Dept. of Systems Biology and Bioinformatics is a part of the University of Rostock, Germany Universität Rostock

2017

Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR
Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments

Journal of Biotechnology
doi.org/10.1016/j.jbiotec.2017.06.1203

Gruening BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Nucleic Acids Research

doi.org/10.1093/nar/gkx409

Bergmann F T, Nickerson D, Waltemath D, Scharm M
SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

Oxford Bioinformatics
doi.org/10.1093/bioinformatics/btw812

Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter A E, Filby A
An open-source solution for advanced imaging flow cytometry data analysis using machine learning

Methods
doi.org/10.1016/j.ymeth.2016.08.018

Lang C, Wolfien M, Langenbach A, Müller P, Wolkenhauer O, Yavari A, Ince H, Steinhoff G, Krause B, David R, Glass Ä
Cardiac cell therapies for the treatment of acute myocardial infarction: A Meta-Analysis from mouse studies

Cellular Physiology and Biochemistry
doi: 10.1159/000477324

Jalili M, Salehzadeh-Yazdi A, Mohammadi S, Yaghmaie M, Ghavamzadeh A, Alimoghaddam K
Meta-Analysis of Gene Expression Profiles in Acute Promyelocytic Leukemia Reveals Involved Pathways

International Journal of Hematology Oncology and Stem Cell Research
open access

Cosseau C, Wolkenhauer O, Padalino G, Geyer KK, Hoffmann KF, Gruna C
(Epi)genetic Inheritance in Schistosoma mansoni: A Systems Approach

Trends in Parasitology
doi.org/10.1016/j.pt.2016.12.002

2016

Sadeghi M, Ranjbar B, Ganjalikhany MR, Khan FM, Schmitz U, Wolkenhauer O
MicroRNA and Transcription Factor Gene Regulatory Network Analysis Reveals Key Regulatory Elements Associated with Prostate Cancer Progression

PLoS ONE 11(12): e0168760. doi:10.1371/journal.pone.0168760
access

Mahdi Jalili, Ali Salehzadeh-Yazdi, Shailendra Gupta, Olaf Wolkenhauer, Marjan Yaghmaie, Osbaldo Resendis-Antonio, Kamran Alimoghaddam
Evolution of centrality measurements for the detection of essential proteins in biological networks

journal.frontiersin.org/article/10.3389/fphys.2016.00375/full

Mahdi Jalili, Ali Salehzadeh-Yazdi, Marjan Yaghmaie, Ardeshir Ghavamzadeh, Kamran Alimoghaddam (2016)
Cancerome: A hidden informative subnetwork of the diseasome

http://www.sciencedirect.com/science/article/pii/S001048251630186X

D Waltemath, R Henkel, R Hoehndorf, T Kacprowski, C Knuepfer, W Liebermeister
Notions of similarity for computational biology models

Open Access article in  Briefings in Bioinformatics (2016) bbw090
DOI: 10.1093/bib/bbw090
URL: http://bib.oxfordjournals.org/content/early/2016/10/11/bib.bbw090

F Schreiber, GD Bader, P Gleeson, M Golebiewski, M Hucka, N Le Novere, C Myers, D Nickerson, B Sommer, D Waltemath
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Open Access article in J Integrative Bioinformatics 2016 13(3)
DOI: doi:10.2390/biecoll-jib-2016-289
URL: http://journal.imbio.de/article.php?aid=289

Touré V, Mazein A, Waltemath D, Balaur I, Saqi M, Henkel R, Pellet J, Auffray C
STON: exploring biological pathways using the SBGN standard and graph databases

Open Access article in BMC Bioinformatics 2016, 17:494
https://dx.doi.org/10.1186/s12859-016-1394-x

Sherry Freiesleben, Michael Hecker, Uwe Klaus Zettl, Georg Fuellen, Leila Tahera
Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms

Scientific Reports (2016) 6: 34512

doi: 10.1038/srep34512

www.nature.com/articles/srep34512

Smita S, Lange F, Wolkenhauer O, Köhling R
Deciphering hallmark processes of aging from interaction networks

Biochim Biophys Acta. 2016; S0304-4165(16)30264-1.
doi: 10.1016/j.bbagen.2016.07.017.

M Scharm, D Waltemath, P Mendes and O Wolkenhauer
COMODI: an ontology to characterise differences in versions of computational models in biology

Open Access article in J of Biomedical Semantics 7:46 (2016)
DOI: 10.1186/s13326-016-0080-2
URL: http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-016-0080-2

Singh J, Dwivedi A, Mujtaba SF, Singh KP, Pal MK, Chopra D, Goyal S, Srivastav AK, Dubey D, Gupta SK, Haldar C, Ray RS
Ambient UV-B exposure reduces the binding of ofloxacin with bacterial DNA gyrase and induces DNA damage mediated apoptosis

The International Journal of Biochemistry and Cell Biology. 2016. pii: S1357-2725(16)30001-2.
doi:10.1016/j.biocel.2016.01.001.

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

Biomaterials. 2016; 84:25-41.
doi: 10.1016/j.biomaterials.2016.01.018.

Wang Y, Alla V, Goody D, Gupta SK, Spitschak A, Wolkenhauer O, Putzer B, Engelmann D
Epigenetic factor EPC1 is a master regulator of DNA damage response by interacting with E2F1 to silence death and activate metastasis-related gene signatures

Nucleic Acids Research. 2016; 44(1):117-33.
doi: 10.1093/nar/gkv885.

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

Molecular Cell

http://www.cell.com/molecular-cell/fulltext/S1097-2765(16)30101-0

D Waltemath, JR Karr, FT Bergmann, V Chelliah et al.
Toward community standards and software for whole-cell modeling

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 2007-14 (2016)
DOI:
10.1109/TBME.2016.2560762
URL: http://ieeexplore.ieee.org/document/7489010/

D Waltemath and O Wolkenhauer
How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine

Open Access article in IEEE Transactions on Biomedical Engineering 63:10, pp. 1999-2006 (2016)
DOI: 10.1109/TBME.2016.2555481
URL: http://ieeexplore.ieee.org/document/7484267/
http://dx.doi.org/10.1109/TBME.2016.2555481

Katja Rateitschak, Lars Kaderali, Olaf Wolkenhauer, Robert Jaster (2016)
Autocrine TGF-beta/ZEB/microRNA-200 signal transduction drives epithelial-mesenchymal transition: Kinetic models predict minimal drug dose to inhibit metastasis

Cellular Signalling
doi:10.1016/j.cellsig.2016.03.002
access

Jonathan Cooper, Martin Scharm, Gary R. Mirams
The Cardiac Electrophysiology Web Lab

Open Access article at the Biophysical Journal.
DOI: 10.1016/j.bpj.2015.12.012
URL: http://www.cell.com/biophysj/references/S0006-3495%2815%2904753-0

M Scharm, O Wolkenhauer and D Waltemath
An algorithm to detect and communicate the differences in computational models describing biological systems

Open Access article in BIOINFORMATICS 32:4, pp. 563-570 (2015)
DOI: 10.1093/bioinformatics/btv484
URL: http://bioinformatics.oxfordjournals.org/content/32/4/563

Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stephan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer (2016)
TRAPLINE: A standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation

BMC Bioinformatics
doi: 10.1186/s12859-015-0873-9
open access

2015

Gupta SK, Jaitly T, Schmitz U, Schuler G, Wolkenauer O, Vera J
Personalized cancer immunotherapy using systems medicine approaches.

Briefings in Bioinformatics 2015. doi: 10.1093/bib/bbv046.

A. Chauhan, H. Weiss, F. Koch, S.M. Ibrahim, J. Vera, O. Wolkenhauer, M. Tiedge (2015)
Dissecting Long-Term Glucose Metabolism Identifies New Susceptibility Period for Metabolic Dysfunction in Aged Mice

Plos One,

doi: 10.1371/journal.pone.0140858

open access

M Hucka, FT Bergmann, A Dräger, ... D Waltemath, DJ Wilkinson
Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

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

DOI: 10.2390/biecoll-jib-2015-271
URL: http://journal.imbio.de/article.php?aid=271

FT Bergmann, J Cooper, N Le Novere, D Nickerson, D Waltemath
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2

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

DOI: 10.2390/biecoll-jib-2015-262
URL: http://journal.imbio.de/article.php?aid=262

F Schreiber, GD Bader, M Golebiewski, ... D Waltemath, S Weise
Specifications of Standards in Systems and Synthetic Biology

Open Access article in J Integrative Bioinformatics 12:2, p. 258 (2015)
DOI: 10.2390/biecoll-jib-2015-258
URL: https://www.ncbi.nlm.nih.gov/pubmed/26528556

R Henkel, O Wolkenhauer, D Waltemath
Combining computational models, semantic annotations and simulation experiments in a graph database

Open Access article in DATABASE bau130 (2015)
DOI: dx.doi.org/10.1093/database/bau130
URL: http://database.oxfordjournals.org/content/2015/bau130.full

Schmitz U, NAderi-Meshkin H, Gupta SK, Wolkenhauer O, Vera J
The RNA world in the 21st century – a systems approach to finding non-coding keys to clinical questions

Briefings in Bioinformatics 2015.
doi: 10.1093/bib/bbv061.

open access

Raheleh A, Schmitz U, Farazmand A, Gupta SK, Ahmadi H, Wolkenhauer O
Naïve Bayes classifier predicts functional microRNA target interactions in colorectal cancer

Molecular BioSystems 2015; 11(8): 2126-34.
doi: 10.1039/c5mb00245a.

Schauer M, Kottek T, Schönherr M, Bhattacharya A, Ibrahim SM, Hirose M, Köhling R, Fuellen G, Schmitz U, Kunz M
A mutation in the NADH-dehydrogenase subunit 2 suppresses fibroblast aging

Oncogene, in press.

access

M Hucka, DP Nickerson, G Bader, ... D Waltemath, N Le Novère
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative

Article in Front. Bioeng. Biotechnol. 3:19 (2015)
DOI: 10.3389/fbioe.2015.00019
URL: http://journal.frontiersin.org/article/10.3389/fbioe.2015.00019/

Vera J, Raatz Y, Wolkenhauer O, Kottek T, Bhattacharaya A, Simon JC, Kunz M
Chk1 and Wee1 control genotoxic-stress induced G2-M arrest in melanoma cells

Accepted for publication in Cellular Signaling (2015).

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

Accepted in Oncotarget.
access

Amirkhah R, Schmitz U, Linnebacher M, Wolkenhauer O, Farazmand A
MicroRNA-mRNA interactions in colorectal cancer and their role in tumor progression

Genes, Chromosomes and Cancer, 54:129–141, doi: 10.1002/gcc.22231.

access

R Alm, D Waltemath, M Wolfien, O Wolkenhauer et al.
Annotation-Based Feature Extraction from Sets of SBML Models

Open Access article in J Biomedical Semantics 6:20 (2015)
DOI: 10.1186/s13326-015-0014-4
URL: http://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-015-0014-4

Kossow C, Rybacki S, Millat T, Rateitschak K, Jaster R, Uhrmacher AM, Wolkenhauer O (2015)
An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers

Mathematical and Computer Modelling of Dynamical Systems.

doi:10.1080/13873954.2015.1033823

open access

2014

Akhoon BA, Singh KP, Varshney M, Gupta SK, Shukla Y, Gupta SK
Understanding the mechanism of Atovaquone drug resistance in Plasmodium falciparum cytochrome b mutation Y268S using computational methods

Plos One 2014; 9(10):e110041
doi: 10.1371/journal.pone.0110041

Meier C, Spitschak A, Abshagen K, Gupta S, Mor JM, Wolkenhauer O, Haier J, Vollmar B, Alla V, Pützer BM
Association of RHAMM with E2F1 promotes tumour cell extravasation by transcriptional up-regulation of fibronectin

Journal of Pathology. 2014; 234(3):351-64.
doi: 10.1002/path.4400.

