Prof. Dr. Falk Schreiber

Prof. Dr. Falk Schreiber
Bioinformatics
Leibniz Institute of Plant Genetics
and Crop Plant Research (IPK)
Corrensstraße 3
06466 Gatersleben
Germany 		Institute of Computer Science
Martin Luther University
Halle-Wittenberg
Von-Seckendorff-Platz 1
06120 Halle
Germany
room: KZH 003
tel.: +49 39482 5753
schreibe@ipk-gatersleben.de 		room: 210
tel.: +49 345 5524770
falk.schreiber@informatik.uni-halle.de
IPK MLU

Personal Topical Research Teaching Software Publications

 Personal
since 2007 Professor (Chair for Bioinformatics)
Institute of Computer Science
Martin Luther University Halle-Wittenberg Germany
and
Coordinator Bioinformatics
Bioinformatics
Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK)
Germany
2006 Habilitation in Computer Science
(Dr. habil.)
2003-2007 Head of Research Group
Department of Molecular Genetics
Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben (IPK)
Germany
2001-2002 Postdoctoral Research Fellow
and Lecturer
with Prof. Peter Eades
School of Information Technologies
The University of Sydney
Australia
2001 Ph.D. in Computer Science
(Dr. rer. nat.)
1997-2001 Research Fellow and Lecturer (Wissenschaftlicher Mitarbeiter)
with Prof. Dr. Franz J. Brandenburg
Faculty of Mathematics and Computer Science
University of Passau
Germany
1997 Diploma in Computer Science
(minor: Medical Computer Science)
at University of Passau
 Topical
SBGN-ED empty space map
SBGN-ED won the SBGN annual competitions 2010 and 2011 best SBGN software support (exactitude, completeness, validation), the map KEGG pathways in SBGN won the competition best SBGN map 2011.
Analysis of Biological Networks Modeling in Systems Biology
Books Analysis of Biological Networks and Modeling in Systems Biology: The Petri Net Approach published.
Integrative Bioinformatics
Next International Symposium on Integrative Bioinformatics (8th symposium) 2-4 April 2012, Hangzhou (China)
Vanted
Vanted 2.0 supporting SBGN, FBA, more data analysis and visualisation pipelines now available!
MetaCrop
MetaCrop 2.0 with extended content, new web-services and SBGN support now online!
Modelling
New crop plant metabolism models and model applications published (see Publications)

 Research
Areas of interest
  • bioinformatics and systems biology
  • visual analytics of biological data
  • modelling and analysing metabolism
  • biological network analysis
  • efficient algorithms for graphs and networks
Current research

My research focuses on two areas: (1) modelling, analysis, and visualisation of biological networks (especially metabolism); and (2) visualisation and visual analytics of multimodal biological data. These research activities aim at supporting the knowledge generation process in the life sciences, developing novel computational methods, and applying them to biological problems. I am particularly interested in plant bioinformatics and plant systems biology, but also have close collaboration with scientists from several other fields.

For an integrative, systems biology directed approach it is not sufficient to consider the biological entities alone but is necessary to study their interactions and link the data from experimental groups to relevant processes such as regulatory, interactomics, and metabolic networks. To support this, I research and develop algorithms, methods and systems in areas such as databases and information systems (to represent networks as well as diverse high-throughput data), data integration and data mining (to combine complex data and networks, and derive knowledge from the data), visual analytics (to help explore and analyse the data/images/networks in 2D to 4D), network analysis (to support hypothesis building), and mathematical modelling and simulation (to evaluate processes and support in silico predictions). My special interest is in metabolism where I have established a comprehensive pipeline of methods and tools. This ranges from multi-level representation of metabolic networks, models and related experimental data (MetaCrop, DBE2) to investigation of experimental data within metabolic networks (Vanted), to simulation and evaluation of these processes (FBA-SimVis), to visualisation and visual analytics methods (Vanted, SBGN-ED). Several applications gave new insights into the metabolism of crop plants. I am interested in theoretical and practical problems from computer science and bioinformatics as well as in the underlying biological and biomedical questions.

Detailed descriptions of current research projects can be found on the project page of my research group.


 Teaching

I have taught computer science and bioinformatics courses at undergraduate and postgraduate levels at the University of Passau (Germany), The University of Sydney (Australia), the University of Dortmund (Germany), the University of Kiel (Germany) and the University of Halle (Germany).

Current courses
winter term
2011/2012
Bioinformatics for Biologists and Agronomists (lecture)
summer term
2012 		Analysis of Biological Networks (lecture)
Programming project

 Software (selected tools)

I have developed/managed the development of several software tools. Major freely available tools are:

Visualisation and analysis of networks containing experimental data
Vanted is a tool for visual exploration and statistical analysis of complex biochemical data sets. For this task it is necessary to integrate and process data from different areas of genome, proteome and metabolome research and to present the results in a user-friendly way. The emphasis is on the linkage of experimental data with metabolic and regulatory networks under consideration of their spatial (3D) and temporal embedding. Vanted can be easily extended by user-developed add-ons, and several add-ons for database access, analysis algorithms (such as CentiLib for computation and evaluation of network centralities), simulation (such as FBA-SimVis for flux balance analysis) and other tasks are available.

SBGN-ED

Editing, translating and validating of SBGN maps
SBGN (Systems Biology Graphical Notation) is the standard for graphical representations of biochemical and cellular processes. SBGN-ED allows to create and edit all three types of SBGN maps (Process Description, Entity Relationship and Activity Flow), to validate these maps according to the SBGN specifications, to translate maps from the KEGG and MetaCrop pathway databases into SBGN, and to export SBGN maps into several file and image formats.

Managing crop plant metabolic pathways and models
MetaCrop is a manually curated repository of high quality information concerning the metabolism of crop plants. This includes pathway diagrams, reactions, locations, transport processes, reaction kinetics, taxonomy and literature. MetaCrop provides detailed information on seven major crop plants and initial information about several other plants. The web interface supports an easy exploration of the information and also allows model creation and automatic data export for detailed models of metabolic pathways therefore supporting systems biology approaches. MetaCrop is based on the Meta-All system.

Editing, processing and visualisation of KGML pathway files
KGML-ED allows the dynamic exploration and editing of KEGG Pathway diagrams. It is a graphical network editor, that provides read- and write-support for the KGML (KEGG Markup Language) file format. Pathway files are loaded and transformed into a graph which may be modified to fulfill user-specific needs and explored with network exploration approaches.

Motifs in networks
Motifs (patterns) in networks may represent building blocks of functional modules that carry out a relatively distinct function in biological networks, and MAVisto is a framework for their analysis. It contains algorithms to recognise multiple appearances of motifs in the target network under different frequency concepts, a motif preserving layout algorithm, and navigation techniques to explore the underlying structure of the network given by the motifs.


 Publications
Selected books
Modeling in Systems Biology

Analysis of Biological Networks

Ina Koch, Wolfgang Reisig and Falk Schreiber: Modeling in Systems Biology: The Petri Net Approach Springer, 2011.
This book deals with modeling of biochemical networks (metabolism, regulation, signaling) 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, 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 general network properties, and the second part studies the usage of these methods for the investigation of different biological networks ranging from molecular networks (gene regulation, protein interaction, metabolism) to ecological and phylogenetical networks.

Articles

F. Schreiber, C. Colmsee, T. Czauderna, E. Grafahrend-Belau, A. Hartmann, A. Junker, B. H. Junker, M. Klapperstück, U. Scholz and S. Weise: MetaCrop 2.0: managing and exploring information about crop plant metabolism Nucleic Acids Research, 40 (1): D1173-D1177, 2012. [pdf]

A. Junker, H. Rohn, T. Czauderna, C. Klukas, A. Hartmann and F. Schreiber: Creating interactive, web-based and data-enriched maps using the Systems Biology Graphical Notation Nature Protocols, 2012 (accepted).

I. Jusufi, C. Klukas, A. Kerren and F. Schreiber: Guiding the interactive exploration of metabolic pathway interconnections Information Visualization, 2012 (accepted).

