SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
Germany
+49 381 498-7571
olaf.wolkenhauer@uni-rostock.de
2024
Challenges and applications in generative AI for clinical tabular data in physiology
Chaithra Umesh, Manjunath Mahendra, Saptarshi Bej, Olaf Wolkenhauer, Markus Wolfien
Bitter peptide prediction using graph neural networks
Prashant Srivastava, Alexandra Steuer, Francesco Ferri, Alessandro Nicoli, Kristian Schultz, Saptarshi Bej, Antonella Di Pizio and Olaf Wolkenhauer
Regulatory Role of IL-6 in Immune-Related Adverse Events During Checkpoint Inhibitor Treatment in Melanoma
Krishna Pal Singh, Anuj Singh, Olaf Wolkenhauer, Shailendra Kumar Gupta
Large-scale knowledge graph representations of disease processes
Hoch M, Wolkenhauer O, Gupta S
Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy.
Lischer C, Eberhardt M, ... , Gupta S, Singh KP, ... , Wolkenhauer O, ... , Vera J
Kreeftforschen mit Mathe un Computers
Olaf Wolkenhauer
Quickborn, 114. Jahrgang, Heft 1, 2024, 36-43
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model.
Singh S, Yadav S, Cavallo C, Mourya D, Singh I, Kumar V, Shukla S, Shukla P, Chaudhary R, Maurya GP, Müller RLJ, Rohde L, Mishra A, Wolkenhauer O, Gupta S, Tripathi A.
Multivariate Functional Linear Discriminant Analysis for the Classification of Short Time Series with Missing Data
Bordoloi R, Réda C, Trautmann O, Bej S, Wolkenhauer O
submitted for publication in arXiv
Whole blood RNA-Seq identifies transcriptional differences between primary sclerosing cholangitis and ulcerative colitis
Wacker EM, Uellendahl-Werth F, Bej S, Wolkenhauer O, Vesterhus M, Lieb W, Franke A, Karlsen TH, Folseraas T, Ellinghaus D
stanscofi and benchscofi: a new standard for drug repurposing by collaborative filtering
Réda C, Vie J-J, Wolkenhauer O
Drug-Target identification in COVID-19 disease mechanisms using computational systems biology approaches
Niarakis A, Ostaszewski M, ... Wolkenhauer O, ..., Kitano H, Barillot E, Auffray C, Balling R, Schneider R
accepted for publication in Frontiers in Immunology
ConvGeN: A convex space learning approach for deep-generative oversampling and imbalanced classification of small tabular datasets
Schultz K, Bej S, Hahn W, Wolfien M, Srivastava P, Wolkenhauer O
2023
Exploring Thiazolopyridine AV25R: Unraveling of Biological Activities, Selective Anti-Cancer Properties and In Silico Target and Binding Prediction in Hematological Neoplasms
Ladwig A, Gupta S, Ehlers P, Sekora A, Alammar M, Koczan D, Wolkenhauer O, Junghanss C, Langer P, Murua Escobar H
Molecules (Special Issue Small Molecules in
Targeted Cancer Therapy)
Logic-based modeling and drug repurposing for the prediction of novel therapeutic targets and combination regimens against E2F1-driven melanoma progression
Singh N, Khan FM, Bala L, Vera J, Wolkenhauer O, Pützer B, Logotheti S, Gupta SK
NaviCenta – The disease map for placental research
Scheel J, Hoch M, Wolfien M, Gupta S
Uncoupling protein 2 deficiency of non-cancerous tissues inhibits the progression of pancreatic cancer in mice
Revskij D, Runst J, Umstätter C, Ehlers L, Rohde S, Zechner D, Bastian M, Müller-Hilke B, Fuellen G, Henze L, Escobar HM, Junghanss C, Kowald A, Walter U, Köhling R, Wolkenhauer O, Jaster R
Integrated systems biology approach to identify key candidate genes, signaling pathways and therapeutic targets of oral squamous cell carcinoma
Choubey J, Wolkenhauer O, Chatterjee T
Accounting for diverse feature-types improves patient stratification on tabular clinical datasets
Bej S, Umesh C, Mahendra M, Schultz K, Sarkar J, Wolkenhauer O