Dammann O, Gray P, Gressens P, Wolkenhauer O, Leviton A
Systems Epidemiology: What's in a Name?

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

J Cooper, JO Vik, D Waltemath
A call for virtual experiments: Accelerating the scientific process

Article in Progress in Biophysics and Molecular Biology 117:1, pp. 99-106 (2014)
DOI: 10.1016/j.pbiomolbio.2014.10.001
URL: http://www.sciencedirect.com/science/article/pii/S0079610714001825 

Wolkenhauer, O
Pushing limits by embracing complexity

IET Syst Biol. 2014 Dec;8(6):244-250.
doi: 10.1049/iet-syb.2014.0031

Knoll S, Fürst K, Kowtharapu B, Schmitz U, Marquardt S, Wolkenhauer O, Martin H, Pützer BM
E2F1 induces miR-224/452 expression to drive EMT through TXNIP downregulation

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

Wollbold J, Jaster R, Müller S, Rateitschak K, Wolkenhauer O
Anti-inflammatory effects of reactive oxygen species – a multi-valued logical model validated by formal concept analysis

BMC Systems Biology, 8:101  doi:10.1186/s12918-014-0101-7.
open access

FT Bergmann, R Adams, ... M Scharm, ... D Waltemath et al.
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Open Access article in BMC Bioinformatics 15:369 (2014)
DOI: 10.1186/s12859-014-0369-z
URL: bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-014-0369-z 

R Alm, D Waltemath, O Wolkenhauer, R Henkel
Annotation-Based Feature Extraction from Sets of SBML Models

Article in Lecture notes in computer science 8574, pp 81-95 (2014)
DOI: 10.1007/978-3-319-08590-6_8

Wolkenhauer O, Auffray C, Brass O, Clairambault J, Deutsch A, Drasdo D, Gervasio F, Preziosi L, et al.
Enabling multiscale modeling in systems medicine

Genome Medicine 2014, 6:21

access

Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta S
Cooperative gene regulation by microRNA pairs and their identification using a computational workflow

Nucleic Acid Research 2014, 42 (12): 7539-7552, doi: 10.1093/nar/gku465.
open access

D Waltemath, FT Bergmann, C Chaouiya et al.
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Open Access article in Standards in Genomic Sciences 9:3 (2014)
DOI: 10.4056/sigs.5279417
URL: http://standardsingenomics.biomedcentral.com/articles/10.4056/sigs.5279417

Ghavami S, Wolkenhauer O, Lahouti F, Ullah M, Linnebacher M
Accounting for randomness in measurement and sampling in studying of cancer cell population dynamics

IET Systems Biology, 8(5):230-41. doi: 10.1049/iet-syb.2013.0031.
access

supplementary material

Müller S, Kaiser, H; Krüger B, Fitzner B, Lange F, Bock CN, Nizze H, Ibrahim SM, Füllen G, Wolkenhauer O, Jaster R
Age-dependent effects of UCP2 deficiency on experimental acute pancreatitis in mice

PLOS ONE 9(4), doi: 10.1371/journal.pone.0094494

Garcia-Salcedo R, Lubitz T, Beltran G, Elbing K, Tian Y, Frey S, Wolkenhauer O, Krantz M, Klipp E, Hohmann S
Glucose de-repression by yeast AMP-activated protein kinase SNF1 is controlled via at least two independent steps

FEBS Journal Feb 15.  281(7): 1901 - 17, doi: 10.111/febs.12753 (Epub 2014 Mar 4)

access

Wolkenhauer, O
Why model?

Front. Physiol. 5:21. doi: 10.3389/fphys.2014.00021
open access

Wolkenhauer, O.
The Role of theory and Modelling in Medical Research

Front. Pysiol. 4:377. doi: 10.3389/fphys.2013.00377
>>access

Chauhan, A. and Vera, J. and Wolkenhauer, O.
The systems biology of mitochondrial fission and fusion and implications for disease and ageing

Biogerontology 15(1): 1 - 12

Pubmed

Nikolov, S. and Wolkenhauer, O. and Vera, J.
Tumors as chaotic attractors

Mol Biosyst. 10 (2):172 - 9 doi: 10.1039/c3mb70331b

Pubmed

Khan FM, Schmitz U, Nikolov S, Engelmann D, Pützer BM,Wolkenhauer O, Vera J
Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic

Biochim Biophys Acta; 1844 (1 Pt B): 289-98. doi:10.1016/j.bbapap.2013.05.007
access

2013

Millat T, Janssen H, Bahl H, Fischer RJ, Wolkenhauer, O (2013)
Integrative modelling of pH-dependent enzyme activity and transcriptomic regulation of the acetone-butanol-ethanol fermentation of Clostridium acetobutylicum in continuous culture

Microbial Biotechnology 6 (5): 526 - 39 doi: 10.1111/1751 - 7915
open access

Singh SB, Biswas D, Rawat J, Sindhwani G, Patras A, Devrani S, Sarkar P, Mitra S, Gupta SK
Ethnicity-tailored novel set of ESAT-6 peptides for differentiating active and latent tuberculosis

Tuberculosis, Volume 93, Issue 6, 618 - 624
»access

Green S, Wolkenhauer O
Tracing organizing principles: Learning from the history of systems biology

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

Minoo P, Wolkenhauer O, Guttentag S
Systems biology and pediatric research

Pediatr Res. 2013 Apr;73(4 Pt 2):499-501, doi: 10.1038/pr.2013.33

Pubmed

Maubach G, O Sokolova, M Wolfien, HJ Rothkötter, M Naumann
Ca2+/calmodulin-dependent kinase II contributes to inhibitor of nuclear factor-kappa B kinase complex activation in Helicobacter pylori infection.

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

Lai X, Bhattacharya A, Schmitz U, Kunz M, Vera J, Wolkenhauer O
A systems biology approach to study microRNA-mediated gene regulatory networks (2013)

BioMed Research International, vol. 2013, doi:10.1155/2013/703849.

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
Do simple models lead to generality in ecology?

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

D Waltemath, O Wolkenhauer, N Le Novère, M Dumontier
Possibilities for Integrating Model-related Data in Computational Biology

Proceedings of the 9th International Conference on Data Integration in the Life Sciences (2013)
URL: http://www2.unb.ca/csas/data/ws/dils2013/papers/DILS-SYS-EC-paper8.pdf (workshop proceedings)

Schmitz Y, Rateitschak K, Wolkenhauer O (2013)
Analysing the impact of nucleo-cytoplasmic shuttling of beta-catenin and its antagonists APC, Axin and GSK3 on Wnt/beta-catenin signalling

Cellular Signalling, 2210:2221

Wolkenhauer O, Green S (2013)
The search for organizing principles as a cure against reductionism in systems medicine

FEBS Journal, 280 (23): 5938-48. doi: 10.111/febs.12311


Pubmed

Wolkenhauer O, Auffray C, Jaster R, Steinhoff G, Dammann O (2013)
The Road from Systems Biology to Systems Medicine

Pediatric Research, 73:502-507

access

D Waltemath, R Henkel, R Hälke, M Scharm, O Wolkenhauer
Improving the reuse of computational models through version control

Article in BIOINFORMATICS 29:6, pp. 742-7 (2014)
DOI: 10.1093/bioinformatics/btt018
URL: bioinformatics.oxfordjournals.org/content/29/6/742

Millat T, Janssen H, Thorn GJ, King JR, Bahl H, Fischer RJ, Wolkenhauer O (2013)
A shift in the dominant phenotype governs the pH-induced metabolic switch of Clostridium acetobutylicum in phosphate-limited continuous cultures

Applied Microbiology & Biotechnology 97: 6451-6466, doi: 10.1007/s00253-013-4860-7
access


Pubmed

Vera J, Schmitz U, Lai X, Engelmann D, Khan FM, Wolkenhauer O, Pützer BM (2013)
Kinetic modeling-based detection of genetic signatures that provide chemoresistance via the E2F1-p73/DNp73-miR-205 network

Cancer Research, doi:10.1158/0008-5472.CAN-12-4095
access

Liebal UW, Millat T, Marles-Wright J, Lewis RJ, Wolkenhauer O (2013)
Simulations of Stressosome Activation Emphasize Allosteric Interactions Between RsbR and RsbT

BMC Systems Biology 7:3
open access

Jablonsky J, Hagemann M, Schwarz D, Wolkenhauer O (2013)
Phosphoglycerate mutases function as reverse regulated isoenzymes in Synechococcus elongatus PCC 7942

PLoS One, doi: 10.1371/journal.pone.0058281

open access

Bader BM, Schmitz Y, Kuznetsov SA, Weiss DG (2013)
Spatio-temporal distribution changes and nucleo-cytoplasmic shuttling rates regulate differentiation in human neural progenitor cells

submitted for publication

2012

Rateitschak K, Winter F, Lange F, Jaster R, Wolkenhauer O (2012)
Parameter Identifiability and Sensitivity Analysis Predict Targets for Enhancement of STAT1 Activity in Pancreatic Cancer and Stellate Cells

PLoS Computational Biology 8: e1002815
open access

Lange F, Rateitschak K, Kossow C, Wolkenhauer O, Jaster R (2012)
Insights into erlotinib action in pancreatic cancer cells using a combined experimental and mathematical approach

World Journal of Gastroenterology 18: 6226-6234
open access

Jones N, Wolkenhauer O (2012)
Diagrams as locality aids for explanation and model construction in cell biology

Biology and Philosophy 27: 705-721
open access

Green S, Wolkenhauer O (2012)
Integration in action

EMBO reports 13: 769-771
open access

Bhattacharya A, Schmitz U, Wolkenhauer O, Schönherr M, Raatz Y, Kunz M (2012)
Regulation of cell cycle checkpoint kinase WEE1 by miR-195 in malignant melanoma

Oncogene, doi: 10.1038/onc.2012.324.
access

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)
Systems Biology and Bioinformatics in Aging Research: A Workshop Report

Rejuvenation Research, Vol 15, No 6, doi: 10.1089/rej.2012.1360.
access

Alla V, Kowtharapu BS, Engelmann D, Emmrich S, Schmitz U, Steder M, Pützer BM (2012)
E2F1 confers anticancer drug resistance by targeting ABC transporter family members and Bcl-2 via the p73/DNp73-miR-205 circuitry

Cell Cycle, 11:1
access

Lai X, Schmitz U, Gupta S, Bhattacharya A, Kunz M, Wolkenhauer O, Vera J (2012)
Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs

Nucleic Acids Research, 40: 8818-8834.

open access

Lao A, Schmidt V, Schmitz Y, Willnow T, Wolkenhauer O (2012)
Multi-compartmental modeling of SORLA's influence on amyloidogenic processing in Alzheimer's disease

BMC Systems Biology 6:74
access

Knops K, Boldt S, Wolkenhauer O, Kriehuber R (2012)
Gene expression in low and high dose-irradiated human peripheral blood lymphocytes: Possible applications for biodosimetry

Radiation Research 178:304-312
open access

Liebal UW, Sappa PK, Millat T, Steil L, Homuth G, Völker U, Wolkenhauer O (2012)
Proteolysis of beta-galactosidase following SigmaB activation in Bacillus subtilis

Molecular Biosystems 8(4):1806-14

access

Guebel DV, Schmitz U, Wolkenhauer O, Vera J (2012)
Analysis of cell adhesion during early stages of colon cancer based on an extended multi-valued logic approach

Molecular Biosystems 8(4):1230-1242

access

Wolkenhauer O, Shibata D, Mesarovic MD (2012)
The role of theorem proving in systems biology

Journal of Theoretical Biology 300: 57-61

access

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

EMBO Journal 31: 187-200

 access

Boldt S, Knops K, Kriehuber R, Wolkenhauer O (2012)
A Frequency Based Gene Selection Method to Identify Robust Biomarkers for Radiation Dose Prediction

