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Publications

featured publications

  • 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

  • COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.

    Molecular systems biology

    Authors: Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Wilighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider