Publications

Books

Ina Koch, Wolfgang Reisig and Falk Schreiber: Modeling in Systems Biology: The Petri Net Approach Springer, 2011.

This book presents the modelling of biochemical and cellular networks (e.g., 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 of Petri nets.


Björn H. Junker and Falk Schreiber:  Analysis of Biological  Networks  Wiley, 2008.


This book presents 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. 


List of publications

2017

•   H. Nim, B. Sommer, K. Klein, A. Flack, K. Safi, M. Nagy, W. Fiedler, M. Wikelski and F. Schreiber: ‘Design considerations for immersive analytics of bird movements obtained by miniaturised GPS sensors’ (Proc.  EG Visual Computing for Biology and Medicine - VCBM), 2017 (to appear).

•  B. Sommer and F. Schreiber: ‘Integration and virtual reality exploration of biomedical data with CmPI and VANTED’ it – Information Technology 59(4): 181-190, 2017. 

•  B. Sommer, D. G. Barnes, S. Boyd, T. Chandler, M. Cordeil, T. Czauderna, M. Klapperstück, K. Klein, T. D. Nguyen, H. Nim, K. Stephens, D. Vohl, S. Wang, E. Wilson, Y. Zhu, J. Li, J. McCormack, K. Mariott, and F. Schreiber: ‘3D-stereoscopic immersive analytics projects at Monash University and University of Konstanz’ (Proc.  IS&T Electronic Imaging - Stereoscopic Displays and Applications XXVIII) Electronic Imaging 5, 179-187, 2017. 

• C. J. Myers, G. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novère, D. P. Nickerson, F. Schreiber and D. Waltemath: 'A brief history of COMBINE’ (Proc. Winter Simulation Conference – WSC), 2017 (to appear).

•   F. Schreiber, E. Grafahrend-Belau, O. Kohlbacher and H. Mi: ‘Metabolic pathways and networks’ in S. I. O'Donoghue and J. B. Procter (eds.), Visualizing biological data - a practical guide, Cambridge University Press, 2017 (to appear).

•   C. Binucci, U. Brandes, T. Dwyer, R. von Hanxleden, P. Mutzel, M. Schaefer and F. Schreiber: ‘10 reasons to get interested in graph drawing’ in Springer LNCS 10000, 2017 (to appear).

•   T. Czauderna and F. Schreiber: ‘Information visualization for biological data’ in J. Keith (ed.), Bioinformatics - Volume II: Structure, Function, and Applications, Springer 403-415, 2017.

2016

•   M. R. Ghaffari, F. Shahinnia, B. Usadel, B. Junker, F. Schreiber, N. Sreenivasulu and M. R. Hajirezaei: ‘The metabolic signature of biomass formation in barley’ Plant and Cell Physiology  57(9): 1943-1960, 2016.

•   D. Waltemath, J. R. Karr, F. T. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C. J. Myers, P. Pir, B. Alaybeyoglu, N. K. Aranganathan, K. Baghalian, A. T. Bittig, P. E. P. Burke, M. Cantarelli, Y. H. Chew, R. S. Costa, J. Cursons, T. Czauderna, H. F. Gomez, J. Hahn, T. Hameri, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knüpfer, M. König, D. Lee, A. Lloret-Villas, N. Mandrik, J. K. Medley, B. Moreau, H. Naderi-Meshkin, S. K. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N. Stanford, J.-H. Song, T. Theile, M. Tokic, N. Tomar, J. Uhlendorf, T. M. Varusai, F. Wendland, M. Wolfien, J. T. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova and F. Schreiber: ‘Toward community standards and software for whole-cell modeling’ IEEE Transactions on Biomedical Engineering 63(10): 2007-2014, 2016.

•   F. Schreiber, G. D. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novère, C. Myers, D. Nickerson, B. Sommer and D. Walthemath: 'Specifications of standards in systems and synthetic biology: status and developments in 2016' special issue Journal of Integrative Bioinformatics 13(3), 132 pages, 2016.