International Journal of Radiation Biology 3:267-276

access

Kossow C, Jose D, Jaster R, Wolkenhauer O, Rateitschak K (2012)
Mathematical modelling unravels regulatory mechanisms of interferon-?-induced STAT1 serine-phosphorylation and MUC4 expression in pancreatic cancer cells

IET System Biology 6: 73-85

access

2011

D Waltemath, R Adams, FT Bergmann, M Hucka et al.
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Open Access article in BMC Systems Biology 2011, 5:198 (2011)
DOI: 10.1186/1752-0509-5-198
URL: http://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-5-198 

Jablonsky J, Bauwe H, Wolkenhauer O (2011)
Modeling the Calvin-Benson cycle

BMC Systems Biology 5: 185
open access

M Courtot, N Juty, C Knüpfer, D Waltemath, A Zhukova et al.
Controlled vocabularies and semantics in systems biology

Open Access article in Nat Molecular Systems Biology 7:543 (2011)
DOI: 10.1038/msb.2011.77
URL: http://msb.embopress.org/content/7/1/543

Isaeva J, Saebo S, Wyller JA, Wolkenhauer O, Martens H (2011)
Nonlinear modelling of curvature by bi-linear metamodelling

Chemometrics and Intelligent Laboratory Systems

access

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

Journal of Clinical Investigation 121: 3924-3931
access

Vera J, Nikolov S, Lai X, Singh A, Wolkenhauer O (2011)
Model-based investigation of the transcriptional activity of p53 and its feedback loop regulation via 14-3-3Σ

IET Systems Biology 5: 293-307
access 

Vera J, Rateitschak K, Lange F, Kossow C, Wolkenhauer O, Jaster R (2011)
Systems Biology Of JAK-STAT Signalling In Human Malignancies

Progress in Biophysics and Molecular Biology 106: 426-434

access

Drack M, Wolkenhauer O (2011)
System approaches of Weiss and Bertalanffy and their relevance for systems biology today

Seminars Cancer Biology 21: 150 - 155
access

D Waltemath, R Adams, DA Beard et al.
Minimum Information About a Simulation Experiment (MIASE)

Open Access article in PLoS Computational Biology 7: 4 (2011)
DOI: 10.1371/journal.pcbi.1001122
URL: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1001122 

Schmitz Y, Wolkenhauer O, Rateitschak K (2011)
Nucleo-cytoplasmic shuttling of APC can maximize beta-catenin/TCF concentration

Journal of Theoretical Biology 279: 132-142
access

Gupta SK, Gupta SK, Smita S, Srivastava M, Lai X, Schmitz U, Rahman Q, Wolkenhauer O, Vera J (2011)
Computational analysis and modeling the effectiveness of "Zanamivir" targeting neuraminidase protein in pandemic H1N1 strains

Infection, Genetics and Evolution 11: 1072 - 1082

access

Lange F, Rateitschak K, Fitzner B, Pohland R, Wolkenhauer O and Jaster R (2011)
Studies on mechanisms of interferon-gamma action in pancreatic cancer using a data-driven and model-based approach

Molecular Cancer 10: 13
open access

Wolkenhauer O, Shibata D, Mesarovic MD (2011)
A stem cell niche dominance theorem

BMC Syst. Biol. 5: 4
open access

Gupta SK, Srivastava M, Akhoon BA, Smita S, Schmitz U, Wolkenhauer O, Vera J, Gupta SK (2011)
Identification of immunogenic consensus T-cell epitopes in globally distributed influenza-A H1N1 neuraminidase

Infection, Genetics and Evolution 11: 308 - 319
access

Haus S, Jabbari S, Millat T, Janssen H, Fischer RJ, Bahl H, King JR, Wolkenhauer O (2011)
A Systems Biology Approach to Investigate the Effect of pH-induced Gene Regulation on Solvent Production by Clostridium acetobutylicum in Continuous Culture

BMC Systems Biology 5: 10
open access

Nikolov S, Vera J, Schmitz U, Wolkenhauer O (2011)
A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks

Theory in Biosciences 130: 55-69
access

Frey S, Sott K, Smedh M, Millat T, Dahl P, Wolkenhauer O, Goksör M (2011)
A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under consideration of bleaching effects and background noise in Saccharomyces cerevisiae

Molecular BioSystems 7: 215-223

access

2010

R Henkel, L Endler, N Le Novère, A Peters, D Waltemath
Ranked Retrieval of Computational Biology Models

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

DOI: 10.1186/1471-2105-11-423
URL: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-423

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

BMC Cancer 10: 560
open access

Raasch P, Schmitz U, Patenge N, Vera J, Kreikemeyer B, Wolkenhauer O (2010)
Non-coding RNA detection methods combined to improve usability, reproducibility and precision

BMC Bioinformatics 11: 491
open access 

Vera J, Rath O, Balsa-Canto E, Banga J, Kolch W, Wolkenhauer (2010)
Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models (2010)

Molecular BioSystems 6: 2174-2191
access

Liebal UW, Millat T, de Jong I, Kuipers O, Völker U, Wolkenhauer O (2010)
How mathematical modelling elucidates signalling in B. subtilis

Molecular Microbiology 77: 1083-1095
access

Pandey R, Gupta S, Tandon S, Wolkenhauer O, Vera J (2010)
Baccoside A suppresses epileptic-like seizure/convulsion in Caenorhabditis elegans

Seizure 19: 439 - 442

access

van Leeuwen I, Vera J, Wolkenhauer O (2010)
Dynamic energy budget approaches for modelling organismal ageing

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

Schultz J, Koczan D, Schmitz U, Ibrahim SM, Pilch D, Landsberg J, Kunz M (2010)
Tumor-promoting role of signal transducer and activator of transcription (Stat)1 in late-stage melanoma growth

Clinical & Experimental Metastasis 27: 133-140
access

Nikolov S, Vera J, Herwig R, Wolkenhauer O, Petrov V (2010)
Dynamics of microRNA regulation of cancer network

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

Rateitschak K, Wolkenhauer O (2010)
Thresholds in transient dynamics of signal transduction pathways

Journal of Theoretical Biology 264: 334 - 346
access

Vera J, Schultz J, Ibrahim S, Wolkenhauer O, Kunz M (2010)
Dynamical effects of epigenetic silencing of 14-3-3s expression

Molecular Biosystems 6: 254-263
access

Sarangi AN, Trivedi N, Rathi B, Gupta S
Mining the proteome of Haemophilus ducreyi for identification of potential drug targets

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

Vera J, Marin-Sanguino A, Torres N (2010)
Optimization of biochemical systems through mathematical programming: methods and applications

Computers & Operations Research 8: 1427-1438
access

Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R (2010)
Mathematical modelling of interferon-gamma signalling in pancreatic stellate cells reflects and predicts dynamics of STAT1 pathway activity

Cellular Signalling 22: 97-105
access

Nikolov S, Lai X, Liebal UW, Wolkenhauer O, Vera J (2010)
Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics

International Journal of Systems Science 41: 81-105
access

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

Rostocker Informatik-Berichte 32: 158-166
open access

2009

Wolkenhauer O, Auffray Ch, Baltrusch S, Blüthgen N, Byrne H et al. (2009)
Systems biologists seek fuller integration of systems biology approaches in new cancer research programs

Cancer Research 70: 12-3
access

Schultz J, Ibrahim SM, Vera J, Kunz M (2009)
14-3-3sigma gene silencing during melanoma progression and its role in cell cycle control and cellular senescence

Molecular Cancer 8: 53
open access

Ullah M, Wolkenhauer O (2009)
Stochastic approaches in systems biology

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

Wolkenhauer O, Fell D, De Meyts P, Bluethgen N, Herzel H, Le Noveere N, Hoefer T, Schuerrle K, van Leeuwen I (2009)
SysBioMed report: Advancing systems biology for medical application

IET Syst. Biol. 3: 131-136
open access

Nikolov S, Lai X, Wolkenhauer O, Vera J (2009)
Time delay and protein modulation analysis in a model of RNA silencing

Communications of SIWN 6: 111-117
open access

additional files

Pattanayak M, Seth PK, Smita S, Gupta SK (2009)
Geraniol and limonene interaction with 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase for their role as cancer chemo-preventive agents

Journal of Proteomics & Bioinformatics 2: 466-474
open access

Aebersold R et al. (including Wolkenhauer O) (2009)
Report on EU - USA Workshop: How Systems Biology Can Advance Cancer Research

Molecular Oncology 3: 9-17

access

Vera J, Kwon T, Schmitz U, Kolch W, Wolkenhauer O (2009)
Exploration of homodimer receptor - homodimer protein interactions

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

additional files

Ullah M, Wolkenhauer O (2009)
Investigating the two-moment characterisation of subcellular biochemical networks

Journal of Theoretical Biology 3: 340-352
access

additional files

Nikolov S, Vera J, Rath O, Kolch W, Wolkenhauer O (2009)
Role of inhibitory proteins as modulators of oscillations in NFkB signalling

IET Systems Biology 3: 59-76
access

Nikolov S, Lai X, Wolkenhauer O, Vera J (2009)
Time delay and Epo dose modulation in a multilevel model for erythropoiesis

Bioautomation 12: 53-69
open access

Lai X, Nikolov S, Wolkenhauer O, Vera J (2009)
A multi-level model accounting for the effects of JAK2-STAT5 signal modulation in erythropoiesis

Computational Biology and Chemistry 4: 312-324

access

2008

Millat T, COSMIC consortium
COSMIC - Systems biology of Clostridium acetobutylicim - A possible answer to dwindling crude oil reserves

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

Vera J, Millat T, Kolch W, Wolkenhauer O (2008)
Dynamics of receptor and protein transducer homodimerisation

BMC Systems Biology 2: 92
open access

Frey S, Millat T, Hohmann S, Wolkenhauer O (2008)
How quantitative measures unravel design principles in multi-stage phosphorylation cascades

J Theor Biol 254: 27-36
open access

Vera J, Bachmann J, Pfeifer A, Becker V, Hormiga J, Torres Darias N, Timmer J, Klingmuller U, Wolkenhauer O (2008)
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway

BMC Systems Biology 2: 38
open access

Pahnke J, Wolkenhauer O, Krohn M, Walker LDK (2008)
Clinico-pathologic function of cerebral ABC transporters - implications for the pathogenesis of Alzheimer's disease

Current Alzheimer Research 5: 396-405

access

Gerber S, Assmus H E, Bakker BM, Klipp E (2008)
Drug-efficacy depends on the inhibitor type and the target position in a metabolic - A systematic study

J.Theoret. Biol. 252: 442-455
access

Schmidt H, Madsen M, Danø S, Cedersund G (2008)
Complexity Reduction of Biochemical Rate Expressions

Bioinformatics 24: 848-854
access

Dell'Orco D, Schmidt H (2008)
Mesoscopic Monte Carlo simulations of stochastic encounters between photoactivated rhodopsin and transducin in the ROS-disc membrane

Journal of Physical Chemistry 112: 4419-4426

access

Wolkenhauer O, Hofmeyr JH (2008)
Ein Beitrag zu einer Theorie lebender Zellen

at - Automatisierungstechnik 5: 225-232
access

Nikolov S, Vera J, Wolkenhauer O, Petrov V (2008)
Dynamic properties of a delayed protein cross talk model

BioSystems 91: 51 - 68

access

Millat T, Sreenath SN, Soebiyanto RP, Avva J, Cho K H, Wolkenhauer O (2008)
The role of dynamic stimulation pattern in the analysis of bistable intracellular networks

BioSystems 92: 270-281
access

2007

Wolkenhauer O (2007)
Defining Systems Biology: An Engineering Perspective

Journal of Biotechnology 2: 329-351
access

Nikolov S, Georgiev G, Kotev V, Wolkenhauer O (2007)
Stability Analysis of a time delay model for the JAK-STAT signalling pathway

