List of works by Edda Klipp

A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle

scientific article

A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae

scientific article

A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae

scientific article published on 21 March 2019

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

scientific article

A framework for mapping, visualisation and automatic model creation of signal-transduction networks

scientific article published on 24 April 2012

A low number of SIC1 mRNA molecules ensures a low noise level in cell cycle progression of budding yeast.

scientific article published on 30 June 2011

A model for the spatiotemporal organization of DNA replication in Saccharomyces cerevisiae.

scientific article published on 22 March 2009

A modelling approach to quantify dynamic crosstalk between the pheromone and the starvation pathway in baker's yeast.

scientific article published in August 2006

A quantitative study of the Hog1 MAPK response to fluctuating osmotic stress in Saccharomyces cerevisiae

scientific article

A stochastic model of epigenetic dynamics in somatic cell reprogramming

scientific article published on 27 June 2012

A systems biological analysis links ROS metabolism to mitochondrial protein quality control

scientific article published on 17 March 2012

A systems biology approach: modelling of Aquaporin-2 trafficking

scientific article published on January 2010

A theory of optimal differential gene expression.

scientific article published in August 2004

A transcriptome-wide analysis deciphers distinct roles of G1 cyclins in temporal organization of the yeast cell cycle

scientific article published on 04 March 2019

A variable fork rate affects timing of origin firing and S phase dynamics in Saccharomyces cerevisiae

scientific article published on 9 July 2013

Acclimation in plants - the Green Hub consortium

scientific article published on 23 December 2020

Alteration of protein levels during influenza virus H1N1 infection in host cells: a proteomic survey of host and virus reveals differential dynamics

scientific article (publication date: 2014)

Alterations of mTOR signaling impact metabolic stress resistance in colorectal carcinomas with BRAF and KRAS mutations.

scientific article

Alternative pathways as mechanism for the negative effects associated with overexpression of superoxide dismutase.

scientific article published on 8 August 2005

Alternative pathways might mediate toxicity of high concentrations of superoxide dismutase.

scientific article published in June 2004

An Antimicrobial Peptide Induces FIG1-Dependent Cell Death During Cell Cycle Arrest in Yeast.

scientific article

Annotation and merging of SBML models with semanticSBML

scientific article

Assessing the advantage of morphological changes in Candida albicans: a game theoretical study

scientific article published on 6 February 2014

Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway

scientific article

Automated generation of bacterial resource allocation models

scientific article published on 09 June 2019

Automatically generated model of a metabolic network.

scientific article published in January 2007

Biochemical network models simplified by balanced truncation.

scientific article published in August 2005

Biochemical network-based drug-target prediction.

scientific article published on 14 June 2010

Biochemical networks with uncertain parameters.

scientific article published in September 2005

Biographer: web-based editing and rendering of SBGN compliant biochemical networks

scientific article

Biophysical properties of Saccharomyces cerevisiae and their relationship with HOG pathway activation

scientific article

BooleSim: an interactive Boolean network simulator

scientific article

Bridging the gaps in systems biology

scientific article published on 13 April 2014

Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

scientific article published on 15 December 2006

Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data

scientific article

Bud-Localization of CLB2 mRNA Can Constitute a Growth Rate Dependent Daughter Sizer

scientific article published on 24 April 2015

Causal influence in linear Langevin networks without feedback ⬇️

scientific article published on 18 April 2017

Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin

scientific article

Cell size at S phase initiation: an emergent property of the G1/S network

scientific article

Cell-to-Cell Communication Circuits: Quantitative Analysis of Synthetic Logic Gates

scientific article published on 25 July 2012

Cellular signaling is potentially regulated by cell density in receptor trafficking networks.

scientific article published on 31 August 2007

Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality

scientific article published on 18 January 2020

Competition for enzymes in metabolic pathways: implications for optimal distributions of enzyme concentrations and for the distribution of flux control.

scientific article published in December 1999

Comprehensive mathematical model of oxidative phosphorylation valid for physiological and pathological conditions.

scientific article published on 24 June 2017

Computational Lipidomics and Lipid Bioinformatics: Filling In the Blanks

scientific article

Computational Modeling of Lipid Metabolism in Yeast

scientific article published on 27 September 2016

Computational yeast systems biology: a case study for the MAP kinase cascade.

scientific article published in January 2011

Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

scientific article

Constitutively active RAS inS. pombecauses persistent Cdc42 signalling but only transient MAPK activation

Constraint-based modeling and kinetic analysis of the Smad dependent TGF-beta signaling pathway

scientific article

Control analysis of unbranched enzymatic chains in states of maximal activity.

scientific article

Data integration strategies for whole-cell modeling

scientific article published in 2024

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems

scientific article

Different groups of metabolic genes cluster around early and late firing origins of replication in budding yeast.

scientific article published on January 2010

Differential T cell response against BK virus regulatory and structural antigens: A viral dynamics modelling approach.

