NTFD - a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data. - Karsten Hiller; André Wegner; Daniel Weindl; Thekla Cordes; Christian M. Metallo; Joanne K. Kelleher; Gregory Stephanopoulos (Bioinform., 2013)

MIA: non-targeted mass isotopolome analysis. - Daniel Weindl; André Wegner; Karsten Hiller (Bioinform., 2016)

LNA++: Linear Noise Approximation with First and Second Order Sensitivities. - Justin Feigelman; Daniel Weindl; Fabian J. Theis; Carsten Marr; Jan Hasenauer (CMSB, 2018)

PESTO: Parameter EStimation TOolbox. - Paul Stapor; Daniel Weindl; Benjamin Ballnus; Sabine Hug; Carolin Loos; Anna Fiedler; Sabrina Krause; Sabrina Hross; Fabian Fröhlich; Jan Hasenauer (Bioinform., 2018)

Community-driven roadmap for integrated disease maps. - Marek Ostaszewski; Stephan Gebel; Inna Kuperstein; Alexander Mazein; Andrei Yu. Zinovyev; Ugur Dogrusoz; Jan Hasenauer; Ronan M. T. Fleming; Nicolas Le Novère; Piotr Gawron; Thomas S. Ligon; Anna Niarakis; et al. (Briefings Bioinform., 2019)

Benchmarking optimization methods for parameter estimation in large kinetic models. - Alejandro Fernández Villaverde; Fabian Fröhlich; Daniel Weindl; Jan Hasenauer; Julio R. Banga (Bioinform., 2019)

Efficient parameterization of large-scale dynamic models based on relative measurements. - Leonard Schmiester; Yannik Schälte; Fabian Fröhlich; Jan Hasenauer; Daniel Weindl (Bioinform., 2020)

AMICI: high-performance sensitivity analysis for large ordinary differential equation models. - Fabian Fröhlich; Daniel Weindl; Yannik Schälte; Dilan Pathirana; Lukasz Paszkowski; Glenn Terje Lines; Paul Stapor; Jan Hasenauer (Bioinform., 2021)

Efficient gradient-based parameter estimation for dynamic models using qualitative data. - Leonard Schmiester; Daniel Weindl; Jan Hasenauer (Bioinform., 2021)

PEtab - Interoperable specification of parameter estimation problems in systems biology. - Leonard Schmiester; Yannik Schälte; Frank T. Bergmann; Tacio Camba; Erika Dudkin; Janine Egert; Fabian Fröhlich; Lara Fuhrmann; Adrian L. Hauber; Svenja Kemmer; Polina A. Lakrisenko; Carolin Loos; et al. (PLoS Comput. Biol., 2021)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - 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 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - 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 006; et al. (Nucleic Acids Res., 2022)

A More Expressive Spline Representation for SBML Models Improves Code Generation Performance in AMICI. - Lorenzo Contento; Paul Stapor; Daniel Weindl; Jan Hasenauer (CMSB, 2023)

Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks. - Polina A. Lakrisenko; Paul Stapor; Stephan Grein; Lukasz Paszkowski; Dilan Pathirana; Fabian Fröhlich; Glenn Terje Lines; Daniel Weindl; Jan Hasenauer (PLoS Comput. Biol., 2023)

pyPESTO: a modular and scalable tool for parameter estimation for dynamic models. - Yannik Schälte; Fabian Fröhlich; Paul J. Jost; Jakob Vanhoefer; Dilan Pathirana; Paul Stapor; Polina A. Lakrisenko; Dantong Wang; Elba Raimúndez-Álvarez; Simon Merkt; Leonard Schmiester; Philipp Städter; et al. (Bioinform., 2023)

Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. - Paul F. Lang; David R. Penas; Julio R. Banga; Daniel Weindl; Béla Novák (PLoS Comput. Biol., 2024)