•   M. Klapperstück, T. Czauderna, C. Goncu, J. Glowacki, T. Dwyer, F. Schreiber and K. Marriott: ‘ContextuWall: peer collaboration using (large) displays’ (Proc. IEEE Big Data Visual Analytics - BDVA) 1-8, 2016.

•   H. T. Nim, M. Wang, Y. Zhu, B. Sommer, F. Schreiber, S. Boyd, S. J. Wang: ‘Communicating the effect of human behaviour on the great barrier reef via mixed reality visualisation’ (Proc. IEEE Big Data Visual Analytics - BDVA) 1-6, 2016.

•   B. Sommer, A. Hamacher, O. Kalutza, T. Czauderna, M. Klapperstück, N. Biere, M. Civico, B. Thomas, D. G. Barnes and F. Schreiber: ‘Stereoscopic space map - semi-immersive configuration of 3D-stereoscopic tours in multi-display environments’ (Proc. IS&T Electronic Imaging - Stereoscopic Displays and Applications XXVII (5)) 1-9, 2016.

•   S. C. Mueller, B. Sommer, C. Backes, J. Haas, B. Meder, E. Meese, A. Keller: ‘From single variants to protein cascades: multi-scale modeling of SNV sets in genetic disorders’ Journal of Biological Chemistry 291(4): 1582-1590, 2016.

2015

•   S. M. Baker, C. H. Poskar, F. Schreiber and B. H. Junker: ‘A unified framework for estimating parameters of kinetic biological models’ BMC Bioinformatics 16: 104.1-21, 2015.

•   H. Rolletschek, E. Grafahrend-Belau, E. Munz, V. Radchuk, R. Kartäusch, H. Tschiersch, G. Melkus, F. Schreiber, P. M. Jakob and L. Borisjuk: ‘Metabolic architecture of the cereal grain and its relevance to maximize carbon use efficiency’ Plant Physiology 169(3): 1698-1713, 2015.

•   J. Schwender, I. Hebbelmann, N. Heinzel, T. Hildebrandt, A. Rogers, D. Naik, M. Klapperstück, H.-P. Braun, F. Schreiber, P. Denolf, L. Borisjuk and H. Rolletschek: ‘Quantitative multilevel analysis of central metabolism in developing oilseeds of oilseed rape during in vitro culture’ Plant Physiology 168(3): 828-848, 2015.

•   Y. Asgari, Z. Zabihinpour, A. Salehzadeh-Yazdi, F. Schreiber and A. Masoudi-Nejad: ‘Alterations in cancer cells metabolism: the Warburg effect and metabolic adaptation’ Genomics, 105(5): 275-281, 2015.

•   C. B. Hill, T. Czauderna, M. Klapperstück, U. Roessner and F. Schreiber: ‘Metabolomics, standards, and metabolic modeling for synthetic biology in plants’ Frontiers in Bioengineering and Biotechnology 3: 167.1-12, 2015.

•   F. Schreiber, G. D. Bader, M. Golebiewski, M. Hucka, B. Kormeier, N. Le Novère, C. Myers, D. Nickerson, B. Sommer, D. Waltemath and S. Weise: ‘Specifications of Standards in Systems and Synthetic Biology’ special issue Journal of Integrative Bioinformatics 12(2), 993 pages, 2015.

•   A. Sorokin, N. Le Novère, A. Luna, T. Czauderna, E. Demir, R. Haw, H. Mi, S. Moodie, F. Schreiber and A. Villéger: ‘Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2’ Journal of Integrative Bioinformatics 12(2): 264.1-59, 2015.

•   H. Mi, F. Schreiber, S. Moodie, T. Czauderna, E. Demir, R. Haw, A. Luna, N. Le Novère, A. Sorokin and A. Villéger: ‘Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2’ Journal of Integrative Bioinformatics 12(2): 265.1-42, 2015.