scientific article

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling

scientific article published on January 2013

Dosage and Dose Schedule Screening of Drug Combinations in Agent-Based Models Reveals Hidden Synergies

scientific article published on January 2015

Drug-efficacy depends on the inhibitor type and the target position in a metabolic network--a systematic study.

scientific article published on 26 September 2007

Dynamic metabolic models in context: biomass backtracking

scientific article

Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress

scientific article

Dynamics of cell wall elasticity pattern shapes the cell during yeast mating morphogenesis

scientific article (publication date: September 2016)

Erratum: Corrigendum: Integrative model of the response of yeast to osmotic shock

scholarly article published in Nature Biotechnology

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data

scientific article

Evolutionary optimization of enzyme kinetic parameters; effect of constraints.

scientific article published in December 1994

Exploratory simulation of cell ageing using hierarchical models

scientific article published on January 2008

Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis.

scientific article published in January 2008

Exploring the impact of osmoadaptation on glycolysis using time-varying response-coefficients.

scientific article published in January 2008

Finding kinetic parameters using text mining.

scientific article published in January 2004

Fkh1 and Fkh2 associate with Sir2 to control CLB2 transcription under normal and oxidative stress conditions

scientific article published on 12 July 2013

Formal representation of the high osmolarity glycerol pathway in yeast

scientific article published in January 2010

Fungal Hsp90: a biological transistor that tunes cellular outputs to thermal inputs

scientific article published on October 2012

G1 and G2 arrests in response to osmotic shock are robust properties of the budding yeast cell cycle

scientific article

General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks.

scientific article published on 20 January 2018

Geospatially Referenced Demographic Agent-Based Modeling of SARS-CoV-2-Infection (COVID-19) Dynamics and Mitigation Effects in a Real-world Community

scientific article published on 06 May 2020

Global dynamic optimization approach to predict activation in metabolic pathways

scientific article

Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism

scientific article published in March 2012

Glucose de-repression by yeast AMP-activated protein kinase SNF1 is controlled via at least two independent steps

scientific article published on 4 March 2014

Graphical analysis and experimental evaluation of Saccharomyces cerevisiae PTRK1|2 and PBMH1|2 promoter region.

scientific article published in January 2010

Identification of 2-[4-[(4-Methoxyphenyl)methoxy]-phenyl]acetonitrile and Derivatives as Potent Oct3/4 Inducers

scientific article published on 7 May 2015

Identification of periodic attractors in Boolean networks using a priori information

scientific article published on 14 January 2022

Identification of small non-coding RNAs responsive to GUN1 and GUN5 related retrograde signals in Arabidopsis thaliana

scientific article published on 08 July 2020

Impact of acute metal stress in Saccharomyces cerevisiae

scientific article (publication date: 2014)

Inferring dynamic properties of biochemical reaction networks from structural knowledge.

scientific article published in January 2004

Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models.

scientific article published on 24 November 2015

Influenza A matrix protein M1 multimerizes upon binding to lipid membranes

scientific article published on August 2014

Information Thermodynamics for Time Series of Signal-Response Models

scientific article published on 14 February 2019

Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system

scientific article published on 19 April 2014

Information theory based approaches to cellular signaling

scientific article published on 23 July 2011

Insights into the network controlling the G1/S transition in budding yeast

scientific article published in January 2007

Integrative model of the response of yeast to osmotic shock

scientific article published on 17 July 2005

Interaction Dynamics Determine Signaling and Output Pathway Responses.

scientific article

Kinetic modelling of DNA replication initiation in budding yeast.

scientific article published in January 2010

Loss of hepatic Mboat7 leads to liver fibrosis

scientific article published on 26 June 2020

MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 March 2020

Mathematical modeling of intracellular signaling pathways ⬇️

scientific article

Mathematical models of mitochondrial aging and dynamics

scientific article

Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Micro- and nano-tubules built from loosely and tightly rolled up thin sheets

scientific article published on 14 December 2015

Minimum Information About a Simulation Experiment (MIASE)

scientific article

Minimum information requested in the annotation of biochemical models (MIRIAM)

scientific article

Model-based inference of biochemical parameters and dynamic properties of microbial signal transduction networks ⬇️

scientific article published on October 20, 2010

ModelMage: a tool for automatic model generation, selection and management

scientific article published in January 2008

Modeling development: spikes of the sea urchin

scientific article published in January 2007

Modeling mechanistic biological networks: an advanced Boolean approach

scientific article published on 22 December 2011

Modelling dynamic processes in yeast.

scientific article published in November 2007

Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast

scientific article published on January 2012

Modelling the dynamics of the yeast pheromone pathway.

scientific article published in July 2004

Modelling the regulation of thermal adaptation in Candida albicans, a major fungal pathogen of humans

scientific article published on 20 March 2012

Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation

scientific article

Molecular insights into reprogramming-initiation events mediated by the OSKM gene regulatory network

scientific article

Monitoring cytochrome P450 activity in living hepatocytes by chromogenic substrates in response to drug treatment or during cell maturation.

