Selected Publications

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2024

A. F. F. Hansel-Frose, M. Friedrichs, J. Allmer
MicroRNA Databases
in L. M. Vaschetto (eds): miRNAs, Human Health and Diseases, Springer Nature Switzerland, 2024.
DOI: 10.1007/978-3-031-64788-8_2
A. F. F. Hansel-Frose, J. Allmer, M. Friedrichs, H. Geremias dos Santos, B. Dallagiovanna, L. Spangenberg
Alternative polyadenylation and dynamic 3' UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs
Front. Mol. Biosci. 11, 2024.
DOI: 10.3389/fmolb.2024.1336336

2023

M. Friedrichs, C. Königs
A web-based platform for the annotation and analysis of NAR-published databases
PLoS ONE 18(10), 2023.
DOI: 10.1371/journal.pone.0293134
J. Allmer, R. Hofestädt
Medizinische Omik
GMS Med Inform Biom Epidemiol 2023.
DOI: 10.3205/mibe000246
M. Friedrichs
A web-based annotation tool for clinical trial failure reasons
GMS Med Inform Biom Epidemiol 2023.
DOI: 10.3205/mibe000241
C. Königs, T. Dietrich
A web-based pathway enrichment analysis module for the PharMeBINet database
GMS Med Inform Biom Epidemiol 2023.
DOI: 10.3205/mibe000243
L. Raupach
Integration of biological molecular data into an existing drug therapy safety workflow used in hospital information systems
GMS Med Inform Biom Epidemiol 2023.
DOI: 10.3205/mibe000242
L. Raupach, C. Königs
PharmoCo: a graph-based visualization of pharmacogenomic plausibility check reports for clinical decision support systems
Journal of Integrative Bioinformatics 2023.
DOI: 10.1515/jib-2023-0026

2022

C. Königs, M. Friedrichs, T. Dietrich
The heterogeneous pharmacological medical biochemical network PharMeBINet
Sci Data 2022.
DOI: 10.1038/s41597-022-01510-3
M. Chen, R. Hofestädt (eds)
Integrative Bioinformatics: History and Future
DOI: 10.1007/978-981-16-6795-4, Springer Singapore, 2022.
- M. Chen, R. Hofestädt, J. Taubert
  Integrative Bioinformatics: History and Perspective
  in M. Chen, R. Hofestädt (eds): Integrative Bioinformatics - History and Future, Springer Singapore, 2022.
  DOI: 10.1007/978-981-16-6795-4_1
- M. Friedrichs
  Automation in Graph-Based Data Integration and Mapping
  in M. Chen, R. Hofestädt (eds): Integrative Bioinformatics - History and Future, Springer Singapore, 2022.
  DOI: 10.1007/978-981-16-6795-4_5
- Y. Zhou, R. Hofestädt, M. Chen
  DaTo: An Integrative Web Portal for Biological Databases and Tools
  in M. Chen, R. Hofestädt (eds): Integrative Bioinformatics - History and Future, Springer Singapore, 2022.
  DOI: 10.1007/978-981-16-6795-4_6
- M. Friedrichs
  Data Integration Applications in Medical Information Systems
  in M. Chen, R. Hofestädt (eds): Integrative Bioinformatics - History and Future, Springer Singapore, 2022.
  DOI: 10.1007/978-981-16-6795-4_11
- C. Brinkrolf, L. Ochel
  Comprehensive Open-Source Petri Net Toolchain for Modeling and Simulation in Systems Biology
  in M. Chen, R. Hofestädt (eds): Integrative Bioinformatics - History and Future, Springer Singapore, 2022.
  DOI: 10.1007/978-981-16-6795-4_13
V. Murali, Y. M. Pradyumna, C. Königs, M. Nair, Sethulekshmi, P. Nedungadi, G. Srinivasa, P. Athri
Predicting Clinical Trial Outcomes Using Drug Bioactivities through Graph Database Integration and Machine Learning
Chemical Biology & Drug Design, 2022.
DOI: 10.1111/cbdd.14092

2021

Md. A. Ahsan, Y. Liu, C. Feng, R. Hofestädt, M. Chen
OverCOVID: an integrative web portal for SARS-CoV-2 bioinformatics resources
Journal of Integrative Bioinformatics, 2021.
DOI: 10.1515/jib-2020-0046
C. Brinkrolf, L. Ochel, R. Hofestädt
VANESA: An open-source hybrid functional Petri net modeling and simulation environment in systems biology
Biosystems, 210:104531, 2021.
DOI: 10.1016/j.biosystems.2021.104531
M. Friedrichs
BioDWH2: an automated graph-based data warehouse and mapping tool
Journal of Integrative Bioinformatics, 2021.
DOI: 10.1515/jib-2020-0033
M Edich, M. Friedrichs
EvoDock: Optimization of protein-ligand binding interfaces
Acta Crystallographica Section A: Foundations and Advances, 2021.
DOI: 10.1107/S0108767321090012

2020

V. Murali, C. Königs, S. Deekshitula, S. Nukala, M. D. Santhi, P. Athri
CompoundDB4j: Integrated Drug Resource of Heterogeneous Chemical Databases
Molecular Informatics, 39(9), 2020.
DOI: 10.1002/minf.202000013
O. Snow, H. Sharifi-Noghabi, J. Lu, O. Zolotareva, M. Lee, M. Ester
BDKANN - Biological Domain Knowledge-based Artificial Neural Network for drug response prediction
bioRxiv, 2020.
DOI: 10.1101/840553
R. Hofestädt
Bioinformatik und Medizinische Informatik
Traumjob it 2021 Hrsg: K. Folz, e-fellows net, München 2020, 27-29
DOI: 10.36193/9783946706670
Y. L. Orlov, O. B. Dobrovolskaya, M. Chen, R. Hofestädt
Bioinformatics of genome regulation and structure – 2020 papers collection
Journal of Integrative Bioinformatics, 17(4), 2020.
DOI: 10.1515/jib-2020-0038

2019

M. Friedrichs, A. Shoshi, P.J. Chmura, J. Ison, V. Schwämmle, F. Schreiber, R. Hofestädt, B. Sommer
JIB.tools 2.0 – A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools
Journal of Integrative Bioinformatics 16(4), 2019.
DOI: 10.1515/jib-2019-0059
M. Friedrichs, A. Shoshi
History and Future of KALIS: Towards Computer-assisted Decision Making in Prescriptive Medicine
Journal of Integrative Bioinformatics 16(3), 2019.
DOI: 10.1515/jib-2019-0011
O. Zolotareva, M. Kleine
A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases
Journal of Integrative Bioinformatics.
DOI: 10.1515/jib-2018-0069
O. Zolotareva, O.V. Saik, C. Königs, E.Y. Bragina, I.A. Goncharova, M.B. Freidin, V.E. Dosenko, V.A. Ivanisenko, R. Hofestädt
Comorbidity of asthma and hypertension may be mediated by shared genetic dysregulation and drug side effects
Scientific reports.
DOI: 10.1038/s41598-019-52762-w
L. Zhu, R. Hofestädt, M. Ester
Tissue-Specific Subcellular Localization Prediction Using Multi-Label Markov Random Fields
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 16(5): 1471-1482.
DOI: 10.1109/TCBB.2019.2897683
Y.L. Orlov, R. Hofestädt, A.V. Baranova
Systems biology research at BGRS-2018
BMC Systems Biology 2019, 13(Suppl 1):21.
DOI: 10.1186/s12918-019-0685-z
R. Hofestädt
Bioinformatik und Medizinische Informatik
Traumjob it Hrsg: K. Folz, e-fellows net, München 2019, 27-29.
M. Chen, R. Hofestädt, J. Taubert
Integrative Bioinformatics: History and Future
Journal of Integrative Bioinformatics, 16 (3), 2019
DOI: 10.1515/jib-2019-2001
H. Sharifi-Noghabi, O. Zolotareva, C.C. Collins, M. Ester
MOLI: multi-omics late integration with deep neural networks for drug response prediction
Bioinformatics, Volume 35, Issue 14, July 2019, Pages i501-i509
DOI: 10.1093/bioinformatics/btz318

