Journals

Journals

2018

Harmonizing semantic annotations for computational models in biology

Neal M, Dräger A, Wolkenhauer O et al.

Brief Bioinform. (Epub ahead of print)

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

Ashtiani M, Salehzadeh-Yazdi A, Razaghi-Moghadam Z, Hennig H, Wolkenhauer O, Mirzaie M and Jafari M

BMC Systems Biology 12:80 (2018)
 

Community-driven data analysis training for biology

Batut B, Hiltemann S, Bagnacani A, …, Wolfien M, ..., Gruening B

Cell Systems

Identifying Frequent Patterns in Biochemical Reaction Networks - a Workflow

Lambusch F, Waltemath D, Wolkenhauer O, Sandkuhl K, Rosenke C, Henkel R

Database, Volume 2018

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

Scharm M, Gebhardt T, Touré V, Bagnacani A, Salehzadeh-Yazdi A, Wolkenhauer O, Waltemath D

BMC Systems Biology 12:53 (2018)

On extension of regular graphs

Banerjee A, Bej S

Whither Systems Medicine?

Apweiler R, Beissbarth T, Berthold MR, ... , Theis FJ, Vera J, Wolkenhauer O

Experimental & Molecular Medicine

A web platform for the network analysis of highthroughput data in melanoma and its use to investigate mechanisms of resistance to anti-PD1 immunotherapy

Dreyer FS, Cantone M, Eberhardt M, Jaitly T,Walter L, Wittmann J, Gupta SK , Khan FM, Wolkenhauer O, Pützer BM, Jäck HM, Heinzerling L, Vera J

Biochimica et Biophysica Acta;2018 Feb 23. pii: S0925-4439(18)30031-0.

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

Jalilia M, Gebhardt T, Wolkenhauer O, Salehzadeh-Yazdi A

Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease

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

Touré V, Le Novère N, Waltemath D, Wolkenhauer O

Plos Computational Biology

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

Singh KP, Baweja L, Wolkenhauer O, Rahman Q, Gupta SK

J Comput Aided Mol Des. 2018;32(3):487-496.

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

Nikolov S, Santos G, Wolkenhauer O, Vera J

Bulletin of Mathematical Biology

Diagnostic potential of imaging flow cytometry

Doan M, Vorobjev I, Rees P, Filby A, Wolkenhauer O, Goldfeld AE, Lieberman J, Barteneva N, Carpenter AE, Hennig H

Trends in Biotechnology

Interaction of anthraquinones of Cassia occidentalis seeds with DNA and Glutathione.

Panigrahi GK, Verma N, Singh N, Asthana S, Gupta SK, Tripathi A, Das M

Toxicol Rep. 2018;5:164-172.

MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance.

Lai X, Gupta SK, Schmitz U, Marquardt S, Knoll S, Spitschak A, Wolkenhauer O, Pützer BM, Vera J

Theranostics. 2018 Jan 1;8(4):1106-1120.

2017

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

Möller S, ..., Bagnacani A, ..., Crusoe MR

Springer Data Science and Engineering

Comprehensive functional enrichment analysis of male infertility

Razavi SM, Sabbaghian M, Jalili M, Divsalar A, Wolkenhauer O, Salehzadeh-Yazdi A

Nature Scientific Reports

Mammalian γ2 AMPK regulates intrinsic heart rate

Yavari A, ..., Wolfien M, ..., Wolkenhauer O, ..., Ashrafian H

Nature Communications

Identification of Antineoplastic Targets with Systems Approaches, Using Resveratrol as an In-Depth Case Study.

Singh N, Freiesleben S, Wolkenhauer O, Shukla Y, Gupta SK

Curr Pharm Des. 2017;23(32):4773-4793.

Stem cells and heart disease - brake or accelerator?

Steinhoff G, Nesteruk J, Wolfien M, Große J, Ruch U, Vasudevan P, Müller P

Advanced Drug Delivery Reviews

(Re-)Programming of Subtype Specific Cardiomyocytes

Hausburg F, Jung JJ, Hoch M, Wolfien M, Yavari A, Rimmbach C, David R

Advanced Drug Delivery Reviews

Data analysis strategies for image-based cell profiling

Caicedo J,…, Hennig H,…, Carpenter AE

Nature Methods 14, 849 (2017)

Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures

Khan FM, Marquardt S, Gupta SK,Knoll S, Schmitz U,Spitschak A, Engelmann D, Vera J, Wolkenhauer O & Pützer BM

Nature Communications

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

Steinhoff G, Nesteruk J, Wolfien M, ... , Hennig H, ... , Wolkenhauer O

EBioMedicine 22, 208-224 (2017)

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

Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR

Journal of Biotechnology

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

Gruening BA, ..., Bagnacani A, Wolfien M, ..., Wolkenhauer O, ..., Backofen R

Nucleic Acids Research

Coloring sums of extensions of certain graphs

Kok J, Bej S

An open-source solution for advanced imaging flow cytometry data analysis using machine learning

Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter A E, Filby A

Methods 112, 201 (2017)

SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

Bergmann FT, Nickerson D, Waltemath D, Scharm M

Oxford Bioinformatics 33:8, pp. 1253–1254 (2017)

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

Winter F, Bludszuweit-Philipp C, Wolkenhauer O

Journal of Cerebral Blood Flow & Metabolism

Cardiac cell therapies for the treatment of acute myocardial infarction: A Meta-Analysis from mouse studies

Lang C, Wolfien M, Langenbach A, Müller P, Wolkenhauer O, Yavari A, Ince H, Steinhoff G, Krause B, David R, Glass Ä

Cellular Physiology and Biochemistry

Aryl Hydrocarbon Receptor Activation Contributes to Benzanthrone-Induced Hyperpigmentation via Modulation of Melanogenic Signaling Pathways.

Abbas S, Alam S, Singh KP, Kumar M, Gupta SK, Ansari KM.