•   M. Hucka, D. P. Nickerson, G. D. Bader, F. T. Bergmann, J. Cooper, E. Demir, A. Garny, M. Golebiewski, C. J. Myers, F. Schreiber, D. Waltemath and N. Le Novère: ‘Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative’ Frontiers in Bioengineering and Biotechnology 3: 19.1-6, 2015.

•   H. Nim, T. Done, F. Schreiber and S. Boyd: ‘Interactive geolocational and coral compositional visualisation of Great Barrier Reef heat stress data’  (Proc. IEEE Big Data Visual Analytics - BDVA) 81-87, 2015.

•   B. Sommer, S. J. Wang, L. Xu, M. Chen and F. Schreiber: ‘Hybrid-dimensional visualization and interaction - integrating 2D and 3D visualization with semi-immersive navigation techniques’ (Proc. IEEE Big Data Visual Analytics - BDVA) 65-72, 2015.

•   T. Chandler, M. Cordeil, T. Czauderna, T. Dwyer, J. Glowacki, C. Goncu, M. Klapperstück, K. Klein, K. Marriott, F. Schreiber and E. Wilson: ‘Immersive Analytics’ (Proc. IEEE Big Data Visual Analytics - BDVA) 73-80, 2015. 

2014

•   K. Baghalian, M.-R. Hajirezaei and F. Schreiber: ‘Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering’ Plant Cell 26: 3847–3866, 2014.

•   A. Hartmann and F. Schreiber: ‘Integrative analysis of metabolic models – from structure to dynamics‘ Frontiers in Bioengineering and Biotechnology 2: 91.1-10, 2014.

•   M. Klapperstück and F. Schreiber. ‘BioNetLink - an architecture for working with network data’ Journal of Integrative Bioinformatics 11(2): 241.1-12, 2014.

•   A. Kerren and F. Schreiber: ‘Why integrate InfoVis and SciVis? An example from systems biology’ IEEE Computer Graphics and Applications 34(6): 69-73, 2014.

•   D. Waltemath, F. T. Bergmann, C. Chaouiya, T. Czauderna, P. Gleeson, C. Goble, M. Golebiewski, M. Hucka, N. Juty, O. Krebs, N. Le Novère, H. Mi, I. I. Moraru, C.J. Myers, D. Nickerson, B. G. Olivier, N. Rodriguez, F. Schreiber, L. Smith, F. Zhang and E. Bonnet. ‘Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)’. Standards in Genomic Sciences 9(3), 1285-1301, 2014.

•   F. Schreiber, A. Kerren, K. Börner, H. Hagen and D. Zeckzer: ‘Heterogeneous networks on multiple levels’ in A. Kerren, H. C. Purchase and M. O. Ward (eds.), Multivariate network visualization, Springer LNCS 8380, 175-206, 2014.

•   C. Krach, A. Junker, H. Rohn, F. Schreiber and B. H. Junker: ‘Flux visualization using Vanted/FluxMap’ in J. O. Krömer, L. K. Nielsen and L. M. Blank (eds.), Methods in Molecular Biology: Metabolic Flux Analysis, Humana Press, 225-233, 2014.

•   K. Lotz, A. Hartmann, E. Grafahrend-Belau, F. Schreiber and 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, 231-252, 2014.

•   E. Grafahrend-Belau, A. Junker, F. Schreiber and B. Junker: ‘Flux balance analysis as an alternative method to estimate fluxes without labeling’ in M. Dieuaide-Noubhani and A. P. Alonso (eds.), Methods in Molecular Biology: Plant Metabolic Flux Analysis, Humana Press, 281-299, 2014.

•   A. Kerren and F. Schreiber: ‘Network visualization for integrative bioinformatics’ in R. Hofestädt and M. Chen (eds.), Approaches in Integrative Bioinformatics: towards the virtual cell, Springer, 173-202, 2014.

•   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, 1109-1125, 2014.