2018

A. Shoshi, R. Hofestädt, O. Zolotareva, M. Friedrichs, A. Maier, V. A. Ivanisenko, V. E. Dosenko, E. Yu. Bragina
GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks
Journal of Integrative Bioinformatics 15(4), 2018.
DOI: 10.1515/jib-2018-0049
O. V. Saik, P. S. Demenkov, T. V. Ivanisenko, E. Yu. Bragina, M. B. Freidin, V. E. Dosenko, O. I. Zolotareva, E. L. Choynzonov, R. Hofestädt, V. A. Ivanisenko
Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature
Journal of Integrative Bioinformatics 15(4), 2018.
DOI: 10.1515/jib-2018-0054
E. Yu. Bragina, I. A. Goncharova, A. F. Garaeva, E. V. Nemerov, A. A. Babovskaya, A. B. Karpov, Y. V. Semenova, I. Z. Zhalsanova, D. E. Gomboeva, O. V. Saik, O. I. Zolotareva, V. A. Ivanisenko, V. E. Dosenko, R. Hofestädt, M. B. Freidin
Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases
Journal of Integrative Bioinformatics 15(4), 2018.
DOI: 10.1515/jib-2018-0052
T. Drevytska, R. Morhachov, L. Tumanovska, G. Portnichenko, V. Nagibin, O. Boldyriev, T. Lapikova-Bryhinska, V. Gurianova, B. Dons'koi, M. Freidin, V. Ivanisenko, E. Yu. Bragina, R. Hofestädt, V. Dosenko
shRNA-Induced Knockdown of a Bioinformatically Predicted Target IL10 Influences Functional Parameters in Spontaneously Hypertensive Rats with Asthma
Journal of Integrative Bioinformatics 15(4), 2018.
DOI: 10.1515/jib-2018-0053
C. Brinkrolf, N. A. Henke, L. Ochel, B. Pucker, O. Kruse, P. Lutter
Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA
Journal of Integrative Bioinformatics 15(3), 2018.
DOI: 10.1515/jib-2018-0018
C. Brinkrolf, P. Reipke
OMPetri - A Software Application for Modeling and Simulation Using Extended Hybrid Petri Nets by Employing OpenModelica
Khomenko V., Roux O. (eds) Application and Theory of Petri Nets and Concurrency. PETRI NETS 2018. Lecture Notes in Computer Science 10877:406-415, 2018.
DOI: 10.1007/978-3-319-91268-4_23
R. Hofestädt, C. Brinkrolf, P. Reipke
OMPetri: A New Petri Net Simulation Environment Based on OpenModelica
Proceedings of the 2018 10th International Conference on Bioinformatics and Biomedical Technology - ICBBT '18. ACM Press. 57-61, 2018.
DOI: 10.1145/3232059.3232073
H. Hamzeiy, R. Suluyayla, C. Brinkrolf, S. J. Janowski, R. Hofestädt, J. Allmer
Visualization and Analysis of miRNAs Implicated in Amyotrophic Lateral Sclerosis Within Gene Regulatory Pathways
IOS Press in the Studies in Health Technologies and Informatics series 253:183-187, 2018.
DOI: 10.3233/978-1-61499-896-9-183
M. Friedrichs, A. Shoshi, M. Kleine
Data-Driven Assessment of Potentially Inappropriate Medication in the Elderly
IOS Press in the Studies in Health Technologies and Informatics series 253:125-129, 2018.
DOI: 10.3233/978-1-61499-896-9-125
N. Biere, M. Ghaffar, A. Doebbe, D. Jäger, N. Rothe, B.M. Friedrich, R. Hofestädt, F. Schreiber, O. Kruse, B. Sommer
Heuristic Modeling and 3D Stereoscopic Visualization of a Chlamydomonas reinhardtii Cell
Journal of Integrative Bioinformatics 15(2), 2018.
DOI: 10.1515/jib-2018-0003
O. V. Saik, P. S. Demenkov, T. V. Ivanisenko, E. Y. Bragina, M. B. Freidin, I. A. Goncharova, V. E. Dosenko, O. I. Zolotareva, R. Hofestädt, I. N. Lavrik, E. I. Rogaev, V. A. Ivanisenko
Novel candidate genes important for asthma and hypertension comorbidity revealed from associative gene networks.
BMC Medical Genomics 11(1):15, 2018.
DOI: 10.1186/s12920-018-0331-4

2017

J. Allmer, C. Brinkrolf, R. Hofestädt, M. D. Saçar Demirci (eds)
Computational Systems Biology: German/Turkish Network of Bioinformatics - Report 2016.
Shaker Verlag, Aachen 2017.
R. Hofestädt
Advantages of Petri-Net Modeling and Simulation for Biological Networks.
Journal of Bioscience, Biochemstry and Bioinformatics 7(4):221-229, 2017.
DOI: 10.17706/ijbbb.2017.7.4.221-229
H. Hamzeiy, R. Suluyayla, C. Brinkrolf, S. Janowski, R. Hofestädt, J. Allmer
Visualization and Analysis of Micro RNAs within KEGG Pathways using VANESA.
Journal of Integrative Bioinformatics 14(1), 2017.
DOI: 10.1515/jib-2016-0004
A. Shoshi, U. Müller, A. Shoshi, V. Ogultarhan, R. Hofestädt
KALIS - An eHealth system for biomedical risk analysis of drugs.
IOS Press in the Studies in Health Technologies and Informatics series 236:128-135, 2017.
DOI: 10.3233/978-1-61499-759-7-128
L. Zhu, M. Ester
Bayesian Collective Markov Random Fields for Subcellular Localization Prediction of Human Proteins.
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics, ACM-BCB '17 ACM Press, pp. 321-329. Boston, Massachusetts, USA, 2017.
DOI: 10.1145/3107411.3107412

2016

Y. L. Orlov, A. V. Baranova, R. Hofestädt, N. A. Kolchanov
Computational genomics at BGRS\SB-2016: introductory note.
BMC Genomics 17:3350, 2016.
DOI: 10.1186/s12864-016-3350-6
A. Winter, R.-D. Hilgers, R. Hofestädt, P. Knaup-Gregori, C. Ose, A. Timmer
Data Integration for Integrated Research and Care.
Methods of Information in Medicine 55(4):365-366, 2016.
DOI: 10.3414/ME2016040001
Q. Li, Y. Zhou, Y. Jiao, Z. Zhang, L. Bai, L. Tong, X. Yang, B. Sommer, R. Hofestädt, M. Chen
DaTo: an atlas of biological databases and tools.
Journal of Integrative Bioinformatics 13(2):297, 2016.
DOI: 10.2390/biecoll-jib-2016-297
V. Ogultarhan, A. Shoshi, R. Magnucki, B. Kormeier, R. Hofestädt
KATIS: An eHealth System for Complementary Medicine.
IOS Press in the Studies in Health Technologies and Informatics series 223:167-173, 2016.
DOI: 10.3233/978-1-61499-645-3-167
S. Mueller, B. Sommer, C. Backes, J. Haas, B. Meder, E. Meese, A. Keller
From single variants to protein cascades multiscale modeling of single nucleotide variant sets in genetic disorders.
Journal of Biological Chemistry 291(4):1582-1590, 2016.
DOI: 10.1074/jbc.M115.695247
G. Kovanci, M. Ghaffar, B. Sommer
Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios.
Journal of Integrative Bioinformatics 13(4):298, 2016
DOI: 10.2390/biecoll-jib-2016-298
B. Sommer, A. Hamacher, O. Kaluza, T. Czauderna, M. Klapperstück, N. Biere, M. Civico, B. Thomas, D. G. Barnes, F. Schreiber
Stereoscopic Space Map—Semi-immersive Configuration of 3D-stereoscopic Tours in Multi-display Environments.
Electronic Imaging 2016(5):1-9, 2016.
DOI: 10.2352/ISSN.2470-1173.2016.5.SDA-429

