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Complete list of publications
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Selected books
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Ina Koch, Wolfgang Reisig and Falk Schreiber:
Modeling in Systems Biology: The Petri Net Approach
Springer, 2010 (to appear).
This book deals with modeling of biochemical networks based on Petri net theory. It serves as text book for biologists who want to model biochemical systems using Petri nets as well as for computer scientists who are interested in biological applications.
Björn H. Junker and Falk Schreiber:
Analysis of Biological Networks
Wiley Series on Bioinformatics, Computational Techniques and Engineering
(Yi Pan and Albert Y. Zomaya, Series Editors), Wiley, 2008.
This book deals with methods for the analysis of biological networks. The first part introduces network analysis algorithms such as centralities,
motifs, clustering and algorithms for special networks (e.g. Petri nets), and the second part studies the usage of these m ethods for the investigation of different biological networks ranging from molecular networks (gene regulation, protein interaction, metabolism) to ecological and phylogenetical networks.
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Selected papers
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N. Le Novère, M. Hucka, H. Mi, S. Moodie, F. Schreiber, A. Sorokin, E. Demir, K. Wegner, M. Aladjem, S. M. Wimalaratne, F. T. Bergman, R. Gauges, P. Ghazal, K. Hideya, L. Li, Y. Matsuoka, A. Villèger,
S. E. Boyd, L. Calzone, M. Courtot, U. Dogrusoz, T. Freeman, A. Funahashi, S. Ghosh, A. Jouraku, S. Kim, F. Kolpakov, A. Luna, S. Sahle, E. Schmidt, S. Watterson, G. Wu, I. Goryanin, D. B. Kell, C. Sander, H. Sauro, J. L. Snoep, K. Kohn and H. Kitano:
The Systems Biology Graphical Notation
Nature Biotechnology, 27: 735-741, 2009.
This paper presents a new set of standards for graphically representing biological information, the biology equivalent of the circuit diagram in electronics. Systems Biology Graphical Notation (SBGN)
as visual language should make it easier to exchange complex information,
so that models are accurate, efficient and readily understandable.
Eva Grafahrend-Belau, Stephan Weise, Dirk Koschützki, Uwe Scholz,
Björn H. Junker and Falk Schreiber:
MetaCrop -
A detailed database of crop plant metabolism
Nucleic Acids Research, 36: D954-D958, 2008.
This paper presents MetaCrop, a comprehensive database for high quality information concerning the metabolism in crop plants on various levels of detail.
Dirk Koschützki, Henning Schwöbbermeyer and Falk Schreiber:
Ranking of network elements based on functional substructures
Journal of Theoretical Biology, 248(3): 471-479, 2007.
This paper presents a novel network centrality algorithm and its application to biological networks, in particular gene regulatory networks.
Christian Klukas and Falk Schreiber:
Dynamic
Exploration and Editing of KEGG Pathway Diagrams
Bioinformatics, 23(3): 344-350, 2007.
This paper presents methods for the interactive visualisation and exploration of KEGG pathways and an editor for the KGML language.
Björn H. Junker, Christian Klukas and Falk Schreiber:
VANTED: A System for Advanced
Data Analysis and Visualization in the Context
of Biological Networks
BMC Bioinformatics 7: 109.1-13, 2006.
This paper presents new methods for the integration, analysis and visualisation of experimental data within biological networks and functional hierarchies, and the tool Vanted which implements these methods.
Falk Schreiber:
High Quality Visualization of
Biochemical Pathways in BioPath
In Silico Biology 2(2): 59-73, 2002.
This paper presents a novel layout (graph drawing) algorithm to produce interactive visualisations of biochemical pathways according to established styles in biochemistry/biology in book printing quality.
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