Series on Biomechanics 1: 52-65
open access

Nikolov S, Yankulova E, Wolkenhauer O, Petrov V (2007)
Principal Difference Between Stability and Structural Stability (Robustness) as Used in Systems Biology

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

Vera J, Sun C, Oertel Y, Wolkenhauer O (2007)
PLMaddon: a power-law module for the Matlab SBToolbox

Bioinformatics 19: 2638 - 2640
access

Vera J, Curto R, Cascante M, Torres NV (2007)
Detection of potential enzyme targets by metabolic modelling and optimization. Application to a simple enzymopathy

Bioinformatics 23: 2281-2289
access

Wolkenhauer O (2007)
Interpreting Rosen

Artificial Life 13: 1-2
access

Nikolov S, Vera J, Wolkenhauer O, Petrov V (2007)
Investigation of dynamic behaviour of receptor tyrosin kinase and protein tyrosine phospatase reaction network using mathematical model

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

Nikolov S, Vera J, Wolkenhauer O, Yankulova E, Petrov V (2007)
Chaos in a delayed protein cross talk model with periodic forcing

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

Schmidt H, Drews G, Vera J, Wolkenhauer O (2007)
SBML Export Interface for Systems Biology Toolbox for Matlab

Bioinformatics 23: 1297-1298
access

Sreenath SN, Soebyanto R, Mesarovic MD, Wolkenhauer O (2007)
Coordination of Crosstalk between MAPK-PKC Pathways: An Exploratory Study

IET Systems Biology 1: 33-40
access

Petrov V, Nikolova E, Wolkenhauer O (2007)
Reduction of Nonlinear Dynamic Systems with an Application to Signal Transduction Pathways

IET Systems Biology 1: 2-9
open access

Rateitschak K, Wolkenhauer O (2007)
Intracellular delay limits cyclic changes in gene expression

Mathematical Biosciences 205: 163-79
access

Vera J, Balsa-Canto E, Wellstead P, Banga J R, Wolkenhauer O (2007)
Power-Law Models of Signal Transduction Pathways

Cellular Signalling 19: 1531-1541
access

Millat T, Bullinger E, Rohwer J, Wolkenhauer O (2007)
Approximations and their Consequences in Dynamic Modelling of Signal Transduction Pathways

Mathematical Biosciences 47: 40-57
access

Wolkenhauer O, Hofmeyr J H (2007)
An Abstract Cell Model that describes the Self-Organization of Cell Function in Living Systems

Journal of Theoretical Biology 246: 461-476
access

Schmitz Y, Baurmann M, Engelen B, Feudel U (2007)
Pattern Formation of Competing Microorganisms in Sediments

Mathematical Modelling of Natural Phenomena 4: 74-104
access

Ullah M, Wolkenhauer O (2007)
Family tree of Markov models in systems biology

IET Systems Biology 1: 247-254
access

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

Proteomics 7: 33-46
open access

Vera J, Kwon T, Schmitz U, Millat T, Wolkenhauer O
Bioinformatics analysis of interactions of receptor homodimers with intracellular protein homodimers

Rostocker Informatik-Berichte, 31, 2007

2006

Lange C, Mix E, Rateitschak K, Rolfs A (2006)
Wnt signal pathways and neural stem cell differentiation

Neurodegenerative Dis. 3: 76-86
access

Assmus HE, Herwig R, Cho KH, Wolkenhauer O (2006)
Dynamics of biological systems: the role of systems biology in medical research

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

Shin SY, Choo SM, Kim D, Baek S J, Wolkenhauer O, Cho KH (2006)
Switching feedback mechanisms realize the dual role of MCIP in the regulation of calcineurin activity

FEBS Letters 580: 5965-5973
access

Dehmer M, Emmert-Streib F, Kilian J (2006)
A similarity measure for graphs with low computational complexity

Applied Mathematics and Computation 1: 447-459

access

Dehmer M, Mehler A (2006)
A new Method of Measuring Similarity for a Special Class of Directed Graphs

Tatra Mountains Mathematical Publications 39: 39-59

open access

Dehmer M (2006)
On the Location of Zeros for complex Polynomials

Journal of Inequalities in Pure and Applied Mathematics 1
open access

Emmert-Streib F, Dehmer M, Liu J, Mühlhäuser M (2006)
Ranking genes from DNA microarray data of cervical cancer by a local tree comparison

International Journal of Biomedical Science 1: 1-6
open access

Dehmer M, Emmert-Streib F, Mehler A, Kilian J (2006)
Measuring the Structural Similarity of Webbased Documents: A novel Approach

International Journal of Computational Intelligence 3: 1

no access

Dehmer M, Emmert-Streib F, Mehler A (2006)
Mining Graph Patterns in Web-based Systems

International Journal of Intelligent Information Technologies 4: 237-253
access

Dehmer M, Emmert-Streib F, Wolkenhauer O (2006)
Perspectives of Graph Mining Techniques

Rostocker Informatik Berichte 30: 47-56

no access

Schmidt H, Jirstrand M, Wolkenhauer O (2006)
Information Technology in Systems Biology

it - Information Technology 3: 133-139
access

Glass A, Koropka T, Wolkenhauer O (2006)
Bioinformatics and The Virtual Cell

it - Information Technology 1: 44-51
access

Ullah M, Schmidt H, Cho KH, Wolkenhauer O (2006)
Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB

IEE Proc Systems Biology 2: 53-60

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additional files

2005

Cho KH, Wolkenhauer O (2005)
Systems Biology: Discovering the Dynamic Behavior of Biochemical Networks

BioSystems Review 1: 9-17
open access

Vogl C, Sanchez-Cabo F, Stocker G, Hubbard S, Wolkenhauer O, Trajanoski Z (2005)
A fully Bayesian model to cluster gene expression profiles

Bioinformatics 2: 130-136
access

Cho KH, Choo SM, Wellstead P, Wolkenhauer O (2005)
A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data

FEBS Letters 579: 4520-4528
access

Petrov V, Nikolova E, Wolkenhauer O (2005)
A driver identification of the Ras/Raf/MEK/ERK signal transduction pathway