2015

J. Allmer, C. Brinkrolf, R. Hofestädt, M. D. Saçar Demirci (eds)
Computational Systems Biology: German/Russian/Turkish Network of Computational Systems Biology - Report 2015
Shaker Verlag, Aachen 2015
B. Sommer, S. J. Wang, L. Xu, M. Chen, F. Schreiber
Hybrid-Dimensional Visualization and Interaction - Integrating 2D and 3D Visualization with Semi-Immersive Navigation Techniques.
In Big Data Visual Analytics (BDVA) 1-8. IEEE, 2015.
DOI: 10.1109/BDVA.2015.7314295
F. Schreiber, G. D. Bader, M. Golebiewski, M. Hucka, B. Kormeier, N. Le Novère, C. Myers, D. Nickerson, B. Sommer, D. Waltemath, S. Weise
Specifications of Standards in Systems and Synthetic Biology.
Journal of integrative Bioinformatics 12(2):258, 2015.
DOI: 10.2390/biecoll-jib-2015-258
L. Zhu, A. Malatras, M. Thorley, I. Aghoghogbe, A. Mer, S. Duguez, G. Butler-Browne, T. Voit, W. Duddy
CellWhere: graphical display of interaction networks organized on subcellular localizations.
Nucleic Acids Research 43 (W1): W571-W575, 2015.
DOI: 10.1093/nar/gkv354
X. Meng, J. Wang, C. Yuan, X. Li, Y. Zhou, R. Hofestädt, M. Chen
CancerNet: a database for decoding multilevel molecular interactions across diverse cancer types.
Oncogenesis 4, e177, 2015.
DOI: 10.1038/oncsis.2015.40
M. Lewinski, A. Hallmann, D. Staiger
Genome-wide identification and phylogenetic analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues.
Molecular Genetics and Genomics, online access, 2015
DOI: 10.1007/s00438-015-1144-1
A. Shoshi, T. Hoppe, B. Kormeier, V. Ogultarhan, R. Hofestädt
GraphSAW: A web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data.
BMC Medical Informatics and Decision Making 15:15, 2015.
DOI: 10.1186/s12911-015-0139-5
A. Shoshi, V. Ogultarhan, T. Hoppe, B. Kormeier, U. Möller, R. Hofestädt
Identifying adverse drug reactions and drug-induced diseases using network-based drug mapping.
Journal of Bioinformatics and Computational Biology 13(1):1540007, 2015.
DOI: 10.1142/S0219720015400077

2014

C. Brinkrolf, S. J. Janowski, B. Kormeier, M. Lewinski, K. Hippe, D. Borck, R. Hofestädt
VANESA - A Software Application for the Visualization and Analysis of Networks in Systems Biology Applications.
Journal of Integrative Bioinformatics 11(2):239, 2014.
DOI: 10.2390/biecoll-jib-2014-239
V. Leder, M. Lummer, K. Tegeker, F. Humpert, M. Lewinski, M. Schüttpelz, D. Staiger
Mutational definition of binding requirements of an hnRNP-like protein in Arabidopsis using fluorescence correlation spectroscopy
Biochemical and Biophysical Research Communications 453(1), 2014
DOI: 10.1016/j.bbrc.2014.09.056
M. Chen, R. Hofestädt
Open Problems in Petri Net Modeling and Simulation of Biological Systems.
it-Information Technology 56(2):76-81, 2014.
DOI: 10.1515/itit-2013-1021
M. Chen, R. Hofestädt (eds)
Approaches in Integrative Bioinformatics - Towards the Virtual Cell
ISBN:3642412807, Springer Verlag Heidelberg New York Dordrecht London, 2014.
- M. Chen, R. Hofestädt
  Integrative Bioinformatics
  in M. Chen, R. Hofestädt (eds): Approaches in Integrative Bioinformatics - Towards the Virtual Cell, ISBN:3642412807, Springer Verlag, 3-20, 2014.
  DOI: 10.1007/978-3-642-41281-3_1
- B. Kormeier
  Data Warehouses in Bioinformatics
  in M. Chen, R. Hofestädt (eds): Approaches in Integrative Bioinformatics - Towards the Virtual Cell, ISBN:3642412807, Springer Verlag, 111-130, 2014.
  DOI: 10.1007/978-3-642-41281-3_4
- S. J. Janowski, B. Kaltschmidt, C. Kaltschmidt
  Biological Netowrk Modeling and Analysis
  in M. Chen, R. Hofestädt (eds): Approaches in Integrative Bioinformatics - Towards the Virtual Cell, ISBN:3642412807, Springer Verlag, 203-244, 2014.
  DOI: 10.1007/978-3-642-41281-3_8
- B. Sommer
  Network Analysis and Integration in a Virtual Cell Environment
  in M. Chen, R. Hofestädt (eds): Approaches in Integrative Bioinformatics - Towards the Virtual Cell, ISBN:3642412807, Springer Verlag, 275-296, 2014.
  DOI: 10.1007/978-3-642-41281-3_10
R. Giegerich, R. Hofestädt, T. Nattkemper (eds)
German Conference on Bioinformatics 2014.
LNI, 235, Köllen Verlag, Bonn 2014.
R. Hofestädt, A. Shoshi (eds)
Computational Systems Biology: german/russian virtual network of bioinformatics - Report 2014.
Shaker Verlag, Aachen 2014.
O. V. Popik, O. V. Saik, E. D. Petrovskiy, B. Sommer, R. Hofestädt, I. N. Lavrik, V. A. Ivanisenko
Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions
BMC Genomics 2014, 15(Suppl 12):S7
DOI: 10.1186/1471-2164-15-S12-S7
B. Sommer (ed)
Proceedings of CELLmicrocosmos neXt 2014
Bielefeld University, Bielefeld, 2014.
DOI: 10.2390/biecoll-next2014-0
B. Sommer, C. Bender, T. Hoppe, C. Gamroth, L. Jelonek
Stereoscopic Cell Visualization: From Mesoscopic to Molecular Scale.
Journal of Electronic Imaging 23(1):011007-1 - 011007-10, 2014
DOI: 10.1117/1.JEI.23.1.011007
T. Waltemate, B. Sommer, M. Botsch
Membrane Mapping: Combining Mesoscopic and Molecular Cell Visualization.
Proceedings of Eurographics Workshop on Visual Computing for Biology and Medicine, pp. 89-96. Vienna, Austria: Eurographics Association, 2014.
DOI: 10.2312/vcbm.20141187

2013

R. Hofestädt, B. Kormeier, M. Lange, F. Schreiber, B. Sommer, S. Weise
Editorial: JIBtools - a Strategy to Reduce the Bioinformatics Analysis Gap.
Journal of Integrative Bioinformatics, 10(1):226, 2013.
DOI: 10.2390/biecoll-jib-2013-226
H.-M. Lee, K.-J. Dietz, R. Hofestädt
Computational construction of specialized biological networks.
Journal of Bioinformatics and Computational Biology, 11(1):1340003, 2013.
DOI: 10.1142/S0219720013400039
G. Lukat, J. Krüger, B. Sommer
APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. Journal of Chemical Information and Modeling, 53(11):2908-25, 2013.
DOI: 10.1021/ci400172g
R. Hofestädt.
Computerunterstützte Diagnose von Erkrankungen.
Management & Krankenhaus, 4/2013:22, 2013.
B. Sommer
Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools.
Computational and Structural Biotechnology Journal, 5(6):e201302014, 2013.
DOI: 10.5936/csbj.201302014
B. Sommer, K. Hippe, P. S. Demenkov, P. Arrigo, B. Kormeier, Ö. Ates, A. V. Kochetov, V. A. Ivanisenko, N. A. Kolchanov, R. Hofestädt
Subcellular Localization Charts: a new visual Methodology for the semi-automatic Localization of protein-related Data Sets.
Journal of Bioinformatics and Computational Biology, 11(1):1340005, 2013.
DOI: 10.1142/S0219720013400052
A. Winter, R.-D. Hilgers, R. Hofestädt, P. Knaup-Gregori, C. Ose, A. Trimmer
More than Four Decades of Medical Informatics Education for Medical Students in Germany.
Methods of Information in Medicine, 52(03):181-183, 2013.
DOI: 10.1055/s-0038-1627057