•   I. Koch, W. Reisig, and F. Schreiber: ‘Petri nets in the biosciences’ special issue it–Information Technology 56(2), Oldenbourg Wissenschaftsverlag, 86 pages,2014;

•   O. Kohlbacher, F. Schreiber and M. O. Ward: ‘Multivariate networks in the life sciences’ in A. Kerren, H. C. Purchase and M. O. Ward (eds.), Multivariate network visualization, Springer LNCS 8380, 61-73, 2014.

2013

•   I. Jusufi, A. Kerren and F. Schreiber: ‘Exploring biological data: mappings between ontology- and cluster-based representations’ Information Visualization 12(3-4): 291-307, 2013.

•   T. Czauderna, M. Wybrow, K. Marriott and F. Schreiber: ‘Conversion of KEGG metabolic pathways to SBGN maps including automatic layout’ BMC Bioinformatics 14: 250.1-17, 2013.

•   S. M. Baker, C. H. Poskar, F. Schreiber and B. H. Junker: ‘An improved constraint filtering technique for inferring hidden states and parameters of a biological model’ Bioinformatics 29: 1052-1059, 2013.

•   T. Vogt, T. Czauderna and F. Schreiber: ‘Translation of SBGN maps: Process Description to Activity Flow’ BMC Systems Biology 7: 115.1-19, 2013.

•   E. Grafahrend-Belau, A. Junker, A. Eschenröder, J. Müller, F. Schreiber and B. H. Junker: ‘Multiscale metabolic modeling: dynamic flux balance analysis on a whole plant scale’ Plant Physiology 163(2): 637-647, 2013.

•   Y. Asgari, A. Salehzadeh-Yazdi, F. Schreiber and A. Masoudi-Nejad: ‘Controllability in cancer metabolic networks according to drug targets as driver nodes’ PLOS One 8: e79397, 2013

•   F. Büchel, N. Rodriguez, N. Swainston, C. Wrzodek, T. Czauderna, R. Keller, F. Mittag, M. Schubert, M. Glont, M. Golebiewski, M. van lersel, S. Keating, M. Rall, M. Wybrow, H. Hermjakob, M. Hucka, D. B. Kell, W. Müller, P. Mendes, A. Zell, C. Chaouiya, J. Saez-Rodriguez,  F. Schreiber, C. Laibe, A. Dräger and N. LeNovère: ‘Path2Models: Large-scale generation of computational models from biochemical pathway maps’ BMC Systems Biology 7: 116.1-19, 2013.

•   C. Colmsee, T. Czauderna, E. Grafahrend-Belau, A. Hartmann, M. Lange, M. Mascher, S. Weise, U. Scholz and F. Schreiber: ‘Optimas-DW, MetaCrop and Vanted: a case study for data integration, curation and visualisation in life sciences’ LNI P-220: 1834-1840 (Proc. Ontologies and Data in Life Sciences – ODLS), 2013.

•   H. Mehlhorn and F. Schreiber: ‘TransID – the flexible identifier mapping service’ (Proc. Integrative Bioinformatics – IB) 112-121, 2013.

•   J. Müller, A. Eschenröder, O. Christen, B. Junker and F. Schreiber: ‘ProNet-CN model: a dynamic and hierarchical process network that couples photosynthesis, primary carbon metabolism and effects of leaf nitrogen status’  (Proc. IEEE Plant Growth Modeling, Simulation, Visualization and Applications – PMA) 289-296, 2013.

•   C. Bachmaier, U. Brandes and F. Schreiber: ‘Biological networks’ in R. Tamassia (ed.), Handbook of graph drawing and visualization, Chapman & Hall/CRC Press, 621-652, 2013.

•   F. Schreiber and N. Le Novère: ‘Exchange formats for systems biology - SBGN’ in W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota (eds.), Encyclopaedia of Systems Biology, Springer, 1893-1895, 2013.

•   H. Mehlhorn and F. Schreiber: ‘Small-world property of networks’ in W. Dubitzky, O. Wolkenhauer, K.-H. Cho and H. Yokota (eds.), Encyclopaedia of Systems Biology, Springer, 1957-1959, 2013.

