), the mRNA profiles were further measured by RT-PCR in laser micro-dissected crypt and villus epithelial cells corresponding to the aforementioned intestinal regions. With respect to differentially regulated transporters, the colon had a distinct expression profile from small intestinal segments. The majority (59 % for p cutoff ≤ 0.05) of transporter mRNA levels were constant across the intestinal sections studied. For the transporter subclass "carrier activity", which contains the majority of known carriers for biologically active compounds, a significant change (p ≤ 0.05) along the anterior-posterior axis was observed. Conclusion All nine transporters examined in laser-dissected material demonstrated good replication of the region-specific profiles revealed by microarray. Furthermore, we suggest that the distribution characteristics of Slc5a8 along the intestinal tract render it a suitable candidate carrier for monocarboxylate drugs in the posterior portion of the intestine. Our findings also predict that there is a significant difference in the absorption of carrier-mediated compounds in the different intestinal segments. The most pronounced differences can be expected between the adjoining segments ileum and colon, but the differences between the other adjoining segments are not negligible. Finally, for the examined genes, profiles measured in whole intestinal tissue extracts are representative of epithelial cell-only gene expression.

Published
2005
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33. Data Descriptor : FANTOM5 CAGE profiles of human and mouse samples

Author

Noguchi, Shuhei, Arakawa, Takahiro, Fukuda, Shiro, Furuno, Masaaki, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Kaida, Kaoru, Kaiho, Ai, Kanamori-Katayama, Mutsumi, Kawashima, Tsugumi, Kojima, Miki, Kubosaki, Atsutaka, Manabe, Ri-ichiroh, Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakazato, Kenichi, Ninomiya, Noriko, Nishiyori-Sueki, Hiromi, Noma, Shohei, Saijyo, Eri, Saka, Akiko, Sakai, Mizuho, Simon, Christophe, Suzuki, Naoko, Tagami, Michihira, Watanabe, Shoko, Yoshida, Shigehiro, Arner, Peter, Axton, Richard A., Babina, Magda, Baillie, J. Kenneth, Barnett, Timothy C., Beckhouse, Anthony G., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Carlisle, Ailsa J., Clevers, Hans C., Davis, Carrie A., Detmar, Michael, Dohi, Taeko, Edge, Albert S. B., Edinger, Matthias, Ehrlund, Anna, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Farach-Carson, Mary C., Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E., Forrester, Lesley M., Fujita, Rie, Furusawa, Jun-ichi, Geijtenbeek, Teunis B., Gingeras, Thomas, Goldowitz, Daniel, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Hasegawa, Yuki, Herlyn, Meenhard, Heutink, Peter, Hitchens, Kelly J., Hume, David A., Ikawa, Tomokatsu, Ishizu, Yuri, Kai, Chieko, Kawamoto, Hiroshi, Kawamura, Yuki I., Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Klein, Sarah, Klinken, S. Peter, Knox, Alan J., Kojima, Soichi, Koseki, Haruhiko, Koyasu, Shigeo, Lee, Weonju, Lennartsson, Andreas, Mackay-sim, Alan, Mejhert, Niklas, Mizuno, Yosuke, Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Morris, Kelly J., Motohashi, Hozumi, Mummery, Christine L., Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Pradhan-Bhatt, Swati, Qin, Xian-Yang, Rehli, Michael, Rizzu, Patrizia, Roy, Sugata, Sajantila, Antti, Sakaguchi, Shimon, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schmidl, Christian, Schneider, Claudio, Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sheng, Guojun, Shin, Jay W., Sugiyama, Daisuke, Sugiyama, Takaaki, Summers, Kim M., Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tomoiu, Andru, Toyoda, Hiroo, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Yamaguchi, Yoko, Yamamoto, Masayuki, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Yonekura, Yohei, Zhang, Peter G., Zucchelli, Silvia, Abugessaisa, Imad, Arner, Erik, Harshbarger, Jayson, Kondo, Atsushi, Lassmann, Timo, Lizio, Marina, Sahin, Serkan, Sengstag, Thierry, Severin, Jessica, Shimoji, Hisashi, Suzuki, Masanori, Suzuki, Harukazu, Kawai, Jun, Kondo, Naoto, Itoh, Masayoshi, Daub, Carsten O., Kasukawa, Takeya, Kawaji, Hideya, Carninci, Piero, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Medicum, University of Helsinki, Forensic Medicine, Department of Forensic Medicine, and PaleOmics Laboratory

Subjects
ENHANCERS, MAMMALIAN-CELLS, UCSC GENOME BROWSER, VISUALIZATION, UPDATE, GROWTH, IN-VITRO, TRANSCRIPTION, 3111 Biomedicine, ATLAS, GENE-EXPRESSION
Abstract

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

Published
2017

34. SPHN – The BioMedIT Network: A Secure IT Platform for Research with Sensitive Human Data.

Author

SCHMID, Diana COMAN, CRAMERI, Katrin, OESTERLE, Sabine, RINN, Bernd, SENGSTAG, Thierry, STOCKINGER, Heinz, ALEXANDER, Leila T., BARDA, Jonathan, BOLLIGER, Christian, BORSTNIK, Urban, BRÄUNLICH, Gerhard, BYRDE, Olivier, DAUVILLIER, Jérôme, ENGLER, Robin, LOPEZ, Pablo ESCOBAR, FLEGEL, Volker, FOX, Martin, GEORGAKOPOULOU, Sofia, HEIKKINEN, Jani, and JACQUOT, Martin

Abstract

The BioMedIT project is funded by the Swiss government as an integral part of the Swiss Personalized Health Network (SPHN), aiming to provide researchers with access to a secure, powerful and versatile IT infrastructure for doing data-driven research on sensitive biomedical data while ensuring data privacy protection. The BioMedIT network gives researchers the ability to securely transfer, store, manage and process sensitive research data. The underlying BioMedIT nodes provide compute and storage capacity that can be used locally or through a federated environment. The network operates under a common Information Security Policy using state-of-the-art security techniques. It utilizes cloud computing, virtualization, compute accelerators (GPUs), big data storage as well as federation technologies to lower computational boundaries for researchers and to guarantee that sensitive data can be processed in a secure and lawful way. Building on existing expertise and research infrastructure at the partnering Swiss institutions, the BioMedIT network establishes a competitive Swiss private-cloud – a secure national infrastructure resource that can be used by researchers of Swiss universities, hospitals and other research institutions. [ABSTRACT FROM AUTHOR]