I. Jusufi, A. Kerren, V. Aleksakhin and F. Schreiber: Visualization of mappings between the gene ontology and cluster trees (VDA), 2012 (accepted).

H. Rohn, C. Klukas and F. Schreiber: Creating views on integrated multi-domain data Bioinformatics, 27(13): 1839-1845, 2011. [pdf]

A. Hartmann, T. Czauderna, R. Hoffmann, N. Stein and F. Schreiber: HTPheno: An image analysis pipeline for high-throughput plant phenotyping BMC Bioinformatics, 12: 148.1-9, 2011. [pdf]

H. Rolletschek, G. Melkus, E. Grafahrend-Belau, J. Fuchs, N. Heinzel, F. Schreiber, P. M. Jakob and L. Borisjuk: Combined non-invasive imaging and modelling approaches reveal metabolic compartmentation in the cereal endosperm Plant Cell 23(8): 3041-3054, 2011.

G. Melkus, H. Rolletschek, J. Fuchs, V. Radchuk, E. Grafahrend-Belau, N. Sreenivasulu, T. Rutten, D. Weier, N. Heinzel, F. Schreiber, T. Altmann, P. Jakob and L. Borisjuk: Dynamic 13C/1H NMR imaging uncovers sugar allocation in the living seed Plant Biotechnology Journal, 9 (9): 1022-1037, 2011.

S. Weise, B. H. Junker, M. Klapperstück, M. Lange, F. Schreiber and U. Scholz: Das Informationssystem MetaCrop zur Unterstützung systembiologischer Forschung an Kulturpflanzen it - Information Technology 53 (5): 234-240, 2011.

H. Rohn, C. Klukas and F. Schreiber: Visual analytics of multimodal biological data 256-261 (IVAPP), 2011.

H. Mehlhorn and F. Schreiber: DBE2 - Management of experimental data for the VANTED system Journal of Integrative Bioinformatics, 8(2): 162.1-10, 2011.

D. Koschützki, B. H. Junker, J. Schwender and F. Schreiber: Structural analysis of metabolic networks based on flux centrality Journal of Theoretical Biology, 265: 261-269, 2010. [pdf]

T. Czauderna, C. Klukas and F. Schreiber: Editing, validating, and translating of SBGN maps Bioinformatics, 26 (18): 2340-2341, 2010. [pdf]

T. F. Sharbel, M.-L. Voigt, J. M. Corral, J. Kumlehn, C. Klukas, F. Schreiber, H. Vogel and B. Rotter: Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns The Plant Cell, 22: 655-671, 2010.

A. Junker, A. Hartmann, F. Schreiber and H. Bäumlein: An engineer's view on regulation of seed development Trends in Plant Science, 15(6): 303-307, 2010. [pdf]

K. Hippe, C. Colmsee, T. Czauderna, E. Grafahrend-Belau, B. H. Junker, C. Klukas, U. Scholz, F. Schreiber and S. Weise: Novel developments of the MetaCrop information system for facilitating systems biological approaches Journal of Integrative Bioinformatics, 7(3): 125.1-9, 2010. [pdf]

M. Scharfe, R. Pielot and F. Schreiber: Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets BMC Bioinformatics 11: 20.1-11, 2010. [pdf]

W. Weidemann, C. Klukas, A. Simm, F. Schreiber and R. Horstkorte: Lessons from GNE-deficient embryonic stem cells: Sialic acid biosynthesis is involved in proliferation and gene expression Glycobiology, 20(1): 107-117, 2010.

C. Klukas and F. Schreiber: Integration of -omics data and networks for biomedical research Journal of Integrative Bioinformatics, 7(2): 112.1-6, 2010. [pdf]

M. Albrecht, A. Kerren, K. Klein, O. Kohlbacher, P. Mutzel, W. Paul, F. Schreiber and M. Wybrow: On open problems in biological network visualization LNCS 5849: 256-267 (GD), 2010. [pdf]

E. Grafahrend-Belau, C. Klukas, B. H. Junker and F. Schreiber: FBASimViz: interactive visualization of constraint-based metabolic models Bioinformatics, 25(20): 2755-2757, 2009. [pdf]

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. Villéger, 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. [pdf]

F. Schreiber: Analyse und Visualisierung biologischer Netzwerke Informatik Spektrum, 32(4): 301-309, 2009. [pdf]

F. Schreiber, T. Dwyer, K. Marriott and M. Wybrow: A generic algorithm for layout of biological networks BMC Bioinformatics, 10: 375.1-12, 2009. [pdf]

S. Omidi, F. Schreiber and A. Masoudi-Nejad: MODA: An efficient algorithm for network motif discovery in biological networks Genes and Genetic Systems 84: 385-395, 2009. [pdf]

E. Grafahrend-Belau, F. Schreiber, D. Koschützki and B. H. Junker: Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism Plant Physiology, 149: 585-598, 2009. [pdf]

Z. R. M. Kashani, H. Ahrabian, E. Elahi, A. Nowzari-Dalini, E. S. Ansari, S. Asadi, S. Mohammadi, F. Schreiber and A. Masoudi-Nejad: Kavosh: a new algorithm for finding network motifs BMC Bioinformatics, 10: 318.1-12, 2009. [pdf]

D. C. Y. Fung, S.-H. Hong, D. Koschützki, F. Schreiber and K. Xu: Visual analysis of overlapping biological networks 337-342 (IEEE IV), 2009. [pdf]

H. Rohn, C. Klukas and F. Schreiber: Integration and visualisation of multimodal biological data LNI P-127: 105-115 (GCB), 2009. [pdf]

T. Fester, F. Schreiber and M. Strickert: CUDA-based multi-core implementation of MDS-based bioinformatics algorithms LNI P-127: 67-79 (GCB), 2009. [pdf]

S. Weise, C. Colmsee, E. Grafahrend-Belau, B. Junker, C. Klukas, M. Lange, U. Scholz and F. Schreiber: An integration and analysis pipeline for systems biology in crop plant metabolism LNBI 5647: 196-203 (DILS), 2009. [pdf]

R. Pielot, U. Seiffert, B. Manz, D. Weier, F. Volke, F. Schreiber and W. Weschke: Multimodal registration of NMR-volumes and histological cross-sections of barley grains on the Cell broadband engine 241-244 (VISAPP), 2009.

S. Weise, C. Colmsee, E. Grafahrend-Belau, B. Junker, C. Klukas, M. Lange, U. Scholz and F. Schreiber: Datenaustausch und Datenintegration zur Modellierung und Analyse metabolischer Netzwerke am Beispiel von Kulturpflanzen LNI P-154: 693-697 (Informatik 2009), 2009.

T. Dwyer, K. Marriott, F. Schreiber, P. J. Stuckey, M. Woodward and M. Wybrow: Exploration of networks using overview+detail with constraint-based cooperative layout IEEE Transactions on Visualization and Computer Graphics, 14(6): 1293-1300 (IEEE InfoVis), 2008. [pdf]

D. C. Y. Fung, S.-H. Hong, D. Koschützki, F. Schreiber and K. Xu: 2.5D Visualisation of overlapping biological networks Journal of Integrative Bioinformatics, 5(1): 90.1-17, 2008. [pdf]

D. Koschützki and F. Schreiber: Centrality analysis methods for biological networks and their application to gene regulatory networks Gene Regulation and Systems Biology, 2: 193-201, 2008. [pdf]

E. Grafahrend-Belau, S. Weise, D. Koschützki, U. Scholz, B. H. Junker and F. Schreiber: MetaCrop - A detailed database of crop plant metabolism Nucleic Acids Research, 36: D954-D958, 2008. [pdf]

E. Grafahrend-Belau, F. Schreiber, M. Heiner, A. Sackmann, B. H. Junker, S. Grunwald, A. Speer, K. Winder and I. Koch: Modularization of biochemical networks based on classification of Petri net t-invariants BMC Bioinformatics, 9: 90.1-17, 2008. [pdf]

