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List of works by Olaf Wolkenhauer

(Epi)genetic Inheritance in Schistosoma mansoni: A Systems Approach

scientific article published on 28 December 2016

2-DE profiling of GDNF overexpression-related proteome changes in differentiating ST14A rat progenitor cells

scientific article published in January 2007

A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples

scientific article published on 27 March 2020

A frequency-based gene selection method to identify robust biomarkers for radiation dose prediction

scientific article published in March 2012

A fully Bayesian model to cluster gene-expression profiles

scientific article published in September 2005

A hybrid systems framework for cellular processes

scientific article published on 15 January 2005

A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in Saccharomyces cerevisiae

scientific article

A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks

scientific article published on 31 August 2010

A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis

scientific article published on 9 July 2009

A shift in the dominant phenotype governs the pH-induced metabolic switch of Clostridium acetobutylicumin phosphate-limited continuous cultures

scientific article published on 3 May 2013

A stem cell niche dominance theorem

scientific article

A system biology approach to understand functional activity of cell communication systems

scientific article published in January 2008

A systematic survey of centrality measures for protein-protein interaction networks

A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture

scientific article (publication date: 19 January 2011)

A systems' biology approach to study microRNA-mediated gene regulatory networks

scientific article (publication date: 2013)

A systems- and signal-oriented approach to intracellular dynamics

article

A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data

scientific article

Accounting for randomness in measurement and sampling in studying cancer cell population dynamics

scientific article published in October 2014

Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis

scientific article

Age-dependent effects of UCP2 deficiency on experimental acute pancreatitis in mice

scientific article

All models are wrong

article

An abstract cell model that describes the self-organization of cell function in living systems

scientific article published on 20 January 2007

An algorithm to detect and communicate the differences in computational models describing biological systems

scientific article published on 21 October 2015

Analysing the impact of nucleo-cytoplasmic shuttling of β-catenin and its antagonists APC, Axin and GSK3 on Wnt/β-catenin signalling

scientific article published on 17 July 2013

Analysis of DNA microarray data

scientific article

Analysis of cell adhesion during early stages of colon cancer based on an extended multi-valued logic approach

scientific article

Annotation-based feature extraction from sets of SBML models

scientific article published in 2015

Anti-inflammatory effects of reactive oxygen species - a multi-valued logical model validated by formal concept analysis

scientific article

Approximations and their consequences for dynamic modelling of signal transduction pathways

scientific article published on 24 August 2006

Association of RHAMM with E2F1 promotes tumour cell extravasation by transcriptional up-regulation of fibronectin

scientific article

Autocrine TGF-β/ZEB/microRNA-200 signal transduction drives epithelial-mesenchymal transition: Kinetic models predict minimal drug dose to inhibit metastasis

scientific article

Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling

scientific article published on 19 November 2021

Baccoside A suppresses epileptic-like seizure/convulsion in Caenorhabditis elegans

COMODI: an ontology to characterise differences in versions of computational models in biology

scientific article published on 11 July 2016

Cardiac Cell Therapies for the Treatment of Acute Myocardial Infarction: A Meta-Analysis from Mouse Studies.

scientific article published on 25 May 2017

Cardiac Function Improvement and Bone Marrow Response -: Outcome Analysis of the Randomized PERFECT Phase III Clinical Trial of Intramyocardial CD133+ Application After Myocardial Infarction

scientific article published on 29 July 2017

Cardiomyocyte Transplantation after Myocardial Infarction Alters the Immune Response in the Heart

scientific article published on 03 August 2020

Chk1 and Wee1 control genotoxic-stress induced G2-M arrest in melanoma cells

scientific article

Clinico-pathologic function of cerebral ABC transporters - implications for the pathogenesis of Alzheimer's disease

scientific article published on August 2008

Clustering of unevenly sampled gene expression time-series data

article

Coenzyme A-transferase-independent butyrate re-assimilation in Clostridium acetobutylicum-evidence from a mathematical model

scientific article published on 23 August 2014

Combining computational models, semantic annotations and simulation experiments in a graph database

scientific article

Comprehensive functional enrichment analysis of male infertility

scientific article published on 17 November 2017

Computational analysis and modeling the effectiveness of 'Zanamivir' targeting neuraminidase protein in pandemic H1N1 strains

scientific article

Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs

scientific article published on 13 July 2012

Cooperative gene regulation by microRNA pairs and their identification using a computational workflow

scientific article published on 29 May 2014

Coordination of crosstalk between MAPK-PKC pathways: an exploratory study

scientific article published in January 2007

Cross-tissue transcriptome-wide association studies identify susceptibility genes shared between schizophrenia and inflammatory bowel disease

scientific article published on 20 January 2022

Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments

scientific article

Deciphering hallmark processes of aging from interaction networks

scientific article

Detection and Analysis of Critical Dynamic Properties of Oligodendrocyte Differentiation

scientific article published in 2022

Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB.

