Czauderna T:

Methoden und Algorithmen für die Systems Biology Graphical Notation. (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2015) 161 pp.

Esch M, Chen J, Colmsee C, Klapperstück M, Grafahrend-Belau E, Scholz U, Lange M:

LAILAPS – the plant science search engine. Plant Cell Physiol. 56 (2015) e8. https://dx.doi.org/10.1093/pcp/pcu185

Hartmann A, Schreiber F:

Integrative analysis of metabolic models - from structure to dynamics. Front. Bioeng. Biotechnol. 2 (2015) 91. https://dx.doi.org/10.3389/fbioe.2014.00091

Baghalian K, Hajirezaei M-R, Schreiber F:

Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering. Plant Cell 26 (2014) 3847-3866. https://dx.doi.org/10.1105/tpc.114.130328

Grafahrend-Belau E, Junker A, Schreiber F, Junker B H:

Flux balance analysis as an alternative method to estimate fluxes without labeling. (Review). In: Dieuaide-Noubhani M, Alonso A P (Eds.): Plant metabolic flux analysis: methods and protocols. (Series: Methods in molecular biology, Vol. 1090) New York [u.a.]: Humana Press (2014) ISBN 978-1-62703-687-0, 281-299. https://dx.doi.org/10.1007/978-1-62703-688-7_17

Grießbach J:

Erweiterung von Vanted zur Simulation und Visualisierung kinetischer Modelle. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2014) 60 pp.

Kerren A, Schreiber F:

Network visualization for integrative bioinformatics. In: Chen M, Hofestädt R (Eds.): Approaches in integrative bioinformatics: towards the virtual cell. Berlin [u.a.]: Springer (2014) ISBN 978-3-642-41280-6, 173-202. https://dx.doi.org/10.1007/978-3-642-41281-3_7

Kerren A, Schreiber F:

Why integrate InfoVis and SciVis?: An example from systems biology. IEEE Comput. Graph. Appl. 34 (2014) 69-73. https://dx.doi.org/10.1109/MCG.2014.122

Klapperstück M, Schreiber F:

BioNetLink - an architecture for working with network data. J. Integr. Bioinform. 11 (2014) 241. https://dx.doi.org/10.2390/biecoll-jib-2014-241

Koch I, Reisig W, Schreiber F (Eds.):

it–Information Technology: Vol. 56., No. 2: Special Issue: Petri nets in the biosciences. Oldenbourg Wissenschaftsverlag (2014) 86 pp.

Koch I, Reisig W, Schreiber F:

Petri nets in the biosciences. it–Information Technology 56 (2014) 43-45. https://dx.doi.org/10.1515/itit-2014-1042

Kohlbacher O, Schreiber F, Ward M O:

Multivariate networks in the life sciences. In: Kerren A, Purchase H C, Ward M O (Eds.): Multivariate network visualization: Dagstuhl Seminar #13201, Dagstuhl Castle, Germany, May 12-17, 2013. (Series: Lecture Notes in Computer Science, Vol. 8380) Cham [u.a.]: Springer (2014) ISBN 978-3-319-06792-6, 61-73. https://dx.doi.org/10.1007/978-3-319-06793-3_4

Krach C, Junker A, Rohn H, Schreiber F, Junker B H:

Flux visualization using VANTED/FluxMap. In: Krömer J O, Nielsen L K, Blank L M (Eds.): Metabolic flux analysis: methods and protocols. (Series: Methods in molecular biology, Vol. 1191) New York [u.a.]: Humana Press (2014) ISBN 978-1-4939-1169-1, 225-233. https://dx.doi.org/10.1007/978-1-4939-1170-7_14

Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz J A, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski P P, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard G-F, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman D J, Stein N, Straub M-L, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet J-L, Wincker P, Scholz U, Neuvéglise C:

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest. Biotechnol. Biofuels 7 (2014) 66. https://dx.doi.org/10.1186/1754-6834-7-66

Lotz K, Hartmann A, Grafahrend-Belau E, Schreiber F, Junker B H:

Elementary flux modes, flux balance analysis, and their application to plant metabolism. In: Sriram G (Ed.): Plant metabolism: methods and protocols. (Series: Methods in molecular biology, Vol. 1083) New York [u.a.]: Humana Press (2014) ISBN 978-1-62703-660-3, 231-252. https://dx.doi.org/10.1007/978-1-62703-661-0_14

Lotz K, Lemke R, Leps M, Junker B, Schreiber F:

In silico prediction of enhanced nutrient content in plants by metabolic modelling. (Industrieanmeldung), Veröffentlichung: 12.06.2014, IPK-Nr. 2013/01. WO2014087361 (2014).

Rohn H, Schreiber F:

Visualization of biological knowledge based on multimodal data. In: Elloumi M, Zomaya A Y (Eds.): Biological knowledge discovery handbook: preprocessing, mining and postprocessing of biological data. (Wiley series on bioinformatics: computational techniques and engineering, Vol. 23) Hoboken, NJ: John Wiley & Sons Ltd. (2014) ISBN 978-1-118-13273-9, 1109-1126. https://dx.doi.org/10.1002/9781118617151.ch48

Schönherr I S:

Assembly and analysis of the transcriptome of the microalga Scenedesmus vacuolatus. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2014) 83 pp.

Schreiber F, Kerren A, Börner K, Hagen H, Zeckzer D:

Heterogeneous networks on multiple levels. In: Kerren A, Purchase H C, Ward M O (Eds.): Multivariate network visualization: Dagstuhl Seminar #13201, Dagstuhl Castle, Germany, May 12-17, 2013. (Series: Lecture Notes in Computer Science, Vol. 8380) Cham [u.a.]: Springer (2014) ISBN 978-3-319-06792-6, 175-206. https://dx.doi.org/10.1007/978-3-319-06793-3_9

Waltemath D, Bergmann F T, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru I I, Myers C J, Nickerson D, Olivier B G, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E:

Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand. Genomic Sci. 9 (2014) https://www.standardsingenomics.org/index.php/sigen/article/view/527.https://dx.doi.org/10.4056/sigs.5279417

Asgari Y, Salehzadeh-Yazdi A, Schreiber F, Masoudi-Nejad A:

Controllability in cancer metabolic networks according to drug targets as driver nodes. PLoS One 8 (2013) e79397. https://dx.doi.org/10.1371/journal.pone.0079397

Bachmaier C, Brandes U, Schreiber F:

Biological networks. In: Tamassia R (Ed.): Handbook of graph drawing and visualization. (Series: Discrete mathematics and its applications) Boca Raton [u.a.]: Chapman & Hall/CRC Press (2013) ISBN 978-1584884125, 621-652.

Baker S M, Poskar C H, Schreiber F, Junker B H:

An improved constraint filtering technique for inferring hidden states and parameters of a biological model. Bioinformatics 29 (2013) 1052-1059. https://dx.doi.org/10.1093/bioinformatics/btt097

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell D B, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novere N:

Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 7 (2013) 116. https://dx.doi.org/10.1186/1752-0509-7-116

Bull F:

Visualization of next-generation sequencing data using Hilbert curves and their application to two species of Lentibulariaceae. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 96 pp.

Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Lange M, Mascher M, Weise S, Scholz U, Schreiber F:

OPTIMAS-DW, MetaCrop and VANTED: a case study for data integration, curation and visualisation in life sciences. In: Horbach M (Ed.): GI-Jahrestagung. (Series: LNI, Vol. 220) (2013) ISBN 978-3-88579-614-5, 1834-1840.

Czauderna T, Wybrow M, Marriott K, Schreiber F:

Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. BMC Bioinformatics 14 (2013) 250. https://dx.doi.org/10.1186/1471-2105-14-250

Esch M:

Effizienzsteigerung des Life-Science-IR-Systems LAILAPS mittels Suchanfragenerweiterung. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 94 pp.

Gellner M:

Evaluating the impact of genome quality on RNA-seq analysis. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 48 pp.

Grafahrend-Belau E:

Rekonstruktion, Analyse und Visualisierung pflanzenbiologischer Stoffwechselprozesse. (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 160 pp.

Grafahrend-Belau E, Junker A, Eschenröder A, Müller J, Schreiber F, Junker B H:

Multiscale metabolic modeling: dynamic flux balance analysis on a whole plant scale. Plant Physiol. 163 (2013) 637-647. https://dx.doi.org/10.1104/pp.113.224006

Grüneisen B:

Graphbasierte Visualisierung medizinischer Ontologie- & Gefäßdaten. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 110 pp.

Hofestädt R, Kormeier B, Lange M, Schreiber F, Sommer B, Weise S:

Editorial. J. Integr. Bioinform. 10 (2013) e226. https://dx.doi.org/10.2390/biecoll-jib-2013-226

Jusufi I, Kerren A, Schreiber F:

Exploring biological data: mappings between ontology- and cluster-based representations. Inform. Visual. 12 (2013) 291-307. https://dx.doi.org/10.1177/1473871612468880

Mehlhorn H, Lange M, Scholz U, Schreiber F:

Extraction and prediction of biomedical database identifier using neural networks towards data network construction. In: Ordóñez de Pablos P, Lytras M D, Tennyson R, Labra Gayo J E (Eds.): Cases on open-linked data and semantic web applications. Hershey: Information Science Reference (2013) ISBN 978-1-4666-2827-4, 58-83.

Mehlhorn H, Schreiber F:

TransID - the flexible identifier mapping service. Proceedings of the 9th International Symposium on Integrative Bioinformatics 2013, March 18 - 20, 2013, Gatersleben, Germany (2013) 112-121.

Mehlhorn H, Schreiber F:

Small-world property. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.): Encyclopedia of systems biology. New York [u.a.]: Springer Reference (2013) ISBN 978-1-4419-9863-7, 1957-1959. https://dx.doi.org/10.1007/978-1-4419-9863-7_2

Müller J, Eschenröder A, Christen O, Junker B H, Schreiber F:

ProNet-CN model: a dynamic and hierarchical process network that couples photosynthesis, primary carbon metabolism and effects of leaf nitrogen status. In: 2012 IEEE Fourth International Symposium on Plant Growth Modeling, Simulation, Visualization and Applications (PMA 2012): Shanghai, China, 31 October - 3 November 2012. Piscataway, NJ: IEEE (2013) ISBN 978-1-4673-0067-4, 289-296.

Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstück M, Czauderna T, Klukas C, Schreiber F:

Vanted 2.0. www.vanted.org (2013).

Schreiber F, Hofestädt R, Lange M, Scholz U, Czauderna T, Schnee R, Weise S (Eds.):

Proceedings of the 9th International Symposium on Integrative Bioinformatics 2013: 18 - 20 March 2013, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben. Gatersleben (2013) 214 pp.

Schreiber F, Le Novère N:

Exchange formats for systems biology - SBGN. In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds.): Encyclopedia of systems biology. New York [u.a.]: Springer Reference (2013) ISBN 978-1-4419-9863-7, 1893-1895.

Ulpinnis C:

Evaluation von Fehlerkorrektur-Algorithmen für Sequenzdaten in komplexen Pflanzengenomen. (Bachelor Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2013) 119 pp.

Vogt T, Czauderna T, Schreiber F:

Translation of SBGN maps: Process description to activity flow. BMC Syst. Biol. 7 (2013) 115. https://dx.doi.org/10.1186/1752-0509-7-115

Arend D:

Konzeption und Implementierung einer Datenhaltungsinfrastruktur zur digitalen Langzeitarchivierung und dauerhaften Zitierbarkeit biologischer Primärdaten am Beispiel von ”Next-Generation-Sequencing“-Daten. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2012) 121 pp.

Baker S M:

A parameter estimation framework for kinetic models of biological systems. (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2012) 150 pp.

Colmsee C, Mascher M, Czauderna T, Hartmann A, Schlüter U, Zellerhoff N, Schmitz J, Bräutigam A, Pick T R, Alter P, Gahrtz M, Witt S, Fernie A R, Börnke F, Fahnenstich H, Bucher M, Dresselhaus T, Weber A P, Schreiber F, Scholz U, Sonnewald U:

OPTIMAS-DW: A comprehensive transcriptomics, metabolomics, ionomics, proteomics and phenomics data resource for maize. BMC Plant Biol. 12 (2012) 245. https://dx.doi.org/10.1186/1471-2229-12-245

Czauderna T, Schreiber F:

SBGN-ED. www.sbgn-ed.org (2012).