E. Grafahrend-Belau, B. H. Junker, D. Koschützki, C. Klukas, S. Weise, U. Scholz and F. Schreiber: Towards systems biology of developing barley grains: a framework for modeling metabolism TICPS Series, 41: 41-44 (WCSB), 2008. [pdf]

C. Klukas and F. Schreiber: Dynamic exploration and editing of KEGG pathway diagrams Bioinformatics, 23(3): 344-350, 2007. [pdf]

D. Koschützki, H. Schwöbbermeyer and F. Schreiber: Ranking of network elements based on functional substructures Journal of Theoretical Biology, 248(3): 471-479, 2007. [pdf]

M. Telgkamp, D. Koschützki, H. Schwöbbermeyer and F. Schreiber: Community-based linking of biological network resources: databases, formats and tools Journal of Integrative Bioinformatics, 4(3): 141-152, 2007. [pdf]

B. H. Junker, D. Koschützki and F. Schreiber: Exploration of biological network centralities with CentiBiN BMC Bioinformatics, 7: 219.1-7, 2006. [pdf]

B. H. Junker, C. Klukas and F. Schreiber: VANTED: A system for advanced data analysis and visualization in the context of biological networks BMC Bioinformatics 7: 109.1-13, 2006. [pdf]

S. Weise, I. Grosse, C. Klukas, D. Koschützki, U. Scholz, F. Schreiber and B. H. Junker: Meta-All: a system for managing metabolic pathway information BMC Bioinformatics, 7: 465.1-9, 2006. [pdf]

B. H. Junker, D. Koschützki and F. Schreiber: Kinetic modelling with the Systems Biology Modelling Environment SyBME Journal of Integrative Bioinformatics, 3(1): 18.1-10, 2006. [pdf]

C. Klukas, B. H. Junker and F. Schreiber: The VANTED software system for transcriptomics, proteomics and metabolomics analysis Journal of Pesticide Science 31(3): 289-292, 2006. [pdf]

T. Dwyer, S.-H. Hong, D. Koschützki, F. Schreiber and K. Xu: Visual analysis of network centralities CRPIT 60: 189-198 (APVIS), 2006. [pdf]

C. Klukas, F. Schreiber and H. Schwöbbermeyer: Coordinated perspectives and enhanced force-directed layout for the analysis of network motifs CRPIT 60: 39-48 (APVIS), 2006. [pdf]

C. Klukas, D. Koschützki and F. Schreiber: Graph pattern analysis with PatternGravisto Journal of Graph Algorithms and Applications 9(1): 19-29, 2005. [pdf]

F. Schreiber and H. Schwöbbermeyer: MAVisto: a tool for the exploration of network motifs Bioinformatics 21(17): 3572-3574, 2005. [pdf]

H. Rolletschek, R. Radchuk, C. Klukas, F. Schreiber, U. Wobus and L. Borisjuk: Evidence of a key role for photosynthetic oxygen release in oil storage in developing soybean seeds New Phytologist 167(3): 777-786, 2005. [pdf]

F. Schreiber and H. Schwöbbermeyer: Frequency Concepts and Pattern Detection for the Analysis of Motifs in Networks Transactions on Computational Systems Biology 3 (LNBI 3737): 89-104, 2005. [pdf]

L. Borisjuk, M.-R. Hajirezaei, C. Klukas, H. Rolletschek and F. Schreiber: Integrating Data from Biological Experiments into Metabolic Networks with the DBE Information System In Silico Biology 5(2): 93-102, 2005. [pdf]

B. H. Junker, D. Koschützki and F. Schreiber: Kinetic Modelling with the Systems Biology Modelling Environment SyBME 49-51 (IB), 2005. [pdf]

U. Brandes, T. Dwyer and F. Schreiber: Visual Understanding of Metabolic Pathways Across Organisms Using Layout in Two and a Half Dimensions Journal of Integrative Bioinformatics 1(1): 119-132, 2004. [pdf]

C. Friedrich and F. Schreiber: Flexible Layering in Hierarchical Drawings with Nodes of Arbitrary Size CRPIT 26: 369-376 (ACSC), 2004. [pdf]

