Zobrazeno 1 - 10
of 23
pro vyhledávání: '"Martin, Scharm"'
Publikováno v:
npj Systems Biology and Applications, Vol 9, Iss 1, Pp 1-9 (2023)
Abstract Genome-scale metabolic models (GEMs) are extensively used to simulate cell metabolism and predict cell phenotypes. GEMs can also be tailored to generate context-specific GEMs, using omics data integration approaches. To date, many integratio
Externí odkaz:
https://doaj.org/article/d4a4b7efb7db4e919ada75208aca142d
Autor:
Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik‐Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle, James C Schaff, Lucian P Smith, Maciej J Swat, Denis Thieffry, Leandro Watanabe, Darren J Wilkinson, Michael L Blinov, Kimberly Begley, James R Faeder, Harold F Gómez, Thomas M Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson L Lister, Daniel Lucio, Eric Mjolsness, Carole J Proctor, Karthik Raman, Nicolas Rodriguez, Clifford A Shaffer, Bruce E Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier‐Schellersheim, Herbert M Sauro, Bernhard Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C Doyle, Michael Hucka, SBML Level 3 Community members, Richard R Adams, Nicholas A Allen, Bastian R Angermann, Marco Antoniotti, Gary D Bader, Jan Červený, Mélanie Courtot, Chris D Cox, Piero Dalle Pezze, Emek Demir, William S Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T Evelo, Christoph Flamm, Ronan MT Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A Harris, Benjamin D Heavner, Ron Henkel, William S Hlavacek, Bin Hu, Daniel R Hyduke, Hidde de Jong, Nick Juty, Peter D Karp, Jonathan R Karr, Douglas B Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T Monteiro, Kedar Nath Natarajan, Poul MF Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D Phair, Tomas Radivoyevitch, Johann M Rohwer, Oliver A Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I Stefan, Devin P Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel von Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, Jeremy Zucker
Publikováno v:
Molecular Systems Biology, Vol 16, Iss 8, Pp 1-21 (2020)
Abstract Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edi
Externí odkaz:
https://doaj.org/article/86e517962df24b21af078b7f951f7487
Publikováno v:
PLoS ONE, Vol 17, Iss 3 (2022)
The evolution of biochemical models is difficult to track. At present, it is not possible to inspect the differences between model versions at the network level. Biochemical models are often constructed in a distributed, non-linear process: collabora
Externí odkaz:
https://doaj.org/article/684d7062ca364217ae30484d43fd5b92
Autor:
Kausthubh Ramachandran, Matthias König, Martin Scharm, Tung V. N. Nguyen, Henning Hermjakob, Dagmar Waltemath, Rahuman S. Malik Sheriff
A major challenge for the dissemination, replication, and reuse of epidemiological forecasting studies during COVID-19 pandemics is the lack of clear guidelines and platforms to exchange models in a Findable, Accessible, Interoperable, and Reusable (
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7e8faec5f0aaa161cd75043b9c977a6e
https://doi.org/10.20944/preprints202206.0137.v1
https://doi.org/10.20944/preprints202206.0137.v1
Autor:
Martin Scharm, Dagmar Waltemath
Publikováno v:
F1000Research, Vol 5 (2016)
COMBINE archives are standardised containers for data files related to a simulation study in computational biology. This manuscript describes a fully featured archive of a previously published simulation study, including (i) the original publication,
Externí odkaz:
https://doaj.org/article/f279e7431cac48b682274cadba37dad5
Publikováno v:
PloS one. 17(3)
