Head: Dr. Björn H. Junker
Systems Biology
Publications
Author
Title
2015
Liiving T:
Subcellular network of starch synthesis in maturing embryos of pea Pisum sativum L. (Fabaceae). (PhD Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg, Naturwissenschaftliche Fakultät I Biowissenschaften, Institut für Pharmazie (2015) 103 pp.
2014
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
Huege J, Götze J, Dethloff F, Junker B H, Kopka J:
Quantification of stable isotope label in metabolites via mass spectrometry. In: Hicks G, Robert S (Eds.): Plant chemical genomics: methods and protocols. (Series: Methods in molecular biology, Vol. 1056) New York [u.a.]: Humana Press (2014) ISBN 978-1-62703-591-0, 213-223. https://dx.doi.org/10.1007/978-1-62703-592-7_20
Keilwagen J, Kilian B, Özkan H, Babben S, Perovic D, Mayer K F, Walther A, Poskar C H, Ordon F, Eversole K, Börner A, Ganal M, Knüpffer H, Graner A, Friedel S:
Separating the wheat from the chaff - a strategy to utilize plant genetic resources from ex situ genebanks. Sci. Rep. 4 (2014) 5231. https://dx.doi.org/10.1038/srep05231
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
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
Poskar C H, Huege J, Krach C, Shachar-Hill Y, Junker B H:
High-throughput data pipelines for metabolic flux analysis in plants. (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, 223-246. https://dx.doi.org/10.1007/978-1-62703-688-7_14
2013
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
Franke M, Hüge J, Tablack P, Junker B H:
Messung von intrazellulären Stoffflüssen in Pflanzen. BIOspektrum 19 (2013) 690-693.
Freier L:
Dynamic metabolic flux analysis (DMFA) applied to the Calvin cycle of Nicotiana tabacum. (Master Thesis) Magdeburg, Otto-von-Guericke Universität Magdeburg (2013) 116 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
Junker B H, Kempa S:
Isotope-based, non-steady state flux analysis. 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, 1056-1057. https://dx.doi.org/10.1007/978-1-4419-9863-7_1148
Klepsch O:
Bedeutung des Lichts im Metabolismus ADP-Glukose Pyrophosphorylase-defizienter Erbsen (Pisum sativum) während der Samenentwicklung. (Bachelor Thesis) Magdeburg, Otto-von-Guericke Universität Magdeburg (2013) 72 pp.
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.
Schumann J:
Der Einfluss von Alanin auf die Berechnung von quantitativen Stoffwechselkarten in Erbsen-Embryos. (Master Thesis) Halle/S., Martin-Luther-Universität Halle-Wittenberg (2013) 99 pp.
Velten S:
Methodische Erweiterung der metabolischen Flussanalyse im steady state (ssMFA) zur Gewinnung von 13C-Markierungsinformationen aus löslichen Stoffwechselintermediaten. (Bachelor Thesis) Magdeburg, Otto-von-Guericke Universität Magdeburg (2013) 172 pp.
2012
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.
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
Huege J, Poskar C H, Franke M, Junker B H:
Towards high throughput metabolic flux analysis in plants. Mol. BioSyst. 8 (2012) 2466-2469. https://dx.doi.org/10.1039/C2MB25068C
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
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
Kumpf A:
Homologe Gene des Brittle1- transporters in Pisum sativum. (Bachelor Thesis) Köthen, Hochschule Anhalt (FH) (2012)
Poskar C H, Huege J, Krach C, Franke M, Shachar-Hill Y, Junker B H:
iMS2Flux - a high-throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis. BMC Bioinformatics 13 (2012) 295. https://dx.doi.org/10.1186/1471-2105-13-295
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
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).