2012

M. Heiner, R. Hofestädt (eds.)
Biological Processes & Petri Nets. Proceedings of the 3rd International Workshop on Biological Processes & Petri Nets, a satellite event of PETRI NETS 2012. CEUR-WS, 2012. Online Journal: http://ceur-ws.org/Vol-852/
R. Hofestädt
Modeling aspects of the virtual cell. Proceedings of the BGRS 2012, Novosibirsk 2012, 122, 2012.
R. Hofestädt, N. Kolchanov N (eds.)
German/Russian Network of Computational Systems Biology: Report 2012. Shaker Verlag, Aachen, 2012.
C. Klenke, S. Janowski, D. Borck, D. Widera, L. A. Ebmeyer, J. Kalinowski, A. Leichtle, R. Hofestädt, T. Upile, C. Kaltschmidt, B. Kaltschmidt, and H. Sudhoff
Identification of Novel Cholesteatoma-related Gene Expression Signatures Using Full-genome Microarrays. PloS One, 2012. Online Journal: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052718
S. Proß, S. J. Janowski, B. Bachmann, C. Kaltschmidt, B. Kaltschmidt
PNlib - A Modelica Library for Simulation of Biological Systems Based on Extended Hybrid Petri Nets. Proceedings of the 3rd International Workshop on Biological Processes and Petri Nets, 852, 2012. Online Journal: http://ceur-ws.org/Vol-826/paper05.pdf
S. Proß, S. J. Janowski, R. Hofestädt, Bachman B
A New Object-Oriented Petri Net Simulation Environment Based On Modelica. Proceedings of the 2012 Winter simulation Conference, IEEE, 2012.
S. Rubert, C. Gamroth, J. Krüger, and B. Sommer
Grid Workflow Approach Using the CELLmicrocosmos 2.2 MembraneEditor and UNICORE to Commit and Monitor GROMACS Jobs. Proceedings of the Grid Workflow Workshop (GWW2011), Cologne, Germany, March 4, 2011. 826. CEUR-WS, 2012. Online Journal: http://ceur-ws.org/Vol-826/paper05.pdf
Al. Shoshi, Ar. Shoshi, R. Hofestädt
KAIS: Ein webbasiertes System zur patientenindividuellen Arzneimittel-Interaktionsprüfung. In: Informatik 2012. Proceedings: Informatik 2012: Was bewegt uns in der/die Zukunft?. LNI P-208:1565-1574, 2012.
B. Sommer, V. Ivanisenko, P. Arrigo and R. Hofestädt
Prediction and 3D visualization of biological networks using cytological disease mapping. EMBnet.journal, Volume 18, Supplement B, 115-116, 2012. Online Journal: http://journal.embnet.org/index.php/embnetjournal/article/view/572

2011

M. Chen, M. Hu, R. Hofestädt
A Systematic Petri Net Approach for Multiple-Scale Modeling and Simulation of Biochemical Processes. Applied Biochemistry and Biotechnology, 164(3):338-352, 2011.
M. Chen, S. Hariharaputran, R. Hofestädt, B. Kormeier, S. Spangardt
Petri net models for the semi-automatic construction of large scale biological networks. Natural Computing, 10(3):1077-1097, 2011.
DOI: 10.1007/s11047-009-9151-y
R. Hofestädt
Petri nets and the simulation of metabolic networks. Studies in health technology and informatics, 162, 2011.
R. Hofestädt
Fundamental Features of Metabolic Computing. Proceedings of MICAI 2011, LNCS (Advances in Soft Computing) 7095:143-152, 2011.
D. Huang, Y. Huang, Y. Bai, D. Chen, R. Hofestadt, C. Klukas, M. Chen
MyBioNet: interactively visualize, edit and merge biological networks on the Web. Bioinformatics, 2011.
DOI: 10.1093/bioinformatics/btr557
S. Janowski, B. Kormeier, T. Töpel, K. Hippe, R. Hofestädt, N. Willassen, R. Friesen, S. Rubert, D. Borck, P. Haugen, M. Chen
Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing. Stud Health Technol Inform, 162, 2011. Online Journal: DOI: 10.3233/978-1-60750-704-8-182
B. Kormeier, K. Hippe, R. Hofestädt
Data Warehouses in Bioinformatics: Integration of Molecular Biological Data. it - Information Technology, 53(5):241-249, 2011.
M. Lange, J. Chen, D. Borck, C. Colmsee, K. Hippe, B. Kormeier, S. Weise, U. Scholz
The LAILAPS Information Retrieval Portal as Scalable and Integrative Database Query Endpoint. Proceedings of the 6th International Symposium on Health Informatics and Bioinformatis 2011, pp. 37, 2011.
B. Sommer, T. Dingersen, C. Gamroth, S.E. Schneider, S. Robert, J. Krueger, K.-J. Dietz
CELLmicrocosmos 2.2 Membrane Editor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems. Journal of Chemical Information and Modeling, 51(5):1165-1182, 2011.
DOI: 10.1021/ci1003619

2010

K. Hippe, B. Kormeier, T. Töpel, S. Janowski, R. Hofestädt
DAWIS-M.D. - A Data Warehouse System for Metabolic Data.
GI Jahrestagung (2) 2010: 720-725.
R. Hofestädt, N. Kolchanov N (eds.)
Computational Systems Biology. Shaker Verlag, Aachen, 2010.
S. Janowski, B. Kormeier, T. Töpel, K. Hippe, R. Hofestädt, N. Willassen, R. Friesen, S. Rubert, D. Borck, P. Haugen, M. Chen.
Modeling of cell-to-cell communication processes with Petri nets using the example of quorum sensing.
In Silico Biology 10:0003, 2010. Online Journal: DOI: 10.3233/ISB-2010-0418
B. Kormeier, K. Hippe, T. Töpel, R, Hofestädt
CardioVINEdb: a data warehouse approach for integration of life science data in cardiovascular diseases. Journal of Integrative Bioinformatics, 7(1):142, 2010. Online Journal: http://journal.imbio.de/index.php?paper_id=142
H. Lee, K.-J. Dietz, R. Hofestädt
Prediction of thioredoxin and glutaredoxin target proteins by identifying reversibly oxidized cysteinyl residues.
IB10 Article, Journal of Integrative Bioinformatics (Special Issue) 7(3), 2010. Online Journal: http://journal.imbio.de/article.php?aid=130
B. Sommer
Membranen für alle. Nachrichten aus der Chemie, 58(10):1030-1032, 2010. Download at: http://Cm2.CELLmicrocosmos.org
B. Sommer, J. Künsemöller, N. Sand, A. Husemann, M. Rumming, B. Kormeier
CELLmicrocosmos 4.1: An interactive approach to Integrating spatially localized metabolic networks into a virtual 3D cell environment.
In Fred, Ana; Filipe, Joaquim; Gamboa, Hugo (eds.): Proceedings of Bioinformatics 2010: 90-95, 2010, ISBN 978-989-674-019-1. Download at: http://Cm4.CELLmicrocosmos.org
B. Sommer, E. S. Tiys, B. Kormeier, K. Hippe, S. Janowski, T. V. Ivanisenko, A. O. Bragin, P. Arrigo, P. S. Demenkov, A. V. Kochetov, V. A. Ivanisenko, N. A. Kolchanov, R. Hofestädt
Visualization and Analysis of a Cardio Vascular Disease- and MUPP1-related Biological Network combining Text Mining and Data Warehouse Approaches.
Journal of Integrative Bioinformatics, 7(1):148, 2010. Online Journal: http://journal.imbio.de/index.php?paper_id=148.
T. Töpel, D. Scheible, F. Trefz, R. Hofestädt
RAMEDIS: a comprehensive information system for variations and corresponding phenotypes of rare metabolic diseases.
Human Mutation, 31(1):E1081-E1088, 2010 (Published Online: 1 Dec 2009).