Chem Res Toxicol. 2017 Feb 20;30(2):625-634.

Factors of edge-chromatic critical graphs: a brief survey and some equivalences

Bej S, Steffen E

Meta-Analysis of Gene Expression Profiles in Acute Promyelocytic Leukemia Reveals Involved Pathways

Jalili M, Salehzadeh-Yazdi A, Mohammadi S, Yaghmaie M, Ghavamzadeh A, Alimoghaddam K

International Journal of Hematology Oncology and Stem Cell Research

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

Cosseau C, Wolkenhauer O, Padalino G, Geyer KK, Hoffmann KF, Gruna C

Trends in Parasitology

2016

Notions of similarity for computational biology models

D Waltemath, R Henkel, R Hoehndorf, T Kacprowski, C Knuepfer, W Liebermeister

Open Access article in Briefings in Bioinformatics (2016) bbw090

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

F Schreiber, GD Bader, P Gleeson, M Golebiewski, M Hucka, N Le Novere, C Myers, D Nickerson, B Sommer, D Waltemath

Open Access article in J Integrative Bioinformatics 2016 13(3)

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

Sadeghi M, Ranjbar B, Ganjalikhany MR, Khan FM, Schmitz U, Wolkenhauer O, Gupta SK

PLoS One. 2016 Dec 22;11(12):e0168760.

STON: exploring biological pathways using the SBGN standard and graph databases

Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C

Open Access article in BMC Bioinformatics 2016, 17:494

Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms

Sherry Freiesleben, Michael Hecker, Uwe Klaus Zettl, Georg Fuellen, Leila Tahera

Scientific Reports (2016) 6: 34512

Deciphering hallmark processes of aging from interaction networks

Smita S, Lange F, Wolkenhauer O, Köhling R

Biochim Biophys Acta. 2016; S0304-4165(16)30264-1.

Evolution of centrality measurements for the detection of essential proteins in biological networks

Mahdi Jalili, Ali Salehzadeh-Yazdi, Shailendra Gupta, Olaf Wolkenhauer, Marjan Yaghmaie, Osbaldo Resendis-Antonio and Kamran Alimoghaddam (2016)

Frontiers in Physiology

Cancerome: A hidden informative subnetwork of the diseasome

Mahdi Jalili, Ali Salehzadeh-Yazdi, Marjan Yaghmaie, Ardeshir Ghavamzadeh, Kamran Alimoghaddam (2016)

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

Scharm M, Waltemath D, Mendes P, and Wolkenhauer O

Open Access article in the Journal of Biomedical Semantics 7:46 (2016)

Ambient UV-B exposure reduces the binding of ofloxacin with bacterial DNA gyrase and induces DNA damage mediated apoptosis

Singh J, Dwivedi A, Mujtaba SF, Singh KP, Pal MK, Chopra D, Goyal S, Srivastav AK, Dubey D, Gupta SK, Haldar C, Ray RS

The International Journal of Biochemistry and Cell Biology. 2016. pii: S1357-2725(16)30001-2.

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

Wang Y, Alla V, Goody D, Gupta SK, Spitschak A, Wolkenhauer O, Putzer B, Engelmann D

Nucleic Acids Research. 2016; 44(1):117-33.

Photoprotective efficiency of PLGA-curcumin nanoparticles versus curcumin through the involvement of ERK/AKT pathway under ambient UV-R exposure in HaCaT cell line

Chopra D, Ray L, Dwivedi A, Tiwari SK, Singh J, Singh KP, Kushwaha HN, Jahan S, Pandey A, Gupta SK, Chaturvedi RK, Pant AB, Ray RS, Gupta KC

Biomaterials. 2016; 84:25-41.

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

Ferdinand von Meyenn, Mario Iurlaro, Ehsan Habibi, Ning Qing Liu, Ali Salehzadeh-Yazdi, Fa´tima Santos, Edoardo Petrini, Ineˆs Milagre, Miao Yu, Zhenqing Xie, Leonie I. Kroeze, Tatyana B. Nesterova, Joop H. Jansen, Hehuang Xie (2016)

Molecular Cell

Toward community standards and software for whole-cell modeling

Waltemath D, Karr JT, Bergmann FT, Chelliah V ... Scharm M et al.

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 2007-14 (2016)

How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine

D Waltemath and O Wolkenhauer

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 1999-2006 (2016)

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

Katja Rateitschak, Lars Kaderali, Olaf Wolkenhauer, Robert Jaster (2016)

Cellular Signalling

The Cardiac Electrophysiology Web Lab

Cooper J, Scharm M, and Mirams GR

Open Access article in the Biophysical Journal 110:2, pp 292-300 (2016)

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

Scharm M, Wolkenhauer O, and Waltemath D

Open Access article in BIOINFORMATICS 32:4, pp. 563-570 (2015)

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

Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stephan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer (2016)

BMC Bioinformatics

Label-free cell cycle analysis for high-throughput imaging flow cytometry

Blasi T, Hennig H, Summers HD, Theis FJ, Davies D, Filby A, Carpenter AE, Rees P

Nature Communications 7, 10256 (2016)

2015

Personalized cancer immunotherapy using systems medicine approaches.

Gupta SK, Jaitly T, Schmitz U, Schuler G, Wolkenhauer O, Vera J

Briefings in Bioinformatics 2015.

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

A. Chauhan, H. Weiss, F. Koch, S.M. Ibrahim, J. Vera, O. Wolkenhauer, M. Tiedge (2015)

PLOS One

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

M Hucka, FT Bergmann, A Dräger, ... D Waltemath, DJ Wilkinson

Open Access article in J Integrative Bioinformatics 12:2 (2015)

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2

FT Bergmann, J Cooper, N Le Novere, D Nickerson, D Waltemath

Open Access article in J Integrative Bioinformatics 12:2 (2015)

Specifications of Standards in Systems and Synthetic Biology

F Schreiber, GD Bader, M Golebiewski, ... D Waltemath, S Weise

Open Access article in J Integrative Bioinformatics 12:2, p. 258 (2015)

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

R Henkel, O Wolkenhauer, D Waltemath

Open Access article in DATABASE bau130 (2015)

The RNA world in the 21st century – a systems approach to finding non-coding keys to clinical questions

Schmitz U, NAderi-Meshkin H, Gupta SK, Wolkenhauer O, Vera J

Briefings in Bioinformatics 2015.