Published
2020
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35. Erratum to: Making sense of big data in health research: towards an EU action plan

Author

Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Ángel, Hose, D Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, I Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A I, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, and Zanetti, Gianluigi

Subjects
Journal Article
Published
2016

36. Die FAIR-Prinzipien für das wissenschaftliche Datenmanagement und Data Stewardship

Author

Wilkinson, Mark D., Dumontier, Michel, Aalbersberg, IJsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan-Willem, da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scott, Evelo, Chris T., Finkers, Richard, Gonzalez-Beltran, Alejandra, Gray, Alasdair J.G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, 't Hoen, Peter A.C., Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, van Schaik, Rene, Sansone, Susanna-Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, van der Lei, Johan, van Mulligen, Erik, Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, Mons, Barend, EcoDM (Funded by BMBF), Rothfritz, Laura, Burkart, Christine, and Bothe, Jasper

Subjects
Datenmanagement, Forschungsdatenmanagement, FAIR-Prinzipien
Abstract

Es besteht dringender Bedarf, die Infrastruktur für die Nachnutzung wissenschaftlicher Daten zu verbessern. Verschiedene Stakeholder aus Hochschulen, Industrieunternehmen, Forschungsförderern und wissenschaftlichen Verlagen haben sich zusammengeschlossen, um gemeinsam einen präzise gefassten Satz von messbaren Prinzipien zu formulieren und zu unterstützen. Diese Prinzipien, die wir als FAIR-Data-Prinzipien bezeichnen, sollen als Leitlinie für die Verbesserung der Nachnutzbarkeit von Datenbeständen dienen. Im Unterschied zu Peer-Initiativen, deren Fokus auf menschlichen Wissenschaftler*innen liegt, richten die FAIR-Prinzipien ein besonderes Augenmerk darauf, Maschinen das automatische Auffinden und die Verwendung von Daten zu erleichtern und somit eine Wiederverwendung durch Menschen zu unterstützen. Dieser Kommentar stellt die erste offizielle Veröffentlichung der FAIR-Prinzipen dar. Er beinhaltet die ihnen zu Grunde liegenden Überlegungen und beispielhaft einige exemplarische Implementierungen innerhalb der Community. Die vorliegende deutsche Übersetzung des Dokuments entstand im Rahmen des Verbundprojektes EcoDM mit der Förderung des Bundesministeriums für Bildung und Forschung (BMBF) unter dem Förderkennzeichen 16DWWQP.

Published
2016
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37. Correction: Making sense of big data in health research: towards an EU action plan (vol 8, pg 71, 2016)

Author

Auffray, Charles, Balling, Rudi, Barroso, Ines, Bencze, Laszlo, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Glynne Gut, Ivo, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Angel, Rod Hose, D., Houwing-Duistermaat, Jeanine, Hubbard, Tim, Helen Janacek, Sophie, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Muller, Werner, Nickel, Dothe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, Redon i Mas, Josep, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A. I., van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Antonio Vizcaino, Juan, Peter Mary Wubbe, John, and Zanetti, Gianluigi

Subjects
Klinisk medicin, Clinical Medicine
Abstract

n/a

Published
2016

38. Exhaustive search for epistatic effects on the human methylome

Author

Egli, Tobias, primary, Vukojevic, Vanja, additional, Sengstag, Thierry, additional, Jacquot, Martin, additional, Cabezón, Rubén, additional, Coynel, David, additional, Freytag, Virginie, additional, Heck, Angela, additional, Vogler, Christian, additional, de Quervain, Dominique J.-F., additional, Papassotiropoulos, Andreas, additional, and Milnik, Annette, additional

Published
2017
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39. FANTOM5 CAGE profiles of human and mouse samples

