COPASI and its applications in biotechnology von Bergmann, Frank T., Hoops, Stefan, Klahn, Brian, Kummer, Ursula, Mendes, Pedro, Pahle, Jürgen, Sahle, Sven

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CoRC: the COPASI R Connector von Förster, Jonas, Bergmann, Frank T., Pahle, Jürgen

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PEtab-Interoperable specification of parameter estimation problems in systems biology von Schmiester, Leonard, Schälte, Yannik, Bergmann, Frank T, Camba, Tacio, Dudkin, Erika, Egert, Janine, Fröhlich, Fabian, Fuhrmann, Lara, Hauber, Adrian L, Kemmer, Svenja, Lakrisenko, Polina, Loos, Carolin, Merkt, Simon, Müller, Wolfgang, Pathirana, Dilan, Raimúndez, Elba, Refisch, Lukas, Rosenblatt, Marcus, Stapor, Paul L, Städter, Philipp, Wang, Dantong, Wieland, Franz-Georg, Banga, Julio R, Timmer, Jens, Villaverde, Alejandro F, Sahle, Sven, Kreutz, Clemens, Hasenauer, Jan, Weindl, Daniel

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COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project von Bergmann, Frank T, Adams, Richard, Moodie, Stuart, Cooper, Jonathan, Glont, Mihai, Golebiewski, Martin, Hucka, Michael, Laibe, Camille, Miller, Andrew K, Nickerson, David P, Olivier, Brett G, Rodriguez, Nicolas, Sauro, Herbert M, Scharm, Martin, Soiland-Reyes, Stian, Waltemath, Dagmar, Yvon, Florent, Le Novère, Nicolas

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EnzymeML—a data exchange format for biocatalysis and enzymology von Range, Jan, Halupczok, Colin, Lohmann, Jens, Swainston, Neil, Kettner, Carsten, Bergmann, Frank T., Weidemann, Andreas, Wittig, Ulrike, Schnell, Santiago, Pleiss, Jürgen

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The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2 von Hucka, Michael, Bergmann, Frank T, Chaouiya, Claudine, Dräger, Andreas, Hoops, Stefan, Keating, Sarah M, König, Matthias, Novère, Nicolas Le, Myers, Chris J, Olivier, Brett G, Sahle, Sven, Schaff, James C, Sheriff, Rahuman, Smith, Lucian P, Waltemath, Dagmar, Wilkinson, Darren J, Zhang, Fengkai

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TinkerCell: modular CAD tool for synthetic biology von Chandran, Deepak, Bergmann, Frank T, Sauro, Herbert M

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SBML Level 3 Package: Flux Balance Constraints version 2 von Olivier, Brett G., Bergmann, Frank T.

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A Novel MIF Signaling Pathway Drives the Malignant Character of Pancreatic Cancer by Targeting NR3C2 von Yang, Shouhui, He, Peijun, Wang, Jian, Schetter, Aaron, Tang, Wei, Funamizu, Naotake, Yanaga, Katsuhiko, Uwagawa, Tadashi, Satoskar, Abhay R, Gaedcke, Jochen, Bernhardt, Markus, Ghadimi, B Michael, Gaida, Matthias M, Bergmann, Frank, Werner, Jens, Ried, Thomas, Hanna, Nader, Alexander, H Richard, Hussain, S Perwez

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NRG1 Fusions in KRAS Wild-Type Pancreatic Cancer von Heining, Christoph, Horak, Peter, Uhrig, Sebastian, Codo, Paula L, Klink, Barbara, Hutter, Barbara, Fröhlich, Martina, Bonekamp, David, Richter, Daniela, Steiger, Katja, Penzel, Roland, Endris, Volker, Ehrenberg, Karl Roland, Frank, Stephanie, Kleinheinz, Kortine, Toprak, Umut H, Schlesner, Matthias, Mandal, Ranadip, Schulz, Lothar, Lambertz, Helmut, Fetscher, Sebastian, Bitzer, Michael, Malek, Nisar P, Horger, Marius, Giese, Nathalia A, Strobel, Oliver, Hackert, Thilo, Springfeld, Christoph, Feuerbach, Lars, Bergmann, Frank, Schröck, Evelin, von Kalle, Christof, Weichert, Wilko, Scholl, Claudia, Ball, Claudia R, Stenzinger, Albrecht, Brors, Benedikt, Fröhling, Stefan, Glimm, Hanno