2009

A. Shoshi, A. Shoshi
KAIS : Ein Krankheiten- und Arzneimittelinformationssystem.
In: 54. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds). Essen, 07.-10.09.2009. Düsseldorf: German Medical Science GMS Publishing House; 2009.
DOI: 10.3205/09gmds311
T. Töpel, D. Scheible, F. Trefz, R. Hofestädt
RAMEDIS: a comprehensive information system for variations and corresponding phenotypes of rare metabolic diseases.
Hum Mutat., 31(1):E1081-E1088, 2010 (Published Online: 1 Dec 2009).
DOI: 10.1002/humu.21169
R. Hofestädt, E.-W. Mayr
Bioinformatik.
In: Informatik Spektrum, Band 32:4, Springer Verlag, 285-286, 2009.
M. Chen, H. Hariharaputran, R. Hofestädt, B. Kormeier, S. Spangardt
Petri Net Models for the Semi-automatic Construction of Large Scale Biological Networks.
Natural Computing, 2009.
DOI: 10.1007/s11047-009-9151-y
R. Hofestädt
DNA-Programming Language of Life. HBSO, 13:1, 68-72, 2009.
M. Chen, R. Hofestädt
Editors: Proceedings International Workshop on Computational & Integrative Biology. University Hanzhou, www.cls.zju.edu.cn/binfo/ib/2009.
R. Hofestädt, K. Kuhn, W. Müller, C. Türker
Daten in den Lebenswissenschaften: Vom Paper über Datenbanken zur integrierten Informationsquelle.
In: Informatik 2009. Proceedings: Informatik 2009 - Im Focus das Leben. LNI 154, 33-34., 2009.
B. Kormeier, K. Hippe, T. Töpel, R. Hofestädt
CARDIOVINEdb: a data warehouse approach for integration of life science in cardiovascular diseases.
In: Informatik 2009. Proceedings: Informatik 2009 - Im Focus das Leben. LNI 154, Seite 40 und 704, 2009.

2008

S. Hariharaputran, T. Töpel, T. Brockschmidt, R. Hofestädt
VINEdb: a data warehouse for integration and interactive exploration of life science data.
Integrative Bioinformatics Yearbook 2007. Shaker Verlag Aachen 2008, 63-74.
F. Trefz, D. Scheible, H. Götz, T. Töpel, R. Hofestädt, G. Frauendienst-Egger: METAGENE and RAMEDIS: databases for metabolic diseases and patients with inborn errors on metabolism. Journal of Inherited Metabolic Disease, 2008, 31:289.
T. Töpel, K. Amling
Informationsfusion biomedizinischer Daten und klinischer Fallberichte im Bereich angeborener Stoffwechselerkrankungen.
In 53. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (gmds). Stuttgart, 15.-19.09.2008. Düsseldorf: German Medical Science GMS Publishing House, 2008.
http://www.egms.de/de/meetings/gmds2008/08gmds133.shtml
S. Hariharaputran; T. Töpel; T. Oberwahrenbrock, R. Hofestädt
Alignment of Linear Biochemical Pathways Using Protein Structural Classification. Nature Precedings, 2008.
DOI: 10.1038/npre.2008.1943.1
T. Töpel, B. Kormeier, A. Klassen and R. Hofestädt
BioDWH: A Data Warehouse Kit for Life Science Data Integration. Journal of Integrative Bioinformatics, 5(2):93, 2008.
DOI: 10.1515/jib-2008-93
T. Töpel
A customizable framework to access and interconnect clinical patient data and molecular biology information.
In Proceedings of The 21th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2008), Jyväskylä, Finland, June 17-19, 2008.
DOI: 10.1109/CBMS.2008.131
R. Hofestädt, T. Töpel (eds.)
Integrative Bioinformatics - Yearbook 2007. Shaker Verlag, 2008.
R. Hofestädt
DNA - Programming Language of Life ?
In: Kolchanov N. and R. Hofestädt. (eds.): BGRS'08, Russian Academy of Science, Novosibirsk 2008, 84. (also VOGiS Herald journal)

2007

R. Hofestädt
Extended Backus-System for the representation and specification of the genome.
Journal of Bioinformatics and Computational Biology, 5-2(b):457-466, 2007.
T. Topel, J. Neumann and R. Hofestadt.
A medical case-based reasoning component for the rare metabolic diseases database RAMEDIS.
In Proceedings of The 20th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2007), Maribor, Slovenia, June 20 - 22, 2007, pp. 7-11, 2007.
S. Hariharaputran, T. Töpel, T. Oberwahrenbrock and R. Hofestädt.
SignAlign: prediction and alignment of biochemical pathways using protein structural information.
In Proceedings of 5th International Conference on Pathways, Networks, and Systems, Greece, June 24 - 29, 2007.
R. Hofestädt and T. Töpel (eds.).
Integrative Bioinformatics - Yearbook 2006.
Shaker Verlag, 2007.
S. Hariharaputran, T. Töpel, B. Brockschmidt, and R. Hofestädt.
VINEdb: a data warehouse for integration and interactive exploration of life science data.
In Proceedings of the 4th Integrative Bioinformatics Workshop (IB 07) , University of Ghent, Belgium, September 10 - 12, 2007.
The NMITLI-BioSuite Team.
BioSuite: A comprehensive bioinformatics software package.
Current Science, 92(1):29-38, 2007.
K. Sivapriya, S. Hariharaputran, V.L. Suhas, N. Chandra, S. Chandrasekaran.
Conformationally locked thiosugars as potent alpha-mannosidase inhibitors: Synthesis, biochemical and docking studies.
Bioorg Med Chem., 15(17):5659-65, 2007.

2006

R. Hofestädt
An extended Backus System for the presentation and analysis of DNA sequences.
Kolchanov N. and R. Hofestädt (eds.): BGRS'06,
Russian Academy of Science, Novosibirsk 2006, Volume I, 48-52.
Kolchanov N. and R. Hofestädt (eds.)
Proceedings of the 5th International Conference on Bioinformatics of Genome Regulation and Structure (BGRS). Volume 1-3,Russian Academy of Science, Novosibirsk 2006.
R. Hofestädt (ed.)
Integrative Bioinformatics.
Shaker Verlag, Aachen 2006.
B. Prins, R. Hofestädt
MILAN - A medical information-system linking agents to metabolic networks.
Journal of Integrative Bioinformatics, 2006.
M. Chen, R. Hofestädt
Prediction and Alignment of Metabolic Pathways.
In Bioinformatics of Genome Regulation and Structure II, N. Kolchanov el al (eds.), pp. 355-365, 2006.
M. Chen, R. Hofestädt
A medical bioinformatics approach for metabolic disorders: Biomedical data prediction, modeling, and systematic analysis.
Journal of Biomedical Informatics, 39(2): 147-159, 2006.
N. Kolchanov, R. Hofestädt, L. Milanesi (eds.)
Bioinformatics of Genome Regulation and Structure II,
Springer, New York, 2006.
T. Töpel, R. Hofestädt, D. Scheible, F. Trefz
RAMEDIS, the rare metabolic diseases database.
Applied Bioinformatics, 5(2):115-118, 2006.