•   H. Mehlhorn, M. Lange, U. Scholz and F. Schreiber: ‘Extraction and prediction of biomedical database identifier using neural networks towards data network construction’ in P. O. de Pablos, M. D. Lytras, R. D. Tennyson and J. E. L. Gayo (eds.), Cases on open-linked data and semantic web applications, IGI Global, 58-83, 2013.

•   F. Schreiber, R. Hofestädt, M. Lange, U. Scholz, T. Czauderna, R. Schnee, S. Weise: ‘Integrative Bioinformatics: proceedings of the 9th international symposium on Integrative Bioinformatics 2013’ IMBio, 224 pages, 2013.

•   R. Hofestädt, B. Kormeier, M. Lange, F. Schreiber, B. Sommer and S. Weise: ‘JIBtools: a strategy to reduce the bioinformatics analysis gap’ special issue Journal of Integrative Bioinformatics 10, (online resource) 2013.

2012

•   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.

•   A. Junker, A. Sorokin, T. Czauderna, F. Schreiber and A. Mazein:  ‘Wiring diagrams in biology: towards the standardized representation of biological information’ Trends in Biotechnology 30(11): 555-557, 2012.

•   H. Rohn, A. Junker, A. Hartmann, E. Grafahrend-Belau, H. Treutler, M. Klapperstück, T. Czauderna, C. Klukas and F. Schreiber: ‘Vanted v2: a framework for systems biology applications’ BMC Systems Biology 6: 139.1-13, 2012.

•   M. P. van Iersel, A. C. Villéger, T. Czauderna, S. E. Boyd, F. T. Bergmann, A. Luna, E. Demir, A. Sorokin, U. Dogrusoz, Y. Matsuoka, A. Funahashi, M. I. Aladjem, H. Mi, S. L. Moodie, H. Kitano, N. Le Novère and F. Schreiber: ‘Software support for SBGN maps: SBGN-ML and LibSBGN’ Bioinformatics 28(15): 2016-2021, 2012.

•   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 7: 579-593, 2012.

•   A. Masoudi-Nejad, F. Schreiber and Z. R. M. Kashani: ‘Building blocks of biological networks: a review on major network motif discovery algorithms’ IET Systems Biology 6(5): 164-174, 2012.

•   J. Gräßler, D. Koschützki and F. Schreiber: ‘CentiLib: comprehensive analysis and exploration of network centralities’ Bioinformatics 28(8): 1178-1179, 2012.

•   A. Junker, H. Rohn and F. Schreiber: ‘Visual analysis of transcriptome data in the context of anatomical structures and biological networks’ Frontiers in Plant Science 3: 252.1-13, 2012.

•   I. Jusufi, C. Klukas, A. Kerren and F. Schreiber: ‘Guiding the interactive exploration of metabolic pathway interconnections’ Information Visualization 11(2): 136-150, 2012.

•   H. Rohn, A. Hartmann, A. Junker, B. H. Junker and F. Schreiber: ‘FluxMap: a Vanted add-on for the visual exploration of flux distributions in biological networks’ BMC Systems Biology 6: 33.1-9, 2012.

•   H. Mehlhorn, M. Lange, U. Scholz and F. Schreiber: ‘IDPredictor: predict database links in biomedical databases’ Journal of Integrative Bioinformatics 9(2): 190.1-15, 2012.

•   C. Colmsee, M. Mascher, T. Czauderna, A. Hartmann, U. Schlüter, N. Zellerhoff, J. Schmitz, A. Bräutigam, T. R. Pick, P. Alter, M. Gahrtz, S. Witt, A. R. Fernie, F. Börnke, H. Fahnenstich, M. Bucher, T. Dresselhaus, A. P. M. Weber, F. Schreiber, U. Scholz and U. Sonnewald: ‘Optimas-DW: a comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize’ BMC Plant Biology 12: 245.1-17, 2012.

•   K. Lotz, F. Schreiber and R. Wünschiers: ‘Nutrilyzer: a tool for deciphering atomic stoichiometry of differentially expressed paralogous proteins’ Journal of Integrative Bioinformatics 9(2): 196.1-7, 2012.

