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Publications

Featured publications

  • Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks.

    PLoS computational biology

    Authors: Polina Lakrisenko, Paul Stapor, Stephan Grein, Łukasz Paszkowski, Dilan Pathirana, Fabian Fröhlich, Glenn Terje Lines, Daniel Weindl, Jan Hasenauer

  • Clinical Impact of Monoclonal Antibodies in the Treatment of High-Risk Patients with SARS-CoV-2 Breakthrough Infections: The ORCHESTRA Prospective Cohort Study.

    Biomedicines

    Authors: Alessia Savoldi, Matteo Morra, Alessandro Castelli, Massimo Mirandola, Matilda Berkell, Mathias Smet, Angelina Konnova, Elisa Rossi, Salvatore Cataudella, Pasquale De Nardo, Elisa Gentilotti, Akshita Gupta, Daniele Fasan, Enrico Gibbin, Filippo Cioli Puviani, Jan Hasenauer, Roy Gusinow, Adriana Tami, Samir Kumar-Singh, Surbhi Malhotra-Kumar, mAb Orchestra Working Group, Evelina Tacconelli

  • Challenges of data sharing in European Covid-19 projects: A learning opportunity for advancing pandemic preparedness and response.

    The Lancet regional health. Europe

    Authors: Evelina Tacconelli, Anna Gorska, Elena Carrara, Ruth Joanna Davis, Marc Bonten, Alex W Friedrich, Corinna Glasner, Herman Goossens, Jan Hasenauer, Josep Maria Haro Abad, José L Peñalvo, Albert Sanchez-Niubo, Anastassja Sialm, Gabriella Scipione, Gloria Soriano, Yazdan Yazdanpanah, Ellen Vorstenbosch, Thomas Jaenisch

  • Histologic Cell Shape Descriptors for the Retinal Pigment Epithelium in Age-Related Macular Degeneration: A Comparison to Unaffected Eyes.

    Translational vision science & technology

    Authors: Leon von der Emde, Marc Vaisband, Jan Hasenauer, Leonie Bourauel, Katharina Bermond, Marlene Saßmannshausen, Rainer Heintzmann, Frank G Holz, Christine A Curcio, Kenneth R Sloan, Thomas Ach

  • Alveolar macrophages in early stage COPD show functional deviations with properties of impaired immune activation.

    Frontiers in immunology

    Authors: Kevin Baßler, Wataru Fujii, Theodore S Kapellos, Erika Dudkin, Nico Reusch, Ari Horne, Benedikt Reiz, Malte D Luecken, Collins Osei-Sarpong, Stefanie Warnat-Herresthal, Lorenzo Bonaguro, Jonas Schulte-Schrepping, Allon Wagner, Patrick Günther, Carmen Pizarro, Tina Schreiber, Rainer Knoll, Lisa Holsten, Charlotte Kröger, Elena De Domenico, Matthias Becker, Kristian Händler, Christian T Wohnhaas, Florian Baumgartner, Meike Köhler, Heidi Theis, Michael Kraut, Marc H Wadsworth, Travis K Hughes, Humberto J Ferreira, Emily Hinkley, Ines H Kaltheuner, Matthias Geyer, Christoph Thiele, Alex K Shalek, Andreas Feißt, Daniel Thomas, Henning Dickten, Marc Beyer, Patrick Baum, Nir Yosef, Anna C Aschenbrenner, Thomas Ulas, Jan Hasenauer, Fabian J Theis, Dirk Skowasch, Joachim L Schultze

  • 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

  • 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