T
Tomáš Helikar
Researcher at University of Nebraska–Lincoln
Publications - 82
Citations - 2067
Tomáš Helikar is an academic researcher from University of Nebraska–Lincoln. The author has contributed to research in topics: Computer science & Biology. The author has an hindex of 19, co-authored 69 publications receiving 1495 citations. Previous affiliations of Tomáš Helikar include University of Nebraska Medical Center & University of Nebraska Omaha.
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Journal ArticleDOI
The Cell Collective: Toward an open and collaborative approach to systems biology
Tomáš Helikar,Bryan Kowal,Sean McClenathan,Mitchell Bruckner,Thaine W. Rowley,Alex Madrahimov,Benjamin Wicks,Manish Shrestha,Kahani Limbu,Jim A. Rogers,Jim A. Rogers +10 more
TL;DR: The Cell Collective is a web-based platform that enables laboratory scientists from across the globe to collaboratively build large-scale models of various biological processes, and simulate/analyze them in real time.
Journal ArticleDOI
Logical Modeling and Dynamical Analysis of Cellular Networks.
Wassim Abou-Jaoudé,Pauline Traynard,Pedro T. Monteiro,Pedro T. Monteiro,Julio Saez-Rodriguez,Tomáš Helikar,Denis Thieffry,Claudine Chaouiya +7 more
TL;DR: A number of recent methodological advances to ease the analysis of large and intricate networks are reviewed, including approaches to determine model attractors and their reachability properties, to assess the dynamical impact of variations of external signals, and to consistently reduce large models.
Journal ArticleDOI
Emergent decision-making in biological signal transduction networks
TL;DR: A large scale model was created with the logical mechanism of each node described completely to allow simulation and dynamical analysis and revealed a robust system capable of clustering widely varying input combinations into equivalence classes of biologically relevant cellular responses.
Journal ArticleDOI
SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating,Sarah M. Keating,Dagmar Waltemath,Matthias König,Fengkai Zhang,Andreas Dräger,Claudine Chaouiya,Claudine Chaouiya,Frank 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,Brett G. Olivier,Brett G. Olivier,Sven Sahle,James C. Schaff,Lucian P. Smith,Lucian P. Smith,Maciej J. Swat,Denis Thieffry,Leandro Watanabe,Darren J. Wilkinson,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 O. Palsson,Hamid Bolouri,Hiroaki Kitano,Akira Funahashi,Henning Hermjakob,John Doyle,Michael Hucka,Richard R. Adams,Nicholas Alexander Allen,Bastian R. Angermann,Marco Antoniotti,Gary D. Bader,Jan Červený,Mélanie Courtot,Christopher 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 M. T. 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 A. Kolpakov,Falko Krause,Martina Kutmon,Camille Laibe,Conor Lawless,Lu Li,Leslie M. Loew,Rainer Machné,Yukiko Matsuoka,Pedro Mendes,Huaiyu Mi,Florian Mittag,Pedro T. Monteiro,Kedar Nath Natarajan,Poul M. F. Nielsen,Tramy Nguyen,Alida Palmisano,Jean-Baptiste Pettit,Thomas Pfau,Robert 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 +146 more
TL;DR: The latest edition of the Systems Biology Markup Language (SBML) is reviewed, a format designed for this purpose that leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models.
Journal ArticleDOI
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
Claudine Chaouiya,Duncan Berenguier,Sarah M. Keating,Aurélien Naldi,Martijn P. van Iersel,Nicolas Rodriguez,Nicolas Rodriguez,Andreas Dräger,Andreas Dräger,Finja Büchel,Thomas Cokelaer,Bryan Kowal,Benjamin Wicks,Emanuel Gonçalves,Julien Dorier,Michel Page,Michel Page,Pedro T. Monteiro,Pedro T. Monteiro,Axel von Kamp,Ioannis Xenarios,Hidde de Jong,Michael Hucka,Steffen Klamt,Denis Thieffry,Nicolas Le Novère,Nicolas Le Novère,Julio Saez-Rodriguez,Tomáš Helikar +28 more
TL;DR: The Systems Biology Markup Language (SBML) Qualitative Models Package (qual) as discussed by the authors is an extension of the SBML Level 3 standard designed for computer representation of qualitative models of biological networks.