2005

R. Hofestädt
Bioinformatik.
In Handbuch der Medizinischen Informatik, Thomas Lehmann (ed.),
Hanser Verlag , 2005, 253-298.
R. Hofestädt (ed.)
Yearbook Bioinformatics 2004.
Magdeburg: IMBio, Informationsmanagement in der Biotechnologie e.V., 2005.
A. Freier, R. Hofestädt, T. Toepel
Investigating the Effective Range of Agents by Using Integrative Modelling.
In Handbook of Toxicogenomics, J. Borlak (ed.).
Wiley-VCH, 2005, 233-252.
Ming Chen, Andreas Freier, Ralf Hofestädt
Bioinformatics Approaches for Metabolic Pathways
In Handbook of Genome Research (Christoph W. Sensen ed.), pp.461-490.
M. Chen and R. Hofestädt
An algorithm for linear metabolic pathway alignment
In Silico Biol. 5(2): 111-128.
R. Hofestädt, T. Töpel
Medical Bioinformatics: Detecting Molecular Diseases with Case-Based Reasoning .
In Bioinformatics using Computational Intelligence Paradigms, U. Seiffert (ed.).
Springer-Verlag, 2005, 1-24.
F. K. Trefz, D. Scheible, G: Frauendienst-Egger, J. Sander, H. Korall, T. Töpel, R. Hofestädt
Harnstoffzykluserkrankungen und Organoazidämien: Aufnahme in das erweiterte Neugeborenen-Screening?
Pädiatrie hautnah, 17( 8): S19-S22, 2005.

2004

N. Kolchanov, R. Hofestädt R. (eds.)
Bioinformatics of Genome Regulation and Structure
Kluewer Academic Publishers , 2004
R. Hofestädt, H.-P. Lenhof (Hrsg.)
Schwerpunktthema Molekulare Bioinformatik
ti Sonderausgabe, Oldenbourg-Verlag, 1, 2004
R. Hofestädt, H.-P. Lenhof
Molekulare Bioinformatik
ti Sonderausgabe, Oldenbourg-Verlag, 1, 2004, 3-4
R. Hofestädt, M. Chen
Metabolic Pathway Prediction/Alignment
Proceedings of the Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004), July 25-30, 2004, Novosibirsk, Russia, Vol. 2: 68-72.
M. Chen, S. Lin, R. Hofestädt
STCDB: Signal Transduction Classification Database
Nucleic Acids Research, 2004, 32(1): D456-D458
M. Chen, R. Hofestädt
Web-based Information Retrieval System for the Prediction of Metabolic Pathways
IEEE Transactions on Nanobioscience, 2004, 3(3): 192-199
M. Chen, R. Hofestädt
PathAligner: Metabolic Pathway Retrieval and Alignment
Applied Bioinformatics, 2004, 3(4): 241-252
D. W. Lorenz, J. Kix
The Benefits of Notebooks in Applied Bioinformatics Education
In Proceedings: EDMEDIA2004. World Conference on Educational Multimedia, Hypermedia & Telecommunications.
Lugano, Schweiz. July 2004.

2003

J. Köhler, S. Philippi, M. Lange
SEMEDA: Ontology Based Semantic Integration of Biological Databases
Bioinformatics, Volume 19(18), pp. 2420-2427
M. Chen, R. Hofestädt
Quantitative Petri net model of gene regulated metabolic networks in the cell.
In Silico Biology. 3, 0030 (2003)
A. Freier, R. Hofestädt, M. Lange
Integrative analysis of gene networks using dynamic process pattern modelling.
Bioinformatics of Genome Regulation and Structure. R. Hofestädt, N. Kolchanov (eds.), Kluwer Academic Publishers.
D. W. Lorenz, A. Rüegg
GenBiLL: Generic Biochemical Learning Laboratories.
In Proceedings: ED-MEDIA 2003 - World Conference on Educational Multimedia, Hypermedia & Telecommunications. Honolulu, USA, June 2003.
D. W. Lorenz, J. Kix
Improving Bioinformatics Education Through Mobile Technology.
In Proceedings: EUNIS 2003. Conference on European University Information Systems. Amsterdam, Netherlands. July 2003.
A. Freier, R. Hofestädt, M. Lange
iUDB: An object-oriented system for modelling, integration and analysis of
gene controlled metabolic networks. In Silico Biology, 3 (0019), IOS Press, 2003.

2002

R. Hofestädt
Bioinformatics.
Yearbook of Medical Informatics. Schattauer 2002, 581-583
J. Collado-Vides, R. Hofestädt (Herausgeber)
Gene Regulation and Metabolism - Post-Genomic Computational Approaches
Cambridge, MA: MIT Press, 2002.
A. Freier, R. Hofestädt, M. Lange, U. Scholz
Information Fusion and Metabolic Network Control
In J. Collado-Vides and R. Hofestädt, Herausgeber, Gene Regulation and Metabolism - Post-Genomic Computational Approaches. Cambridge, MA: MIT Press, 2002.
R. Hofestädt, T. Töpel
Case-based Support of Information Retrieval and Analysis of Molecular Data.
In Proceedings of The 15th IEEE Symposium on Computer-Based Medical Systems (CBMS 2002), Maribor, Slovenia, June 4-7, 2002, S. 129-133, 2002.
T. Töpel, R. Hofestädt
Architecture for Information Retrieval and Analysis of Integrated Molecular Data.
In Medizinische Genetik, Band 14, Nr. 3, S. 315, 2002.
T. Töpel, U. Mischke, D. Scheible, F. Trefz, R. Hofestädt
RAMEDIS: Vernetzte Forschung am Beispiel angeborener Stoffwechselerkrankungen.
In Informatik, Biometrie und Epidemiologie in Medizin und Biologie, Band 33, Nr. 2-3, S. 79-80, 2002.
T. Töpel, U. Scholz, U. Mischke, D. Scheible, R. Hofestädt, F. Trefz
Supporting genotype-phenotype correlation with the rare metabolic diseases database Ramedis
In Silico Biology, 2, 0036, 2002.
Online Journal: http://www.bioinfo.de/isb/2002/02/0036/
A. Freier, R. Hofestädt, M. Lange, U. Scholz, A. Stephanik
BioDataServer: A SQL-based service for the online integration of life science data.
In Silico Biology, 2(0005), 2002.
Online Journal: http://www.bioinfo.de/isb/2002/02/0005
R. Hofestädt, Kolchanov N. und Reinitz J.:
Information and Simulation Systems for the Analysis of Gene Regulation and Metablic Pathways. In Silico Biology, 2, 0005, 2002. 35-36
A. Freier, R. Hofestädt, M. Lange
(2002) IIUDB: An Object-oriented System for Modelling, Integration and Analysis of Gene Controlled Metabolic Networks
Proceedings of the Third International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'02) Novosibirsk, Russia July 14-20, vol. 2, pp.123-125, ICG Novosibirsk.
R. Hofestädt, R. Schnee
Studien und Forschungsführer Bioinformatik.
Spektrum Akademischer Verlag, Heidelberg, 2002
R. Hofestädt, T. Töpel
Case-based Support of Information Retrieval and Analysis of Molecular Data.
In Proceedings of The 15th IEEE Symposium on Computer-Based Medical Systems (CBMS 2002), Maribor, Slovenia, 129-133, 2002.
M. Chen, A. Freier, J. Köhler, A. Rüegg
The Biology Petri Net Markup Language.
In: Jörg Desel, Mathias Weske (Hrsg.), Lecture Notes in Informatics - proceedings of Promise'2002, Oct. 9-11, Potsdam, Germany, Vol. 21: 150-161
M. Chen
Modelling and Simulation of Metabolic Networks: Petri Nets Approach and Perspective, in the proceeding of "ESM 2002, 16th European Simulation Multiconference" , 2002, June 3-5, Darmstadt, Germany, 441-444
S. Döhr et al
Modeling of gene regulatory networks for genotype-phenotype information.
Progress Report German Human Genome Project, BMBF 2002, 68-69
D. Lorenz
Das generische Labor.
In Beck U., Sommer W. (ed.), Proceeding of "LEARNTEC 2002, 10. Europäischer Kongress und Fachmesse für Bildungs- und Informationstechnologie", 595-601, Karsruhe, Germany, 2002