Machine Learning with Applications
(Volume 14, 2023)
CCR2 macrophage response determines the functional outcome following cardiomyocyte transplantation
Vasudevan P, Wolfien M, Lemcke H, Lang CI, Skorska A, Gaebel R, Galow AM, Koczan D, Lindner T, Bergmann W, Mueller-Hilke B, Vollmar B, Krause BJ, Wolkenhauer O, Steinhoff G, David R
Metabolic function-based normalization improves transcriptome data-driven reduction of genome-scale metabolic models
Salehzadeh-Yazdi A, Jalili M, Scharm M, Wolkenhauer O
Ten topics to get started in Medical Informatics research
Wolfien M, Ahmadi N, Fitzer K, Grummt S, Heine KL, Jung IC, Krefting D, Kühn A, Peng Y, Reinecke I, Scheel J, Schmidt T, Schmücker P, Schüttler 7, Waltemath D, Zoch M, Sedlmayr M
J Med Internet Res. (Epub ahead of print)
DOI: 10.2196/45948
Uncoupling protein 2 deficiency of non-cancerous tissues inhibits the progression of pancreatic cancer in mice
Revskij D, Runst J, Umstätter C, Ehlers L, Rohde S, Zechner D, Bastian M, Müller-Hilke B, Fuellen G, Henze L, Escobar HM , Junghanss C, Kowald A, Walter U, Köhling R, Wolkenhauer O, Jaster R
Leptin deficiency-caused behavioral change -a comparative analysis using EthoVision and DeepLabCut
Bühler D, Power-Guerra N, Müller L, Wolkenhauer O, Düffer M, Vollmar B, Kuhla A, Wolfien M
Cell-Type-Specific Gene Regulatory Networks of Pro-Inflammatory and Pro-Resolving Lipid Mediator Biosynthesis in the Immune System
Hoch M, Jannik R, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Valerio C, Gupta S
Network analyses reveal new insights into the effect of multicomponent Tr14 compared to single-component diclofenac in an acute inflammation model
Hoch M, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Gupta S
DOI: 10.1186/s12950-023-00335-0
Pubmed: 36973809
Construction of a three-component regulatory network of transcribed ultraconserved regions for the identification of prognostic biomarkers in gastric cancer
Khalafiyan A, Emadi-Baygi M, Wolfien M, Salehzadeh-Yazdi A, Nikpour P
DOI: 10.1002/jcb.30373
2022
In silico investigation of molecular networks linking gastrointestinal diseases, malnutrition, and sarcopenia
Hoch M, Ehlers L, Bannert K, Stanke C, Brauer C, Caton V, Lamprecht G, Wolkenhauer O, Jaster R, Wolfien M
Frontiers in Nutrition (2022)
Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence
Vera J, Lai X, Baur A, Erdmann M, Gupta S, Guttà C, Heinzerling L, Heppt MV, Kazmierczak PM, Kunz M, Lischer C, Pützer BM, Rehm M, Ostalecki C, Retzlaff J, Witt S, Wolkenhauer O, Berking C
Briefings in Bioinformatics (2022)
Perspectives of (/Memorandum for) Systems Thinking on Covid-19 Pandemic and Pathology
Wolkenhauer O
A workflow for the creation of regulatory networks integrating miRNAs and lncRNAs associated with exposure to ionizing radiation using open source data and tools
Freiesleben S, Unverricht-Yeboah M, Gütebier L, Waltemath D, Kriehuber R, Wolkenhauer O
accepted for publication in Frontiers in Systems Biology
Detection and Analysis of Critical Dynamic Properties of Oligodendrocyte Differentiation
Nikolov SG, Wolkenhauer O, Nenov M, Vera J
Mathematics (2022)
Contribution of Synthetic Data Generation towards an Improved Patient Stratification in Palliative Care
Hahn W, Schütte K, Schultz K, Wolkenhauer O, Sedlmayr M, Schuler U, Eichler M, Bej S, Wolfien M
JPM (2022)
Identification and epidemiological characterization of Type-2 Diabetes sub-population using an unsupervised machine learning approach
Bej S, Sarkar J, Biswas S, Mitra P, Chakrabarti P, Wolkenhauer O
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps
Hoch M, Smita S, Cesnulevicius K, Lescheid D, Schultz M, Wolkenhauer O, Gupta S
On the role of data, statistics and decisions in a pandemic
Jahn B, Friedrich S, Behnke J, Engel J, Garczarek U, Münnich R, Pauly M, Wilhelm A, Wolkenhauer O, Zwick M, Siebert U, Friede T
Exploring the evolution of biochemical models at the network level
Gebhardt T, Touré V, Waltemath D, Wolkenhauer O, Scharm M
PLOS ONE (2022)
Attention retrieval model for entity relation extraction from biological literature
Srivastava P, Bej S, Schultz K, Yordanova K, Wolkenhauer O
IEEE Xplore (2022)
Monitoring the maturation of the sarcomere network: a super-resolution microscopy-based approach
Skorska A, Johann L, Chabanovska O, Vasudevan P, Kussauer S, Hillemanns M, Wolfien M, Jonitz-Heincke A, Wolkenhauer O, Bader R, Lang H, David R, Lemcke H
CLMS (2022)
Single extracellular vesicle analysis in human amniotic fluid shows evidence of phenotype alterations in preeclampsia
Gebara N, Scheel J, Skovronova R, Grange C, Marozio L, Gupta S, Giorgione V, Caicci F, Benedetto C, Khalil A, Bussolati B
bioRxiv (2022)
The Prognostic and Predictive Role of Xeroderma Pigmentosum Gene Expression in Melanoma
Fischer S, Hamid M, Emmert S, Wolkenhauer O, Fuellen G, Thiem A
Frontiers in Oncology (2022)
Computational Models for Clinical Applications in Personalized Medicine—Guidelines and Recommendations for Data Integration and Model Validation
Collin CB, Gebhardt T, Golebiewski M, Karaderi T, Hillemanns M, Khan FM, Salehzadeh-Yazdi A, Kirschner K, Krobitsch S, EU-STANDSPM consortium, Kuepfer L
MDPI JPM (2022)
Cross-tissue transcriptome-wide association studies identify susceptibility genes shared between schizophrenia and inflammatory bowel disease
Uellendahl-Werth F, Maj C, Borisov O, Wacker EM, Bej S, Wolkenhauer O, Degenhardt F, Ellinghaus D et al.
Nature Comms Bio (2022)
2021
Overexpression of microRNAs miR-25-3p, miR-185-5p and miR-132-3p in Late Onset Fetal Growth Restriction, Validation of Results and Study of the Biochemical Pathways Involved
Loscalzo G, Scheel J, Ibañez-Cabellos J S, García-Lopez E, Gupta S, García-Gimenez J L, Mena-Mollá S, Perales-Marín A, Morales-Roselló J
IJMS (2021)
Personalized cell therapy for patients with peripheral arterial diseases in the context of genetic alterations: Artificial intelligence-based responder and non-responder prediction
Salybekov AA, Wolfien M, Kobayashi S, Steinhoff G, Asahara T
Cells 2021
Automated annotation of rare-cell types from single-cell RNA-sequencing data through synthetic oversampling
Bej S, Galow AM, David R, Wolfien M, Wolkenhauer O
BMC Bioinformatics 2021
Self-attention based models for the extraction of molecular interactions from biological texts
Srivastava P, Bej S, Yordanova K, Wolkenhauer O
Biomolecules 2021
Imagining the Future of Learning in Healthcare: The GAME 2019 #FuturistForum
Murray S, Koksma J, Haramati A, Bonnefoy E, Zary N, Bill W, Wolkenhauer O, Price S & Kummerle D
Comprehensive Characterization of Multitissue Expression Landscape, Co-Expression Networks and Positive Selection in Pikeperch
Nguinkal JA, Verleih M, de los Ríos-Pérez L, Brunner RM, Sahm A, Bej S, Rebl A, Goldammer T
Cells 2021
Fibroblast Growth Factor 21 as a Potential Biomarker for Improved Locomotion and Olfaction Detection Ability after Weight Reduction in Obese Mice
Power Guerra N, Parveen A, Bühler D, Brauer DL, Müller L, Pilz K, Witt M, Glass Ä, Bajorat R, Janowitz D, Wolkenhauer O, Vollmar B, Kuhla A
Nutrients 2021
COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms
Ostaszewski M, Niarakis A, Mazein A, Wolkenhauer O et al.