•   A. Kerren and F. Schreiber: ‘Towards the role of interaction in visual analytics’  (Proc. Winter Simulation Conference – WSC) 420.1-13, 2012.

•   A. Hartmann, H. Rohn, K. Pucknat and F. Schreiber: ‘Petri nets in Vanted: simulation of barley seed metabolism’ CEUR-WS 852: 20-28 (Proc. Biological Processes and Petri Nets – BioPPN), 2012.

•   I. Jusufi, A. Kerren, V. Aleksakhin and F. Schreiber: ‘Visualization of mappings between the gene ontology and cluster trees’ SPIE 8294: 82940N (Proc. Visualization and Data Analysis – VDA, part of IS&T/SPIE Electronic Imaging), 2012

•   C. Krach, E. Grafahrend-Belau, H. Poskar, K. Schallau, F. Schreiber and 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, 387-406, 2012

•    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, 345-366, 2012.

2011

•   H. Rohn, C. Klukas and F. Schreiber: ‘Creating views on integrated multidomain data’ Bioinformatics 27(13): 1839–1845, 2011.

•   H. Rolletschek, G. Melkus, E. Grafahrend-Belau, J. Fuchs, N. Heinzel, F. Schreiber, P. M. Jakob and L. Borisjuk: ‘Combined non-invasive imaging and modeling approaches reveal metabolic compartmentation in the barley 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.

•   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.

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

•   H. Rohn, C. Klukas and F. Schreiber: ‘Visual analytics of multimodal biological data’ (Proc. Information Visualization Theory and Applications – IVAPP) 256-261, 2011.

•   M. R. Hajirezaei, M. R. Ghaffari, B. H. Junker, J. Müller, B. Usadel, M. Leps, R. Lemke and F. Schreiber: ‘Multiscale metabolic modeling of cereals – an integrated systems biology approach for research biomass’ in G. E. Zaikov, D. P. Pudel and G. Spychalski (eds.) Renewable Resources and Biotechnology for Material Applications, Nova Science Publishers, 325-331, 2011.

•   I. Koch, W. Reisig and F. Schreiber: ‘Modeling in systems biology: the Petri net approach’ Springer Book Series Computational Biology, Springer, 364 pages, 2011.

2010


•   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.
 
•   T. Czauderna, C. Klukas and F. Schreiber: ‘Editing, validating, and translating of SBGN maps’ Bioinformatics 26(18): 2340-2341, 2010.

•   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.

•   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.

•   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.

•   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.

•   M. Albrecht, A. Kerren, K. Klein, O. Kohlbacher, P. Mutzel, W. Paul, F. Schreiber and M. Wybrow: ‘On open problems in biological network visualization’ LNCS5849: 256-267  (Proc. Graph Drawing – GD), 2010.

•   M.R. Hajirezaei, M.R. Ghaffari, B. Junker, J. Müller, B. Usadel, M. Leps, R. Lemke, F. Schreiber: ‘Multiscale metabolic modeling of cereals – an integrated systems biology approach for research biomass’ (Proc. Renewable Resources and Plant Biotechnology – NAROSSA) 325-331, 2010.

•   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 and C. Wiuf (eds.), Statistical and evolutionary analysis of biological networks, Imperial College Press/World Scientific, 45-64, 2010.

2009

•   E. Grafahrend-Belau, C. Klukas, B. H. Junker and F. Schreiber: ‘FBA-SimVis: interactive visualisation of constraint-based metabolic models’ Bioinformatics 25(20): 2755-2757, 2009.

•   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.

•   F. Schreiber: ‘Analyse und Visualisierung biologischer Netzwerke’ Informatik Spektrum 32(4): 301-309, 2009.

•   F. Schreiber, T. Dwyer, K. Marriott and M. Wybrow: ‘A generic algorithm for layout of biological networks’ BMC Bioinformatics 10: 375.1-12, 2009.

•   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.

•   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.

•   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.