2001

A. Freier, R. Hofestädt, M. Lange
The electronical infrastructure for the analysis of metabolic networks.
In Abstracts' Book of the Workshop on CORBA and XML: Towards a Bioinformatics Integrated Network Evironment, NETTAB 2001 - Network Tools and Applications in Biology, S. 38-43, 2001.
R. Hofestädt, M. Lange, U. Scholz
Molecular Information Fusion for Metabolic Networks.
In G.X. Xue, Y.B. Xue, Z.H. Xu, R. Holmes, G. Hammond und H.A. Lim, Herausgeber, Gene Families: Studies of DNA, RNA, Enzymes and Proteins, S. 221-232. Singapore et al: World Scientific Press, 2001.
R. Hofestädt, J. Reinitz, N. Kolchanov.
Information and Simulation Systems for the Analysis of Gene Regulation and Metabolic Pathways
Report No. 313 of the Dagstuhl-Seminar No. 01261, Schloss Dagstuhl, 24. 6. - 29. 6. 2001.
http://www.dagstuhl.de/01261/, zipped PS, zipped PDF
R. Kauert, T. Töpel, U. Scholz, R. Hofestädt
Information System for the Support of Research, Diagnosis and Therapy of Inborn Metabolic Diseases.
In MedInfo 2001: Proceedings of the 10th World Congress on Health and Medical Informatics, London, September 2 - 5, 2001, S. 353-356. Amsterdam: IOS Press, 2001.
A. Stephanik, R. Hofestädt, M. Lange, A. Freier
Metabolic Information Control System.
In Proceedings of the World Multiconference on Systemics, Cybernetics and Informatics (SCI 2001), Orlando, Florida, USA, July 22-25, 2001.
U. Mischke, U. Scholz, T. Töpel, D. Scheible, R. Hofestädt, F. K. Trefz
RAMEDIS - Rare Metabolic Diseases Publishing Tool for Genotype-Phenotype Correlation.
In MedInfo 2001: Proceedings of the 10th World Congress on Health and Medical Informatics, London, September 2 - 5, 2001, S. 970-974. Amsterdam: IOS Press, 2001.

2000

A. Freier, R. Hofestädt, M. Lange, U. Scholz
An integrated architecture for modelling and simulation of metabolic networks.
In Proceedings of the BIOTECHNOLOGY 2000, S. 210-211. DECHEMA e.V., 2000.
J.M. Hills, J.C. Thomason, H. Davis, J. Köhler, E. Millett
Exploratory behaviour of barnacle larvae in field conditions.
Biofouling, Volume 16 (2-4), pp 171 - 179, 2000.
R. Hofestädt
Electronical infrastructure for the detection of inborn errors.
In Proceedings of the Second International Conference on Bioinformatics of Genome Regulation and Structure (BRGS2000), ICG Novisibirsk, Vol.1, 212-213, 2000.
R. Hofestädt, K. Lautenbach, M. Lange, Herausgeber.
Modellierung und Simulation Metabolischer Netzwerke: DFG-Workshop im Rahmen des DFG-Schwerpunktes Informatikmethoden zur Analyse und Interpretation großer genomischer Datenmengen, Magdeburg, 19. - 20. Mai 2000, Preprint Nr. 10. Fakultät für Informatik, Universität Magdeburg, 2000.
R. Hofestädt, U. Mischke und U. Scholz.
Knowledge acquisition, management and representation for the diagnostic support in human inborn errors of metabolism.
In A. Hasman, B. Blobel, J. Dudeck, R. Engelbrecht, G. Gell und H.-U. Prokosch, Herausgeber, Medical Infobahn for Europe: Proceedings of MIE2000 and GMDS2000, Hannover, August 27 - September 1, S. 857-862. Amsterdam et al: IOS Press, 2000.
R. Hofestädt, K.-P. Pleißner und A. Stephanik, Herausgeber.
Informationssysteme in der Biotechnologie. Fakultät für Informatik, Universität Magdeburg, 2000.
J. Köhler, M. Lange, R. Hofestädt und S. Schulze-Kremer.
Logical and Semantic Database Integration.
In BIBE 2000: IEEE International Symposium on Bio-Informatic & Biomedical Engineering, Washington, D.C., U.S.A., November 8-10, S. 77-80. IEEE Computer Society, 2000.

1999

J. Collado-Vides, R. Hofestädt, M. Mavrovouniotis, G. Michal
Modeling and simulation of gene regulation and metabolic pathways.
Bio Systems, Vol. 49, N^o 1, pp. 79-82, 1999.
A. Freier, R. Hofestädt, M. Lange, U. Scholz
MARGBench - An Approach for Integration, Modeling and Animation of Metabolic Networks
In Giegerich, R.; R. Hofestädt; Lengauer, T.; Mewes, W.; Schomburg, D.; Vingron, M.; Wingender, E. (Eds.): Proceedings of the German Conference on Bioinformatics (GCB '99), Hannover, October 4th - 6th, pp. 190-194, 1999.
R. Hofestädt, M. Lange, U. Scholz
Molecular Information Fusion for Metabolic Networks
Courses of The First International Bioinformatics Summer School (IBSS '99), Magdeburg, September 5th -10th, 1999.
R. Hofestädt; U. Mischke, M. Prüß, U. Scholz
Metabolic Drug Pointing and Information Processing.
Medical Informatics Europe, Vol. 68, pp. 12-15, 1999.
R. Hofestädt (Ed.):
Bioinformatik 2000 - Forschungsführer Informatik in den Biowissenschaften. Berlin: BIOCOM, 1999.
R. Hofestädt:
Bioinformatik 2000 - Von der Molekularen Biologie zum Metabolic Engineering.
Informatik Spektrum, Vol. 22, N^o 5, pp. 385-390, 1999.
R. Hofestädt:
Das Bioinformatik-Dilemma.
Laborjournal, Vol. 99, N^o 10, pp. 12-13, 1999.
J. Köhler, P.D. Hansen und M. Wahl
Colonization patterns at the substratum-water interface: How does surface microtopography influence recruitment patterns of sessile organisms?
Biofouling, Volume 14 (3), pp. 237- 248, 1999.

1998

J. Collado-Vides, R. Hofestädt, M. Mavrovouniotis, G. Michal (ed.).
Modelling and Simulation of Gene and Cell Regulation and Metabolic Pathways.
Schloss Dagstuhl, International Conference and Research Center for Computer Science, Seminar N^o. 98251, Report N^o. 215, 1998.
A. Freier, M. Höding, R. Hofestädt, M. Lange, U. Scholz.
Molecular Database Integration: Analysis of Metabolic Network Control.
In: Proceedings of the First International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'98) Novosibirsk - Altai Mountains, Russia August 24-31, Volume 1, pp 86-89, ICG Novosibirsk, 1998.
M. Höding, R. Hofestädt, G. Saake, U. Scholz.
Scheme Derivation for WWW Information Sources and their Integration with Databases in Bioinformatics
In: W. Litwin, T. Morzy, G. Vossen (eds.), Second East-European Symposium on Advances in Databases and Information Systems (ADBIS'98), September 8th -11th, 1998, Poznan, Poland, LNCS No.1475, Springer Publishing, Berlin, pp 296-304, 1998.
R. Hofestädt (ed.).
Molekulare Bioinformatik: Workshop der GI'98 Jahrestagung
in Series: Medizinische Informatik und Bioinformatik, Shaker Publishing, Aachen, 1998.
R. Hofestädt.
An Integrative Molecular Information System.
In: Proceedings of The 9th World Congress on Medical Informatics, Editors: B. Cesnik, A. McCray, J. Scherrer, ISO Press, pp 361-365, 1998.
R. Hofestädt, M. Prüß, U. Scholz, H. Urban.
Molekulare Bioinformatik- Molekulare Informationssysteme zur Erkennung von angeborenen Stoffwechselerkrankungen.
Magdeburger Wissenschaftsjournal 3(1):29-40, 1998.
See also Preprint N^o. 9 (German) of Faculty for CS, Otto-von-Guericke University Magdeburg
R. Hofestädt, U. Scholz.
Information Processing for the Analysis of Metabolic Pathways and Inborn Errors.
BioSystems, 47, pp 91-102, 1998.
R. Hofestädt, S. Thelen.
Quantitative Modeling of Biochemical Networks.
In Silico Biology 1(1), pp 39-53, IOS Press, 1998.
Available online via URL: http://www.bioinfo.de/isb/1998/01/0006/.