Naïve Bayes classifier predicts functional microRNA target interactions in colorectal cancer

Raheleh A, Schmitz U, Farazmand A, Gupta SK, Ahmadi H, Wolkenhauer O

Molecular BioSystems 2015; 11(8): 2126-34.

Annotation-Based Feature Extraction from Sets of SBML Models

R Alm, D Waltemath, M Wolfien, O Wolkenhauer et al.

Open Access article in J Biomedical Semantics 6:20 (2015)

A mutation in the NADH-dehydrogenase subunit 2 suppresses fibroblast aging

Schauer M, Kottek T, Schönherr M, Bhattacharya A, Ibrahim SM, Hirose M, Köhling R, Fuellen G, Schmitz U, Kunz M

Oncogene, in press.

Systems Epidemiology: What's in a Name?

Dammann O, Gray P, Gressens P, Wolkenhauer O, Leviton A

Online J Public Health Inform. 2014, 6(3):e198

Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

M Hucka, DP Nickerson, G Bader, ... D Waltemath, N Le Novère

Article in Front. Bioeng. Biotechnol. 3:19 (2015)

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

Vera J, Raatz Y, Wolkenhauer O, Kottek T, Bhattacharaya A, Simon JC, Kunz M

Accepted for publication in Cellular Signalling (2015).

A call for virtual experiments: Accelerating the scientific process

J Cooper, JO Vik, D Waltemath

Article in Progress in Biophysics and Molecular Biology 117:1, pp. 99-106 (2014)

miR-638 promotes melanoma metastasis and protects melanoma cells from apoptosis and autophagy

Bhattacharya A, Schmitz U, Raatz Y, Schönherr M, Kottek T, Schauer M, Franz S, Saalbach A, Anderegg U, Wolkenhauer O, Schadendorf D, Simon JC, Magin T, Vera J, Kunz M

Accepted in Oncotarget.

2014

Pushing limits by embracing complexity

Wolkenhauer, O

IET Syst Biol. 2014 Dec, 8(6):244-250.

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

Amirkhah R, Schmitz U, Linnebacher M, Wolkenhauer O, Farazmand A

Genes, Chromosomes and Cancer, 54:129–141,

Understanding the mechanism of Atovaquone drug resistance in Plasmodium falciparum cytochrome b mutation Y268S using computational methods

Akhoon BA, Singh KP, Varshney M, Gupta SK, Shukla Y, Gupta SK

PLOS One 2014; 9(10):e110041

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

Knoll S, Fürst K, Kowtharapu B, Schmitz U, Marquardt S, Wolkenhauer O, Martin H, Pützer BM

EMBO reports, 15 (12), pp.1315-1329.

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

Wollbold J, Jaster R, Müller S, Rateitschak K, Wolkenhauer O

BMC Systems Biology, 8:101

Annotation-Based Feature Extraction from Sets of SBML Models

R Alm, D Waltemath, O Wolkenhauer, R Henkel

Article in Lecture notes in computer science 8574, pp 81-95 (2014)

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Bergmann FT, Adams R, ... Scharm M, ... Waltemath D et al.

Open Access article in BMC Bioinformatics 15:369 (2014)

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

Meier C, Spitschak A, Abshagen K, Gupta S, Mor JM, Wolkenhauer O, Haier J, Vollmar B, Alla V, Pützer BM

Journal of Pathology. 2014; 234(3):351-64.

Enabling multiscale modeling in systems medicine

Wolkenhauer O, Auffray C, Brass O, Clairambault J, Deutsch A, Drasdo D, Gervasio F, Preziosi L, et al.

Genome Medicine 2014, 6:21

Synchronization in human musical rhythms and mutually interacting complex systems

Hennig H

Proceedings of the National Academy of Sciences of the USA 111, 12974-12979 (2014)

Ethnicity-tailored novel set of ESAT-6 peptides for differentiating active and latent tuberculosis

Singh SB, Biswas D, Rawat J, Sindhwani G, Patras A, Devrani S, Sarkar P, Mitra S, Gupta SK

Tuberculosis, Volume 93, Issue 6, 618 - 624

Tracing organizing principles: Learning from the history of systems biology

Green S, Wolkenhauer O

History and Philosophy of the Life Sciences, 35 (4), 553 - 576

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

Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta S

Nucleic Acids Research 2014, 42 (12): 7539-7552,

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

D Waltemath, FT Bergmann, C Chaouiya et al.

Open Access article in Standards in Genomic Sciences 9:3 (2014)

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

Garcia-Salcedo R, Lubitz T, Beltran G, Elbing K, Tian Y, Frey S, Wolkenhauer O, Krantz M, Klipp E, Hohmann S

FEBS Journal Feb 15. 281(7): 1901 - 17, (Epub 2014 Mar 4)

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

Müller S, Kaiser, H; Krüger B, Fitzner B, Lange F, Bock CN, Nizze H, Ibrahim SM, Füllen G, Wolkenhauer O, Jaster R

PLOS ONE 9(4),

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

Ghavami S, Wolkenhauer O, Lahouti F, Ullah M, Linnebacher M

IET Systems Biology, 8(5):230-41.

Why model?

Wolkenhauer, O

Front. Physiol. 5:21.

2013

Tumors as chaotic attractors

Nikolov, S. and Wolkenhauer, O. and Vera, J.

Mol Biosyst. 10 (2):172 - 9

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

Chauhan, A. and Vera, J. and Wolkenhauer, O.