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Cancer Cell-Autonomous TRAIL-R Signaling Promotes KRAS-Driven Cancer Progression, Invasion, and Metastasis von von Karstedt, Silvia, Conti, Annalisa, Nobis, Max, Montinaro, Antonella, Hartwig, Torsten, Lemke, Johannes, Legler, Karen, Annewanter, Franka, Campbell, Andrew D., Taraborrelli, Lucia, Grosse-Wilde, Anne, Coy, Johannes F., El-Bahrawy, Mona A., Bergmann, Frank, Koschny, Ronald, Werner, Jens, Ganten, Tom M., Schweiger, Thomas, Hoetzenecker, Konrad, Kenessey, Istvan, Hegedüs, Balazs, Bergmann, Michael, Hauser, Charlotte, Egberts, Jan-Hendrik, Becker, Thomas, Röcken, Christoph, Kalthoff, Holger, Trauzold, Anna, Anderson, Kurt I., Sansom, Owen J., Walczak, Henning

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SBtab: a flexible table format for data exchange in systems biology von Lubitz, Timo, Hahn, Jens, Bergmann, Frank T, Noor, Elad, Klipp, Edda, Liebermeister, Wolfram

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Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language von Waltemath, Dagmar, Adams, Richard, Bergmann, Frank T, Hucka, Michael, Kolpakov, Fedor, Miller, Andrew K, Moraru, Ion I, Nickerson, David, Sahle, Sven, Snoep, Jacky L, Le Novère, Nicolas

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Yes-Associated Protein Up-regulates Jagged-1 and Activates the NOTCH Pathway in Human Hepatocellular Carcinoma von Tschaharganeh, Darjus Felix, Chen, Xin, Latzko, Philipp, Malz, Mona, Gaida, Matthias Martin, Felix, Klaus, Ladu, Sara, Singer, Stephan, Pinna, Federico, Gretz, Norbert, Sticht, Carsten, Tomasi, Maria Lauda, Delogu, Salvatore, Evert, Matthias, Fan, Biao, Ribback, Silvia, Jiang, Lijie, Brozzetti, Stefania, Bergmann, Frank, Dombrowski, Frank, Schirmacher, Peter, Calvisi, Diego Francesco, Breuhahn, Kai

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Minimum Information About a Simulation Experiment (MIASE) von Waltemath, Dagmar, Adams, Richard, Beard, Daniel A, Bergmann, Frank T, Bhalla, Upinder S, Britten, Randall, Chelliah, Vijayalakshmi, Cooling, Michael T, Cooper, Jonathan, Crampin, Edmund J, Garny, Alan, Hoops, Stefan, Hucka, Michael, Hunter, Peter, Klipp, Edda, Laibe, Camille, Miller, Andrew K, Moraru, Ion, Nickerson, David, Nielsen, Poul, Nikolski, Macha, Sahle, Sven, Sauro, Herbert M, Schmidt, Henning, Snoep, Jacky L, Tolle, Dominic, Wolkenhauer, Olaf, Le Novère, Nicolas

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Induction of Chromosome Instability by Activation of Yes-Associated Protein and Forkhead Box M1 in Liver Cancer von Weiler, Sofia M.E, Pinna, Federico, Wolf, Thomas, Lutz, Teresa, Geldiyev, Aman, Sticht, Carsten, Knaub, Maria, Thomann, Stefan, Bissinger, Michaela, Wan, Shan, Rössler, Stephanie, Becker, Diana, Gretz, Norbert, Lang, Hauke, Bergmann, Frank, Ustiyan, Vladimir, Kalin, Tatiana V, Singer, Stephan, Lee, Ju-Seog, Marquardt, Jens U, Schirmacher, Peter, Kalinichenko, Vladimir V, Breuhahn, Kai

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Piecewise parameter estimation for stochastic models in COPASI von Bergmann, Frank T, Sahle, Sven, Zimmer, Christoph

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EnzymeML: seamless data flow and modeling of enzymatic data von Lauterbach, Simone, Dienhart, Hannah, Range, Jan, Malzacher, Stephan, Spöring, Jan-Dirk, Rother, Dörte, Pinto, Maria Filipa, Martins, Pedro, Lagerman, Colton E., Bommarius, Andreas S., Høst, Amalie Vang, Woodley, John M., Ngubane, Sandile, Kudanga, Tukayi, Bergmann, Frank T., Rohwer, Johann M., Iglezakis, Dorothea, Weidemann, Andreas, Wittig, Ulrike, Kettner, Carsten, Swainston, Neil, Schnell, Santiago, Pleiss, Jürgen

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Most Pancreatic Cancer Resections are R1 Resections von Esposito, Irene, Kleeff, Jörg, Bergmann, Frank, Reiser, Caroline, Herpel, Esther, Friess, Helmut, Schirmacher, Peter, Büchler, Markus W.

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Enucleation: A treatment alternative for branch duct intraductal papillary mucinous neoplasms von Kaiser, Joerg, MD, Fritz, Stefan, MD, Klauss, Miriam, MD, Bergmann, Frank, MD, Hinz, Ulf, MSc, Strobel, Oliver, MD, Schneider, Lutz, MD, Büchler, Markus W., MD, Hackert, Thilo, MD

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