Grafahrend-Belau E, Junker B H, Schreiber F:

Plant metabolic pathways: database and pipeline for stoichiometric analysis. In: Agrawal G K, Rakwal R (Eds.): Seed development: OMICS technologies toward improvement of seed quality and crop yield. Dordrecht [u.a.]: Springer (2012) ISBN 978-94-007-4748-7, 345-366. https://dx.doi.org/10.1007/978-94-007-4749-4_17

Gräßler J, Koschützki D, Schreiber F:

CentiLib: comprehensive analysis and exploration of network centralities. Bioinformatics 28 (2012) 1178-1179. https://dx.doi.org/10.1093/bioinformatics/bts106

Grischau I:

Die Anwendung von magischen Linsen im Kontext metabolischer Netzwerke. (Diploma Thesis) Magdeburg, Otto-von-Guericke Universität (2012) 68 pp.

Hartmann A, Rohn H, Pucknat K, Schreiber F:

Petri nets in VANTED: Simulation of barley seed metabolism. Proc. 3rd Int. Workshop on Biological Processes & Petri Nets (BioPPN), CEUR Workshop Proc. 852 (2012) 20-28.

Junker A, Bäumlein H:

Multifunctionality of the LEC1 transcription factor during plant development. Plant Signal. Behav. 7 (2012) 1718-1720. https://dx.doi.org/10.4161/psb.22365

Junker A, Junker B H:

Synthetic gene networks in plant systems. In: Weber G, Fussenegger M (Eds.): Synthetic gene networks: methods and protocols. (Series: Methods in molecular biology, Vol. 813) New York [u.a.]: Humana Press (2012) ISBN 978-1-61779-411-7, 343-258. https://dx.doi.org/10.1007/978-1-61779-412-4_21

Junker A, Mönke G, Rutten T, Keilwagen J, Seifert M, Thi T M, Renou J P, Balzergue S, Viehover P, Hähnel U, Ludwig-Müller J, Altschmied L, Conrad U, Weisshaar B, Bäumlein H:

Elongation-related functions of LEAFY COTYLEDON1 during the development of Arabidopsis thaliana. Plant J. 71 (2012) 427-442. https://dx.doi.org/10.1111/j.1365-313X.2012.04999.x

Junker A, Rohn H, Czauderna T, Klukas C, Hartmann A, Schreiber F:

Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. Nat. Protoc. 7 (2012) 579-593. https://dx.doi.org/10.1038/nprot.2012.002

Junker A, Rohn H, Schreiber F:

Visual analysis of transcriptome data in the context of anatomical structures and biological networks. Front. Plant Sci. 3 (2012) 252. https://dx.doi.org/10.3389/fpls.2012.00252

Junker A, Sorokin A, Czauderna T, Schreiber F, Mazein A:

Wiring diagrams in biology: towards the standardized representation of biological information. Trends Biotechnol. 30 (2012) 555-557. https://dx.doi.org/10.1016/j.tibtech.2012.08.003

Jusufi I, Kerren A, Aleksakhin V, Schreiber F:

Visualization of mappings between the gene ontology and cluster trees. Proc. SPIE 8294, Visualization and Data Analysis 2012 (2012) 82940N. https://dx.doi.org/10.1117/12.906700

Jusufi I, Klukas C, Kerren A, Schreiber F:

Guiding the interactive exploration of metabolic pathway interconnections. Inform. Visual. 11 (2012) 136-150. https://dx.doi.org/10.1177/1473871611405677

Kerren A, Schreiber F:

Towards the role of interaction in visual analytics. In: Laroque C (Ed.): Proceedings of the 2012 Winter Simulation Conference (WSC 2012): Berlin, Germany, 9 - 12 December 2012. Piscataway, NJ: IEEE (2012) ISBN 978-1-4673-4779-2, 1-13. https://dx.doi.org/10.1109/WSC.2012.6465208

Krach C, Grafahrend-Belau E, Poskar H, Schallau K, Schreiber F, Junker B H:

Using systems approaches to analyze metabolic networks involved in storage reserve synthesis in developing seeds. In: Agrawal G K, Rakwal R (Eds.): Seed development: OMICS technologies toward improvement of seed quality and crop yield. Dordrecht [u.a.]: Springer (2012) ISBN 978-94-007-4748-7, 387-406. https://dx.doi.org/10.1007/978-94-007-4749-4_19

Kutz D:

Editorerstellung für VANTED am Beispiel von SBML. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2012) 114 pp.

Lotz K, Schreiber F, Wünschiers R:

Nutrilyzer: a tool for deciphering atomic stoichiometry of differentially expressed paralogous proteins. J. Integr. Bioinform. 9 (2012) 196. https://dx.doi.org/10.2390/biecoll-jib-2012-196

Masoudi-Nejad A, Schreiber F, Kashani Z R:

Building blocks of biological networks: a review on major network motif discovery algorithms. IET Syst. Biol. 6 (2012) 164-174. https://dx.doi.org/10.1049/iet-syb.2011.0011

Mehlhorn H, Lange M, Scholz U, Schreiber F:

IDPredictor: predict database links in biomedical database. J. Integr. Bioinform. 9 (2012) e190. https://dx.doi.org/10.2390/biecoll-jib-2012-190

Mirschel S:

Interactive visualization of complex structures in modular models for systems biology. (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2012) 111 pp.

Mönke G, Seifert M, Keilwagen J, Mohr M, Grosse I, Hähnel U, Junker A, Weisshaar B, Conrad U, Bäumlein H, Altschmied L:

Toward the identification and regulation of the Arabidopsis thaliana ABI3 regulon. Nucleic Acids Res. 40 (2012) 8240-8254. https://dx.doi.org/10.1093/nar/gks594

Pucknat K:

Erweiterung der Software VANTED zum Editieren und Simulieren biologischer Petri-Netze. (Master Thesis) Hochschule Ostwestfalen-Lippe (2012) 77 pp.