Author

Noguchi, Shuhei, primary, Arakawa, Takahiro, additional, Fukuda, Shiro, additional, Furuno, Masaaki, additional, Hasegawa, Akira, additional, Hori, Fumi, additional, Ishikawa-Kato, Sachi, additional, Kaida, Kaoru, additional, Kaiho, Ai, additional, Kanamori-Katayama, Mutsumi, additional, Kawashima, Tsugumi, additional, Kojima, Miki, additional, Kubosaki, Atsutaka, additional, Manabe, Ri-ichiroh, additional, Murata, Mitsuyoshi, additional, Nagao-Sato, Sayaka, additional, Nakazato, Kenichi, additional, Ninomiya, Noriko, additional, Nishiyori-Sueki, Hiromi, additional, Noma, Shohei, additional, Saijyo, Eri, additional, Saka, Akiko, additional, Sakai, Mizuho, additional, Simon, Christophe, additional, Suzuki, Naoko, additional, Tagami, Michihira, additional, Watanabe, Shoko, additional, Yoshida, Shigehiro, additional, Arner, Peter, additional, Axton, Richard A., additional, Babina, Magda, additional, Baillie, J. Kenneth, additional, Barnett, Timothy C., additional, Beckhouse, Anthony G., additional, Blumenthal, Antje, additional, Bodega, Beatrice, additional, Bonetti, Alessandro, additional, Briggs, James, additional, Brombacher, Frank, additional, Carlisle, Ailsa J., additional, Clevers, Hans C., additional, Davis, Carrie A., additional, Detmar, Michael, additional, Dohi, Taeko, additional, Edge, Albert S.B., additional, Edinger, Matthias, additional, Ehrlund, Anna, additional, Ekwall, Karl, additional, Endoh, Mitsuhiro, additional, Enomoto, Hideki, additional, Eslami, Afsaneh, additional, Fagiolini, Michela, additional, Fairbairn, Lynsey, additional, Farach-Carson, Mary C., additional, Faulkner, Geoffrey J., additional, Ferrai, Carmelo, additional, Fisher, Malcolm E., additional, Forrester, Lesley M., additional, Fujita, Rie, additional, Furusawa, Jun-ichi, additional, Geijtenbeek, Teunis B., additional, Gingeras, Thomas, additional, Goldowitz, Daniel, additional, Guhl, Sven, additional, Guler, Reto, additional, Gustincich, Stefano, additional, Ha, Thomas J., additional, Hamaguchi, Masahide, additional, Hara, Mitsuko, additional, Hasegawa, Yuki, additional, Herlyn, Meenhard, additional, Heutink, Peter, additional, Hitchens, Kelly J., additional, Hume, David A., additional, Ikawa, Tomokatsu, additional, Ishizu, Yuri, additional, Kai, Chieko, additional, Kawamoto, Hiroshi, additional, Kawamura, Yuki I., additional, Kempfle, Judith S., additional, Kenna, Tony J., additional, Kere, Juha, additional, Khachigian, Levon M., additional, Kitamura, Toshio, additional, Klein, Sarah, additional, Klinken, S. Peter, additional, Knox, Alan J., additional, Kojima, Soichi, additional, Koseki, Haruhiko, additional, Koyasu, Shigeo, additional, Lee, Weonju, additional, Lennartsson, Andreas, additional, Mackay-sim, Alan, additional, Mejhert, Niklas, additional, Mizuno, Yosuke, additional, Morikawa, Hiromasa, additional, Morimoto, Mitsuru, additional, Moro, Kazuyo, additional, Morris, Kelly J., additional, Motohashi, Hozumi, additional, Mummery, Christine L., additional, Nakachi, Yutaka, additional, Nakahara, Fumio, additional, Nakamura, Toshiyuki, additional, Nakamura, Yukio, additional, Nozaki, Tadasuke, additional, Ogishima, Soichi, additional, Ohkura, Naganari, additional, Ohno, Hiroshi, additional, Ohshima, Mitsuhiro, additional, Okada-Hatakeyama, Mariko, additional, Okazaki, Yasushi, additional, Orlando, Valerio, additional, Ovchinnikov, Dmitry A., additional, Passier, Robert, additional, Patrikakis, Margaret, additional, Pombo, Ana, additional, Pradhan-Bhatt, Swati, additional, Qin, Xian-Yang, additional, Rehli, Michael, additional, Rizzu, Patrizia, additional, Roy, Sugata, additional, Sajantila, Antti, additional, Sakaguchi, Shimon, additional, Sato, Hiroki, additional, Satoh, Hironori, additional, Savvi, Suzana, additional, Saxena, Alka, additional, Schmidl, Christian, additional, Schneider, Claudio, additional, Schulze-Tanzil, Gundula G., additional, Schwegmann, Anita, additional, Sheng, Guojun, additional, Shin, Jay W., additional, Sugiyama, Daisuke, additional, Sugiyama, Takaaki, additional, Summers, Kim M., additional, Takahashi, Naoko, additional, Takai, Jun, additional, Tanaka, Hiroshi, additional, Tatsukawa, Hideki, additional, Tomoiu, Andru, additional, Toyoda, Hiroo, additional, van de Wetering, Marc, additional, van den Berg, Linda M., additional, Verardo, Roberto, additional, Vijayan, Dipti, additional, Wells, Christine A., additional, Winteringham, Louise N., additional, Wolvetang, Ernst, additional, Yamaguchi, Yoko, additional, Yamamoto, Masayuki, additional, Yanagi-Mizuochi, Chiyo, additional, Yoneda, Misako, additional, Yonekura, Yohei, additional, Zhang, Peter G., additional, Zucchelli, Silvia, additional, Abugessaisa, Imad, additional, Arner, Erik, additional, Harshbarger, Jayson, additional, Kondo, Atsushi, additional, Lassmann, Timo, additional, Lizio, Marina, additional, Sahin, Serkan, additional, Sengstag, Thierry, additional, Severin, Jessica, additional, Shimoji, Hisashi, additional, Suzuki, Masanori, additional, Suzuki, Harukazu, additional, Kawai, Jun, additional, Kondo, Naoto, additional, Itoh, Masayoshi, additional, Daub, Carsten O., additional, Kasukawa, Takeya, additional, Kawaji, Hideya, additional, Carninci, Piero, additional, Forrest, Alistair R.R., additional, and Hayashizaki, Yoshihide, additional

Published
2017
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40. The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome

Author

Hurst, Laurence D., Ghanbarian, Avazeh T., Forrest, Alistair R R, Huminiecki, Lukasz, Rehli, Michael, Kenneth Baillie, J., de Hoon, Michiel J L, Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicolas, Jørgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Alam, Intikhab, Albanese, Davide, Altschuler, Gabriel M., Arakawa, Takahiro, Archer, John A C, Arner, Peter, Babina, Magda, Baker, Sarah, Balwierz, Piotr J., Beckhouse, Anthony G., Pradhan, Swati Bhatt, Blake, Judith A., Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Maxwell Burroughs, A., Califano, Andrea, Cannistraci, Carlo V., Carbajo, Daniel, Chen, Yun, Chierici, Marco, Ciani, Yari, Clevers, Hans C., Dalla, Emiliano, Davis, Carrie A., Detmar, Michael, Diehl, Alexander D., Dohi, Taeko, Drabløs, Finn, Edge, Albert S B, Edinger, Matthias, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Fagiolini, Michela, Fairbairn, Lynsey, Fang, Hai, Farach-Carson, Mary C., Faulkner, Geoffrey J., Favorov, Alexander V., Fisher, Malcolm E., Frith, Martin C., Fujita, Rie, Fukuda, Shiro, Furlanello, Cesare, Furuno, Masaaki, Furusawa, Jun ichi, Geijtenbeek, Teunis B., Gibson, Andrew, Gingeras, Thomas, Goldowitz, Daniel, Gough, Julian, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J., Hamaguchi, Masahide, Hara, Mitsuko, Harbers, Matthias, Harshbarger, Jayson, Hasegawa, Akira, Hasegawa, Yuki, Hashimoto, Takehiro, Herlyn, Meenhard, Hitchens, Kelly J., Ho Sui, Shannan J., Hofmann, Oliver M., Hoof, Ilka, Hori, Fumi, Iida, Kei, Ikawa, Tomokatsu, Jankovic, Boris R., Jia, Hui, Joshi, Anagha, Jurman, Giuseppe, Kaczkowski, Bogumil, Kai, Chieko, Kaida, Kaoru, Kaiho, Ai, Kajiyama, Kazuhiro, Kanamori, Mutsumi Katayama, Kasianov, Artem S., Kasukawa, Takeya, Katayama, Shintaro, Kato, Sachi, Kawaguchi, Shuji, Kawamoto, Hiroshi, Kawamura, Yuki I., Kawashima, Tsugumi, Kempfle, Judith S., Kenna, Tony J., Kere, Juha, Khachigian, Levon M., Kitamura, Toshio, Peter Klinken, S., Knox, Alan J., Kojima, Miki, Kojima, Soichi, Kondo, Naoto, Koseki, Haruhiko, Koyasu, Shigeo, Krampitz, Sarah, Kubosaki, Atsutaka, Kwon, Andrew T., Laros, Jeroen F J, Lee, Weonju, Lennartsson, Andreas, Li, Kang, Lilje, Berit, Lipovich, Leonard, Mackay, Alan sim, Manabe, Riichiroh, Mar, Jessica C., Marchand, Benoit, Mathelier, Anthony, Mejhert, Niklas, Meynert, Alison, Mizuno, Yosuke, de Lima Morais, David A., Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Motakis, Efthymios, Motohashi, Hozumi, Mummery, Christine L., Murata, Mitsuyoshi, Nagao, Sayaka Sato, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nakazato, Kenichi, van Nimwegen, Erik, Ninomiya, Noriko, Nishiyori, Hiromi, Noma, Shohei, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohmiya, Hiroko, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada, Mariko Hatakeyama, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A., Pain, Arnab, Passier, Robert, Patrikakis, Margaret, Persson, Helena, Piazza, Silvano, Prendergast, James G D, Rackham, Owen J L, Ramilowski, Jordan A., Rashid, Mamoon, Ravasi, Timothy, Rizzu, Patrizia, Roncador, Marco, Roy, Sugata, Rye, Morten B., Saijyo, Eri, Sajantila, Antti, Saka, Akiko, Sakaguchi, Shimon, Sakai, Mizuho, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schneider, Claudio, Schultes, Erik A., Schulze-Tanzil, Gundula G., Schwegmann, Anita, Sengstag, Thierry, Sheng, Guojun, Shimoji, Hisashi, Shimoni, Yishai, Shin, Jay W., Simon, Christophe, Sugiyama, Daisuke, Sugiyama, Takaaki, Suzuki, Masanori, Suzuki, Naoko, Swoboda, Rolf K., 't Hoen, Peter A C, Tagami, Michihira, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tatum, Zuotian, Thompson, Mark, Toyoda, Hiroo, Toyoda, Tetsuro, Valen, Eivind, van de Wetering, Marc, van den Berg, Linda M., Verardo, Roberto, Vijayan, Dipti, Vorontsov, Ilya E., Wasserman, Wyeth W., Watanabe, Shoko, Wells, Christine A., Winteringham, Louise N., Wolvetang, Ernst, Wood, Emily J., Yamaguchi, Yoko, Yamamoto, Masayuki, Yoneda, Misako, Yonekura, Yohei, Yoshida, Shigehiro, Zabierowski, Suzan E., Zhang, Peter G., Zhao, Xiaobei, Zucchelli, Silvia, Summers, Kim M., Suzuki, Harukazu, Daub, Carsten O., Kawai, Jun, Heutink, Peter, Hide, Winston, Freeman, Tom C., Lenhard, Boris, Bajic, Vladimir B., Taylor, Martin S., Makeev, Vsevolod J., Sandelin, Albin Gustav, Hume, David A., Carninci, Piero, Hayashizaki, Yoshihide, Hubrecht Institute for Developmental Biology and Stem Cell Research, Barton, Nick H, Amsterdam institute for Infection and Immunity, Infectious diseases, and Experimental Immunology

Subjects
Male, Medical and Health Sciences, Essential, Models, Gene expression, Databases, Genetic, Biology (General), Non-U.S. Gov't, X-linked recessive inheritance, X chromosome, Cells, Cultured, Regulation of gene expression, Genetics, Sex Characteristics, Dosage compensation, Tumor, Cultured, Genes, Essential, Genome, Agricultural and Biological Sciences(all), General Neuroscience, Research Support, Non-U.S. Gov't, Biological Sciences, Organ Specificity, Female, General Agricultural and Biological Sciences, Research Article, Human, X Chromosome, Retroelements, QH301-705.5, Neuroscience(all), 1.1 Normal biological development and functioning, Cells, Down-Regulation, Biology, Research Support, General Biochemistry, Genetics and Molecular Biology, Chromosomes, Cell Line, Databases, Genetic, Species Specificity, Underpinning research, Immunology and Microbiology(all), Cell Line, Tumor, Journal Article, Animals, Humans, Comparative Study, Gene, Chromosomes, Human, X, Autosome, General Immunology and Microbiology, Agricultural and Veterinary Sciences, Models, Genetic, Biochemistry, Genetics and Molecular Biology(all), Genome, Human, Mammalian, Human Genome, Chromosomes, Mammalian, Genes, Gene Expression Regulation, Human genome, FANTOM consortium, Developmental Biology
Abstract

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X’s gene content, gene expression, and evolution., Laurence Hurst, Lukasz Huminiecki, and the FANTOM5 consortium propose a new explanation for the peculiar expression properties of genes on the human X chromosome, based on the premise that very high expression levels cannot be achieved on a haploid-expressed chromosome., Author Summary Genes located on the human X chromosome are not a random mix of genes: they tend to be expressed in relatively few tissues or are specific for a particular set of tissues, e.g., brain regions. Prior attempts to explain this skewed gene content have hypothesized that the X chromosome might be peculiar because it has to balance mutations that are advantageous to one sex but deleterious to the other, or because it has to shut down during the process of sperm manufacture in males. Here we suggest and test a third possible explanation: that genes on the X chromosome are limited in their transcription levels and thus tend to be genes that are lowly or specifically expressed. We consider the suggestion that since these genes can only be expressed from one chromosome, as males only have one X, the ability to express a gene at very high rates is limited owing to potential transcriptional traffic jams. As predicted, we find that human X-located genes have maximal expression rates far below that of genes residing on autosomes. When we look at genes that have moved onto or off the X chromosome during recent evolution, we find the maximal expression is higher when not on the X chromosome. We also find that X-located genes that are relatively highly expressed are not able to increase their expression level further. Our model explains both the enrichment for tissue specificity and the paucity of certain tissues with X-located genes. Genes underrepresented on the X are either expressed in many tissues—such genes tend to have high maximal expression—or are from tissues that require a lot of transcription (e.g., fast secreting tissues like the liver). Just as many of the findings cannot be explained by the two earlier models, neither can the traffic jam model explain all the peculiar features of the genes found on the X chromosome. Indeed, we find evidence of a reproduction-related bias in X-located genes, even after allowing for the traffic jam problem.

Published
2015
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41. FANTOM5 CAGE profiles of human and mouse samples

Author

Noguchi, Shuhei, Arakawa, Takahiro, Fukuda, Shiro, Furuno, Masaaki, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Kaida, Kaoru, Kaiho, Ai, Kanamori-Katayama, Mutsumi, Kawashima, Tsugumi, Kojima, Miki, Kubosaki, Atsutaka, Manabe, Ri-ichiroh, Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakazato, Kenichi, Ninomiya, Noriko, Nishiyori-Sueki, Hiromi, Noma, Shohei, Saijyo, Eri, Saka, Akiko, Sakai, Mizuho, Simon, Christophe, Suzuki, Naoko, Tagami, Michihira, Watanabe, Shoko, Yoshida, Shigehiro, Arner, Peter, Axton, Richard A, Babina, Magda, Baillie, J Kenneth, Barnett, Timothy C, Beckhouse, Anthony G, Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Carlisle, Ailsa J, Clevers, Hans C, Davis, Carrie A, Detmar, Michael, Dohi, Taeko, Edge, Albert S B, Edinger, Matthias, Ehrlund, Anna, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Farach-Carson, Mary C, Faulkner, Geoffrey J, Ferrai, Carmelo, Fisher, Malcolm E, Forrester, Lesley M, Fujita, Rie, Furusawa, Jun-ichi, Geijtenbeek, Teunis B, Gingeras, Thomas, Goldowitz, Daniel, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J, Hamaguchi, Masahide, Hara, Mitsuko, Hasegawa, Yuki, Herlyn, Meenhard, Heutink, Peter, Hitchens, Kelly J, Hume, David A, Ikawa, Tomokatsu, Ishizu, Yuri, Kai, Chieko, Kawamoto, Hiroshi, Kawamura, Yuki I, Kempfle, Judith S, Kenna, Tony J, Kere, Juha, Khachigian, Levon M, Kitamura, Toshio, Klein, Sarah, Klinken, S Peter, Knox, Alan J, Kojima, Soichi, Koseki, Haruhiko, Koyasu, Shigeo, Lee, Weonju, Lennartsson, Andreas, Mackay-Sim, Alan, Mejhert, Niklas, Mizuno, Yosuke, Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Morris, Kelly J, Motohashi, Hozumi, Mummery, Christine L, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A, Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Pradhan-Bhatt, Swati, Qin, Xian-Yang, Rehli, Michael, Rizzu, Patrizia, Roy, Sugata, Sajantila, Antti, Sakaguchi, Shimon, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schmidl, Christian, Schneider, Claudio, Schulze-Tanzil, Gundula G, Schwegmann, Anita, Sheng, Guojun, Shin, Jay W, Sugiyama, Daisuke, Sugiyama, Takaaki, Summers, Kim M, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tomoiu, Andru, Toyoda, Hiroo, van de Wetering, Marc, van den Berg, Linda M, Verardo, Roberto, Vijayan, Dipti, Wells, Christine A, Winteringham, Louise N, Wolvetang, Ernst, Yamaguchi, Yoko, Yamamoto, Masayuki, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Yonekura, Yohei, Zhang, Peter G, Zucchelli, Silvia, Abugessaisa, Imad, Arner, Erik, Harshbarger, Jayson, Kondo, Atsushi, Lassmann, Timo, Lizio, Marina, Sahin, Serkan, Sengstag, Thierry, Severin, Jessica, Shimoji, Hisashi, Suzuki, Masanori, Suzuki, Harukazu, Kawai, Jun, Kondo, Naoto, Itoh, Masayoshi, Daub, Carsten O, Kasukawa, Takeya, Kawaji, Hideya, Carninci, Piero, Forrest, Alistair R R, Hayashizaki, Yoshihide, Noguchi, Shuhei, Arakawa, Takahiro, Fukuda, Shiro, Furuno, Masaaki, Hasegawa, Akira, Hori, Fumi, Ishikawa-Kato, Sachi, Kaida, Kaoru, Kaiho, Ai, Kanamori-Katayama, Mutsumi, Kawashima, Tsugumi, Kojima, Miki, Kubosaki, Atsutaka, Manabe, Ri-ichiroh, Murata, Mitsuyoshi, Nagao-Sato, Sayaka, Nakazato, Kenichi, Ninomiya, Noriko, Nishiyori-Sueki, Hiromi, Noma, Shohei, Saijyo, Eri, Saka, Akiko, Sakai, Mizuho, Simon, Christophe, Suzuki, Naoko, Tagami, Michihira, Watanabe, Shoko, Yoshida, Shigehiro, Arner, Peter, Axton, Richard A, Babina, Magda, Baillie, J Kenneth, Barnett, Timothy C, Beckhouse, Anthony G, Blumenthal, Antje, Bodega, Beatrice, Bonetti, Alessandro, Briggs, James, Brombacher, Frank, Carlisle, Ailsa J, Clevers, Hans C, Davis, Carrie A, Detmar, Michael, Dohi, Taeko, Edge, Albert S B, Edinger, Matthias, Ehrlund, Anna, Ekwall, Karl, Endoh, Mitsuhiro, Enomoto, Hideki, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Farach-Carson, Mary C, Faulkner, Geoffrey J, Ferrai, Carmelo, Fisher, Malcolm E, Forrester, Lesley M, Fujita, Rie, Furusawa, Jun-ichi, Geijtenbeek, Teunis B, Gingeras, Thomas, Goldowitz, Daniel, Guhl, Sven, Guler, Reto, Gustincich, Stefano, Ha, Thomas J, Hamaguchi, Masahide, Hara, Mitsuko, Hasegawa, Yuki, Herlyn, Meenhard, Heutink, Peter, Hitchens, Kelly J, Hume, David A, Ikawa, Tomokatsu, Ishizu, Yuri, Kai, Chieko, Kawamoto, Hiroshi, Kawamura, Yuki I, Kempfle, Judith S, Kenna, Tony J, Kere, Juha, Khachigian, Levon M, Kitamura, Toshio, Klein, Sarah, Klinken, S Peter, Knox, Alan J, Kojima, Soichi, Koseki, Haruhiko, Koyasu, Shigeo, Lee, Weonju, Lennartsson, Andreas, Mackay-Sim, Alan, Mejhert, Niklas, Mizuno, Yosuke, Morikawa, Hiromasa, Morimoto, Mitsuru, Moro, Kazuyo, Morris, Kelly J, Motohashi, Hozumi, Mummery, Christine L, Nakachi, Yutaka, Nakahara, Fumio, Nakamura, Toshiyuki, Nakamura, Yukio, Nozaki, Tadasuke, Ogishima, Soichi, Ohkura, Naganari, Ohno, Hiroshi, Ohshima, Mitsuhiro, Okada-Hatakeyama, Mariko, Okazaki, Yasushi, Orlando, Valerio, Ovchinnikov, Dmitry A, Passier, Robert, Patrikakis, Margaret, Pombo, Ana, Pradhan-Bhatt, Swati, Qin, Xian-Yang, Rehli, Michael, Rizzu, Patrizia, Roy, Sugata, Sajantila, Antti, Sakaguchi, Shimon, Sato, Hiroki, Satoh, Hironori, Savvi, Suzana, Saxena, Alka, Schmidl, Christian, Schneider, Claudio, Schulze-Tanzil, Gundula G, Schwegmann, Anita, Sheng, Guojun, Shin, Jay W, Sugiyama, Daisuke, Sugiyama, Takaaki, Summers, Kim M, Takahashi, Naoko, Takai, Jun, Tanaka, Hiroshi, Tatsukawa, Hideki, Tomoiu, Andru, Toyoda, Hiroo, van de Wetering, Marc, van den Berg, Linda M, Verardo, Roberto, Vijayan, Dipti, Wells, Christine A, Winteringham, Louise N, Wolvetang, Ernst, Yamaguchi, Yoko, Yamamoto, Masayuki, Yanagi-Mizuochi, Chiyo, Yoneda, Misako, Yonekura, Yohei, Zhang, Peter G, Zucchelli, Silvia, Abugessaisa, Imad, Arner, Erik, Harshbarger, Jayson, Kondo, Atsushi, Lassmann, Timo, Lizio, Marina, Sahin, Serkan, Sengstag, Thierry, Severin, Jessica, Shimoji, Hisashi, Suzuki, Masanori, Suzuki, Harukazu, Kawai, Jun, Kondo, Naoto, Itoh, Masayoshi, Daub, Carsten O, Kasukawa, Takeya, Kawaji, Hideya, Carninci, Piero, Forrest, Alistair R R, and Hayashizaki, Yoshihide