Biogerontology 15(1): 1 - 12

Systems biology and pediatric research

Minoo P, Wolkenhauer O, Guttentag S

Pediatric Res. 2013 Apr, 73(4 Pt 2):499-501,

The Role of theory and Modelling in Medical Research

Wolkenhauer, O.

Front. Pysiol. 4:377.

Ca2+/calmodulin-dependent kinase II contributes to inhibitor of nuclear factor-kappa B kinase complex activation in Helicobacter pylori infection.

Maubach G, O Sokolova, M Wolfien, HJ Rothkötter, M Naumann

Int J Cancer. Epub ahead of print 5 March 2013. IF: 5,444

A systems biology approach to study microRNA-mediated gene regulatory networks (2013)

Lai X, Bhattacharya A, Schmitz U, Kunz M, Vera J, Wolkenhauer O

BioMed Research International, vol. 2013,

Do simple models lead to generality in ecology?

Evans MR, Grimm V, Johst K, Knuuttila T, de Langhe R, Lessells CM, Merz M, O'Malley MA, Orzack SH, Weisberg M, Wilkinson DJ, Wolkenhauer O, Benton TG

Trends Ecol Evol. 2013 Oct; 28(10):578-83

Possibilities for Integrating Model-related Data in Computational Biology

D Waltemath, O Wolkenhauer, N Le Novère, M Dumontier

Proceedings of the 9th International Conference on Data Integration in the Life Sciences (2013)

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

Schmitz Y, Rateitschak K, Wolkenhauer O (2013)

Cellular Signalling, 2210:2221

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

Khan FM, Schmitz U, Nikolov S, Engelmann D, Pützer BM,Wolkenhauer O, Vera J

Biochim Biophys Acta; 1844 (1 Pt B): 289-98.

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

Wolkenhauer O, Green S (2013)

FEBS Journal, 280 (23): 5938-48.

An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers

Kossow C, Rybacki S, Millat T, Rateitschak K, Jaster R, Uhrmacher AM, Wolkenhauer O (2015)

Mathematical and Computer Modelling of Dynamical Systems.

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

Millat T, Janssen H, Bahl H, Fischer RJ, Wolkenhauer, O (2013)

Microbial Biotechnology 6 (5): 526 - 39

The Road from Systems Biology to Systems Medicine

Wolkenhauer O, Auffray C, Jaster R, Steinhoff G, Dammann O (2013)

Pediatric Research, 73:502-507

COSMIC - Systems biology of Clostridium acetobutylicim - A possible answer to dwindling crude oil reserves

Millat T, COSMIC consortium

9th International Conference on Systems Biology (ICSB), Gothenborg (Sweden), 23 August - 27 August 2008

Improving the reuse of computational models through version control

Waltemath D, Henkel R, Hälke R, Scharm M, and Wolkenhauer O

Article in BIOINFORMATICS 29:6, pp. 742-7 (2014)

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

Millat T, Janssen H, Thorn GJ, King JR, Bahl H, Fischer RJ, Wolkenhauer O (2013)

Applied Microbiology & Biotechnology 97: 6451-6466,

Spatio-temporal distribution changes and nucleo-cytoplasmic shuttling rates regulate differentiation in human neural progenitor cells

Bader BM, Schmitz Y, Kuznetsov SA, Weiss DG (2013)

submitted for publication

2012

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

Vera J, Schmitz U, Lai X, Engelmann D, Khan FM, Wolkenhauer O, Pützer BM (2013)

Cancer Research,

Simulations of Stressosome Activation Emphasize Allosteric Interactions Between RsbR and RsbT

Liebal UW, Millat T, Marles-Wright J, Lewis RJ, Wolkenhauer O (2013)

BMC Systems Biology 7:3

Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells

Rateitschak K, Winter F, Lange F, Jaster R, Wolkenhauer O (2012)

PLOS Computational Biology 8: e1002815

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

Jablonsky J, Hagemann M, Schwarz D, Wolkenhauer O (2013)

PLOS One,

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

Lange F, Rateitschak K, Kossow C, Wolkenhauer O, Jaster R (2012)

World Journal of Gastroenterology 18: 6226-6234

Integration in action

Green S, Wolkenhauer O (2012)

EMBO reports 13: 769-771

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

Jones N, Wolkenhauer O (2012)

Biology and Philosophy 27: 705-721

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

Bhattacharya A, Schmitz U, Wolkenhauer O, Schönherr M, Raatz Y, Kunz M (2012)

Oncogene,

Systems Biology and Bioinformatics in Aging Research: A Workshop Report

Fuellen G, Dengjel J, Hoeflich A, Hoeijmakers J, Kestler H, Kowald A, Priebe S, Rebholz-Schuhmann D, Schmeck B, Schmitz U, Stolzing A, Sühnel J, Wuttke D, Vera J (2012)

Rejuvenation Research, Vol 15, No 6,

E2F1 confers anticancer drug resistance by targeting ABC transporter family members and Bcl-2 via the p73/DNp73-miR-205 circuitry

Alla V, Kowtharapu BS, Engelmann D, Emmrich S, Schmitz U, Steder M, Pützer BM (2012)

Cell Cycle, 11:1

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

Lai X, Schmitz U, Gupta S, Bhattacharya A, Kunz M, Wolkenhauer O, Vera J (2012)

Nucleic Acids Research, 40: 8818-8834.

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

Kossow C, Jose D, Jaster R, Wolkenhauer O, Rateitschak K (2012)

IET System Biology 6: 73-85

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

Lao A, Schmidt V, Schmitz Y, Willnow T, Wolkenhauer O (2012)

BMC Systems Biology 6:74

Gene expression in low and high dose-irradiated human peripheral blood lymphocytes: Possible applications for biodosimetry

Knops K, Boldt S, Wolkenhauer O, Kriehuber R (2012)

Radiation Research 178:304-312

Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis

Liebal UW, Sappa PK, Millat T, Steil L, Homuth G, Völker U, Wolkenhauer O (2012)

Molecular Biosystems 8(4):1806-14

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

D Waltemath, R Adams, FT Bergmann, M Hucka et al.