Rohn H:

Integrative Visualisierung multimodaler biologischer Experimentaldaten. (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik der Naturwissenschaftlichen Fakultät III (2012) 119 pp.

Rohn H, Hartmann A, Junker A, Junker B H, Schreiber F:

FluxMap: A VANTED add-on for the visual exploration of flux distributions in biological networks. BMC Syst. Biol. 6 (2012) 33. https://dx.doi.org/10.1186/1752-0509-6-33

Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstück M, Czauderna T, Klukas C, Schreiber F:

Vanted 2.0. www.vanted.org (2012).

Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstück M, Czauderna T, Klukas C, Schreiber F:

VANTED v2: a framework for systems biology applications. BMC Syst. Biol. 6 (2012) 139. https://dx.doi.org/10.1186/1752-0509-6-139

Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Klapperstück M, Scholz U, Weise S:

MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acids Res. 40 (2012) D1173-D1177. https://dx.doi.org/10.1093/nar/gkr1004

Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Koschützki D, Scholz U, Weise S:

MetaCrop 2.0. metacrop.ipk-gatersleben.de (2012).

van Iersel M P, Villéger A C, Czauderna T, Boyd S E, Bergmann F T, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem M I, Mi H, Moodie S L, Kitano H, Le Novère N, Schreiber F:

Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 28 (2012) 2016-2021. https://dx.doi.org/10.1093/bioinformatics/bts270

Czauderna T, Schreiber F:

SBGN-ED. www.sbgn-ed.org (2011).

Fröhlich S:

Modellprüfung biologischer Systeme. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2011) 100 pp.

Hartmann A, Czauderna T, Hoffmann R, Stein N, Schreiber F:

HTPheno: An image analysis pipeline for high-throughput plant phenotyping. BMC Bioinformatics 12 (2011) 148. https://dx.doi.org/10.1186/1471-2105-12-148

Koch I, Reisig W, Schreiber F:

Modeling in systems biology: the Petri net approach. (Series: Computational biology, Vol. 16) London [u.a.]: Springer (2011) ISBN: 978-1-84996-473-9, 364 pp. https://www.springer.com/computer/bioinformatics/book/978-1-84996-473-9

Koch I, Schreiber F:

Introduction. In: Koch I, Reisig W, Schreiber F (Eds.): Modeling in systems biology: the petri net approach. Springer Book Series Computational Biology, Vol. 16. London Ltd.: Springer-Verlag (2011) ISBN: 978-1-84996-473-9, 3-18. http://www.springer.com/computer/bioinformatics/book/978-1-84996-473-9

Koschützki D:

Zentralitätsanalyse molekularbiologischer Netzwerke. (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2011) 110 pp.

Mehlhorn H, Schreiber F:

DBE2 - management of experimental data for the VANTED system. J. Integr. Bioinform. 8 (2011) 162. https://dx.doi.org/10.2390/biecoll-jib-2011-162

Melkus G, Rolletschek H, Fuchs J, Radchuk V, Grafahrend-Belau E, Sreenivasulu N, Rutten T, Weier D, Heinzel N, Schreiber F, Altmann T, Jakob P M, Borisjuk L:

Dynamic (13) C/(1) H NMR imaging uncovers sugar allocation in the living seed. Plant Biotechnol. J. 9 (2011) 1022-1037. https://dx.doi.org/10.1111/j.1467-7652.2011.00618.x

Rohn H, Klukas C, Schreiber F:

Vanted 2.0. www.vanted.org (2011).

Rohn H, Klukas C, Schreiber F:

Creating views on integrated multidomain data. Bioinformatics 27 (2011) 1839-1845. https://dx.doi.org/10.1093/bioinformatics/btr282

Rohn H, Klukas C, Schreiber F:

Visual analytics of multimodal biological data. Proceedings of the International Conference on Information Visualization Theory and Applications (IVAPP’11). SciTePress (2011) 256-261.

Rolletschek H, Melkus G, Grafahrend-Belau E, Fuchs J, Heinzel N, Schreiber F, Jakob P M, Borisjuk L:

Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm. Plant Cell 23 (2011) 3041-3054. https://dx.doi.org/10.1105/tpc.111.087015

Schönherr I S:

Assemblierung und Analyse des Vitis vinifera Genoms der Rebsorte Riesling. (Bachelor Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Institut für Informatik (2011) 40 pp.

Schreiber F, Colmsee C, Czauderna T, Grafahrend-Belau E, Hartmann A, Junker A, Junker B H, Koschützki D, Scholz U, Weise S:

MetaCrop 2.0. metacrop.ipk-gatersleben.de (2011).

van Iersel M P, Boyd S E, Bergmann F, Moodie S, Schreiber F, Czauderna T, Demir E, Le Novère N, Sorokin A, Mi H, Luna A, Dogrusoz U, Matsuoka Y, Funahashi A, Kitano H, Aladjem M I, Blinov M L, Villéger A C:

LibSBGN. libsbgn.sourceforge.net (2011).

Vogt T:

Entwicklung und Implementierung eines Algorithmus zur Übersetzung von SBGN Process Description Diagrammen in SBGN Activity Flow Diagramme. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2011) 62 pp.

Weise S, Chen J, Junker B H, Klapperstück M, Lange M, Schreiber F, Scholz U:

Das Informationssystem MetaCrop zur Unterstützung systembiologischer Forschung an Kulturpflanzen. it - Information Technology 53 (2011) 234-240. https://dx.doi.org/10.1524/itit.2011.0648

Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H:

Meta-All: A system for managing metabolic pathway information. meta-all.ipk-gatersleben.de (2011).

Albrecht M, Kerren A, Klein K, Kohlbacher O, Mutzel P, Paul W, Schreiber F, Wybrow M:

On open problems in biological network visualization. In: Eppstein D, Gansner E R (Eds.): Graph drawing: 17th international symposium, GD 2009, Chicago, IL, USA, September 22 - 25, 2009. (Series: Lecture Notes in Computer Science, Vol. 5849) Berlin [u.a.]: Springer (2010) ISBN 978-3-642-11804-3, 256-267. https://dx.doi.org/10.1007/978-3-642-11805-0_25

Banaei Moghaddam A M, Fuchs J, Czauderna T, Houben A, Mette M F:

Intraspecific hybrids of Arabidopsis thaliana revealed no gross alterations in endopolyploidy, DNA methylation, histone modifications and transcript levels. Theor. Appl. Genet. 120 (2010) 215-226. https://dx.doi.org/10.1007/s00122-009-1127-x

Czauderna T, Klukas C, Schreiber F:

SBGN-ED. vanted.ipk-gatersleben.de/addons/sbgn-ed/ (2010).