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

no access

Wolkenhauer O, Mesarovic M (2005)
Feedback dynamics and cell function: Why systems biology is called Systems Biology

Molecular BioSystems, Royal Society of Chemistry1: 14-16
access

Wolkenhauer O, Ullah M, Wellstead P, Cho KH (2005)
The dynamic systems approach to control and regulation of intracellular networks

FEBS Letters 579: 1846-1853
access

Wolkenhauer O, Sreenath S, Wellstead P, Ullah M, Cho KH (2005)
A systems- and signal-oriented approach to intracellular dynamics

Biochemical Society Transactions 3: 507-515
no access

Moller-Levet C, Klawonn F, Cho KH, Yin H, Wolkenhauer O (2005)
Clustering of unevenly sampled gene expression time-series data

Fuzzy Sets and Systems 152: 49-66
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additional files

Cho KH, Johansson KH, Wolkenhauer O (2005)
A hybrid systems framework for cellular processes

BioSystems 3: 273-282
access

2004 and older

Kutalik Z, Razaz M, Inwald J, Gordon S V, Wolkenhauer O (2004)
A novel statistical approach in comparative genomics to reveal new immunogenic antigens in M. bovis

Tissue Antigens 4: 427-427
open access

Wolkenhauer O, Ullah M, Kolch W, Cho KH (2004)
Modeling and simulation of intracellular dynamics: choosing an appropriate framework

IEEE Transactions on NanoBioScience 3: 200-207
open access

additional files

Hackl H, Sanchez-Cabo F, Sturn A, Wolkenhauer O, Trajanoski Z (2004)
Analysis of DNA microarray data

Curr. Top. Med. Chem. 4: 1355-1368
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Kutalik Z, Cho KH, Wolkenhauer O (2004)
Optimal sampling time selection for parameter estimation in dynamic pathway modeling

BioSystems 75: 43-55
access

additional files

Guebel DV, Torres NV (2004)
Interactive Astrocytic-Neuronal Sulphur Amino Acid Metabolism in mammalian brain:its assessment by a Mathematical Hybrid Model

Biochimica et Biophysica Acta 1674: 12-28
access

Kutalik Z, Inwald J, Gordon SV, Hewinson RG, Butcher P, Hinds J, Cho KH, Wolkenhauer O (2004)
Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis

Bioinformatics 3: 357-363

access

additional files

Cho KH, Wolkenhauer O (2003)
Analysis and modelling of signal transduction pathways in systems biology

Biochemical Society Transactions 6: 503-1509
access

Vera J, Torres NV (2003)
MetMAP: An integrated Matlab package for analysis and optimisation of metabolic systems

Silico Biology 4: 001
open access

Nunez-Garcia J, Mersinias V, Cho KH, Smith CP, Wolkenhauer O (2003)
The statistical distribution of the intensity of pixels within spots of DNA microarrays: what is the appropriate single-value representative?

Applied Bioinformatics 4: 229-239

no access

Vera J, Torres NV, Moles CG, Banga JR (2003)
Integrated nonlinear optimization of bioprocesses via linear programming

AIChE Journal 12: 3173-3187
open access

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

Simulation 12: 726-739
access

Sanchez-Cabo F, Cho KH, Hinds J, Wolkenhauer O (2004)
Assessing the efficiency of dye-swap normalization to remove systematic bias from two-color microarray data

Applied Bioinformatics
open access

additional files

Müller-Levet C, Cho KH, Wolkenhauer O (2003)
Microarray data clustering based on temporal variation: FCV with TSD preclustering

Open Mind Journals. Applied Bioinformatics 1: 35-45
open access

additional files

Nunez-Garcia J, Kutalik Z, Cho KH, Wolkenhauer O (2003)
Level sets and minimum volume sets of probability density functions

Approximate Reasoning 1: 25-47
access

Cho KH, Shin SY, Lee HW, Wolkenhauer O (2003)
Investigations into the analysis and modeling of the TNF alpha-mediated NF-kappa B-signaling pathway

Genome Research 13: 2413-2422
open access

Wolkenhauer O, Kitano H, Cho KH (2003)
An introduction to systems biology

IEEE Control Systems Magazine 4: 38-48

no access

Vera J, de Atauri P, Cascante M, Torres NV (2003)
Multicriteria optimization of biochemical systems by linear programming: Application to production of ethanol by Saccharomyces cerevisiae

Biotechnology and Bioengineering 3: 335-343

open access

Wolkenhauer O, Müller-Levet C, Sanchez-Cabo F (2002)
The curse of normalisation

Comparative and Functional Genomics 3: 375-379

open access

Cai Y, Dodson CJT, Doig A, Wolkenhauer O (2002)
Information-theoretic analysis of protein sequences shows that amino acids self-cluster

Journal of Theoretical Biology 218: 409-418

access

Wolkenhauer O (2002)
Mathematical modelling in the post-genome era: understanding genome expression and regulation - a system theoretic approach

BioSystems 1: 1-18

access

Nunez-Garcia J, Wolkenhauer O (2002)
Random set system identification

IEEE Transactions on Fuzzy Systems 3: 287-296

no access

Sidhu KS, Sangvanich P, Brancia F L, Sullivan A G, Gaskell SJ, Wolkenhauer O, Oliver SG, Hubbard S J (2001)
Bioinformatic assessment of mass spectrometric chemical derivatisation techniques for proteome database searching

Proteomics 11: 1368-1377

open access

Wolkenhauer O (2001)
Systems Biology: the reincarnation of systems theory applied in biology? Briefings in Bioinformatics

Henri Stewart Publications 3: 258-270

access

Wolkenhauer O, Edmunds J (1997)
Dynamic Systems Reliability Evaluation using Uncertainty Techniques for Performance Monitoring

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

access

Wolkenhauer O, Edmunds J (1997)
Possibilistic testing of distribution functions for change detection

Elsevier Science 2: 119-127

access

Wolkenhauer O, Edmunds J (1997)
A Critique of Fuzzy Logic in Control

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

no access