Open Access article in BMC Systems Biology 2011, 5:198 (2011)

A Frequency Based Gene Selection Method to Identify Robust Biomarkers for Radiation Dose Prediction

Boldt S, Knops K, Kriehuber R, Wolkenhauer O (2012)

International Journal of Radiation Biology 3:267-276

Controlled vocabularies and semantics in systems biology

M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova et al.

Open Access article in Nat Molecular Systems Biology 7:543 (2011)

The role of theorem proving in systems biology

Wolkenhauer O, Shibata D, Mesarovic MD (2012)

Journal of Theoretical Biology 300: 57-61

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

Schmidt V, Baum K, Lao A, Rateitschak K, Schmitz Y, Teichmann A, Wiesner B, Petersen CM, Nykjaer A, Wolf J, Wolkenhauer O, Willnow T (2012)

EMBO Journal 31: 187-200

2011

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

Guebel DV, Schmitz U, Wolkenhauer O, Vera J (2012)

Molecular Biosystems 8(4):1230-1242

Nonlinear modelling of curvature by bi-linear metamodelling

Isaeva J, Saebo S, Wyller JA, Wolkenhauer O, Martens H (2011)

Chemometrics and Intelligent Laboratory Systems

Modeling the Calvin-Benson cycle

Jablonsky J, Bauwe H, Wolkenhauer O (2011)

BMC Systems Biology 5: 185

Cerebral amyloid-beta proteostasis is regulated by the membrane transport protein ABCC1 in mice

Krohn M, Lange C, Hofrichter J, Scheffler K, Stenzel J, Steffen J, Schumacher T, Bräunung T, Plath A S, Alfen F, Schmidt A, Winter F, Rateitschak K, Wree A, Gsponer J, Walker L C, Pahnke J (2011)

Journal of Clinical Investigation 121: 3924-3931

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

Vera J, Nikolov S, Lai X, Singh A, Wolkenhauer O (2011)

IET Systems Biology 5: 293-307

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

Gupta SK, Gupta SK, Smita S, Srivastava M, Lai X, Schmitz U, Rahman Q, Wolkenhauer O, Vera J (2011)

Infection, Genetics and Evolution 11: 1072 - 1082

Systems Biology Of JAK-STAT Signalling In Human Malignancies

Vera J, Rateitschak K, Lange F, Kossow C, Wolkenhauer O, Jaster R (2011)

Progress in Biophysics and Molecular Biology 106: 426-434

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

Schmitz Y, Wolkenhauer O, Rateitschak K (2011)

Journal of Theoretical Biology 279: 132-142

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

Drack M, Wolkenhauer O (2011)

Seminars Cancer Biology 21: 150 - 155

Minimum Information About a Simulation Experiment (MIASE)

D Waltemath, R Adams, DA Beard et al.

Open Access article in PLoS Computational Biology 7: 4 (2011)

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

Gupta SK, Srivastava M, Akhoon BA, Smita S, Schmitz U, Wolkenhauer O, Vera J, Gupta SK (2011)

Infection, Genetics and Evolution 11: 308 - 319

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

Nikolov S, Vera J, Schmitz U, Wolkenhauer O (2011)

Theory in Biosciences 130: 55-69

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

Lange F, Rateitschak K, Fitzner B, Pohland R, Wolkenhauer O and Jaster R (2011)

Molecular Cancer 10: 13

A Systems Biology Approach to Investigate the Effect of pH-induced Gene Regulation on Solvent Production by Clostridium acetobutylicum in Continuous Culture

Haus S, Jabbari S, Millat T, Janssen H, Fischer RJ, Bahl H, King JR, Wolkenhauer O (2011)

BMC Systems Biology 5: 10

A stem cell niche dominance theorem

Wolkenhauer O, Shibata D, Mesarovic MD (2011)

BMC Syst. Biol. 5: 4

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

Frey S, Sott K, Smedh M, Millat T, Dahl P, Wolkenhauer O, Goksör M (2011)

Molecular BioSystems 7: 215-223

2010

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

Schult C, Dahlhaus M, Ruck S, Sawitzky M, Amoroso F, Lange S, Etro D, Glass A, Fuellen G, Boldt S, Wolkenhauer O, Neri LM, Freund M, Junghanss C (2010)

BMC Cancer 10: 560

Dynamic energy budget approaches for modelling organismal ageing

van Leeuwen I, Vera J, Wolkenhauer O (2010)

Phil. Trans. R. Soc. B 365: 3443-3454

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

Raasch P, Schmitz U, Patenge N, Vera J, Kreikemeyer B, Wolkenhauer O (2010)

BMC Bioinformatics 11: 491

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

Pandey R, Gupta S, Tandon S, Wolkenhauer O, Vera J (2010)

Seizure 19: 439 - 442

Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models (2010)

Vera J, Rath O, Balsa-Canto E, Banga J, Kolch W, Wolkenhauer (2010)

Molecular BioSystems 6: 2174-2191

Ranked Retrieval of Computational Biology Models

R Henkel, L Endler, N Le Novère, A Peters, D Waltemath

Open Access article in BMC Bioinformatics 11:423 (2010)

Optimization of biochemical systems through mathematical programming: methods and applications

Vera J, Marin-Sanguino A, Torres N (2010)

Computers & Operations Research 8: 1427-1438

How mathematical modelling elucidates signalling in B. subtilis

Liebal UW, Millat T, de Jong I, Kuipers O, Völker U, Wolkenhauer O (2010)

Molecular Microbiology 77: 1083-1095

Thresholds in transient dynamics of signal transduction pathways

Rateitschak K, Wolkenhauer O (2010)

Journal of Theoretical Biology 264: 334 - 346

Tumor-promoting role of signal transducer and activator of transcription (Stat)1 in late-stage melanoma growth