D. Koschützki and F. Schreiber: Comparison of Centralities for Biological Networks LNI P-53: 199-206 (GCB), 2004. [pdf]

T. Dwyer and F. Schreiber: Optimal Leaf Ordering for Two and a Half Dimensional Phylogenetic Tree Visualisation CRPIT 35: 109-115 (InVis.au), 2004. [pdf]

F. Schreiber and H. Schwöbbermeyer: Towards Motif Detection in Networks: Frequency Concepts and Flexible Search 91-102 (NETTAB), 2004. [pdf]

U. Brandes, T. Dwyer and F. Schreiber: Visual Triangulation of Network-based Phylogenetic Trees 75-84 (VisSym), 2004. [pdf]

T. Dwyer, H. Rolletschek and F. Schreiber: Representing Experimental Biological Data in Metabolic Networks CRPIT 29: 13-20 (APBC), 2004. [pdf]

F. Schreiber: Visual Comparison of Metabolic Pathways Journal of Visual Languages and Computing 14(4): 327-340, 2003. [pdf]

C. Friedrich and F. Schreiber: Visualisation and navigation methods for typed protein-protein interaction networks Applied Bioinformatics 2(S3): 19-24, 2003. [pdf]

U. Brandes, T. Dwyer and F. Schreiber: Visualizing Related Metabolic Pathways in Two and a Half Dimensions LNCS 2912: 111-122 (GD), 2003. [pdf]

F. Schreiber: Comparison of Metabolic Pathways using Constraint Graph Drawing CRPIT 19: 105-110 (APBC), 2003. [pdf]

M. Forster, A. Pick, M. Raitner, F. Schreiber and F. J. Brandenburg: The System Architecture of the BioPath system In Silico Biology 2(3): 415-426, 2002. [pdf]

F. Schreiber: High Quality Visualization of Biochemical Pathways in BioPath In Silico Biology 2(2): 59-73, 2002. [pdf]

F. J. Brandenburg, M. Forster, A. Pick, M. Raitner and F. Schreiber: BioPath - Visualization of Biochemical Pathways 11-15 (GCB), 2001. [html]

F. Schreiber and K. Skodinis: NP-Completeness of some Tree-Clustering Problems LNCS 1547: 288-301 (GD), 1998. [pdf]

F. J. Brandenburg, B. Gruber, M. Himsolt and F. Schreiber: Automatische Visualisierung biochemischer Informationen 24-38 (MB/GI Informatik), 1998. [pdf]

J. Knoop and F. Schreiber: Type Analysis and Type-test Elimination in Oberon-2 240-250 (PLFP), 1997. [pdf]

J. Knoop and F. Schreiber: Analysing and Optimizing Strongly Typed Object-Oriented Languages: A Generic Approach and its Application to Oberon-2 252-266 (WOON), 1997. [pdf]

M. v. d. Beeck, V. Braun, A. Claßen, A. Dannecker, C. Friedrich, D. Koschützki, T. Margaria, F. Schreiber and B. Steffen: Graphs in METAFrame: The Unifying Power of Polymorphism LNCS 1217: 112-129 (TACAS), 1997. [pdf]

Books, conference proceedings and theses

I. Koch, W. Reisig and F. Schreiber: Modeling in Systems Biology: The Petri Net Approach Springer Book Series Computational Biology, Springer, 364 pages, 2011. [html]

I. Grosse, S. Neumann, S. Posch, F. Schreiber and P. Stadler: Proceedings of the German Bioinformatics Conference 2009 Lecture Notes in Informatics Series (157), GI Verlag, 228 pages, 2009.

B. H. Junker and F. Schreiber: Analysis of Biological Networks Wiley Series on Bioinformatics, Computational Techniques and Engineering, Wiley, 368 pages, 2008. [html]

R. Hofestädt, J. Köhler, M. Lange, U. Scholz, F. Schreiber, P. Verrier: Integrative Bioinformatics: Proceedings of the 5th International Symposium on Integrative Bioinformatics 2008 IMBio, 345 pages, 2008

F. Schreiber: Visual Analysis of Biological Networks Habilitation thesis, University of Passau (Germany), 194 pages, 2006.

