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2020 – today
- 2024
[j20]Martin Golebiewski
, Gary D. Bader, Padraig Gleeson, Thomas E. Gorochowski, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber:
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024. J. Integr. Bioinform. 21(1) (2024)- 2023
- [j19]Matthias König, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath, Falk Schreiber:
Specifications of standards in systems and synthetic biology: status and developments in 2022 and the COMBINE meeting 2022. J. Integr. Bioinform. 20(1) (2023) - [j18]Justas Birgiolas, Vergil Haynes, Padraig Gleeson, Richard C. Gerkin, Suzanne W. Dietrich, Sharon M. Crook:
NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML. PLoS Comput. Biol. 19(3) (2023) - 2022
- [j17]John D. Griffiths, Kelly Shen, Padraig Gleeson:
Editorial: Neuroinformatics of large-scale brain modelling. Frontiers Neuroinformatics 16 (2022) - [j16]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [i1]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [j15]Falk Schreiber, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of standards in systems and synthetic biology: status and developments in 2021. J. Integr. Bioinform. 18(3) (2021) - 2020
- [j14]Dagmar Waltemath, Martin Golebiewski, Michael L. Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M. Keating, Matthias König, Olga Krebs, Rahuman S. Malik-Sheriff, David P. Nickerson, Ernst Oberortner, Herbert M. Sauro, Falk Schreiber, Lucian P. Smith, Melanie I. Stefan, Ulrike Wittig, Chris J. Myers:
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J. Integr. Bioinform. 17(2-3) (2020) - [j13]Kael Dai, Juan Hernando, Yazan N. Billeh, Sergey L. Gratiy, Judit Planas, Andrew P. Davison, Salvador Dura-Bernal, Padraig Gleeson, Adrien Devresse, Benjamin K. Dichter, Michael Gevaert, James Gonzalo King, Werner Van Geit, Arseny V. Povolotsky, Eilif Müller, Jean-Denis Courcol, Anton Arkhipov:
The SONATA data format for efficient description of large-scale network models. PLoS Comput. Biol. 16(2) (2020)
2010 – 2019
- 2019
- [j12]Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath:
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20(2): 540-550 (2019) - [j11]Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j10]Inga Blundell, Romain Brette, Thomas A. Cleland, Thomas G. Close, Daniel Coca, Andrew P. Davison, Sandra Diaz-Pier, Carlos Fernandez Musoles, Padraig Gleeson, Dan F. M. Goodman, Michael L. Hines, Michael W. Hopkins, Pramod S. Kumbhar, David R. Lester, Bóris Marin, Abigail Morrison, Eric Müller, Thomas Nowotny, Alexander Peyser, Dimitri Plotnikov, Paul Richmond, Andrew Rowley, Bernhard Rumpe, Marcel Stimberg, Alan B. Stokes, Adam R. Tomkins, Guido Trensch, Michael Marmaduke Woodman, Jochen Martin Eppler:
Code Generation in Computational Neuroscience: A Review of Tools and Techniques. Frontiers Neuroinformatics 12: 68 (2018) - [j9]Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. J. Integr. Bioinform. 15(1) (2018) - 2017
- [c1]Chris J. Myers, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, David P. Nickerson, Falk Schreiber, Dagmar Waltemath:
A brief history of COMBINE. WSC 2017: 884-895 - 2016
- [j8]Falk Schreiber, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novère, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath:
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. J. Integr. Bioinform. 13(3) (2016) - 2014
- [j7]Balazs Szigeti, Padraig Gleeson, Michael Vella, Sergey Khayrulin, Andrey Palyanov, Jim Hokanson, Michael Currie, Matteo Cantarelli, Giovanni Idili, Stephen D. Larson:
OpenWorm: an open-science approach to modeling Caenorhabditis elegans. Frontiers Comput. Neurosci. 8: 137 (2014) - [j6]Michael Vella, Robert C. Cannon, Sharon M. Crook, Andrew P. Davison, Gautham Ganapathy, Hugh P. C. Robinson, R. Angus Silver, Padraig Gleeson:
libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience. Frontiers Neuroinformatics 8: 38 (2014) - [j5]Robert C. Cannon, Padraig Gleeson, Sharon M. Crook, Gautham Ganapathy, Bóris Marin, Eugenio Piasini, R. Angus Silver:
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Frontiers Neuroinformatics 8: 79 (2014) - [j4]Matteo Farinella, Daniel T. Ruedt, Padraig Gleeson, Frederic Lanore, R. Angus Silver:
Glutamate-Bound NMDARs Arising from In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model. PLoS Comput. Biol. 10(4) (2014) - [r5]Sharon M. Crook, Padraig Gleeson, Robert C. Cannon, Michael Vella, Angus Silver:
NeuroML. Encyclopedia of Computational Neuroscience 2014 - [r4]Padraig Gleeson:
Software Tools for Modelling in Computational Neuroscience: Overview. Encyclopedia of Computational Neuroscience 2014 - [r3]Padraig Gleeson:
Synthetic Neuronal Circuits/Networks. Encyclopedia of Computational Neuroscience 2014 - [r2]Padraig Gleeson:
neuroConstruct. Encyclopedia of Computational Neuroscience 2014 - [r1]Padraig Gleeson, Angus Silver, Matteo Cantarelli:
Open Source Brain. Encyclopedia of Computational Neuroscience 2014 - 2010
- [j3]Padraig Gleeson, Sharon M. Crook, Robert C. Cannon, Michael L. Hines, Guy O. Billings, Matteo Farinella, Thomas M. Morse, Andrew P. Davison, Subhasis Ray, Upinder S. Bhalla, Simon R. Barnes, Yoana D. Dimitrova, Angus Silver:
NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail. PLoS Comput. Biol. 6(6) (2010)
2000 – 2009
- 2008
- [p1]Cengiz Günay, Tomasz G. Smolinski, William W. Lytton, Thomas M. Morse, Padraig Gleeson, Sharon M. Crook, Volker Steuber, Angus Silver, Horatiu Voicu, Peter Andrews, Hemant Bokil, Hiren Maniar, Catherine Loader, Samar Mehta, David Kleinfeld, David J. Thomson, Partha P. Mitra, Gloster Aaron, Jean-Marc Fellous:
Computational Intelligence in Electrophysiology: Trends and Open Problems. Applications of Computational Intelligence in Biology 2008: 325-359 - 2007
- [j2]Sharon M. Crook, Padraig Gleeson, Fredrick W. Howell, Joseph Svitak, Angus Silver:
MorphML: Level 1 of the NeuroML Standards for Neuronal Morphology Data and Model Specification. Neuroinformatics 5(2): 96-104 (2007) - [j1]Robert C. Cannon, Marc-Oliver Gewaltig, Padraig Gleeson, Upinder S. Bhalla, Hugo Cornelis, Michael L. Hines, Fredrick W. Howell, Eilif Mueller, Joel R. Stiles, Stefan Wils, Erik De Schutter:
Interoperability of Neuroscience Modeling Software: Current Status and Future Directions. Neuroinformatics 5(2): 127-138 (2007)
Coauthor Index
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