Publikationen

Autoren Titel
2016
Arend D, Lange M, Pape J-M, Weigelt-Fischer K, Arana-Ceballos F, Mücke I, Klukas C, Altmann T, Scholz U, Junker A Quantitative monitoring of Arabidopsis thaliana growth and development using high-throughput plant phenotyping. Sci. Data 3 (2016) 160055. dx.doi.org/10.1038/sdata.2016.55
Ćwiek-Kupczyńska H, Altmann T, Arend D, Arnaud E, Chen D, Cornut G, Fiorani F, Frohmberg W, Junker A, Klukas C, Lange M, Mazurek C, Nafissi A, Neveu P, van Oeveren J, Pommier C, Poorter H, Rocca-Serra P, Sansone S-A, Scholz U, van Schriek M, Seren Ü, Usadel B, Weise S, Kersey P, Krajewski P Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods 12 (2016) 44. dx.doi.org/10.1186/s13007-016-0144-4
Pape J-M Ein Klassifikationssystem zur quantitativen Analyse von Krankheitssymptomen im Kontext der Hochdurchsatz-Phänotypisierung von Pflanzen. (Master Thesis) Magdeburg, Fakultät für Informatik, Otto-von-Guericke-Universität (2016) 84 pp.
Scharr H, Minervini M, French A P, Klukas C, Kramer D M, Liu X, Luengo I, Pape J-M, Polder G, Vukadinovic D, Yin X, Tsaftaris S A Leaf segmentation in plant phenotyping: a collation study. Mach. Vision Appl. 27 (2016) 585-606. dx.doi.org/10.1007/s00138-015-0737-3
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 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
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
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 v2: a framework for systems biology applications. BMC Syst. Biol. 6 (2012) 139. dx.doi.org/10.1186/1752-0509-6-139
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).
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 Visual analytics of multimodal biological data. Proceedings of the International Conference on Information Visualization Theory and Applications (IVAPP’11). SciTePress (2011) 256-261.
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
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 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. dx.doi.org/10.1093/bioinformatics/btq407
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