Abstract

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

Published
2017

42. Mutant huntingtin's effects on striatal gene expression in mice recapitulate changes observed in human Huntington's disease brain and do not differ with mutant huntingtin length or wild-type huntingtin dosage

Author

Kuhn, Alexandre, Goldstein, Darlene R., Hodges, Angela, Strand, Andrew D., Sengstag, Thierry, Kooperberg, Charles, Becanovic, Kristina, Pouladi, Mahmoud A., Sathasivam, Kirupa, Cha, Jang-Ho J., Hannan, Anthony J., Hayden, Michael R., Leavitt, Blair R., Dunnett, Stephen B., Ferrante, Robert J., Albin, Roger, Shelbourne, Peggy, Delorenzi, Mauro, Augood, Sarah J., Faull, Richard L.M., Olson, James M., Bates, Gillian P., Jones, Lesley, Luthi-Carter, Ruth, Kuhn, Alexandre, Goldstein, Darlene R., Hodges, Angela, Strand, Andrew D., Sengstag, Thierry, Kooperberg, Charles, Becanovic, Kristina, Pouladi, Mahmoud A., Sathasivam, Kirupa, Cha, Jang-Ho J., Hannan, Anthony J., Hayden, Michael R., Leavitt, Blair R., Dunnett, Stephen B., Ferrante, Robert J., Albin, Roger, Shelbourne, Peggy, Delorenzi, Mauro, Augood, Sarah J., Faull, Richard L.M., Olson, James M., Bates, Gillian P., Jones, Lesley, and Luthi-Carter, Ruth