F. Schreiber: Visualisierung biochemischer Reaktionsnetze PhD thesis, University of Passau (Germany), 290 pages, 2001. [pdf]

Book chapters

H. Rohn and F. Schreiber: Visualization of biological knowledge based on multimodal data In M. Elloumi (Ed.), Biological knowledge discovery handbook: preprocessing, mining and postprocessing of biological data, Wiley, 2012 (to appear).

C. Bachmaier, U. Brandes and F. Schreiber: Biological Networks In R. Tamassia (Ed.), Handbook of Graph Drawing and Visualization, Chapman & Hall/CRC Press, 2012 (in press). [pdf]

K. Lotz, A. Hartmann, E. Grafahrend-Belau, F. Schreiber, B. H. Junker: Elementary flux modes, flux balance analysis and their application to plant metabolism In G. Sriram (Ed.), Methods in Molecular Biology: Plant Metabolism, Humana Press, 2012 (in press).

F. Schreiber and N. Le Novère: Exchange formats for systems biology - SBGN In W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota (Eds.), Encyclopedia of Systems Biology, Springer, 2012 (to appear).

H. Mehlhorn and F. Schreiber: Small-world property of networks In W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota (Eds.), Encyclopedia of Systems Biology, Springer, 2012 (to appear).

C. Krach, E. Grafahrend-Belau, H. Poskar, K. Schallau, F. Schreiber, B. H. Junker: Using systems approaches to analyze metabolic networks involved in storage reserve synthesis in developing seeds In G. K. Agrawal and R. Rakwal (Eds.), Seed development: omics technologies toward improvement of seed quality and crop yield, Springer, 2012 (in press).

E. Grafahrend-Belau, B. H. Junker and F. Schreiber: Plant metabolic pathways: databases and pipeline for stoichiometric analysis In G. K. Agrawal and R. Rakwal (Eds.), Seed development: omics technologies toward improvement of seed quality and crop yield, Springer, 2012 (in press).

F. Schreiber: Representation and analysis of biological networks with the Vanted toolsuite In R. Hofestädt and N. Kolchanov (Eds.), German/Russian Network of Computational Systems Biology, Berichte aus der Medizinischen Informatik und Bioinformatik, Shaker Verlag, 47-50, 2010.

F. Schreiber and H. Schwöbbermeyer: Motifs in biological networks In M. Stumpf, C. Wiuf (Eds.), Statistical and Evolutionary Analysis of Biological Network Data, Imperial College Press/World Scientific, 45-64, 2010. [pdf]

C. E. Wheelock, S. Goto, L. Yetukuri, F. L. D'Alexandri, C. Klukas, F. Schreiber and M. Oresic: Bioinformatics strategies for the analysis of lipids In D. Armstrong (Ed.) Methods in Molecular Biology: Lipidomics, Humana Press, 339-368, 2009. [pdf]

E. Grafahrend-Belau, B. H. Junker, C. Klukas, D. Koschützki, F. Schreiber and H. Schwöbbermeyer: Topology of plant metabolic networks In J. Schwender (Ed.), Plant Metabolic Networks, Springer, 173-209, 2009.

F. Schreiber: Visualization In J. Keith (Ed.), Methods in Molecular Biology: Bioinformatics, Humana Press, 441-450, 2008.

F. J. Brandenburg, M. Forster, A. Pick, M. Raitner and F. Schreiber: BioPath - Exploration and Visualization of Biochemical Pathways In M. Jünger, P. Mutzel (Eds.), Graph Drawing Software, Springer Mathematics and Visualization Series, 215-236, 2004. [pdf]

F. J. Brandenburg, M. Jünger, J. Marks, P. Mutzel and F. Schreiber: Graph-Drawing Contest Report In J. Krachtochvil (Ed.), Graph Drawing, Springer LNCS 1731, 400-409, 1999.

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