scientific article published in March 2006

Diagnostic Potential of Imaging Flow Cytometry.

scientific article published on 30 January 2018

Diagrams as locality aids for explanation and model construction in cell biology

article

Dissecting Long-Term Glucose Metabolism Identifies New Susceptibility Period for Metabolic Dysfunction in Aged Mice

scientific article published on 5 November 2015

Do simple models lead to generality in ecology?

scientific article published in July 2013

Drug Repositioning Inferred from E2F1-Coregulator Interactions Studies for the Prevention and Treatment of Metastatic Cancers

Dynamic energy budget approaches for modelling organismal ageing

scientific article

Dynamic properties of a delayed protein cross talk model

scientific article published on 18 July 2007

Dynamical effects of epigenetic silencing of 14-3-3sigma expression

scientific article

Dynamics of a miRNA Model with Two Delays

article

Dynamics of biological systems: role of systems biology in medical research

scientific article published on November 2006

Dynamics of receptor and protein transducer homodimerisation

scientific article published on 31 October 2008

E2F1 induces miR-224/452 expression to drive EMT through TXNIP downregulation

scientific article

Ein Beitrag zu einer Theorie lebender Zellen (A Contribution towards a Theory of Living Cells)

Enabling multiscale modeling in systems medicine

scientific article

Epigenetic factor EPC1 is a master regulator of DNA damage response by interacting with E2F1 to silence death and activate metastasis-related gene signatures

scientific article published on 8 September 2015

Evolution of computational models in BioModels Database and the Physiome Model Repository

scientific article published on 12 April 2018

Exploring the evolution of biochemical models at the network level

scientific article published on 21 March 2022

Family tree of Markov models in systems biology.

scientific article published on July 2007

Feedback dynamics and cell function: Why systems biology is called Systems Biology

scientific article published on 8 April 2005

From Networks to Systems to Complex Systems: A Signaling Pathway Coordination Case Study

Gene Expression in Low- and High-Dose-Irradiated Human Peripheral Blood Lymphocytes: Possible Applications for Biodosimetry

article

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

Harmonizing semantic annotations for computational models in biology

Hematopoietic stem-cell senescence and myocardial repair - Coronary artery disease genotype/phenotype analysis of post-MI myocardial regeneration response induced by CABG/CD133+ bone marrow hematopoietic stem cell treatment in RCT PERFECT Phase 3

scientific article published on 03 July 2020

How mathematical modelling elucidates signalling in Bacillus subtilis

scientific article published on September 2010

How quantitative measures unravel design principles in multi-stage phosphorylation cascades

article by Simone Frey et al published September 2008 in Journal of Theoretical Biology

Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic

scientific article published on 18 May 2013

Identification of antineoplastic targets with systems approaches, using resveratrol as an in-depth case study

scientific article published on 10 July 2017

Identification of immunogenic consensus T-cell epitopes in globally distributed influenza-A H1N1 neuraminidase

scientific article published in 2011

Identifying frequent patterns in biochemical reaction networks - a workflow

Identifying frequent patterns in biochemical reaction networks - a workflow

Identifying frequent patterns in biochemical reaction networks - a workflow

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide

scientific article published on 3 February 2018

Improving the reuse of computational models through version control

scientific article published on 18 January 2013

Inbred mouse strains reveal biomarkers that are pro-longevity, antilongevity or role switching

scientific article

Information-theoretic analysis of protein sequences shows that amino acids self-cluster

scientific article published on 01 October 2002

Insights into erlotinib action in pancreatic cancer cells using a combined experimental and mathematical approach

scientific article

Integration in action

scientific article published on 17 August 2012

Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics

article

Integrative Cluster Analysis of Whole Hearts Reveals Proliferative Cardiomyocytes in Adult Mice

scientific article published on 06 May 2020

Integrative modelling of pH-dependent enzyme activity and transcriptomic regulation of the acetone-butanol-ethanol fermentation of Clostridium acetobutylicum in continuous culture

