Publikationen

Autoren Titel
2015
Castellini A, Edlich-Muth C, Muraya M, Klukas C, Altmann T, Selbig J Towards a graph-theoretic approach to hybrid performance prediction from large-scale phenotypic data. In: Lones M, Tyrrell A, Smith S, Fogel G (Eds.): Information Processing in Cells and Tissues.10th International Conference, IPCAT 2015, San Diego, CA, USA, September 14-16, 2015, Proceedings. (Series: Lecture Notes in Computer Science, Vol. 9303) Cham: Springer (2015) 173-184. dx.doi.org/10.1007/978-3-319-23108-2_15 ISBN 978-3-319-23107-5
Guo Z, Chen D, Schnurbusch T Variance components, heritability and correlation analysis of anther and ovary size during the floral development of bread wheat. J. Exp. Bot. 66 (2015) 3099-3111. dx.doi.org/10.1093/jxb/erv117
Junker A, Muraya M M, Weigelt-Fischer K, Arana-Ceballos F, Klukas C, Melchinger A E, Meyer R C, Riewe D, Altmann T Optimizing experimental procedures for quantitative evaluation of crop plant performance in high throughput phenotyping systems. Front. Plant Sci. 5 (2015) 770. dx.doi.org/10.3389/fpls.2014.00770
Krajewski P, Chen D, Ćwiek H, van Dijk A D J, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap J P, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S Towards recommendations for metadata and data handling in plant phenotyping. J. Exp. Bot. 66 (2015) 5417-5427. dx.doi.org/10.1093/jxb/erv271
Muscolo A, Junker A, Klukas C, Weigelt-Fischer K, Riewe D, Altmann T Phenotypic and metabolic responses to drought and salinity of four contrasting lentil accessions. J. Exp. Bot. 66 (2015) 5467-5480. dx.doi.org/10.1093/jxb/erv208
Neumann K, Klukas C, Friedel S, Rischbeck P, Chen D, Entzian A, Stein N, Graner A, Kilian B Dissecting spatio-temporal biomass accumulation in barley under different water regimes using high-throughput image analysis. Plant Cell Environ. 38 (2015) 1980-1996. dx.doi.org/10.1111/pce.12516
Pape J M, Klukas C Utilizing machine learning approaches to improve the prediction of leaf counts and individual leaf segmentation of rosette plant images. In: Tsaftaris S A, Scharr H, Pridmore T (Eds.): Proceedings of the Computer Vision Problems in Plant Phenotyping (CVPPP). : BMVA Press (2015) 3.1-3.12. dx.doi.org/10.5244/C.29.CVPPP.3 ISBN 1-901725-55-3
Pape J M, Klukas C 3-D histogram-based segmentation and leaf detection for rosette plants. In: Fleet D, Pajdla T, Schiele B, Tuytelaars T (Eds.): Computer Vision – ECCV 2014 Workshops: 13th European Conference, Zurich, Switzerland, September 6-12, 2014, proceedings, part IV (Series: Lecture Notes in Computer Science) Cham: Springer (2015) 61-74. doi.org/10.1007/978-3-319-16220-1_5 ISBN 978-3-319-16219-5
Rahaman M M, Chen D, Gillani Z, Klukas C, Chen M Advanced phenotyping and phenotype data analysis for the study of plant growth and development. Front. Plant Sci. 6 (2015) 619. dx.doi.org/10.3389/fpls.2015.00619
Schilling S, Gramzow L, Lobbes D, Kirbis A, Weilandt L, Hoffmeier A, Junker A, Weigelt-Fischer K, Klukas C, Wu F, Meng Z, Altmann T, Theissen G Non-canonical structure, function and phylogeny of the B MADS-box gene OsMADS30 of rice (Oryza sativa). Plant J. 84 (2015) 1059-1072. dx.doi.org/10.1111/tpj.13055
Yuan C, Wang J, Harrison A P, Meng X, Chen D, Chen M Genome-wide view of natural antisense transcripts in Arabidopsis thaliana. DNA Res. 22 (2015) 233-243. dx.doi.org/10.1093/dnares/dsv008
2014
Chen D, Chen M, Altmann T, Klukas C Bridging genomics and phenomics. In: Chen M, Hofestädt R (Eds.): Approaches in integrative bioinformatics: towards the virtual cell. Berlin [u.a.]: Springer (2014) 299-333. dx.doi.org/10.1007/978-3-642-41281-3_11 ISBN 978-3-642-41280-6
Chen D, Fu L Y, Zhang Z, Li G, Zhang H, Jiang L, Harrison A P, Shanahan H P, Klukas C, Zhang H Y, Ruan Y, Chen L L, Chen M Dissecting the chromatin interactome of microRNA genes. Nucleic Acids Res. 42 (2014) 3028-3043. dx.doi.org/10.1093/nar/gkt1294
Chen D, Neumann K, Friedel S, Kilian B, Chen M, Altmann T, Klukas C Dissecting the phenotypic components of crop plant growth and drought responses based on high-throughput image analysis. Plant Cell 26 (2014) 4636-4655. dx.doi.org/10.1105/tpc.114.129601
Harshavardhan V T, Van Son L, Seiler C, Junker A, Weigelt-Fischer K, Klukas C, Altmann T, Sreenivasulu N, Bäumlein H, Kuhlmann M AtRD22 and AtUSPL1, members of the plant-specific BURP domain family involved in Arabidopsis thaliana drought tolerance. PLoS One 9 (2014) e110065. dx.doi.org/10.1371/journal.pone.0110065
Klukas C, Chen D, Pape J M Integrated Analysis Platform: an open-source information system for high-throughput plant phenotyping. Plant Physiol. 165 (2014) 506-518. dx.doi.org/10.1104/pp.113.233932
2013
Chen D, Chen M, Klukas C Phenomics collaboration website. phenomics.cn (2013).