Schultz J, Koczan D, Schmitz U, Ibrahim SM, Pilch D, Landsberg J, Kunz M (2010)

Clinical & Experimental Metastasis 27: 133-140

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

Nikolov S, Lai X, Liebal UW, Wolkenhauer O, Vera J (2010)

International Journal of Systems Science 41: 81-105

Dynamics of microRNA regulation of cancer network

Nikolov S, Vera J, Herwig R, Wolkenhauer O, Petrov V (2010)

Comptes rendus de l'Académie Bulgare des Sciences Tome 63: No 1

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

Vera J, Schultz J, Ibrahim S, Wolkenhauer O, Kunz M (2010)

Molecular Biosystems 6: 254-263

Mining the proteome of Haemophilus ducreyi for identification of potential drug targets

Sarangi AN, Trivedi N, Rathi B, Gupta S

The Open Bioinformatics Journal, 4: 1-4, 2010

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

Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R (2010)

Cellular Signalling 22: 97-105

2009

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

Wolkenhauer O, Rateitschak K, Auffray Ch, Baltrusch S, Blüthgen N, Byrne H et al. (2009)

Cancer Research 70: 12-3

Stochastic approaches in systems biology

Ullah M, Wolkenhauer O (2009)

Wiley Interdisciplinary Reviews: Systems Biology and Medicine 4: 385-397

Investigating the two-moment characterisation of subcellular biochemical networks

Ullah M, Wolkenhauer O (2009)

Journal of Theoretical Biology 3: 340-352

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Geraniol and limonene interaction with 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase for their role as cancer chemo-preventive agents

Pattanayak M, Seth PK, Smita S, Gupta SK (2009)

Journal of Proteomics & Bioinformatics 2: 466-474

Effective ncRNA detection

Raasch P, Schmitz U, Kreikemeyer B, Wolkenhauer O (2010)

Rostocker Informatik-Berichte 32: 158-166

ISBN 13 (print): 9783832540050

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

Lai X, Nikolov S, Wolkenhauer O, Vera J (2009)

Computational Biology and Chemistry 4: 312-324

14-3-3sigma gene silencing during melanoma progression and its role in cell cycle control and cellular senescence

Schultz J, Ibrahim SM, Vera J, Kunz M (2009)

Molecular Cancer 8: 53

Exploration of homodimer receptor - homodimer protein interactions

Vera J, Kwon T, Schmitz U, Kolch W, Wolkenhauer O (2009)

International Journal of Bioinformatics Research and Applications 4: 447-457

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Time delay and protein modulation analysis in a model of RNA silencing

Nikolov S, Lai X, Wolkenhauer O, Vera J (2009)

Communications of SIWN 6: 111-117

SysBioMed report: Advancing systems biology for medical application

Wolkenhauer O, Fell D, De Meyts P, Bluethgen N, Herzel H, Le Noveere N, Hoefer T, Schuerrle K, van Leeuwen I (2009)

IET Syst. Biol. 3: 131-136

Role of inhibitory proteins as modulators of oscillations in NFkB signalling

Nikolov S, Vera J, Rath O, Kolch W, Wolkenhauer O (2009)

IET Systems Biology 3: 59-76

Time delay and Epo dose modulation in a multilevel model for erythropoiesis

Nikolov S, Lai X, Wolkenhauer O, Vera J (2009)

Bioautomation 12: 53-69

2008

Report on EU - USA Workshop: How Systems Biology Can Advance Cancer Research

Aebersold R et al. (including Wolkenhauer O) (2009)

Molecular Oncology 3: 9-17

Dynamics of receptor and protein transducer homodimerisation

Vera J, Millat T, Kolch W, Wolkenhauer O (2008)

BMC Systems Biology 2: 92

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

Pahnke J, Wolkenhauer O, Krohn M, Walker LDK (2008)

Current Alzheimer Research 5: 396-405

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

Gerber S, Assmus H E, Bakker BM, Klipp E (2008)

J.Theoret. Biol. 252: 442-455

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

Millat T, Sreenath SN, Soebiyanto RP, Avva J, Cho K H, Wolkenhauer O (2008)

BioSystems 92: 270-281

Ein Beitrag zu einer Theorie lebender Zellen

Wolkenhauer O, Hofmeyr JH (2008)

at - Automatisierungstechnik 5: 225-232

Mesoscopic Monte Carlo simulations of stochastic encounters between photoactivated rhodopsin and transducin in the ROS-disc membrane

Dell'Orco D, Schmidt H (2008)

Journal of Physical Chemistry 112: 4419-4426

Complexity Reduction of Biochemical Rate Expressions

Schmidt H, Madsen M, Danø S, Cedersund G (2008)

Bioinformatics 24: 848-854
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How quantitative measures unravel design principles in multi-stage phosphorylation cascades

Frey S, Millat T, Hohmann S, Wolkenhauer O (2008)

J Theor Biol 254: 27-36

A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway

Vera J, Bachmann J, Pfeifer A, Becker V, Hormiga J, Torres Darias N, Timmer J, Klingmuller U, Wolkenhauer O (2008)

BMC Systems Biology 2: 38

Dynamic properties of a delayed protein cross talk model

Nikolov S, Vera J, Wolkenhauer O, Petrov V (2008)

BioSystems 91: 51 - 68

2007

Stability Analysis of a time delay model for the JAK-STAT signalling pathway

Nikolov S, Georgiev G, Kotev V, Wolkenhauer O (2007)

Series on Biomechanics 1: 52-65

Investigation of dynamic behaviour of receptor tyrosin kinase and protein tyrosine phospatase reaction network using mathematical model

Nikolov S, Vera J, Wolkenhauer O, Petrov V (2007)

International Electronic Journal of Bioautomation (IEJB) 8: 105-114

Principal Difference Between Stability and Structural Stability (Robustness) as Used in Systems Biology