2011
Baker S M, Poskar C H, Junker B H:
Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models. EURASIP J. Bioinform. Syst. Biol. 2011 (2011) 7. https://dx.doi.org/10.1186/1687-4153-2011-7
Huege J, Goetze J, Schwarz D, Bauwe H, Hagemann M, Kopka J:
Modulation of the major paths of carbon in photorespiratory mutants of Synechocystis. PLoS One 6 (2011) e16278. https://dx.doi.org/10.1371/journal.pone.0016278
Junker B H:
Steady-state-13C-Flussanalysen in Pflanzen. Biospektrum 17 (2011) 230-232. https://dx.doi.org/10.1007/s12268-011-0034-2
Liiving T, Baker S M, Junker B H:
Biochemical fundamentals. In: Koch I, Reisig W, Schreiber F (Eds.): Modeling in systems biology: the Petri net approach. (Series: Computational biology, Vol. 16) London [u.a.]: Springer (2011) ISBN 978-1-8499-6473-9, 19-36. https://dx.doi.org/10.1007/978-1-84996-474-6_2
Peter V:
Vorhersage der subzellulären Verteilung von Enzymaktivitäten im Erbsensamen auf Basis von Expressionsdaten. (Bachelor Thesis) Mittweida, Hochschule Mittweida (FH) (2011) 79 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).
Schuster S, Junker B H:
Topological analysis of metabolic and regulatory networks. In: Koch I, Reisig W, Schreiber F (Eds.): Modeling in systems biology: the Petri net approach. (Series: Computational biology, Vol. 16) London [u.a.]: Springer (2011) ISBN 978-1-8499-6473-9, 209-224. https://dx.doi.org/10.1007/978-1-84996-474-6_10
Weber S:
Validierung einer neuen Enzymkinetik-Approximation am Citratzyklus von Erbsensamen (Diploma Thesis) Magdeburg, Otto-von-Guericke Universität (2011) 263 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).
2010
Baker S M, Junker B H:
Adaptive unscented Kalman filter for estimation of parameters in kinetic metabolic models. In: Chen L, Zhang X-S, Shen B, Wu L-Y, Wang Y H (Eds.): Computational systems biology. 4th International Conference on Computational Systems Biology (ISB2010) Suzhou, China, September 9-11, 2010, proceedings. (Series: Lecture notes in operations research Vol. 13) Beijing: World Publishing Corporation (2010) 185-186.
Baker S M, Poskar H, Junker B H:
Unscented Kalman filter for estimation of multiple parameters in kinetic models. In: Nykter M, Ruusuvuori P, Carlberg C, Yli-Harja O (Eds.): 7th International Workshop on Computational Systems Biology, WCSB 2010, June 16–18, 2010, Luxembourg, proceedings. (TICSP series, Vol. 51) Tampere: Tampere International Center for Signal Processing (2010) ISBN 978-952-15-2384-7, 19-22.
Baker S M, Schallau K, Junker B H:
Comparison of different algorithms for simultaneous estimation of multiple parameters in kinetic metabolic models. J. Integr. Bioinform. 7 (2010) e133. https://dx.doi.org/10.2390/biecoll-jib-2010-133
Floss D M, Schallau K, Rose-John S, Conrad U, Scheller J:
Elastin-like polypeptides revolutionize recombinant protein expression and their biomedical application. Trends Biotechnol. 28 (2010) 37-45. https://dx.doi.org/10.1016/j.tibtech.2009.10.004
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).
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
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.
Schallau K, Junker B H:
Simulating plant metabolic pathways with enzyme-kinetic models. Plant Physiol. 152 (2010) 1763-1771. https://dx.doi.org/10.1104/pp.109.149237
Sreenivasulu N, Borisjuk L, Junker B H, Mock H-P, Rolletschek H, Seiffert U, Weschke W, Wobus U:
Barley grain development toward an integrative view. Int. Rev. Cell Mol. Biol. 281 (2010) 49-89. https://dx.doi.org/10.1016/S1937-6448(10)81002-0
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).
2009
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).
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.
Steuer R, Junker B H:
Computational models of metabolism: stability and regulation in metabolic networks. Adv. Chem. Phys. 142 (2009) 105-251. https://dx.doi.org/10.1002/9780470475935.ch3
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
2008
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).
Junker B H:
Networks in biology. 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, 3-14.
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.
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).
2007
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
2006
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, Junker B H, Schreiber F:
The VANTED software system for transcriptomics, proteomics and metabolomics analysis. J. Pestic. Sci. 31 (2006) 289-292.
Weise S, Grosse I, Klukas C, Koschützki D, Scholz U, Schreiber F, Junker B H:
Meta-All: a system for managing metabolic pathway information. BMC Bioinformatics 7 (2006) 465. https://dx.doi.org/10.1186/1471-2105-7-465