scientific article

Interpreting Rosen

scientific article published in January 2007

Intracellular delay limits cyclic changes in gene expression

scientific article published on 24 August 2006

Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models

scientific article published on 18 August 2010

Investigating the two-moment characterisation of subcellular biochemical networks

scientific article published on 3 June 2009

Investigations into the analysis and modeling of the TNF alpha-mediated NF-kappa B-signaling pathway

scientific article

Kinetic modeling-based detection of genetic signatures that provide chemoresistance via the E2F1-p73/DNp73-miR-205 network

scientific article published on 27 February 2013

Label-Free Identification of White Blood Cells Using Machine Learning

scientific article published on 13 May 2019

Label-Free Leukemia Monitoring by Computer Vision

scientific article published on 24 February 2020

Level sets and minimum volume sets of probability density functions

Mammalian γ2 AMPK regulates intrinsic heart rate

scientific article

Mathematical Modeling of the Influence of RKIP on the ERK Signaling Pathway

Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer's disease

scientific article

Mathematical modelling in the post-genome era: understanding genome expression and regulation--a system theoretic approach

scientific article published in February 2002

Mathematical modelling of interferon-gamma signalling in pancreatic stellate cells reflects and predicts the dynamics of STAT1 pathway activity

scientific article published on 23 September 2009

Mathematical modelling unravels regulatory mechanisms of interferon-γ-induced STAT1 serine-phosphorylation and MUC4 expression in pancreatic cancer cells

scientific article

Methods in In Silico Biology: Modeling Feedback Dynamics in Pathways

MicroRNA and Transcription Factor Gene Regulatory Network Analysis Reveals Key Regulatory Elements Associated with Prostate Cancer Progression

scientific article

MicroRNA-Regulated Networks: The Perfect Storm for Classical Molecular Biology, the Ideal Scenario for Systems Biology ⬇️

scientific article published on January 1, 2013

MicroRNA-mRNA interactions in colorectal cancer and their role in tumor progression

scientific article

Microarray data clustering based on temporal variation: FCV with TSD preclustering.

scientific article

Minimum Information About a Simulation Experiment (MIASE)

scientific article

Model-Based Phenotypic Signatures Governing the Dynamics of the Stem and Semi-differentiated Cell Populations in Dysplastic Colonic Crypts

scientific article published on 7 December 2017

Model-based investigation of the transcriptional activity of p53 and its feedback loop regulation via 14-3-3σ.

scientific article published in September 2011

Modeling and simulation of intracellular dynamics: choosing an appropriate framework

scientific article

Modeling miRNA Regulation in Cancer Signaling Systems: miR-34a Regulation of the p53/Sirt1 Signaling Module ⬇️

scientific article published on January 1, 2012

Modeling of cellular processes: methods, data, and requirements

scientific article

Modeling the Calvin-Benson cycle

scientific article

Modelling gene expression time-series with radial basis function neural networks

article

Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease

scientific article

Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps

scientific article published on 26 April 2022

Network-Assisted Disease Classification and Biomarker Discovery

scientific article published on January 2016

Non-coding RNA detection methods combined to improve usability, reproducibility and precision

scientific article

Nonlinear modelling of curvature by bi-linear metamodelling

Nucleo-cytoplasmic shuttling of APC can maximize β-catenin/TCF concentration

scientific article published on 23 March 2011

Objective assessment of stored blood quality by deep learning

scientific article published on 24 August 2020

Optimal sampling time selection for parameter estimation in dynamic pathway modeling

scientific article published in July 2004

PLMaddon: a power-law module for the Matlab SBToolbox

scientific article published on 11 May 2007

Parameter identifiability and sensitivity analysis predict targets for enhancement of STAT1 activity in pancreatic cancer and stellate cells

scientific article

Pathway maps enable straightforward yet customized and semi-automated yet insightful analyses of omics data

Phosphoglycerate mutases function as reverse regulated isoenzymes in Synechococcus elongatus PCC 7942.

scientific article

Possibilistic Testing of Distribution Functions for Change Detection

Power-law models of signal transduction pathways

scientific article (publication date: July 2007)

Principal difference between stability and structural stability (robustness) as used in systems biology

scientific article published on October 2007

Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression

scientific article published on 09 November 2019

Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis

scientific article published on 17 April 2012

Pushing limits by embracing complexity

scientific article published on December 2014

Quantitative modelling of amyloidogenic processing and its influence by SORLA in Alzheimer's disease

scientific article

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.