Nikolov S, Yankulova E, Wolkenhauer O, Petrov V (2007)

Nonlinear Dynamics, Psychology, and Life Sciences 4: 413-433

Power-Law Models of Signal Transduction Pathways

Vera J, Balsa-Canto E, Wellstead P, Banga J R, Wolkenhauer O (2007)

Cellular Signalling 19: 1531-1541

Family tree of Markov models in systems biology

Ullah M, Wolkenhauer O (2007)

IET Systems Biology 1: 247-254

Detection of potential enzyme targets by metabolic modelling and optimization. Application to a simple enzymopathy

Vera J, Curto R, Cascante M, Torres NV (2007)

Bioinformatics 23: 2281-2289

Interpreting Rosen

Wolkenhauer O (2007)

Artificial Life 13: 1-2

An Abstract Cell Model that describes the Self-Organization of Cell Function in Living Systems

Wolkenhauer O, Hofmeyr J H (2007)

Journal of Theoretical Biology 246: 461-476

Reduction of Nonlinear Dynamic Systems with an Application to Signal Transduction Pathways

Petrov V, Nikolova E, Wolkenhauer O (2007)

IET Systems Biology 1: 2-9

SBML Export Interface for Systems Biology Toolbox for Matlab

Schmidt H, Drews G, Vera J, Wolkenhauer O (2007)

Bioinformatics 23: 1297-1298

PLMaddon: a power-law module for the Matlab SBToolbox

Vera J, Sun C, Oertel Y, Wolkenhauer O (2007)

Bioinformatics 19: 2638 - 2640

Chaos in a delayed protein cross talk model with periodic forcing

Nikolov S, Vera J, Wolkenhauer O, Yankulova E, Petrov V (2007)

Comptes rendus de lAcademie bulgare des Sciences 2: 127-132

Approximations and their Consequences in Dynamic Modelling of Signal Transduction Pathways

Millat T, Bullinger E, Rohwer J, Wolkenhauer O (2007)

Mathematical Biosciences 47: 40-57

Defining Systems Biology: An Engineering Perspective

Wolkenhauer O (2007)

Journal of Biotechnology 2: 329-351
access

Intracellular delay limits cyclic changes in gene expression

Rateitschak K, Wolkenhauer O (2007)

Mathematical Biosciences 205: 163-79

Pattern Formation of Competing Microorganisms in Sediments

Schmitz Y, Baurmann M, Engelen B, Feudel U (2007)

Mathematical Modelling of Natural Phenomena 4: 74-104
access

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

Hoffrogge R, Beyer S, Hübner R, Mikkat S, Mix E, Scharf C, Schmitz U, Pauleweit S, Berth M, Zbrzycki IZ, Christoph H, Pahnke J, Wolkenhauer O, Uhrmacher A, Völker U, Rolfs R (2007)

Proteomics 7: 33-46

Bioinformatics analysis of interactions of receptor homodimers with intracellular protein homodimers

Vera J, Kwon T, Schmitz U, Millat T, Wolkenhauer O

Rostocker Informatik-Berichte, 31, 2007

Coordination of Crosstalk between MAPK-PKC Pathways: An Exploratory Study

Sreenath SN, Soebyanto R, Mesarovic MD, Wolkenhauer O (2007)

IET Systems Biology 1: 33-40

2006

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

Assmus HE, Herwig R, Cho KH, Wolkenhauer O (2006)

Expert Rev. Mol. Diagn. 6: 891-902

A new Method of Measuring Similarity for a Special Class of Directed Graphs

Dehmer M, Mehler A (2006)

Tatra Mountains Mathematical Publications 39: 39-59

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

Shin SY, Choo SM, Kim D, Baek S J, Wolkenhauer O, Cho KH (2006)

FEBS Letters 580: 5965-5973

Measuring the Structural Similarity of Webbased Documents: A novel Approach

Dehmer M, Emmert-Streib F, Mehler A, Kilian J (2006)

International Journal of Computational Intelligence 3: 1

A similarity measure for graphs with low computational complexity

Dehmer M, Emmert-Streib F, Kilian J (2006)

Applied Mathematics and Computation 1: 447-459

Wnt signal pathways and neural stem cell differentiation

Lange C, Mix E, Rateitschak K, Rolfs A (2006)

Neurodegenerative Dis. 3: 76-86

Ranking genes from DNA microarray data of cervical cancer by a local tree comparison

Emmert-Streib F, Dehmer M, Liu J, Mühlhäuser M (2006)

International Journal of Biomedical Science 1: 1-6

Information Technology in Systems Biology

Schmidt H, Jirstrand M, Wolkenhauer O (2006)

it - Information Technology 3: 133-139

Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB

Ullah M, Schmidt H, Cho KH, Wolkenhauer O (2006)

IEE Proc Systems Biology 2: 53-60

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Perspectives of Graph Mining Techniques

Dehmer M, Emmert-Streib F, Wolkenhauer O (2006)

Rostocker Informatik Berichte 30: 47-56

Mining Graph Patterns in Web-based Systems

Dehmer M, Emmert-Streib F, Mehler A (2006)

International Journal of Intelligent Information Technologies 4: 237-253

On the Location of Zeros for complex Polynomials

Dehmer M (2006)

Journal of Inequalities in Pure and Applied Mathematics 1

Bioinformatics and The Virtual Cell

Glass A, Koropka T, Wolkenhauer O (2006)

it - Information Technology 1: 44-51

2005

A fully Bayesian model to cluster gene expression profiles

Vogl C, Sanchez-Cabo F, Stocker G, Hubbard S, Wolkenhauer O, Trajanoski Z (2005)

Bioinformatics 2: 130-136

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

Cho KH, Choo SM, Wellstead P, Wolkenhauer O (2005)

FEBS Letters 579: 4520-4528

A hybrid systems framework for cellular processes

Cho KH, Johansson KH, Wolkenhauer O (2005)