The evolution of biochemical models is difficult to track. At present, it is not possible to inspect the differences between model versions at the network level. Biochemical models are often constructed in a distributed, non-linear process: collabora
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2b366fbf89eef9e2a86bde9b87c408a2
https://pubmed.ncbi.nlm.nih.gov/35312734
https://pubmed.ncbi.nlm.nih.gov/35312734
Autor:
Edda Klipp, Marco Antoniotti, Frank Bergmann, James C. Schaff, Peter D. Karp, Daniel Lucio, Kedar Nath Natarajan, Thomas M. Hamm, Leandro Watanabe, Henning Hermjakob, David Tolnay, John Wagner, Joerg Stelling, Alida Palmisano, Falk Schreiber, Yukiko Matsuoka, Harold F. Gómez, Huaiyu Mi, Carole J. Proctor, Ulrike Wittig, Neil Swainston, Jan Červený, Denis Thieffry, Piero Dalle Pezze, Julio Saez-Rodriguez, Maciej J. Swat, Bin Hu, Martina Kutmon, Thomas Pfau, Bas Teusink, Sarah M. Keating, Fedor A. Kolpakov, Andreas Dräger, Pedro Mendes, Martin Scharm, Emek Demir, Ioannis Xenarios, Christoph Flamm, Axel von Kamp, Darren J. Wilkinson, Nick Juty, Fengkai Zhang, Leonard A. Harris, Michael Schubert, Dagmar Waltemath, Lucian P. Smith, Steffen Klamt, Herbert M. Sauro, Ali Ebrahim, Wolfram Liebermeister, Christian Knüpfer, Nicolas Rodriguez, Tramy Nguyen, Naoki Tanimura, Christopher Cox, Stuart C. Sealfon, Nicholas Alexander Allen, Clemens Wrzodek, Bastian R. Angermann, Martin Meier-Schellersheim, Anna Zhukova, Jean-Baptiste Pettit, Hovakim Grabski, Devin P. Sullivan, Claudine Chaouiya, Michael L. Blinov, John Doyle, Ilya Kiselev, Roman Schulte, Alex Gutteridge, Mélanie Courtot, Eric Mjolsness, Finja Wrzodek, Rahuman S Malik-Sheriff, Ronan M. T. Fleming, Bruce E. Shapiro, Kimberly Begley, Leslie M. Loew, Colin S. Gillespie, Ibrahim Vazirabad, Michael Hucka, Akira Funahashi, Bernhard O. Palsson, Hamid Bolouri, Tomáš Helikar, Camille Laibe, William S. Denney, Chris T. Evelo, Florian Mittag, William S. Hlavacek, Ron Henkel, Harish Dharuri, Julien Dorier, Karthik Raman, Martina Fröhlich, Conor Lawless, Rainer Machné, Falko Krause, Damon Hachmeister, Matthias König, Clifford A. Shaffer, Benjamin D. Heavner, Douglas B. Kell, Jonathan R. Karr, Mihai Glont, Lukas Endler, Melanie I. Stefan, Robert Phair, Lu Li, Henning Schmidt, Dirk Drasdo, Johan Elf, Allyson L. Lister, Hiroaki Kitano, Richard R. Adams, Oliver A. Ruebenacker, Roland Keller, Sven Sahle, Ion I. Moraru, Gary D. Bader, Poul M. F. Nielsen, Johann M. Rohwer, Johannes Eichner, Daniel R. Hyduke, James R. Faeder, Stefan Hoops, Emanuel Gonçalves, Yuichiro Inagaki, Aurélien Naldi, Koichi Takahashi, Sylvain Soliman, Brett G. Olivier, Kieran Smallbone, Stuart L. Moodie, Pedro T. Monteiro, Chris J. Myers, Martin Golebiewski, Tomas Radivoyevitch, Jeremy Zucker, Hidde de Jong, Andrew Finney
Publikováno v:
Molecular Systems Biology
Molecular Systems Biology, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Molecular systems biology, vol 16, iss 8
Molecular Systems Biology, EMBO Press, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Keating, S M, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, F T, Finney, A, Gillespie, C S, Helikar, T, Hoops, S, Malik-Sheriff, R S, Moodie, S L, Moraru, I I, Myers, C J, Naldi, A, Olivier, B G, Sahle, S, Schaff, J C, Smith, L P, Swat, M J, Thieffry, D, Watanabe, L, Wilkinson, D J, Blinov, M L, Begley, K, Faeder, J R, Gómez, H F, Hamm, T M, Inagaki, Y, Liebermeister, W, Lister, A L, Lucio, D, Mjolsness, E, Proctor, C J, Raman, K, Rodriguez, N, Shaffer, C A, Shapiro, B E, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier-Schellersheim, M, Sauro, H M, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, J C, Hucka, M, Adams, R