scientific article published on 15 February 2018

RNA Systems Biology for Cancer: From Diagnosis to Therapy

scientific article published on January 2016

RNA-Based Strategies for Cardiac Reprogramming of Human Mesenchymal Stromal Cells

scientific article published on 22 February 2020

Random set system identification

Reduced adolescent-age spatial learning ability associated with elevated juvenile-age superoxide levels in complex I mouse mutants

scientific article

Reduction of nonlinear dynamic systems with an application to signal transduction pathways

scientific article published in January 2007

Regulation of cell cycle checkpoint kinase WEE1 by miR-195 in malignant melanoma

scientific article

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008)

scientific article

Reverse Engineering of Biochemical Reaction Networks Using Co-evolution with Eng-Genes

article

Role of inhibitory proteins as modulators of oscillations in NFB signalling

scientific article published in March 2009

SBML export interface for the systems biology toolbox for MATLAB.

scientific article published on 23 March 2007

Simulations of stressosome activation emphasize allosteric interactions between RsbR and RsbT.

scientific article

Single Nuclei Sequencing of entire Mammalian Hearts: Strain-dependent Cell Type Composition and Velocity

scientific article published on 03 April 2020

Single-Nucleus Sequencing of an Entire Mammalian Heart: Cell Type Composition and Velocity

scientific article published on 28 January 2020

Stochastic approaches in systems biology

scientific article published on July 2010

Studies on mechanisms of interferon-gamma action in pancreatic cancer using a data-driven and model-based approach

scientific article

Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model

scientific article published in 2024

Switching feedback mechanisms realize the dual role of MCIP in the regulation of calcineurin activity.

scientific article published on 5 October 2006

SysBioMed report: advancing systems biology for medical applications.

scientific article published on May 2009

System approaches of Weiss and Bertalanffy and their relevance for systems biology today

scientific article published on 14 May 2011

Systems approach to the study of brain damage in the very preterm newborn

scientific article

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs

scientific article

Systems biology and pediatric research

scientific article published in April 2013

Systems biology of JAK-STAT signalling in human malignancies

scientific article published on 06 July 2011

Systems biology to battle vascular disease

scientific article published on 03 February 2010

Systems medicine and integrated care to combat chronic noncommunicable diseases

scientific article

TGF-ß1 Induces Changes in the Energy Metabolism of White Adipose Tissue-Derived Human Adult Mesenchymal Stem/Stromal Cells In Vitro

scientific article published on 07 February 2020

TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation

scientific article

The Complexity of Cell-Biological Systems

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

scientific article published on 05 June 2017

The curse of normalization

scientific article published on January 2002

The dynamic systems approach to control and regulation of intracellular networks

scientific article

The multikinase inhibitor Sorafenib displays significant antiproliferative effects and induces apoptosis via caspase 3, 7 and PARP in B- and T-lymphoblastic cells

scientific article published on 15 October 2010

The road from systems biology to systems medicine

scientific article published on 11 January 2013

The role of dynamic stimulation pattern in the analysis of bistable intracellular networks

scientific article

The role of theorem proving in systems biology

scientific article published on 30 December 2011

The role of theory and modeling in medical research

scientific article published on 19 December 2013

The search for organizing principles as a cure against reductionism in systems medicine ⬇️

scientific article published on May 24, 2013

The statistical distribution of the intensity of pixels within spots of DNA microarrays: what is the appropriate single-value representative?

scientific article published in January 2003

The systems biology of mitochondrial fission and fusion and implications for disease and aging

scientific article published on February 2014

The timing of contact restrictions and pro-active testing balances the socio-economic impact of a lockdown with the control of infections

scientific article published on 13 May 2020

Thresholds in transient dynamics of signal transduction pathways

scientific article published on 6 February 2010

Tools for Understanding miRNA-mRNA Interactions for Reproducible RNA Analysis

scientific article published on 01 January 2019

Tracing organizing principles: learning from the history of systems biology

scientific article

Tumors as chaotic attractors

scientific article published in February 2014

Unveiling network-based functional features through integration of gene expression into protein networks

scientific article published on 18 February 2018

Web resources for microRNA research

scientific article published on January 2013

Whither systems medicine?

scientific article published on 2 March 2018

Why model?

scientific article published on 28 January 2014

Workflow Development for the Functional Characterization of ncRNAs

article

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