1997

R. Hofestädt.
Computer Science and Biology.
Biosystems, 43, 1997, pp 69-71.
R. Hofestädt.
Herausforderungen des elektronischen Krankenhausmanagements.
In: C. Steigner (ed.), Arbeitsplatz-Rechensysteme, Fölbach Publishing, 1997, pp 285-292.
R. Hofestädt.
Algorithms for the Microscopic and Macroscopic Analysis of Metabolic Processes (Diseases).
In: Proceedings European Congress on Intelligent Techniques and Soft Computing, Publishing Mainz, Vol. 3, pp 2293-2297.
R. Hofestädt, T. Lengauer, M. Löffler, D. Schomburg (ed.).
Bioinformatics.
LNCS, 1278, Springer Publishing, 1997.
R. Hofestädt, H. Lim (ed.).
Molecular Bioinformatics: Sequence Analysis - The Human Genome Project.
Shaker Publishing, Aachen 1997.

1996

J. Collado-Vides, R. Hofestädt, M. Löffler, M. Mavrovouniotis (ed.).
Modelling and Simulation of Gene and Cell Regulation.
Dagstuhl-Seminar-Report, 130, 1996.
R. Hofestädt, J. Collado-Vides, M. Mavrovouniotis.
Modelling and Simulation of Metabolic Pathways, Gene Regulation and Cell Differentiation.
BioEssays, 18, 1996, 333-335.
R. Hofestädt et al.
Integrative Database Analysis for the Detection of Inborn Errors.
In: J. Brender et al. (ed.): Medical Informatics Europe '96, IOS Press, 1996, 542-546.
R. Hofestädt et al..
Simulation of load balancing with cellular automata.
Simulation Practice and Theory, 4, 1996, 81-96.
R. Hofestädt, T. Lengauer, M. Löffler (ed.).
Informatik in den Biowissenschaften.
it+ti Sonderausgabe, Oldenbourg-Verlag, 5, 1996.
H. Herre, R. Hofestädt, F. Trefz (ed.).
Computerunterstützte Erkennung von Stoffwechselerkrankungen.
Informatik-Berichte, 9, University of Leipzig, 1996.
R. Hofestädt, T. Lengauer, M. Löffler, D. Schomburg (ed.).
Computer Science and Biology - Proceedings of the German Conference on Bioinformatics.
IMISE Report, 1, University of Leipzig, 1996.

1995

R. Hofestädt, M. Löffler, K. Möller (ed.).
Modellierung des Immunsystems.
Informatik Bericht, Universität Bonn, 88, 1995.
R. Hofestädt.
Computer Science, Supercomputing and Biology - Bioinformatics.
Journal EUROSIM - Simulation News Europe, 13, 7-15, 1995.
R. Hofestädt, F. Meinecke.
Interactive Modelling and Simulation of Biochemical Networks.
Computers in Biology and Medicine, 25, 321-334, 1995.
R. Hofestädt.
Metabolic Engineering.
In: Sydow A. (ed.), International IMACS-Symposium on Systems Analysis and Simulation, Elsevier, 1995 , 321-326 (See also SAMS, 18, 1995, 99-102).
R. Hofestädt.
A Rule Based System for the Detection of Metabolic Diseases.
In: Greenes R., Peterson H. und Protti D. (ed.), Proceedings of the Eighth World Congress on Medical Informatics, North-Holland, 1995, 994-999.
R. Hofestädt, X. Huang.
Automaton-Based Load Balancing Simulation in a Workstation Cluster.
Proceedings APPT'95 International Workshop on Advanced Parallel Processing Technologies, Publishing House of Electronics Industry, Beijing 1995, 344-347.
R. Hofestädt et al (ed.).
Artificial Life.
GMD-Studien, 271, St. Augustin, 1995

1994

R. Hofestädt
A Petri Net Application to Model Metabolic Processes.
In Barahona P., Veloso M. und Bryant J. (ed.): Proceedings 12th International Congress of the European for Medical Informatics, Lissabon 1994, 115-120.
Extended Version: Journal of Systems Analysis Modelling Simulation, 16, 1994, 113-122.
R. Hofestädt, U. Hörkens.
CASS - Simulation Shell for Cellular Automata.
Journal of Systems Analysis Modelling Simulation, 14, 1, 1994, 1-15.
R. Hofestädt.
Detection and Animation of Metabolic Bottlenecks.
In Lim H. (ed.): Proceedings Third International Conference on Bioinformatics and Genome Research, Talahassee 1994, World Scientific, 331-340.
R. Hofestädt.
Modellierung und Simulation molekulargenetischer Prozesse.
In Kampe G., Zeitz M. (ed.): Proceedings ASIM 1994 Simulationstechnik, Vieweg Publishing, Stuttgart 1994, 1-8.
K.-E. Großpietsch, R. Hofestädt, C. Steigner (Hrsg.).
Parallele Datenverarbeitung in Cluster-Workstations.
Informatik Berichte, University of Koblenz, Heft 9, 1994.
D. Beerbohm, S. Bresken, R. Hofestädt, X. Huang.
Automatengesteuertes skalierbares Verfahren zum Lastausgleich.
In Flieger R., Grebe R. (ed.): Parallele Datenverarbeitung aktuell, IOS Press, London 1994, 100-108.
R. Hofestädt.
Computer-Aided Metabolic Engineering.
it+ti Nachrichten, Heft 6, 1994, 66-70.
U. Ashauer, R. Hofestädt.
Ein wissensbasierter Ansatz zur Diagnose genetisch verursachter Stoffwechselkrankheiten.
In Kunath H. et al. (ed.): Proceedings 39. Jahrestagung der Deutschen Gesellschaft für Medizinische Informatik, Biometrie und Epidemiologie (GMDS), MMV Medizin Publishing Munich, 1994, 115-119.
D. Beerbohm, S. Bresken, R. Hofestädt, X. Huang.
Dynamic load balancing based on the theory of cellular automata.
In Dekker L., Smit W. und Zuidervaart J. (ed.): Proceedings Conference on Massively Parallel Processing, Elsevier, Amsterdam 1994, 235-242.

1993

R. Hofestädt, F. Krückeberg, T. Lengauer (ed.).
Informatik in den Biowissenschaften.
Informatik Aktuell, Springer Publishing, Heidelberg, 1993.
D. Beerbohm, R. Hofestädt, X. Huang.
Dynamischer Lastausgleich mit Zellularautomaten.
In Proceedings of the PARS 1993, PARS Notes No. 12, 1993, 92-101.
R. Hofestädt.
Grammatical Formalization of Metabolic Processes.
In L. Hunter, Searls D. and Shavlik J. (ed.): Proceedings First International Conference of Intelligent Systems for Molecular Biology, MIT/AAAI Press California, Washington D.C. 1993, 181-189.
R. Hofestädt.
Formale Sprachen zur Beschreibung von Zellstoffwechselprozessen.
In Pöppl S., Lipinski H.-G. und Mansky T. (ed.): Medizinische Informatik, MMV Medizin Publishing, Munich 1993, 245-249.
R. Hofestädt.
Modelling molecular counters with stochastic cellular grammars.
Informatik, Biometrie und Epidemiologie in Medizin und Biologie, 4, 1993, 169-177.
R. Hofestädt.
A Simulation Shell to Model Metabolic Pathways.
In Journal of Systems Analysis Modelling Simulation, Vol. 11, 1993, 253-262.
R. Hofestädt, K. Lautenbach, M. Löffler (ed.).
Modellierung der Zelldifferenzierung.
Informatik Berichte, University of Koblenz, 11, 1993