•   H. Rohn, C. Klukas and F. Schreiber: ‘Integration and visualisation of multimodal biological data’ LNI P-127: 105-115 (Proc. German Conf. Bioinformatics –GCB), 2009.

•   T. Fester, F. Schreiber and M. Strickert: ‘CUDA-based multi-core implementation of MDS-based bioinformatics algorithms’ LNI P-127: 67-79 (Proc. German Conf.Bioinformatics – GCB), 2009.

•   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 (Proc. Data Integration in the Life Sciences – DILS), 2009.

•   D. C. Y. Fung, S.-H. Hong, D. Koschützki, F. Schreiber and K. Xu: ‘Visual analysis of overlapping biological networks’ 337-342 (Proc. IEEE Information Visualisation – IV), 2009.

•   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’ (Proc. Computer Vision Theory and Applications – VISAPP) 241-244, 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 (Proc. Informatik 2009), 2009.

•   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.

•   C. E. Wheelock, S. Goto, L. Yetukuri, F. L. D’Alexandri, C. Klukas, F. Schreiber and M. Orešic: ‘Bioinformatics strategies for the analysis of lipids’ in D. Armstrong (ed.), Methods in Molecular Biology: Lipidomics, Humana Press, 339-368, 2009.

•   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

2008

•   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, 2008.

•   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.

•   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.

•   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.

•   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.

•   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 modelling metabolism’ TICPS 41: 41-44 (Proc. Computational Systems Biology – WCSB), 2008.

•   F. Schreiber: ‘Visualization’ in J. Keith (ed.), Methods in Molecular Biology: Bioinformatics, Humana Press, 441-450, 2008.

•   B. H. Junker and F. Schreiber: ‘Analysis of biological networks’ Wiley Book Series on Bioinformatics, Computational Techniques and Engineering, Wiley, 368 pages, 2008.

•   R. Hofestädt, J. Köhler, M. Lange, U. Scholz, F. Schreiber and P. Verrier: ‘Integrative Bioinformatics: proceedings of the 5th international symposium on Integrative Bioinformatics 2008’ IMBio, 345 pages, 2008.

2007

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

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

•   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.

2006

•   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.

•   B. H. Junker, D. Koschützki and F. Schreiber: ‘Kinetic modelling with the systems biology modelling environment SyBME’ Journal of Integrative Bioinformatics3(1): 18.1-10, 2006.

•   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.

•   D. Koschützki and F. Schreiber: ‘Exploration of biological network centralities with CentiBiN’ BMC Bioinformatics 7: 219.1-7, 2006.

•   C. Klukas, B. H. Junker and F. Schreiber: ‘The Vanted software system for transcriptomics, proteomics and metabolomics analysis’ Journal of Pesticide Science31(3): 289-292, 2006.

•   T. Dwyer, S.-H. Hong, D. Koschützki, F. Schreiber and K. Xu: ‘Visual analysis of network centralities’ CRPIT 60: 189-198 (Proc. Asia-Pacific Information Visualisation – APVIS, now IEEE PacificVis), 2006.

•   C. Klukas, F. Schreiber and H. Schwöbbermeyer: ‘Coordinated perspectives and enhanced force-directed layout for the analysis of network motifs’ CRPIT 60: 39-48 (Proc. Asia-Pacific Information Visualisation – APVIS, now IEEE PacificVis), 2006.

•   F. Schreiber: ‘Visual analysis of biological networks’ Habilitation thesis, University of Passau, 194 pages, 2006.

2005

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

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

•   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.

•   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.

•   L. Borisjuk, M. 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.

•   B. H. Junker, D. Koschützki and F. Schreiber: ‘Kinetic modelling with the systems biology modelling environment SyBME’ (Proc. Integrative Bioinformatics– IB) 49-51, 2005.

2004

•   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.
 
•   U. Brandes, T. Dwyer and F. Schreiber: ‘Visual triangulation of network-based phylogenetic trees’ 75-84 (Proc. EG-IEEE Data Visualization – VisSym, now EuroVis), 2004.