Abstract

To test the hypotheses that mutant huntingtin protein length and wild-type huntingtin dosage have important effects on disease-related transcriptional dysfunction, we compared the changes in mRNA in seven genetic mouse models of Huntington's disease (HD) and postmortem human HD caudate. Transgenic models expressing short N-terminal fragments of mutant huntingtin (R6/1 and R6/2 mice) exhibited the most rapid effects on gene expression, consistent with previous studies. Although changes in the brains of knock-in and full-length transgenic models of HD took longer to appear, 15- and 22-month CHL2Q150/Q150, 18-month HdhQ92/Q92 and 2-year-old YAC128 animals also exhibited significant HD-like mRNA signatures. Whereas it was expected that the expression of full-length huntingtin transprotein might result in unique gene expression changes compared with those caused by the expression of an N-terminal huntingtin fragment, no discernable differences between full-length and fragment models were detected. In addition, very high correlations between the signatures of mice expressing normal levels of wild-type huntingtin and mice in which the wild-type protein is absent suggest a limited effect of the wild-type protein to change basal gene expression or to influence the qualitative disease-related effect of mutant huntingtin. The combined analysis of mouse and human HD transcriptomes provides important temporal and mechanistic insights into the process by which mutant huntingtin kills striatal neurons. In addition, the discovery that several available lines of HD mice faithfully recapitulate the gene expression signature of the human disorder provides a novel aspect of validation with respect to their use in preclinical therapeutic trials

Published
2017

43. Regional and cellular gene expression changes in human Huntington's disease brain

Author

Hodges, Angela, Strand, Andrew D., Aragaki, Aaron K., Kuhn, Alexandre, Sengstag, Thierry, Hughes, Gareth, Elliston, Lyn A., Hartog, Cathy, Goldstein, Darlene R., Thu, Doris, Hollingsworth, Zane R., Collin, Francois, Synek, Beth, Holmans, Peter A., Young, Anne B., Wexler, Nancy S., Delorenzi, Mauro, Kooperberg, Charles, Augood, Sarah J., Faull, Richard L.M., Olson, James M., Jones, Lesley, Luthi-Carter, Ruth, Hodges, Angela, Strand, Andrew D., Aragaki, Aaron K., Kuhn, Alexandre, Sengstag, Thierry, Hughes, Gareth, Elliston, Lyn A., Hartog, Cathy, Goldstein, Darlene R., Thu, Doris, Hollingsworth, Zane R., Collin, Francois, Synek, Beth, Holmans, Peter A., Young, Anne B., Wexler, Nancy S., Delorenzi, Mauro, Kooperberg, Charles, Augood, Sarah J., Faull, Richard L.M., Olson, James M., Jones, Lesley, and Luthi-Carter, Ruth

Abstract

Huntington's disease (HD) pathology is well understood at a histological level but a comprehensive molecular analysis of the effect of the disease in the human brain has not previously been available. To elucidate the molecular phenotype of HD on a genome-wide scale, we compared mRNA profiles from 44 human HD brains with those from 36 unaffected controls using microarray analysis. Four brain regions were analyzed: caudate nucleus, cerebellum, prefrontal association cortex [Brodmann's area 9 (BA9)] and motor cortex [Brodmann's area 4 (BA4)]. The greatest number and magnitude of differentially expressed mRNAs were detected in the caudate nucleus, followed by motor cortex, then cerebellum. Thus, the molecular phenotype of HD generally parallels established neuropathology. Surprisingly, no mRNA changes were detected in prefrontal association cortex, thereby revealing subtleties of pathology not previously disclosed by histological methods. To establish that the observed changes were not simply the result of cell loss, we examined mRNA levels in laser-capture microdissected neurons from Grade 1 HD caudate compared to control. These analyses confirmed changes in expression seen in tissue homogenates; we thus conclude that mRNA changes are not attributable to cell loss alone. These data from bona fide HD brains comprise an important reference for hypotheses related to HD and other neurodegenerative diseases

Published
2017

44. The FAIR Guiding Principles for scientific data management and stewardship

Author

Wilkinson, Mark D., Dumontier, Michel, Aalbersberg, IJsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan-Willem, da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scott, Evelo, Chris T., Finkers, Richard, Gonzalez-Beltran, Alejandra, Gray, Alasdair J.G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, ’t Hoen, Peter A.C, Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, van Schaik, Rene, Sansone, Susanna-Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, van der Lei, Johan, van Mulligen, Erik, Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, Mons, Barend, Wilkinson, Mark D., Dumontier, Michel, Aalbersberg, IJsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan-Willem, da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scott, Evelo, Chris T., Finkers, Richard, Gonzalez-Beltran, Alejandra, Gray, Alasdair J.G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, ’t Hoen, Peter A.C, Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, van Schaik, Rene, Sansone, Susanna-Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, van der Lei, Johan, van Mulligen, Erik, Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, and Mons, Barend

Published
2016
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45. Making sense of big data in health research: Towards an EU action plan

Author

Auffray, Charles, Balling, Rudi, Barroso, Ines, Bencze, Laszlo, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Glynne Gut, Ivo, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Angel, Rod Hose, D., Houwing-Duistermaat, Jeanine, Hubbard, Tim, Helen Janacek, Sophie, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Mueller, Werner, Nickel, Dorthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, Redon i Mas, Josep, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A. I., van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Antonio Vizcaino, Juan, Peter Mary Wubbe, John, Zanetti, Gianluigi, Auffray, Charles, Balling, Rudi, Barroso, Ines, Bencze, Laszlo, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Glynne Gut, Ivo, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Angel, Rod Hose, D., Houwing-Duistermaat, Jeanine, Hubbard, Tim, Helen Janacek, Sophie, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Mueller, Werner, Nickel, Dorthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, Redon i Mas, Josep, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A. I., van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Antonio Vizcaino, Juan, Peter Mary Wubbe, John, and Zanetti, Gianluigi

Abstract

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health arid healthcare for all Europearis., Funding Agencies|European Union [115568, 603160, 282510, 664691, 115749, 305033, 305397, 288028, 242189, 211601]; European Molecular Biology Laboratory; Wellcome Trust [WT098051]; [115372]; [257082]; [291814]; [291728]; [321567]; [262055]; [115446]; [602552]; [644753]; [634143]; [261357]; [305280]; [115525]; [2011 23 02]; [270089]; [278433]; [602525]; [201418]; [242135]; [260558]; [223411]; [305626]; [115621]; [611388]; [306000]; [354457]; [305564]; [115010]; [269978]

Published
2016
Full Text
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46. The FAIR Guiding Principles for scientific data management and stewardship