R, Allen, N A, Angermann, B R, Antoniotti, M, Bader, G D, Červený, J, Courtot, M, Cox, C D, Dalle Pezze, P, Demir, E, Denney, W S, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, C T, Flamm, C, Fleming, R M T, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, L A, Heavner, B D, Henkel, R, Hlavacek, W S, Hu, B, Hyduke, D R, de Jong, H, Juty, N, Karp, P D, Karr, J R, Kell, D B, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, L M, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, P T, Natarajan, K N, Nielsen, P M F, Nguyen, T, Palmisano, A, Pettit, J B, Pfau, T, Phair, R D, Radivoyevitch, T, Rohwer, J M, Ruebenacker, O A, Saez-Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, S C, Smallbone, K, Soliman, S, Stefan, M I, Sullivan, D P, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, von Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A & Zucker, J 2020, ' SBML Level 3 : an extensible format for the exchange and reuse of biological models ', Molecular Systems Biology, vol. 16, no. 8, e9110, pp. 1-21 . https://doi.org/10.15252/msb.20199110
MOLECULAR SYSTEMS BIOLOGY
Molecular Systems Biology, Vol 16, Iss 8, Pp n/a-n/a (2020)
Molecular Systems Biology, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Molecular systems biology, vol 16, iss 8
Molecular Systems Biology, EMBO Press, 2020, 16 (8), pp.1-21. ⟨10.15252/msb.20199110⟩
Keating, S M, Waltemath, D, König, M, Zhang, F, Dräger, A, Chaouiya, C, Bergmann, F T, Finney, A, Gillespie, C S, Helikar, T, Hoops, S, Malik-Sheriff, R S, Moodie, S L, Moraru, I I, Myers, C J, Naldi, A, Olivier, B G, Sahle, S, Schaff, J C, Smith, L P, Swat, M J, Thieffry, D, Watanabe, L, Wilkinson, D J, Blinov, M L, Begley, K, Faeder, J R, Gómez, H F, Hamm, T M, Inagaki, Y, Liebermeister, W, Lister, A L, Lucio, D, Mjolsness, E, Proctor, C J, Raman, K, Rodriguez, N, Shaffer, C A, Shapiro, B E, Stelling, J, Swainston, N, Tanimura, N, Wagner, J, Meier-Schellersheim, M, Sauro, H M, Palsson, B, Bolouri, H, Kitano, H, Funahashi, A, Hermjakob, H, Doyle, J C, Hucka, M, Adams, R R, Allen, N A, Angermann, B R, Antoniotti, M, Bader, G D, Červený, J, Courtot, M, Cox, C D, Dalle Pezze, P, Demir, E, Denney, W S, Dharuri, H, Dorier, J, Drasdo, D, Ebrahim, A, Eichner, J, Elf, J, Endler, L, Evelo, C T, Flamm, C, Fleming, R M T, Fröhlich, M, Glont, M, Gonçalves, E, Golebiewski, M, Grabski, H, Gutteridge, A, Hachmeister, D, Harris, L A, Heavner, B D, Henkel, R, Hlavacek, W S, Hu, B, Hyduke, D R, de Jong, H, Juty, N, Karp, P D, Karr, J R, Kell, D B, Keller, R, Kiselev, I, Klamt, S, Klipp, E, Knüpfer, C, Kolpakov, F, Krause, F, Kutmon, M, Laibe, C, Lawless, C, Li, L, Loew, L M, Machne, R, Matsuoka, Y, Mendes, P, Mi, H, Mittag, F, Monteiro, P T, Natarajan, K N, Nielsen, P M F, Nguyen, T, Palmisano, A, Pettit, J B, Pfau, T, Phair, R D, Radivoyevitch, T, Rohwer, J M, Ruebenacker, O A, Saez-Rodriguez, J, Scharm, M, Schmidt, H, Schreiber, F, Schubert, M, Schulte, R, Sealfon, S C, Smallbone, K, Soliman, S, Stefan, M I, Sullivan, D P, Takahashi, K, Teusink, B, Tolnay, D, Vazirabad, I, von Kamp, A, Wittig, U, Wrzodek, C, Wrzodek, F, Xenarios, I, Zhukova, A & Zucker, J 2020, ' SBML Level 3 : an extensible format for the exchange and reuse of biological models ', Molecular Systems Biology, vol. 16, no. 8, e9110, pp. 1-21 . https://doi.org/10.15252/msb.20199110
MOLECULAR SYSTEMS BIOLOGY
Molecular Systems Biology, Vol 16, Iss 8, Pp n/a-n/a (2020)
Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aa48af775634bdfd1c248e236b20ef61
http://hdl.handle.net/10281/282956
http://hdl.handle.net/10281/282956
Publikováno v:
Journal of Personalized Medicine
Volume 11