Czauderna T, Klukas C, Schreiber F:

Editing, validating and translating of SBGN maps. Bioinformatics 26 (2010) 2340-2341. https://dx.doi.org/10.1093/bioinformatics/btq407

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2010).

Gräßler J:

Optimierung und Weiterentwicklung von Algorithmen und einer Bibliothek zur Berechnung von Netzwerk-Zentralitäten. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2010) 59 pp.

Gräßler J, Koschützki D, Schreiber F:

CentiLib. centilib.ipk-gatersleben.de (2010).

Hartmann A, Czauderna T, Schreiber F:

HTPheno. htpheno.ipk-gatersleben.de (2010).

Hippe K, Colmsee C, Czauderna T, Grafahrend-Belau E, Junker B H, Klukas C, Scholz U, Schreiber F, Weise S:

Novel developments of the MetaCrop information system for facilitating systems biological approaches. J. Integr. Bioinform. 7 (2010) e125. https://dx.doi.org/10.2390/biecoll-jib-2010-125

Junker A, Hartmann A, Schreiber F, Bäumlein H:

An engineers view on regulation of seed development. Trends Plant Sci. 15 (2010) 303-307. https://dx.doi.org/10.1016/j.tplants.2010.03.005

Klukas C, Schreiber F:

VANTED. vanted.ipk-gatersleben.de (2010).

Klukas C, Schreiber F:

Integration of -omics data and networks for biomedical research with VANTED. J. Integr. Bioinform. 7 (2010) 112. https://dx.doi.org/10.2390/biecoll-jib-2010-112

Koschützki D, Junker B H, Schwender J, Schreiber F:

Structural analysis of metabolic networks based on flux centrality. J. Theor. Biol. 265 (2010) 261-269. https://dx.doi.org/10.1016/j.jtbi.2010.05.009

Lemke R, Hajirezaei M-R, Junker B H, Müller J, Usadel B, Leps M, Schreiber F:

MMM – Mehrskalen-Stoffwechselmodelle zur Systembiologie in Getreiden – ein integrativer Ansatz für die Biomasseforschung. Systembiologie.de 2 (2010) 51-53.

Mehlhorn H, Schreiber F:

DBE2. vanted.ipk-gatersleben.de/addons/DBE2/ (2010).

Pucknat K, Rohn H, Schreiber F:

Anaglyph Canvas3D. sourceforge.net/projects/anaglyphcanvas3/ (2010).

Rohn H, Klukas C, Schreiber F:

HIVE. vanted.ipk-gatersleben.de/addons/hive/ (2010).

Scharfe M, Pielot R, Schreiber F:

Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets. BMC Bioinformatics 11 (2010) Article ID:20. https://dx.doi.org/10.1186/1471-2105-11-20

Schreiber F:

Representation and analysis of biological networks with the Vanted toolsuite. In: Hofestädt R, Kolchanov N (Eds.): German/Russian Network of Computational Systems Biology. (Series: Berichte aus der Medizinischen Informatik und Bioinformatik) Aachen: Shaker (2010) ISBN 978-3-8322-9695-7, 47-50.

Schreiber F, Schwöbbemeyer H:

Motifs in biological networks. In: Stumpf M P H, Wiuf C (Eds.): Statistical and evolutionary analysis of biological networks. London: Imperial College Press (2010) ISBN 978-1-84816-433-8, 45-64.

Sharbel T F, Voigt M L, Corral J M, Galla G, Kumlehn J, Klukas C, Schreiber F, Vogel H, Rotter B:

Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns (Hofmann, N.R.: Apomixis and gene expression in Boechera. Plant Cell (2010) 22:539. Highlight of Sharbel et al. 2010 by Plant Cell scientific editor). Plant Cell 22 (2010) 655-671. https://dx.doi.org/10.1105/tpc.109.072223

Weidemann W, Klukas C, Klein A, Simm A, Schreiber F, Horstkorte R:

Lessons from GNE-deficient embryonic stem cells: Sialic acid biosynthesis is involved in proliferation and gene expression. Glycobiology 20 (2010) 107-117. https://dx.doi.org/10.1093/glycob/cwp153

Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H:

Meta-All: A system for managing metabolic pathway information. meta-all.ipk-gatersleben.de (2010).

Bargsten J:

Nutzerprofilgestütztes Schätzen von Rankingparametern für Suchmaschinen-Anfragen an integrierte biologische Datenbanken. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2009) 103 pp.

del Rio G, Koschutzki D, Coello G:

How to identify essential genes from molecular networks? BMC Syst. Biol. 3 (2009) 102. https://dx.doi.org/10.1186/1752-0509-3-102

Fester T, Schreiber F, Strickert M:

CUDA-based multi-core implementation of MDS-based bioinformatics algorithms. In: German Conference on Bioinformatics 2009: 28 - 30 September 2009, Halle/S., Germany, proceedings (Series: Lecture notes in informatics, Vol. 157) Bonn: Ges. für Informatik (2009) ISBN 978-3-88579-251-2, 67-79.

Fung D C Y, Hong S-H, Koschützki D, Schreiber F, Xu K:

Visual analysis of overlapping biological networks. In: Banissi E (Ed.): 13th International Conference Information Visualisation, 2009: IV 2009, 15 - 17 July 2009, Barcelona, Spain, proceedings. Piscataway, NJ: IEEE (2009) ISBN 978-1-4244-4556-1, 337-342. https://dx.doi.org/10.1109/IV.2009.55

Grafahrend-Belau E, Junker B H, Klukas C, Koschützki D, Schreiber F, Schwöbbemeyer H:

Topology of plant metabolic networks. In: Schwender J (Ed.): Plant metabolic networks. Dordrecht [u.a.]: Springer (2009) ISBN 978-0-387-78744-2, 173-209. https://dx.doi.org/10.1007/978-0-387-78745-9_7

Grafahrend-Belau E, Klukas C, Junker B H, Schreiber F:

FBASimViz: dynamic visualization of constraint-based metabolic models. fbasimviz.ipkgatersleben.de (2009).