Klukas C, Chen D, Pape J-M IAP – The Integrated Analysis Platform for High-Througput Plant Phenotyping. iap.ipk-gatersleben.de (2013).
Lu X, Chen D, Shu D, Zhang Z, Wang W, Klukas C, Chen L L, Fan Y, Chen M, Zhang C The differential transcription network between embryo and endosperm in the early developing maize seed. Plant Physiol. 162 (2013) 440-455. dx.doi.org/10.1104/pp.113.214874
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).
2012
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. dx.doi.org/10.1038/nprot.2012.002
Jusufi I, Klukas C, Kerren A, Schreiber F Guiding the interactive exploration of metabolic pathway interconnections. Inform. Visual. 11 (2012) 136-150. dx.doi.org/10.1177/1473871611405677
Klukas C, Pape J M, Entzian A Analysis of high-throughput plant image data with the information system IAP. J. Integr. Bioinform. 9 (2012) 191. dx.doi.org/10.2390/biecoll-jib-2012-191
Neumann K, Stein N, Graner A, Klukas C, Entzian A, Kilian B Non-destructive phenotyping using the high-throughput LemnaTec-Scanalyzer 3D platform to investigate drought tolerance in barley. In: Börner A, Kobijlski B (Eds.): Proceedings of the 15th International EWAC Conference, 7 - 11 November 2011, Novi Sad, Serbia. (Series: European Wheat Aneuploid Co-operative newsletter, Vol. 15) Gatersleben: Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (2012) 158-160.
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. dx.doi.org/10.1186/1752-0509-6-139
2011
Huang D, Huang Y, Bai Y, Chen D, Hofestädt R, Klukas C, Chen M MyBioNet: interactively visualize, edit and merge biological networks on the Web. Bioinformatics 27 (2011) 3321-3322. dx.doi.org/10.1093/bioinformatics/btr557
Pape J-M Automatische Erkennung und Quantifizierung von phänotypischen Pflanzenmerkmalen und Strukturen. (Bachelor Thesis) Magdeburg, Fakultät für Informatik, Otto-von-Guericke-Universität (2011) 67 pp.
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. 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.
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
Czauderna T, Klukas C, Schreiber F Editing, validating and translating of SBGN maps. Bioinformatics 26 (2010) 2340-2341. dx.doi.org/10.1093/bioinformatics/btq407
Czauderna T, Klukas C, Schreiber F SBGN-ED. vanted.ipk-gatersleben.de/addons/sbgn-ed/ (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. dx.doi.org/10.2390/biecoll-jib-2010-125
Huang D, Huang Y, Klukas C, Hofestädt R, Chen M PBSK Browser: navigate biological pathways of PSI-MI, BioPAX, SBML and KGML formats. In: di Bernado D (Ed.): IEEE International Conference on Bioinformatics and Biomedicine workshops (BIBMW 2010): Hong Kong, China, 18 - 21 December 2010, proceedings. Piscataway, NJ: IEEE (2010) 13-18. dx.doi.org/10.1109/BIBMW.2010.5703766 ISBN 978-1-4244-8303-7
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. dx.doi.org/10.2390/biecoll-jib-2010-112
Rohn H, Klukas C, Schreiber F HIVE. vanted.ipk-gatersleben.de/addons/hive/ (2010).
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. 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. 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).
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) 173-209. dx.doi.org/10.1007/978-0-387-78745-9_7 ISBN 978-0-387-78744-2
Grafahrend-Belau E, Klukas C, Junker B H, Schreiber F FBA-SimVis: Interactive visualisation of constraint-based metabolic models. Bioinformatics 25 (2009) 2755-2757. dx.doi.org/10.1093/bioinformatics/btp408
Grafahrend-Belau E, Klukas C, Junker B H, Schreiber F FBASimViz: dynamic visualization of constraint-based metabolic models. fbasimviz.ipkgatersleben.de (2009).
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.
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) 105-115. ISBN 978-3-88579-251-2
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) 693-697. ISBN 978-3-88579-248-2
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) 196-203. dx.doi.org/10.1007/978-3-642-02879-3_16 ISBN 978-3-642-02878-6
Wheelock C E, Goto S, Yetukuri L, D'Alexandri 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) 339-368. dx.doi.org/10.1007/978-1-60761-325-1_19 ISBN 978-1-60761-324-4
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) 41-44. ISBN 978-952-15-1988-8
Klukas C VANTED - visualization and analysis of networks containing experimental data. vanted.ipk-gatersleben.de (2008).
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
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. dx.doi.org/10.1093/bioinformatics/btl611
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. dx.doi.org/10.1111/j.1365-313X.2007.03155.x
2006
Junker B H, Klukas C, Schreiber F VANTED: Datenauswertung im Netzwerk-Kontext. GenomXPress 1 (2006) 16-18.
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. dx.doi.org/10.1186/1471-2105-7-109
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 Coordinated perspectives and enhanced force-directed layout for the analysis of network motifs. 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) 39-48. ISBN 1-920682-41-4
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. dx.doi.org/10.1186/1471-2105-7-465