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Systems Biology in Practice: Concepts, Implementation and Application

1. Aufl., 2008

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

Nature communications, 2019-03, Vol.10 (1), p.1308-1308, Article 1308

2019

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

Nature communications, 2017-12, Vol.8 (1), p.2032-12, Article 2032

2017

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Information theory based approaches to cellular signaling

Biochimica et biophysica acta, 2011-10, Vol.1810 (10), p.924-932

2011

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kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models

BMC bioinformatics, 2023-06, Vol.24 (1), p.246-246, Article 246

2023

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Identification of periodic attractors in Boolean networks using a priori information

PLoS computational biology, 2022-01, Vol.18 (1), p.e1009702-e1009702

2022

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

Bioinformatics, 2010-06, Vol.26 (12), p.1528-1534

2010

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

PLoS computational biology, 2021-07, Vol.17 (7), p.e1009109-e1009109

2021

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Modeling indicates degradation of mRNA and protein as a potential regulation mechanisms during cold acclimation

Journal of plant research, 2021-07, Vol.134 (4), p.873-883

2021

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Deep Hidden Physics Modeling of Cell Signaling Networks

Current genomics, 2021-12, Vol.22 (4), p.239-243

2021

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

PLoS computational biology, 2018-04, Vol.14 (4), p.e1006075-e1006075

2018

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Systematic construction of kinetic models from genome-scale metabolic networks

PloS one, 2013-11, Vol.8 (11), p.e79195-e79195

2013

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Integrative model of the response of yeast to osmotic shock

Nature biotechnology, 2005-08, Vol.23 (8), p.975-982

2005

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

PloS one, 2007-09, Vol.2 (9), p.e936-e936

2007

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

Theoretical biology and medical modelling, 2006-12, Vol.3 (1), p.41-41, Article 41

2006

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Mathematical modeling of intracellular signaling pathways

BMC neuroscience, 2006-10, Vol.7 Suppl 1 (Suppl 1), p.S10-S10, Article S10

2006

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Nonalcoholic fatty liver disease stratification by liver lipidomics

Journal of lipid research, 2021-01, Vol.62, p.100104-100104, Article 100104

2021

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Impact of acute metal stress in Saccharomyces cerevisiae

PloS one, 2014-01, Vol.9 (1), p.e83330

2014

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Information Thermodynamics for Time Series of Signal-Response Models

Entropy (Basel, Switzerland), 2019-02, Vol.21 (2), p.177

2019

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A dynamical stochastic model of yeast translation across the cell cycle

Heliyon, 2023-02, Vol.9 (2), p.e13101-e13101, Article e13101

2023

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Quantitative Study of the Hog1 MAPK Response to Fluctuating Osmotic Stress in Saccharomyces cerevisiae

PloS one, 2010-03, Vol.5 (3), p.e9522-e9522

2010

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

Scientific reports, 2019-03, Vol.9 (1), p.3343-3343, Article 3343

2019

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

Physical biology, 2015-11, Vol.12 (6), p.066014-066014

2015

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Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality

Entropy (Basel, Switzerland), 2020-01, Vol.22 (1), p.117

2020

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Systems Biology in Practice: Concepts, Implementation and Application

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

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

Information theory based approaches to cellular signaling

kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models

Identification of periodic attractors in Boolean networks using a priori information

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

Loss of hepatic Mboat7 leads to liver fibrosis

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

Modeling indicates degradation of mRNA and protein as a potential regulation mechanisms during cold acclimation

Deep Hidden Physics Modeling of Cell Signaling Networks

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

Systematic construction of kinetic models from genome-scale metabolic networks

Integrative model of the response of yeast to osmotic shock

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

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

Mathematical modeling of intracellular signaling pathways

Nonalcoholic fatty liver disease stratification by liver lipidomics

Impact of acute metal stress in Saccharomyces cerevisiae

Information Thermodynamics for Time Series of Signal-Response Models

A dynamical stochastic model of yeast translation across the cell cycle

Quantitative Study of the Hog1 MAPK Response to Fluctuating Osmotic Stress in Saccharomyces cerevisiae

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

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

Chemical Reaction Networks Possess Intrinsic, Temperature-Dependent Functionality

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