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Publications

featured publications

  • BioSimulators: a central registry of simulation engines and services for recommending specific tools.

    Nucleic acids research

    Authors: 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 Haiman, Jan Hasenauer, Joseph L Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C Ison, Diego Jahn, Henry V Jakubowski, Ryann Jordan, Matúš Kalaš, Matthias König, Wolfram Liebermeister, Rahuman S Malik Sheriff, Synchon Mandal, Robert McDougal, J Kyle Medley, Pedro Mendes, Robert Müller, Chris J Myers, Aurelien 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 S Saglam, Dilawar Singh, Ankur Sinha, Jacky Snoep, Hugh Sorby, Ryan Spangler, Jörn Starruß, Payton J Thomas, David 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

  • Identifiability analysis for models of the translation kinetics after mRNA transfection.

    Journal of mathematical biology

    Authors: Susanne Pieschner, Jan Hasenauer, Christiane Fuchs

  • Combining gene expression analysis of gastric cancer cell lines and tumor specimens to identify biomarkers for anti-HER therapies-the role of HAS2, SHB and HBEGF.

    BMC cancer

    Authors: Karolin Ebert, Ivonne Haffner, Gwen Zwingenberger, Simone Keller, Elba Raimúndez, Robert Geffers, Ralph Wirtz, Elena Barbaria, Vanessa Hollerieth, Rouven Arnold, Axel Walch, Jan Hasenauer, Dieter Maier, Florian Lordick, Birgit Luber

  • Top publication

    A protocol for dynamic model calibration.

    Briefings in bioinformatics

    Authors: Alejandro F Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R Banga

  • Top publication

    Mini-batch optimization enables training of ODE models on large-scale datasets.

    Nature communications

    Authors: Paul Stapor, Leonard Schmiester, Christoph Wierling, Simon Merkt, Dilan Pathirana, Bodo M H Lange, Daniel Weindl, Jan Hasenauer

  • Efficient gradient-based parameter estimation for dynamic models using qualitative data.

    Bioinformatics (Oxford, England)

    Authors: Leonard Schmiester, Daniel Weindl, Jan Hasenauer

  • The mesoscale organization of syntaxin 1A and SNAP25 is determined by SNARE-SNARE interactions.

    eLife

    Authors: Jasmin Mertins, Jérôme Finke, Ricarda Sies, Kerstin M Rink, Jan Hasenauer, Thorsten Lang

  • SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.

    Bioinformatics (Oxford, England)

    Authors: Andreas Dräger, Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, Juilee Thakar

  • Seroepidemiology and model-based prediction of SARS-CoV-2 in Ethiopia: longitudinal cohort study among front-line hospital workers and communities.

    The Lancet. Global health

    Authors: Esayas Kebede Gudina, Solomon Ali, Eyob Girma, Addisu Gize, Birhanemeskel Tegene, Gadissa Bedada Hundie, Wondewosen Tsegaye Sime, Rozina Ambachew, Alganesh Gebreyohanns, Mahteme Bekele, Abhishek Bakuli, Kira Elsbernd, Simon Merkt, Lorenzo Contento, Michael Hoelscher, Jan Hasenauer, Andreas Wieser, Arne Kroidl

  • AMICI: high-performance sensitivity analysis for large ordinary differential equation models.

    Bioinformatics (Oxford, England)

    Authors: Fabian Fröhlich, Daniel Weindl, Yannik Schälte, Dilan Pathirana, Łukasz Paszkowski, Glenn Terje Lines, Paul Stapor, Jan Hasenauer