Grafahrend-Belau E, Klukas C, Junker B H, Schreiber F:

FBA-SimVis: Interactive visualisation of constraint-based metabolic models. Bioinformatics 25 (2009) 2755-2757. https://dx.doi.org/10.1093/bioinformatics/btp408

Grafahrend-Belau E, Schreiber F, Koschützki D, Junker B H:

Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism. Plant Physiol. 149 (2009) 585-598. https://dx.doi.org/10.1104/pp.108.129635

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2009).

Gräßler J, Koschützki D, Schreiber F:

CentiLib. centilib.ipk-gatersleben.de (2009).

Grosse I, Neumann S, Posch S, Schreiber F, Stadler P (Eds.):

German Conference on Bioinformatics 2009: 28 - 30 September 2009, Martin Luther University Halle-Wittenberg, Germany, proceedings. (Series: Lecture notes in informatics, Vol. 157) Bonn: Ges. für Informatik (2009) ISBN 978-3-88579-251-2, 228 pp.

Hartmann A:

Automatisierte Datenaufnahme und Bildverarbeitung zur Hochdurchsatz-Phänotypisierung von Gerste. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2009) 105 pp.

Kashani Z R, Ahrabian H, Elahi E, Nowzari-Dalini A, Ansari E S, Asadi S, Mohammadi S, Schreiber F, Masoudi-Nejad A:

Kavosh: a new algorithm for finding network motifs. BMC Bioinformatics 10 (2009) 318. https://dx.doi.org/10.1186/1471-2105-10-318

Klukas C:

Analyse und Visualisierung von Experimentdaten im Kontext biologischer Netzwerke. (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2009) 100 pp.

Klukas C, Rohn H, Schreiber F:

Vanted and Vanted3D. vanted.ipk-gatersleben.de (2009).

Klukas C, Schreiber F:

Integration of -omics data and networks for biomedical research. In: Proceedings of the International Workshop in Computational & Integrative Biology: a satellite meeting of the International Conference of Integrative Biology, 18.-20.09.2009, Hangzhou, China. Hanzhou (2009) 14-19.

Kormeier B, Hippe K, Töpel T, Hofestädt R:

CardioVINEdb: a data warehouse approach for integration of life science data in cardiovascular diseases. In: Fischer S, Maehle E, Reischuk R (Eds.): Informatik 2009: im Focus das Leben, Beiträge der 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 28.9. - 2.10.2009 in Lübeck. (Series: GI-Edition, Lecture notes in informatics, Vol. 154) Bonn: Ges. für Informatik (2009) ISBN 978-3-88579-248-2, 704-708.

Le Novere N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem M I, Wimalaratne S M, Bergman F T, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villeger A, Boyd S E, Calzone L, Courtot M, Dogrusoz U, Freeman T C, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell D B, Sander C, Sauro H, Snoep J L, Kohn K, Kitano H:

The Systems Biology Graphical Notation. Nat. Biotechnol. 27 (2009) 735-741. https://dx.doi.org/10.1038/nbt.1558

Le Novère N, Moodie S, Sorokin A, Schreiber F, Mi H:

Systems Biology Graphical Notation: Entity Relationship Language Level 1. sbgn.org and Nature Precedings npre.2009.3719.1 (https://precedings.nature.com/documents/3719/version/1) (2009).

Lemke R, Hajirezaei M-R, Junker B H, Müller J, Usadel B, Wünschiers R, Schreiber F:

Mehrskalen-Stoffwechselmodelle von Getreiden - Ein integrativer systembiologischer Ansatz für die Biomasseforschung. GenomXpress 4 (2009) 16-18.

Lotz K:

Ökologische Stöchiometrie: Einfluss der Nährstoffverfügbarkeit auf die Genexpression von Paralogen. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2009) 77 pp.

Mi H, Schreiber F, Le Novère N, Moodie S, Sorokin A:

Systems Biology Graphical Notation: Activity Flow Language Level 1. sbgn.org and Nature Precedings npre.2009.3724.1 (https://precedings.nature.com/documents/3724/version/1) (2009).

Omidi S, Schreiber F, Masoudi-Nejad A:

MODA: An efficient algorithm for network motif discovery in biological networks. Genes Genet. Syst. 84 (2009) 385-395. https://dx.doi.org/10.1266/ggs.84.385

Pielot R, Seiffert U, Manz B, Weier D, Volke F, Schreiber F, Weschke W:

Multimodal registration of NMR-volumes and histological cross-sections of barley grains on the cell broadband engine. In: Ranchordas A K (Ed.): Proceedings of the Fourth International Conference on Computer Vision Theory and Applications (VISAPP 2009): Vol.1, Lisboa, Portugal, February 05 - 08, 2009. Setúbal: INSTICC Press (2009) ISBN 978-989-8111-69-2, 241-244.

Pucknat K:

Implementierung eines interaktiven Anaglyph-Stereomodus für Java3D. (Bachelor Thesis) Ostwestfalen-Lippe, Hochschule (2009) 43 pp.

Rohn H, Klukas C, Schreiber F:

Integration and visualisation of multimodal biological data. In: German Conference on Bioinformatics 2009: 28 - 30 September 2009, Martin Luther University Halle-Wittenberg, Germany, proceedings (Series: Lecture notes in informatics, Vol. 157) Bonn: Ges. für Informatik (2009) ISBN 978-3-88579-251-2, 105-115.

Schreiber F:

Analyse und Visualisierung biologischer Netzwerke. Informatik Spektrum 32 (2009) 301-309.