scientific article

Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network

scientific article published on 23 August 2009

Moonlighting proteins - an approach to systematize the concept

scientific article published on 23 November 2019

Nested uncertainties in biochemical models

scientific article published on January 2009

Network reconstruction and validation of the Snf1/AMPK pathway in baker's yeast based on a comprehensive literature review

scientific article

Network-based selectivity of antiparasitic inhibitors

scientific article published on 01 January 2002

New types of experimental data shape the use of enzyme kinetics for dynamic network modeling

scientific article

Onset of immune senescence defined by unbiased pyrosequencing of human immunoglobulin mRNA repertoires

scientific article

Osmolyte homeostasis controls single-cell growth rate and maximum cell size of Saccharomyces cerevisiae

scientific article published on 26 September 2019

Parameter balancing in kinetic models of cell metabolism

scientific article

Phosphoproteomic analyses reveal novel cross-modulation mechanisms between two signaling pathways in yeast

scientific article

Prediction of enzyme kinetic parameters based on statistical learning.

scientific article published in January 2006

Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities.

scientific article published in November 2002

Propagating semantic information in biochemical network models

scientific article

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing

scientific article published on 01 April 2020

Quantitative analysis of glycerol accumulation, glycolysis and growth under hyper osmotic stress

scientific article

Quantitative analysis of transient and sustained transforming growth factor-β signaling dynamics.

scientific article

Reaction-contingency based bipartite Boolean modelling

scientific article

Replication origins and timing of temporal replication in budding yeast: how to solve the conundrum?

scientific article published on May 2010

Retrieval, alignment, and clustering of computational models based on semantic annotations

scientific article published on 19 July 2011

Robustness and fragility in the yeast high osmolarity glycerol (HOG) signal-transduction pathway

scientific article published on 16 June 2009

Role of M1 Self-Organization in Influenza Virus Assembly: A Combined Rics and AFM Study

Role of gB and pUS3 in Equine Herpesvirus 1 Transfer between Peripheral Blood Mononuclear Cells and Endothelial Cells: a Dynamic In Vitro Model

scientific article

SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

scientific article published on 22 August 2006

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool

scientific article

SBMLmerge, a system for combining biochemical network models.

scientific article published on January 2006

SBtab: a flexible table format for data exchange in systems biology

scientific article

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology

scientific article

Selective benefits of damage partitioning in unicellular systems and its effects on aging

scholarly article

SensA: web-based sensitivity analysis of SBML models

scientific article published on 5 June 2014

Short-term volume and turgor regulation in yeast

scientific article published on January 2008

Shutting the MAP Off - and On Again?

Sic1 plays a role in timing and oscillatory behaviour of B-type cyclins.

scientific article published on 18 September 2011

Signal integration in budding yeast

scientific article published on October 2010

Signaling pathways in context

scientific article published on 08 April 2019

Size homeostasis can be intrinsic to growing cell populations and explained without size sensing or signalling

scientific article published on 22 October 2012

Spatial modeling of the membrane-cytosolic interface in protein kinase signal transduction.

scientific article published on 9 April 2018

Sperm migration in the genital tract—In silico experiments identify key factors for reproductive success

scientific article published on 15 July 2021

Steady state analysis of signal response in receptor trafficking networks.

scientific article published in January 2007

Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks

scientific article published on 11 August 2015

Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology

Superoxide production by cytochrome bc1 complex: a mathematical model

scientific article published on 7 June 2014

Systematic construction of kinetic models from genome-scale metabolic networks

scientific article

Systems Level Analysis of the Yeast Osmo-Stat

scientific article published on 12 August 2016

Systems biology standards—the community speaks

TIde: a software for the systematic scanning of drug targets in kinetic network models

scientific article

The MYpop toolbox: Putting yeast stress responses in cellular context on single cell and population scales

scientific article published on 8 March 2016

The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression

scientific article published on March 2016

Theoretical approaches to the evolutionary optimization of glycolysis: thermodynamic and kinetic constraints.

scientific article published in January 1997

Time-dependent quantitative multicomponent control of the G₁-S network by the stress-activated protein kinase Hog1 upon osmostress

scientific article published in September 2011

Timing matters

scientific article published on December 2009

Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation

scientific article

Transcriptional timing and noise of yeast cell cycle regulators-a single cell and single molecule approach.

scientific article published on 21 May 2018

Triple-negative breast cancer: present challenges and new perspectives

scientific article published on 24 April 2010

Unraveling interactions of cell cycle-regulating proteins Sic1 and B-type cyclins in living yeast cells: a FLIM-FRET approach

scientific article

Using Confocal Microscopy and Computational Modeling to Investigate the Cell-Penetrating Properties of Antimicrobial Peptides

scientific article published in January 2017

Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency

scientific article

What influences DNA replication rate in budding yeast?

scientific article

Yeast mating and image-based quantification of spatial pattern formation

scientific article

Zooming in on yeast osmoadaptation

scientific article published on January 2012

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