SBML-PET: a Systems Biology Markup Language-based parameter estimation tool. - Zhike Zi; Edda Klipp (Bioinform., 2006)

Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network. - Matteo Barberis; Edda Klipp; Marco Vanoni; Lilia Alberghina (PLoS Comput. Biol., 2007)

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool. - Zhike Zi; Yanan Zheng; Ann E. Rundell; Edda Klipp (BMC Bioinform., 2008)

Systems Biology - a Textbook. - Edda Klipp; Wolfram Liebermeister; Christoph K. Wierling; Axel Kowald; Hans Lehrach (Wiley, 2009)

Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. - Roberta Alfieri; Matteo Barberis; Ferdinando Chiaradonna; Daniela Gaglio; Luciano Milanesi; Marco Vanoni; Edda Klipp; Lilia Alberghina (BMC Bioinform., 2009)

TIde: a software for the systematic scanning of drug targets in kinetic network models. - Marvin Schulz; Barbara M. Bakker; Edda Klipp (BMC Bioinform., 2009)

Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. - Clemens Kühn; Christoph K. Wierling; Alexander Kühn; Edda Klipp; Georgia Panopoulou; Hans Lehrach; Albert J. Poustka (BMC Syst. Biol., 2009)

Annotation and merging of SBML models with semanticSBML. - Falko Krause; Jannis Uhlendorf; Timo Lubitz; Marvin Schulz; Edda Klipp; Wolfram Liebermeister (Bioinform., 2010)

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation. - Wolfram Liebermeister; Jannis Uhlendorf; Edda Klipp (Bioinform., 2010)

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology. - Szymon Stoma; Martina Fröhlich; Susanne Gerber; Edda Klipp (BMC Bioinform., 2011)

Minimum Information About a Simulation Experiment (MIASE). - Dagmar Waltemath; Richard R. Adams; Daniel A. Beard; Frank T. Bergmann; Upinder S. Bhalla; Randall Britten; Vijayalakshmi Chelliah; Mike T. Cooling; Jonathan Cooper; Edmund J. Crampin; Alan Garny; Stefan Hoops; et al. (PLoS Comput. Biol., 2011)

Modeling mechanistic biological networks: An advanced Boolean approach. - Thomas Handorf; Edda Klipp (Bioinform., 2012)

Propagating semantic information in biochemical network models. - Marvin Schulz; Edda Klipp; Wolfram Liebermeister (BMC Bioinform., 2012)

Biographer: web-based editing and rendering of SBGN compliant biochemical networks. - Falko Krause; Marvin Schulz; Ben Ripkens; Max Flöttmann; Marcus Krantz; Edda Klipp; Thomas Handorf (Bioinform., 2013)

Reaction-contingency based bipartite Boolean modelling. - Max Flöttmann; Falko Krause; Edda Klipp; Marcus Krantz (BMC Syst. Biol., 2013)

Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress. - Elzbieta Petelenz-Kurdziel; Clemens Kühn; Bodil Nordlander; Dagmara Klein; Kuk-Ki Hong; Therese Jacobson; Peter Dahl; Jörg Schaber; Jens Nielsen; Stefan Hohmann; Edda Klipp (PLoS Comput. Biol., 2013)

BooleSim: an interactive Boolean network simulator. - Matthias Bock; Till Scharp; Chaitanya Talnikar; Edda Klipp (Bioinform., 2014)

SensA: web-based sensitivity analysis of SBML models. - Max Flöttmann; Jannis Uhlendorf; Till Scharp; Edda Klipp; Thomas W. Spiesser (Bioinform., 2014)

Global dynamic optimization approach to predict activation in metabolic pathways. - Gundián M. de Hijas-Liste; Edda Klipp; Eva Balsa-Canto; Julio R. Banga (BMC Syst. Biol., 2014)

Yeast Mating and Image-Based Quantification of Spatial Pattern Formation. - Christian Diener; Gabriele Schreiber; Wolfgang Giese; Gabriel del Rio; Andreas Schröder 001; Edda Klipp (PLoS Comput. Biol., 2014)

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. - Andreas Raue; Bernhard Steiert; Max Schelker; Clemens Kreutz; Tim Maiwald; Helge Hass; Joep Vanlier; Christian Tönsing; Lorenz Adlung; Raphael Engesser; Wolfgang Mader 002; Tim Heinemann; et al. (Bioinform., 2015)

Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks. - Tomoya Mori; Max Flöttmann; Marcus Krantz; Tatsuya Akutsu; Edda Klipp (BMC Syst. Biol., 2015)

Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer. - Thomas W. Spiesser; Clemens Kühn; Marcus Krantz; Edda Klipp (PLoS Comput. Biol., 2015)

SBtab: a flexible table format for data exchange in systems biology. - Timo Lubitz; Jens Hahn; Frank T. Bergmann; Elad Noor; Edda Klipp; Wolfram Liebermeister (Bioinform., 2016)

The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression. - Katarzyna M. Tyc; Sanna E. Herwald; Jennifer A. Hogan; Jessica V. Pierce; Edda Klipp; Carol A. Kumamoto (BMC Syst. Biol., 2016)

Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks. - Josch Pauling; Edda Klipp (J. Integr. Bioinform., 2016)

A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae. - Susanne Gerber; Martina Fröhlich; Hella Lichtenberg-Fraté; Sergey Shabala; Lana Shabala; Edda Klipp (PLoS Comput. Biol., 2016)

Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency. - Max Schelker; Caroline Maria Mair; Fabian Jolmes; Robert-William Welke; Edda Klipp; Andreas Herrmann; Max Flöttmann; Christian Sieben (PLoS Comput. Biol., 2016)

Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach. - Arturo Blazquez-Navarro; Thomas Schachtner; Ulrik Stervbo; Anett Sefrin; Maik Stein; Timm H. Westhoff; Petra Reinke; Edda Klipp; Nina Babel; Avidan U. Neumann; Michal Or-Guil (PLoS Comput. Biol., 2018)

Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction. - Wolfgang Giese; Gregor Milicic; Andreas Schröder 001; Edda Klipp (PLoS Comput. Biol., 2018)

Information Thermodynamics for Time Series of Signal-Response Models. - Andrea Auconi; Andrea Giansanti; Edda Klipp (Entropy, 2019)

Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality. - Stephan O. Adler; Edda Klipp (Entropy, 2020)

Moonlighting proteins - an approach to systematize the concept. - Maria Krantz; Edda Klipp (Silico Biol., 2020)

Sperm migration in the genital tract - In silico experiments identify key factors for reproductive success. - Jorin Diemer; Jens Hahn; Björn Goldenbogen; Karin Müller 005; Edda Klipp (PLoS Comput. Biol., 2021)

Identification of periodic attractors in Boolean networks using a priori information. - Ulrike Münzner; Tomoya Mori; Marcus Krantz; Edda Klipp; Tatsuya Akutsu (PLoS Comput. Biol., 2022)

kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models. - Willow Carretero Chavez; Marcus Krantz; Edda Klipp; Irina Kufareva (BMC Bioinform., 2023)