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Anna Zhukova
Researcher at Pasteur Institute
Publications - 38
Citations - 1373
Anna Zhukova is an academic researcher from Pasteur Institute. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 9, co-authored 29 publications receiving 1028 citations. Previous affiliations of Anna Zhukova include European Bioinformatics Institute & University of Bordeaux.
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Journal ArticleDOI
Modeling sample variables with an Experimental Factor Ontology
James Malone,Ele Holloway,Tomasz Adamusiak,Misha Kapushesky,Jie Zheng,Nikolay Kolesnikov,Anna Zhukova,Alvis Brazma,Helen Parkinson +8 more
TL;DR: The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way.
Journal ArticleDOI
Controlled vocabularies and semantics in systems biology
Mélanie Courtot,Nick Juty,Christian Knüpfer,Dagmar Waltemath,Anna Zhukova,Andreas Dräger,Michel Dumontier,Andrew Finney,Martin Golebiewski,Janna Hastings,Stefan Hoops,Sarah M. Keating,Douglas B. Kell,Samuel Kerrien,James R. Lawson,Allyson L. Lister,James Lu,Rainer Machné,Pedro Mendes,Matthew Pocock,Nicolas Rodriguez,Alice Villéger,Darren J. Wilkinson,Sarala M. Wimalaratne,Camille Laibe,Michael Hucka,Nicolas Le Novère +26 more
TL;DR: Three ontologies created specifically to address the needs of the systems biology community are described, including the Systems Biology Ontology, which provides semantic information about the model components, and the Kinetic Simulation Algorithm Ontology and the Terminology for the Description of Dynamics, which categorizes dynamical features of the simulation results and general systems behavior.
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
A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios
TL;DR: PastML was applied to the phylogeography of Dengue serotype 2 (DENV2), and the evolution of drug resistances in a large HIV data set, and showed the uncertainty of the human-sylvatic DENV2 geographic origin.
Journal ArticleDOI
Toward Community Standards and Software for Whole-Cell Modeling
Dagmar Waltemath,Jonathan R. Karr,Frank Bergmann,Vijayalakshmi Chelliah,Michael Hucka,Marcus Krantz,Wolfram Liebermeister,Pedro Mendes,Chris J. Myers,Pınar Pir,Begum Alaybeyoglu,Naveen K. Aranganathan,Kambiz Baghalian,Arne T. Bittig,Paulo E. Pinto Burke,Matteo Cantarelli,Yin Hoon Chew,Rafael S. Costa,Joseph Cursons,Tobias Czauderna,Arthur P. Goldberg,Harold F. Gómez,Jens Hahn,Tuure Hameri,Daniel Federico Hernandez Gardiol,Denis Kazakiewicz,Ilya Kiselev,Vincent Knight-Schrijver,Christian Knüpfer,Matthias König,Daewon Lee,Audald Lloret-Villas,Nikita Mandrik,J. Kyle Medley,Bertrand Moreau,Hojjat Naderi-Meshkin,Sucheendra K. Palaniappan,Daniel Alejandro Priego-Espinosa,Martin Scharm,Mahesh C. Sharma,Kieran Smallbone,Natalie J. Stanford,Je-Hoon Song,Tom Theile,Milenko Tokic,Namrata Tomar,Vasundra Touré,Jannis Uhlendorf,Thawfeek M. Varusai,Leandro Watanabe,Florian Wendland,Markus Wolfien,James T. Yurkovich,Yan Zhu,Argyris Zardilis,Anna Zhukova,Falk Schreiber +56 more
TL;DR: The 2015 Whole-Cell Modeling Summer School was organized to teach WC modeling and evaluate the need for new WC modeling standards and software by recoding a recently published WC model in the Systems Biology Markup Language.