BioSystems 3: 273-282

A systems- and signal-oriented approach to intracellular dynamics

Wolkenhauer O, Sreenath S, Wellstead P, Ullah M, Cho KH (2005)

Biochemical Society Transactions 3: 507-515

A driver identification of the Ras/Raf/MEK/ERK signal transduction pathway

Petrov V, Nikolova E, Wolkenhauer O (2005)

Comptes Rendus d. l'Acad. Bulg. Sci., Tome 58, 6: 639-644

Systems Biology: Discovering the Dynamic Behavior of Biochemical Networks

Cho KH, Wolkenhauer O (2005)

BioSystems Review 1: 9-17

Clustering of unevenly sampled gene expression time-series data

Moller-Levet C, Klawonn F, Cho KH, Yin H, Wolkenhauer O (2005)

Fuzzy Sets and Systems 152: 49-66

The dynamic systems approach to control and regulation of intracellular networks

Wolkenhauer O, Ullah M, Wellstead P, Cho KH (2005)

FEBS Letters 579: 1846-1853

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

Wolkenhauer O, Mesarovic M (2005)

Molecular BioSystems, Royal Society of Chemistry1: 14-16

2004

A novel statistical approach in comparative genomics to reveal new immunogenic antigens in M. bovis

Kutalik Z, Razaz M, Inwald J, Gordon S V, Wolkenhauer O (2004)

Tissue Antigens 4: 427-427

Analysis of DNA microarray data

Hackl H, Sanchez-Cabo F, Sturn A, Wolkenhauer O, Trajanoski Z (2004)

Curr. Top. Med. Chem. 4: 1355-1368

Interactive Astrocytic-Neuronal Sulphur Amino Acid Metabolism in mammalian brain:its assessment by a Mathematical Hybrid Model

Guebel DV, Torres NV (2004)

Biochimica et Biophysica Acta 1674: 12-28

Modeling and simulation of intracellular dynamics: choosing an appropriate framework

Wolkenhauer O, Ullah M, Kolch W, Cho KH (2004)

IEEE Transactions on NanoBioScience 3: 200-207

Optimal sampling time selection for parameter estimation in dynamic pathway modeling

Kutalik Z, Cho KH, Wolkenhauer O (2004)

BioSystems 75: 43-55

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Assessing the efficiency of dye-swap normalization to remove systematic bias from two-color microarray data

Sanchez-Cabo F, Cho KH, Hinds J, Wolkenhauer O (2004)

Applied Bioinformatics

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

Kutalik Z, Inwald J, Gordon SV, Hewinson RG, Butcher P, Hinds J, Cho KH, Wolkenhauer O (2004)

Bioinformatics 3: 357-363

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2003

MetMAP: An integrated Matlab package for analysis and optimisation of metabolic systems

Vera J, Torres NV (2003)

Silico Biology 4: 001
open access

Integrated nonlinear optimization of bioprocesses via linear programming

Vera J, Torres NV, Moles CG, Banga JR (2003)

AIChE Journal 12: 3173-3187

Experimental design in systems biology, based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNF alpha-mediated NF-kappa B signal transduction pathway

Cho KH, Shin SY, Kolch W, Wolkenhauer O (2003)

Simulation 12: 726-739

Level sets and minimum volume sets of probability density functions

Nunez-Garcia J, Kutalik Z, Cho KH, Wolkenhauer O (2003)

Approximate Reasoning 1: 25-47

Analysis and modelling of signal transduction pathways in systems biology

Cho KH, Wolkenhauer O (2003)

Biochemical Society Transactions 6: 503-1509

Multicriteria optimization of biochemical systems by linear programming: Application to production of ethanol by Saccharomyces cerevisiae

Vera J, de Atauri P, Cascante M, Torres NV (2003)

Biotechnology and Bioengineering 3: 335-343

An introduction to systems biology

Wolkenhauer O, Kitano H, Cho KH (2003)

IEEE Control Systems Magazine 4: 38-48

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

Nunez-Garcia J, Mersinias V, Cho KH, Smith CP, Wolkenhauer O (2003)

Applied Bioinformatics 4: 229-239

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

Müller-Levet C, Cho KH, Wolkenhauer O (2003)

Open Mind Journals. Applied Bioinformatics 1: 35-45

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

Cho KH, Shin SY, Lee HW, Wolkenhauer O (2003)

Genome Research 13: 2413-2422

2002

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

Cai Y, Dodson CJT, Doig A, Wolkenhauer O (2002)

Journal of Theoretical Biology 218: 409-418

The curse of normalisation

Wolkenhauer O, Müller-Levet C, Sanchez-Cabo F (2002)

Comparative and Functional Genomics 3: 375-379

Random set system identification

Nunez-Garcia J, Wolkenhauer O (2002)

IEEE Transactions on Fuzzy Systems 3: 287-296

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

Wolkenhauer O (2002)

BioSystems 1: 1-18

2001

Bioinformatic assessment of mass spectrometric chemical derivatisation techniques for proteome database searching

Sidhu KS, Sangvanich P, Brancia F L, Sullivan A G, Gaskell SJ, Wolkenhauer O, Oliver SG, Hubbard S J (2001)

Proteomics 11: 1368-1377

Systems Biology: the reincarnation of systems theory applied in biology? Briefings in Bioinformatics

Wolkenhauer O (2001)

Henri Stewart Publications 3: 258-270

1997

A Critique of Fuzzy Logic in Control

Wolkenhauer O, Edmunds J (1997)

IJEEE (International Journal of Electrical Engineering Education) 3: 235-242

Dynamic Systems Reliability Evaluation using Uncertainty Techniques for Performance Monitoring

Wolkenhauer O, Edmunds J (1997)

IEE Proc.- Control Theory Appl. 1: 103-108

Possibilistic testing of distribution functions for change detection

Wolkenhauer O, Edmunds J (1997)

Elsevier Science 2: 119-127