Issue 6
Journal of Personalized Medicine, Vol 11, Iss 496, p 496 (2021)
Volume 11
Issue 6
Journal of Personalized Medicine, Vol 11, Iss 496, p 496 (2021)
Metabolic heterogeneity is a hallmark of cancer and can distinguish a normal phenotype from a cancer phenotype. In the systems biology domain, context-specific models facilitate extracting physiologically relevant information from high-quality data.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cb99f0f6cbccd1a4178ef6eaa3eb9e34
https://doi.org/10.3390/jpm11060496
https://doi.org/10.3390/jpm11060496
Autor:
Natalie J, Stanford, Martin, Scharm, Paul D, Dobson, Martin, Golebiewski, Michael, Hucka, Varun B, Kothamachu, David, Nickerson, Stuart, Owen, Jürgen, Pahle, Ulrike, Wittig, Dagmar, Waltemath, Carole, Goble, Pedro, Mendes, Jacky, Snoep
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2049
Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating datasets and integrating them into models involves a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::689a90901a87bc461fda4c292a10a7f7
https://pubmed.ncbi.nlm.nih.gov/31602618
https://pubmed.ncbi.nlm.nih.gov/31602618
Autor:
Jacky L. Snoep, Brett G. Olivier, Maxwell Lewis Neal, Vasundra Touré, Samuel H. Friedman, Daniel L. Cook, Alan Garny, Chris J. Myers, Martin Golebiewski, David P. Nickerson, Michael T. Cooling, Olaf Wolkenhauer, Sharon M. Crook, Nick Juty, Goksel Misirli, Miguel de Alba, John H. Gennari, Martin Scharm, Koray Atalag, Herbert M. Sauro, Vijayalakshmi Chelliah, Dagmar Waltemath, Reza Kalbasi, Matthias König, Padraig Gleeson, Anil Wipat, Michael Hucka, Andreas Dräger
Publikováno v:
Neal, M L, König, M, Nickerson, D, Misirli, G, Kalbasi, R, Dräger, A, Atalag, K, Chelliah, V, Cooling, M T, Cook, D L, Crook, S, De Alba, M, Friedman, S H, Garny, A, Gennari, J H, Gleeson, P, Golebiewski, M, Hucka, M, Juty, N, Myers, C, Olivier, B G, Sauro, H M, Scharm, M, Snoep, J L, Touré, V, Wipat, A, Wolkenhauer, O & Waltemath, D 2019, ' Harmonizing semantic annotations for computational models in biology ', Briefings in Bioinformatics, vol. 20, no. 2, pp. 540-550 . https://doi.org/10.1093/bib/bby087
Neal, M L, König, M, Nickerson, D, Misirli, G, Kalbasi, R, Dräger, A, Atalag, K, Chelliah, V, Cooling, M T, Cook, D L, Crook, S, De Alba, M, Friedman, S H, Garny, A, Gennari, J H, Gleeson, P, Golebiewski, M, Hucka, M, Juty, N, Myers, C, Olivier, B G, Sauro, H M, Scharm, M, Snoep, J L, Touré, V, Wipat, A, Wolkenhauer, O & Waltemath, D 2019, ' Harmonizing semantic annotations for computational models in biology ', Briefings in bioinformatics, vol. 20, no. 2, pp. 540-550 . https://doi.org/10.1093/bib/bby087
Briefings in bioinformatics, 20(2), 540-550. Oxford University Press
Briefings in Bioinformatics
Neal, M L, König, M, Nickerson, D, Misirli, G, Kalbasi, R, Dräger, A, Atalag, K, Chelliah, V, Cooling, M T, Cook, D L, Crook, S, De Alba, M, Friedman, S H, Garny, A, Gennari, J H, Gleeson, P, Golebiewski, M, Hucka, M, Juty, N, Myers, C, Olivier, B G, Sauro, H M, Scharm, M, Snoep, J L, Touré, V, Wipat, A, Wolkenhauer, O & Waltemath, D 2019, ' Harmonizing semantic annotations for computational models in biology ', Briefings in bioinformatics, vol. 20, no. 2, pp. 540-550 . https://doi.org/10.1093/bib/bby087
Briefings in bioinformatics, 20(2), 540-550. Oxford University Press
Briefings in Bioinformatics
Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability and reusability of such models as well as for
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1210d470e96241cc9cb2513126ecaef8
https://eprints.keele.ac.uk/5519/1/bby087.pdf
https://eprints.keele.ac.uk/5519/1/bby087.pdf