Schreiber F, Dwyer T, Marriott K, Wybrow M:

A generic algorithm for layout of biological networks. BMC Bioinformatics 10 (2009) 375. https://dx.doi.org/10.1186/1471-2105-10-375

Weise S, Colmsee C, Grafahrend-Belau E, Junker B, Klukas C, Lange M, Scholz U, Schreiber F:

Datenaustausch und Datenintegration zur Modellierung und Analyse metabolischer Netzwerke am Beispiel von Kulturpflanzen. In: Fischer S, Maehle E, Reischuk R (Eds.): Informatik 2009: im Focus das Leben, Beiträge der 39. Jahrestagung der Gesellschaft für Informatik e.V. (GI), 28.9. - 2.10.2009 in Lübeck. (Series: GI-Edition, Lecture notes in informatics, Vol. 154) Bonn: Ges. für Informatik (2009) ISBN 978-3-88579-248-2, 693-697.

Weise S, Colmsee C, Grafahrend-Belau E, Junker B, Klukas C, Lange M, Scholz U, Schreiber F:

An integration and analysis pipeline for systems biology in crop plant metabolism. In: Paton N W, Missier P, Hedeler C (Eds.): Data integration in the life sciences: 6th international workshop, DILS 2009, Manchester, UK, July 20-22, 2009, proceedings. (Series: Lecture Notes in Computer Science, Vol. 5647) Berlin [u.a.]: Springer (2009) ISBN 978-3-642-02878-6, 196-203. https://dx.doi.org/10.1007/978-3-642-02879-3_16

Wheelock C E, Goto S, Yetukuri L, DAlexandri F L, Klukas C, Schreiber F, Oresic M:

Bioinformatics strategies for the analysis of lipids. In: Armstrong D (Ed.): Lipidomics, Vol. 2: methods and protocols. (Series: Methods in molecular biology, Vol. 580) New York, NY: Humana Press (2009) ISBN 978-1-60761-324-4, 339-368. https://dx.doi.org/10.1007/978-1-60761-325-1_19

Bollenbeck F, Seiffert U:

Fast registration-based automatic segmentation of serial section images for high-resolution 3-D plant seed modeling. IEEE International Symposium on Biomedical Imaging (2008) 352-355.

Dwyer T, Marriott K, Schreiber F, Stuckey P, Woodward M, Wybrow M:

Exploration of networks using overview+detail with constraint-based cooperative layout. IEEE Trans. Vis. Comput. Graph 14 (2008) 1293-1300. https://dx.doi.org/10.1109/TVCG.2008.130

Fung D C Y, Hong S-H, Koschützki D, Schreiber F, Xu K:

2.5D visualisation of overlapping biological networks. J. Integr. Bioinform. 5 (2008) https://dx.doi.org/10.2390/biecoll-jib-2008-90

Grafahrend-Belau E, Junker B H, Koschützki D, Klukas C, Weise S, Scholz U, Schreiber F:

Towards systems biology of developing barley grains: a framework for modeling metabolism. In: Ahdesmäki M, Strimmer K, Radde N, Rahnenführer J, Klemm K, Lähdesmäki H, Yli-Harja O (Eds.): 5th International Workshop on Computational Systems Biology, WCSB 2008, June 11–13, 2008, Leipzig, Germany, proceedings. (TICSP series, Vol. 41) Tampere: Tampere International Center for Signal Processing (2008) ISBN 978-952-15-1988-8 41-44.

Grafahrend-Belau E, Schreiber F, Heiner M, Sackmann A, Junker B H, Grunwald S, Speer A, Winder K, Koch I:

Modularization of biochemical networks based on classification of Petri net t-invariants. BMC Bioinformatics 9 (2008) 90. https://dx.doi.org/10.1186/1471-2105-9-90

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res. 36 (2008) D954-D958. https://dx.doi.org/10.1093/nar/gkm835

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop: a detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2008).

Hofestädt R, Köhler J, Lange M, Scholz U, Schreiber F, Verrier P (Eds.):

Proceedings of the 5th International Symposium on Integrative Bioinformatics 2008: 20 - 22 August 2008 Leucorea, Lutherstadt Wittenberg, Germany. Wittenberg (2008) 345 pp.

Junker B H, Schreiber F (Eds.):

Analysis of biological networks. (Wiley series on bioinformatics) New York, NY: Wiley-Interscience (2008) ISBN 978-0-470-04144-4, 368 pp.

Klukas C:

VANTED - visualization and analysis of networks containing experimental data. vanted.ipk-gatersleben.de (2008).

Koschützki D:

Network centralities. In: Junker B H, Schreiber F (Eds.): Analysis of biological networks. (Wiley series on bioinformatics) New York, NY: Wiley-Interscience (2008) ISBN 978-0-470-04144-4, 65-84.

Koschützki D, Schreiber F:

Centrality analysis methods for biological networks and their application to gene regulatory networks. Gene Regul. Syst. Biol. 2 (2008) 193-201.

Le Novère N, Moodie S, Sorokin A, Hucka M, Schreiber F, Demir E, Mi H, Matsuoka Y, Wegner K, Kitano H:

Systems Biology Graphical Notation: Process Diagram Level 1. sbgn.org and Nature Precedings npre.2008.2320.1 (https://precedings.nature.com/documents/2320/version/1) (2008).

Pielot R, Seiffert U, Manz B, Weier D, Volke F, Weschke W:

4D warping for analysing morphological changes in seed development of barley grains. In: Ranchordas A, Araujo H (Eds.): Proceedings of the Third International Conference on Computer Vision Theory and Applications (VISAPP2008), 22.-25.01.2008, Funchal, Madeira/Portugal, Vol. 1. [Setúbal]: INSTICC Press (2008) ISBN 978-989-8111-21-0, 335-340.

Schreiber F:

Visualization. In: Keith J M (Ed.): Bioinformatics. (Series: Methods in molecular biology, Vol. 453) New York, NY: Humana Press (2008) ISBN 978-1-60327-428-9, 441-450. https://dx.doi.org/10.1007/978-1-60327-429-6_23

Schreiber F:

Graph theory. In: Junker B H, Schreiber F (Eds.): Analysis of biological networks. (Wiley series on bioinformatics: computational techniques and engineering) New York, NY: Wiley-Interscience (2008) ISBN 978-0-470-04144-4, 15-28.