•   C. Friedrich and F. Schreiber: ‘Flexible layering in hierarchical drawings with nodes of arbitrary size’ CRPIT 26: 369-376 (Proc. Australasian Computer Science Conf. – ACSC), 2004.

•   D. Koschützki and F. Schreiber: ‘Comparison of centralities for biological networks’ LNI P-53: 199-206 (Proc. German Conf. Bioinformatics – GCB), 2004.

•   T. Dwyer and F. Schreiber: ‘Optimal leaf ordering for two and a half dimensional phylogenetic tree visualisation’ CRPIT 35: 109-115 (Proc. Australasian Information Visualisation – InVis.au), 2004.

•   F. Schreiber and H. Schwöbbermeyer: ‘Towards motif detection in networks: frequency concepts and flexible search’ 91-102 (Proc. Network Tools and Applications in Biology – NETTAB), 2004.

•   T. Dwyer, H. Rolletschek and F. Schreiber: ‘Representing experimental biological data in metabolic networks’ CRPIT 29: 13-20 (Proc. Asia-Pacific Bioinformatics Conf. – APBC), 2004.

•   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.

2003

•   F. Schreiber: ‘Visual comparison of metabolic pathways’ Journal of Visual Languages and Computing 14(4): 327-340, 2003.

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

•   U. Brandes, T. Dwyer and F. Schreiber: ‘Visualizing related metabolic pathways in two and a half dimensions’ LNCS 2912: 111-122 (Proc. Graph Drawing – GD), 2003.

•   F. Schreiber: ‘Comparison of metabolic pathways using constraint graph drawing’ CRPIT 19: 105-110 (Proc. Asia-Pacific Bioinformatics Conf. – APBC), 2003.

2002

•   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.

•   F. Schreiber: ‘High quality visualization of biochemical pathways in BioPath’ In Silico Biology 2(2): 59-73, 2002.

•   F. J. Brandenburg, M. Forster, A. Pick, M. Raitner and F. Schreiber: ‘BioPath’ (Software Exhibition) LNCS 2265: 455-456 (Proc. Graph Drawing – GD), 2002.

2001

•   F. Schreiber: ‘Visualisierung biochemischer Reaktionsnetze’ PhD thesis, University of Passau, 290 pages, 2001.

•   F. J. Brandenburg, M. Forster, A. Pick, M. Raitner and F. Schreiber: ‘BioPath – visualization of biochemical pathways’ 11-15 (Proc. German Conf. Bioinformatics – GCB), 2001.

1999

 •   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.

•   C.-C. Kanne, F. Schreiber and D. Trümbach: ‘Electronic Biochemical Pathways’, LNCS 1731: 418-419 (Proc. Graph Drawing – GD), 1999.

1998

•   F. Schreiber and K. Skodinis: ‘NP-completeness of some tree-clustering problems’ LNCS 1547: 288-301 (Proc. Graph Drawing – GD), 1998.

•   F. J. Brandenburg, B. Gruber, M. Himsolt and F. Schreiber: ‘Automatische Visualisierung biochemischer Informationen’ 24-38 (Proc. Molekulare Bioinformatik), 1998.

1997

•   J. Knoop and F. Schreiber: ‘Type analysis and type-test elimination in Oberon-2’ 240-250 (Proc. Programming Languages and Fundamentals of Programming), 1997.

•   J. Knoop and F. Schreiber: ‘Analysing and optimizing strongly typed object-oriented languages: a generic approach and its application to Oberon-2’ 252-266 (Proc. Object-Oriented Technology – WOON), 1997.

•   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 (Proc. Tools and Algorithms for the Construction and Analysis of Systems – TACAS), 1997.

Publication indices

 (head and postdoctoral research fellows)

 Google Scholar  DBLP Bibliography Server  PubMed  
Prof. Dr. Falk Schreiber LinkLinkLink
Dr. Karsten KleinLinkLinkLink
Dr. Björn SommerLinkLinkLink