Quality control in scRNA-Seq can discriminate pacemaker cells – the mtDNA bias
Galow AM, Kussauer S, Wolfien M, Brunner R, Goldammer T, David R, Hoeflich A
AMES: Automated evaluation of sarcomere structures in cardiomyocytes
Hillemanns M, Lemcke H, David R, Martinetz T, Wolfien M, Wolkenhauer O
bioRxiv 2021
A Metabolic Model of Intestinal Secretions: The Link between Human Microbiota and Colorectal Cancer Progression
Salahshouri P, Emadi-Baygi M, Jalili N , Khan F.M, Wolkenhauer O and Salehzadeh-Yazdi A
Metabolites 2021
A multi-schematic classifier-independent oversampling approach for imbalanced datasets
Bej S, Schultz K, Srivastava P, Wolfien M, Wolkenhauer O
IEEE Access 2021
Placental mitochondrial function as a driver of angiogenesis and placental dysfunction
Correia Y, Scheel J, Gupta S, Wang K
De Gruyter BioChem (2021)
Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models
Jalili M, Scharm M, Wolkenhauer O, Damaghi M and Salehzadeh-Yazdi A
The role of epigenetic modifications for the pathogenesis of Crohn's disease
Hornschuh M, Wirthgen E, Wolfien M, Singh KP, Wolkenhauer O, Däbritz J
Clinical Epigenetics 2021
A New Perspective on Teaching the Natural Exponential to Engineering Students
Ullah M, Aman MN, Wolkenhauer O, Iqbal J
The quest for systems-theoretical medicine in the COVID-19 era
Tretter F, Wolkenhauer O, Meyer-Hermann M, Dietrich JW, Green S, Marcum J, Weckwerth W
2020
Towards biomarkers for outcomes after pancreatic ductal anocarcinoma and ischemic stroke, with focus on (co-)morbidity and aging / cellular senescence (SASKit): protocol for a prospective cohort study
Henze L, Walter U, Murua Escobar H, Junghanß C, Jaster R, Köhling R, Lange F, Salehzadeh-Yazdi A, Wolkenhauer O, Hamed M, Barrantes I, Palmer D, Möller S, Kowald A, Heussen N, Fuellen G
BMJ Open 2020
LoRAS: An oversampling approach for imbalanced datasets
Bej S, Davtyan N, Wolfien M, Nassar M, Wolkenhauer O
Machine Learning 2020
COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity's fight
Auffray C, Balling R, Blomberg N, ..., Wolkenhauer O, Wouters E
F1000Research 2020, 9:1130
The Atlas of Inflammation-Resolution (AIR)
Serhan CN, Gupta SK, ... , Smita S, Schopohl P, Hoch M, Gjorgevikj D, Khan FM, Brauer D, ... , Wolkenhauer O
Enzyme-constrained models and omics analysis of Streptomyces coelicolor reveal metabolic changes that enhance heterologous production
Sulheim S, Kumelj T, van Dissel D, Salehzadeh-Yazdi A, Du Ch, P. van Wezel G, Nieselt K, Almaas E, Wentzel A, Kerkhoven E
iScience 2020
Hamiltonian cycles in annular decomposable Barnette graphs
Bej S
Cardiomyocyte Transplantation after Myocardial Infarction Alters the Immune Response in the Heart
Vasudevan P, Wolfien M, Lemcke H, Lang CI, Skorska A, Gaebel R, Koczan D, Lindner T, Engelmann R, Vollmar B, Krause BJ, Wolkenhauer O, Lang H, Steinhoff G, David R
Cells 2020, 9(8), 1825
LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1
Logotheti S, Marquardt S, Gupta SK, Richter C, Edelhäuser BAH, Engelmann D, Brenmoehl J, Söhnchen C, Murr N, Alpers M, Singh KP, Wolkenhauer O, Heckl D, Spitschak A, Pützer BM
Theranostics 2020; 10(21):9620-9643.
An integrative network-driven pipeline for systematic identification of lncRNA-associated regulatory network motifs in metastatic melanoma
Singh N, Eberhardt M, Wolkenhauer O, Vera J, Gupta SK
BMC Bioinformatics 2020, 21 (1), 1-17
Objective assessment of stored blood quality by deep learning
Doan M, ..., Wolkenhauer O, Hennig H, ..., Carpenter AE
PNAS 2020
Hematopoietic Stem-Cell Senescence and Myocardial Repair
Wolfien M, Klatt D, Salybekov, ... , Wolkenhauer O, Schambach A, Asahara T, Steinhoff G
EBioMedicine 2020
Omics Integration Analyses Reveal the Early Evolution of Malignancy in Breast Cancer
Sarhadi Sh, Salehzadeh-Yazdi A, Damaghi M, Zarghami N, Wolkenhauer O and Hosseini H
Cancers 2020, 12(6), 1460
Integrative cluster analysis of whole hearts reveals proliferative cardiomyocytes in adult mice
Galow AM, Wolfien M, Müller P, Bartsch M, Brunner RM, Hoeflich A, Wolkenhauer O, David R, Goldammer T
Cells 2020, 9 (5), 1144
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
Ostaszewski M, Mazein A, Gillespie, ME, Wolkenhauer O et al.
The role of cooperativity in a p53-miR34 dynamical mathematical model
Nikolov S, Wolkenhauer O, Vera J, Nenov M
A benchmark of hemoglobin blocking during library preparation for mRNA-Sequencing of human blood samples
Uellendahl-Werth F, Wolfien M, Franke A, Wolkenhauer O, Ellinghaus D
Scientific Reports 2020, 10, 5630
Single Nuclei Sequencing of entire Mammalian Hearts: Strain-dependent Cell Type Composition and Velocity
Wolfien M, Galow AM, Müller P, Bartsch M, Brunner RM, Goldammer T, Wolkenhauer O, Hoeflich A, David R
RNA-Based Strategies for Cardiac Reprogramming of Human Mesenchymal Stromal Cells
Mueller P, Wolfien M, Ekat K, Lang CI, Koczan D, Wolkenhauer O, Hahn O, Peters K, Lang H, David R, Lemcke H
Cells 2020, 9 (2), 504
Label-free leukemia monitoring by computer vision
Doan M, Case M, Masic D, Hennig H, ... Wolkenhauer O, ... Irving J
Cytometry Part A 2020
https://github.com/carpenterlab/2019_doan_leukemia_submitted
TGF-ß1 induces changes in the energy metabolism of white adipose tissue-derived human adult mesenchymal stem/stromal cells in vitro
Hahn O, Ingwersen LC, Soliman A, Hamed M, Fuellen G, Wolfien M, Scheel J, Wolkenhauer O, Koczan D, Kamp G, Peters K
Metabolites 2020, 10 (2), 59
GEMtractor: Extracting Views into Genome-scale Metabolic Models
Scharm M, Wolkenhauer O, Jalili M, Salehzadeh-Yazdi A
Single Nuclei Sequencing of an entire Mammalian Heart: Cell Type Composition and Velocity
Wolfien M, Galow AM, Müller P, Bartsch M, Brunner RM, Goldammer T, Wolkenhauer O, Hoeflich A, David R
Cells 2020, 9, 318
2019
C. elegans protein interaction network analysis probes RNAi validated pro-longevity effect of nhr-6, a human homolog of tumor suppressor Nr4a1
Akhoon BA, Gupta SK, Tiwari S, Rathor L, Pant A, Singh N, Gupta SK, Dandekar T, Pandey R
Sci Rep. 2019 Oct 31;9(1):15711.
Protein-coding variants contribute to the risk of atopic dermatitis and skin-specific gene expression
Mucha S, ... Bej S, ..., Wolfien M, ..., Wolkenhauer O, ..., Ellinghaus D
Vom Anfang und Ende der Systembiologie
Wolkenhauer O
BIOspektrum 05.19 Springer
A systems appraoch to investigate inflammation resolution by multicomponent medicinal product TR14
Schopohl P, Smita S, Khan F, Gebhardt T, Hoch M, Brauer D, Cesnulevicius D, Schultz M, Wolkenhauer O, Gupta S
Label-Free Identification of White Blood Cells Using Machine Learning
Nassar M, Doan M, Filby A, Wolkenhauer O, Fogg DK, Piasecka J, Thornton CA, Carpenter AE, Summers HD, Rees P, Hennig H
Cytometry part A
The RNA workbench 2.0: next generation RNA data analysis
Fallmann J, Pavankumar V, Bagnacani A, ..., Gruening BA
Nucleic Acid Research
DOI: 10.1093/nar/gkz353
Recent advancement in the early detection of melanoma using computerized tools: An image analysis perspective
Singh N, Gupta SK
Skin Res Technol. 2019;25(2):129-141
Drug Repositioning Inferred from E2F1-Coregulator Interactions Studies for the Prevention and Treatment of Metastatic Cancers.
Goody D, Gupta SK, Engelmann D, Spitschak A, Marquardt S, Mikkat S, Meier C, Hauser C, Gundlach JP, Egberts JH, Martin H, Schumacher T, Trauzold A, Wolkenhauer O, Logotheti S, Pützer BM.
Theranostics. 2019 Feb 20;9(5):1490-1509.
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
Community-driven data analysis training for biology
Batut B, Hiltemann S, Bagnacani A, …, Wolfien M, ..., Gruening B
Cell Systems 2018
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)
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, 80(2) 360-384
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
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, (2018) Vol. 38 (2) 304-316
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 2017, 22, 208-224
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
DOI: 10.1093/nar/gkx409
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)
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
DOI: 10.1159/000477324
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 Taher
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
Jalili M, Salehzadeh-Yazdi A, Gupta S, Wolkenhauer O, Yaghmaie M, Resendis-Antonio O and Alimoghaddam K
Frontiers in Physiology
Cancerome: A hidden informative subnetwork of the diseasome
Jalili M, Salehzadeh-Yazdi A, Yaghmaie M, Ghavamzadeh A, Alimoghaddam K
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)
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.
DOI: 10.1093/nar/gkv885
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.
DOI: 10.1093/bib/bbv046
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.
DOI: 10.1039/c5mb00245a
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.
DOI: 10.1049/iet-syb.2013.0031
URL: http://digital-library.theiet.org/content/journals/10.1049/iet-syb.2013.0031
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,
DOI: 10.1038/pr.2013.33
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
DOI: 10.1002/ijc.28148
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,
DOI: 10.1155/2013/703849
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)
- DILS-SYS-EC-paper8.pdf (workshop proceedings)
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
DOI: 10.1016/j.jtbi.2009.05.022
URL: http://www.sciencedirect.com/science/article/pii/S0022519309002471
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
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
access
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
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
DOI: 10.1042/BST0330507
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
DOI: 10.1016/j.biosystems.2004.03.007
URL: http://www.sciencedirect.com/science/article/pii/S0303264704000395
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
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