Author

Wilkinson, Mark Denis, Dumontier, Michel, Aalbersberg, IJsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan-Willem, Da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scotr, Evelo, Chris T., Finkers, Richard, González Beltrán, Alejandra, Gray, Alasdair J.G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, Hoen, Peter A.C't, Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, Van Schaik, Rene, Sansone, Susanna-Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, Van Der Lei, Johan, Van Mulligen, Erik M., Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, Mons, Barend, Wilkinson, Mark Denis, Dumontier, Michel, Aalbersberg, IJsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan-Willem, Da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scotr, Evelo, Chris T., Finkers, Richard, González Beltrán, Alejandra, Gray, Alasdair J.G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, Hoen, Peter A.C't, Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, Van Schaik, Rene, Sansone, Susanna-Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, Van Der Lei, Johan, Van Mulligen, Erik M., Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, and Mons, Barend

Abstract

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community

Published
2016

47. Erratum to: Making sense of big data in health research: towards an EU action plan

Author

Biostatistiek Onderzoek, Circulatory Health, JC onderzoeksprogramma Infectieziekten, JC onderzoeksprogramma Methodologie, Child Health, Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Ángel, Hose, D Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, I Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A I, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, Zanetti, Gianluigi, Biostatistiek Onderzoek, Circulatory Health, JC onderzoeksprogramma Infectieziekten, JC onderzoeksprogramma Methodologie, Child Health, Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Ángel, Hose, D Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, I Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A I, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, and Zanetti, Gianluigi

Published
2016

48. Making sense of big data in health research: Towards an EU action plan

Author

Biostatistiek Onderzoek, Circulatory Health, JC onderzoeksprogramma Infectieziekten, JC onderzoeksprogramma Methodologie, Child Health, Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk Jan, Guo, Yi Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf Dieter, Honrado, Ángel, Hose, D. Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, i Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A I, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, Zanetti, Gianluigi, Biostatistiek Onderzoek, Circulatory Health, JC onderzoeksprogramma Infectieziekten, JC onderzoeksprogramma Methodologie, Child Health, Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk Jan, Guo, Yi Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf Dieter, Honrado, Ángel, Hose, D. Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, i Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A I, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, and Zanetti, Gianluigi

Published
2016

49. The FAIR Guiding Principles for scientific data management and stewardship : Comment

Author

Wilkinson, Mark D., Dumontier, Michel, Aalbersberg, Ijsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan Willem, Da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scott, Evelo, Chris T., Finkers, Richard, Gonzalez-Beltran, Alejandra, Gray, Alasdair J.G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, 't Hoen, Peter A.C., Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, van Schaik, Rene, Sansone, Susanna Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, van der Lei, Johan, van Mulligen, Erik, Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, Mons, Barend, Wilkinson, Mark D., Dumontier, Michel, Aalbersberg, Ijsbrand Jan, Appleton, Gabrielle, Axton, Myles, Baak, Arie, Blomberg, Niklas, Boiten, Jan Willem, Da Silva Santos, Luiz Bonino, Bourne, Philip E., Bouwman, Jildau, Brookes, Anthony J., Clark, Tim, Crosas, Mercè, Dillo, Ingrid, Dumon, Olivier, Edmunds, Scott, Evelo, Chris T., Finkers, Richard, Gonzalez-Beltran, Alejandra, Gray, Alasdair J.G., Groth, Paul, Goble, Carole, Grethe, Jeffrey S., Heringa, Jaap, 't Hoen, Peter A.C., Hooft, Rob, Kuhn, Tobias, Kok, Ruben, Kok, Joost, Lusher, Scott J., Martone, Maryann E., Mons, Albert, Packer, Abel L., Persson, Bengt, Rocca-Serra, Philippe, Roos, Marco, van Schaik, Rene, Sansone, Susanna Assunta, Schultes, Erik, Sengstag, Thierry, Slater, Ted, Strawn, George, Swertz, Morris A., Thompson, Mark, van der Lei, Johan, van Mulligen, Erik, Velterop, Jan, Waagmeester, Andra, Wittenburg, Peter, Wolstencroft, Katherine, Zhao, Jun, and Mons, Barend

Abstract

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Published
2016

50. Making sense of big data in health research: Towards an EU action plan

Author

Auffray, Charles, primary, Balling, Rudi, additional, Barroso, Inês, additional, Bencze, László, additional, Benson, Mikael, additional, Bergeron, Jay, additional, Bernal-Delgado, Enrique, additional, Blomberg, Niklas, additional, Bock, Christoph, additional, Conesa, Ana, additional, Del Signore, Susanna, additional, Delogne, Christophe, additional, Devilee, Peter, additional, Di Meglio, Alberto, additional, Eijkemans, Marinus, additional, Flicek, Paul, additional, Graf, Norbert, additional, Grimm, Vera, additional, Guchelaar, Henk-Jan, additional, Guo, Yi-Ke, additional, Gut, Ivo Glynne, additional, Hanbury, Allan, additional, Hanif, Shahid, additional, Hilgers, Ralf-Dieter, additional, Honrado, Ángel, additional, Hose, D. Rod, additional, Houwing-Duistermaat, Jeanine, additional, Hubbard, Tim, additional, Janacek, Sophie Helen, additional, Karanikas, Haralampos, additional, Kievits, Tim, additional, Kohler, Manfred, additional, Kremer, Andreas, additional, Lanfear, Jerry, additional, Lengauer, Thomas, additional, Maes, Edith, additional, Meert, Theo, additional, Müller, Werner, additional, Nickel, Dörthe, additional, Oledzki, Peter, additional, Pedersen, Bertrand, additional, Petkovic, Milan, additional, Pliakos, Konstantinos, additional, Rattray, Magnus, additional, i Màs, Josep Redón, additional, Schneider, Reinhard, additional, Sengstag, Thierry, additional, Serra-Picamal, Xavier, additional, Spek, Wouter, additional, Vaas, Lea A. I., additional, van Batenburg, Okker, additional, Vandelaer, Marc, additional, Varnai, Peter, additional, Villoslada, Pablo, additional, Vizcaíno, Juan Antonio, additional, Wubbe, John Peter Mary, additional, and Zanetti, Gianluigi, additional

Published
2016
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