Schwöbbermeyer H:

Network motifs. In: Junker B H, Schreiber F (Eds.): Analysis of biological networks. (Wiley series on bioinformatics) New York, NY: Wiley-Interscience (2008) ISBN 978-0-470-04144-4, 85-111.

Thiel J, Weier D, Sreenivasulu N, Strickert M, Weichert N, Melzer M, Czauderna T, Wobus U, Weber H, Weschke W:

Different hormonal regulation of cellular differentiation and function in nucellar projection and endosperm transfer cells - a microdissection-based transcriptome study of young barley grains. Plant Physiol. 148 (2008) 1436-1452. https://dx.doi.org/10.1104/pp.108.127001

Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H:

Meta-All: A system for managing metabolic pathway Information. meta-all.ipk-gatersleben.de (2008).

Grafahrend-Belau E, Weise S, Koschützki D, Scholz U, Junker B H, Schreiber F:

MetaCrop – A detailed database of crop plant metabolism. metacrop.ipk-gatersleben.de (2007).

Junker B H, Lonien J, Heady L E, Rogers A, Schwender J:

Parallel determination of enzyme activities and in vivo fluxes in Brassica napus embryos grown on organic or inorganic nitrogen source. Phytochemistry 68 (2007) 2232-2242. https://dx.doi.org/10.1016/j.phytochem.2007.03.032

Klukas C:

VANTED - visualization and analysis of networks containing experimental data. vanted.ipk-gatersleben.de (2007).

Klukas C, Schreiber F:

Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics 23 (2007) 344-350. https://dx.doi.org/10.1093/bioinformatics/btl611

Koschützki D, Schwöbbermeyer H, Schreiber F:

Ranking of network elements based on functional substructures. J. Theor. Biol. 248 (2007) 471-479. https://dx.doi.org/10.1016/j.jtbi.2007.05.038

Rolletschek H, Nguyen T H, Häusler R E, Rutten T, Göbel C, Feussner I, Radchuk R, Tewes A, Claus B, Klukas C, Linemann U, Weber H, Wobus U, Borisjuk L:

Antisense inhibition of the plastidial glucose-6-phosphate/phosphate translocator in Vicia seeds shifts cellular differentiation and promotes protein storage. Plant J. 51 (2007) 468-484. https://dx.doi.org/10.1111/j.1365-313X.2007.03155.x

Telgkamp M:

? Generating networks from data sources. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2007)

Telgkamp M, Koschützki D, Schwöbbermeyer H, Schreiber F:

Community-based linking of biological network resources: databases, formats and tools. J. Integr. Bioinform. 4 (2007) 71. https://dx.doi.org/10.2390/biecoll-jib-2007-71

Telgkamp M, Koschützki D, Schwöbbermeyer H, Schreiber F:

BiNCo-Wiki - Community-based Linking of Biological Network Resources. pgrc.ipk-gatersleben.de/BiNCO-wiki (2007).

Weschke W, Mock H-P, Pietsch C, Radchuk V, Röder M S, Schreiber F, Seiffert U, Sreenivasulu N, Strickert M, Witzel K, Wobus U:

Genetical Genomics der Gerstenkornentwicklung - von der Genexpression zu landwirtschaftlich bedeutsamen Merkmalen. GenomXPress 1 (2007) 12-16.

Wobus U, Mock H-P, Pietsch C, Radchuk V, Röder M, Schreiber F, Seiffert U, Sreenivasulu N, Strickert M, Weschke W, Witzel K:

GABI-SEED: Genetische Grundlagen komplexer agronomischer Merkmale im Getreidekorn entschlüsseln. GenomXPress Sonderausgabe März (2007) 19.

Ahmed A, Dwyer T, Forster M, Fu X Y, Ho J, Hong S H, Koschützki D, Murray C, Nikolov N S, Taib R, Tarassov A, Xu K:

GEOMI: GEOmetry for maximum insight. Proc. Intl. Symp. Graph Drawing. Lect. Notes Comput. Sci. 3843 (2006) 468-479. https://dx.doi.org/10.1007/11618058_42

Ast V:

Interaktive Visualisierungsverfahren zur Untersuchung netzbasierter Bäume. (Diploma Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2006)

Dwyer T, Hong S H, Koschützki D, Schreiber F, Xu F:

Visual analysis of network centralities. In: Misue K, Sugiyama K, Tanaka J (Eds.): Information Visualisation 2006: proceedings of the Asia Pacific Symposium on Information Visualisation (APVIS2006). (Series: Conferences in research and practice in information technology, Vol. 60) Tokyo: ACS (2006) ISBN 1-920682-41-4, 189-197.

Junker B H, Klukas C, Schreiber F:

VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7 (2006) 109. https://dx.doi.org/10.1186/1471-2105-7-109

Junker B H, Klukas C, Schreiber F:

VANTED: Datenauswertung im Netzwerk-Kontext. GenomXPress 1 (2006) 16-18.

Junker B H, Koschützki D, Schreiber F:

Exploration of biological network centralities with CentiBiN. BMC Bioinformatics 7 (2006) 219. https://dx.doi.org/10.1186/1471-2105-7-219

Junker B H, Koschützki D, Schreiber F:

Kinetic modelling with the Systems Biology Modelling Environment SyBME. J. Integr. Bioinform. (2006) e0018. https://dx.doi.org/10.2390/biecoll-jib-2006-18

Junker B H, Wuttke R, Nunes-Nesi A, Steinhäuser D, Schauer N, Büssis D, Willmitzer L, Fernie A R:

Enhancing vacuolar sucrose cleavage within the developing potato tuber has only minor effects on metabolism. Plant Cell Physiol. 47 (2006) 277-289. https://dx.doi.org/10.1093/pcp/pci247

Klukas C:

KGML-ED - a graphical KGML pathway editor. kgml-ed.ipk-gatersleben.de (2006).

Klukas C, Junker B H, Schreiber F:

The VANTED software system for transcriptomics, proteomics and metabolomics analysis. J. Pestic. Sci. 31 (2006) 289-292.

Klukas C, Schreiber F:

VANTED - visualization and analysis of networks containing experimental data. vanted.ipk-gatersleben.de (2006).

Klukas C, Schreiber F, Schwöbbermeyer H:

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