our knowledge united

Méret, M., Kopetzki, D., Degenkolbe, T., Kleessen, S., Nikoloski, Z., Tellstroem, V., Barsch, A., Kopka, J., Antonietti, M., Willmitzer, L. (2014). From System Biology to System Chemistry: Metabolomic procedures enable insights into complex chemical reaction networks in water. RSC Advances. doi: 10.1039/C3RA42384K.

Schulz, P., Jansseune, K., Degenkolbe, T., Méret, M., Claeys, H., Skirycz, A., Teige, M, Willmitzer, L., Hannah, M. A. (2014). Poly(ADP-Ribose)Polymerase Activity Controls Plant Growth by Promoting Leaf Cell Number. PLoS One. doi: 10.1371/journal.pone.0090322.

Degenkolbe, T., Do, P. T., Kopka, J., Zuther, E., Hincha, D. K., Köhl, K. I. (2013). Identification of Drought Tolerance Markers in a Diverse Population of Rice Cultivars by Expression and Metabolite Profiling. PLoS One, 8(5): e63637. doi:10.1371/journal.pone.0063637.

Do, P. T., Degenkolbe, T., Erban, A., Heyer, A. G., Kopka, J., Köhl, K. I., Hincha, D. K., Zuther, E. (2013). Dissecting Rice Polyamine Metabolism under Controlled Long-Term Drought Stress. PLoS One, 8(4), e60325. doi:10.1371/journal.pone.0060325.

Degenkolbe, T., Giavalisco, P., Zuther, E., Seiwert, B., Hincha, D. K., Willmitzer, L. (2012). Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana. Plant Journal, 72, 972-982. doi:10.1111/tpj.12007.

Hubberten, H.-M., Klie, S., Caldana, C., Degenkolbe, T., Willmitzer, L., Hoefgen, R. (2012). An additional role of O-acetylserine as a sulphur status independent regulator during plant growth. Plant Journal, 70(4), 666-677. doi:10.1111/j.1365-313X.2012.04905.x.

Caldana, C., Degenkolbe, T., Cuadros-Inostroza, A., Klie, S., Sulpice, R., Leisse, A., Steinhauser, D., Fernie, A. R., Willmitzer, L., Hannah, M. A. (2011). High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions. The Plant Journal, 67(5), 869-884. doi:10.1111/j.1365-313X.2011.04640.x.

Burgos, A., Szymanski, J., Seiwert, B., Degenkolbe, T., Hannah, M. A., Giavalisco, P., Willmitzer, L. (2011). Analysis of short-term changes in the Arabidopsis thaliana glycerolipidome in response to temperature and light. Plant Journal, 66(4), 656-668. doi:10.1111/j.1365-313X.2011.04531.x.

Espinoza, C., Degenkolbe, T., Caldana, C., Zuther, E., Leisse, A., Willmitzer, L., Hincha, D. K., Hannah, M. A. (2010). Interaction with diurnal and circadian regulation results in dynamic metabolic and transcriptional changes during cold acclimation in Arabidopsis. PLoS One, 5(11), e14101. doi:10.1371/journal.pone.0014101.

Willmitzer, L., Degenkolbe, T., Caldana, C., Hannah, M. (2009). Systems response to environmental conditions as studied by metabolome analysis. New Biotechnology, 25, S317-S317.

Degenkolbe, T., Do, P. T., Zuther, E., Repsilber, D., Walther, D., Hincha, D. K., Koehl, K. I. (2009). Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Molecular Biology, 69(1-2), 133-153. doi:10.1007/s11103-008-9412-7.

Degenkolbe, T., Hannah, M. A., Freund, S., Hincha, D. K., Heyer, A. G., Koehl, K. I. (2005). A quality-controlled microarray method for gene expression profiling. Analytical Biochemistry, 346(2), 217-224. doi:10.1016/j.ab.2005.08.027.

Freilich, S., Lev, S., Gonda, I., Reuveni, E., Portnoy, V., Oren, E., Lohse M. … Katzir, N. (2015). Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits. BMC Plant Biology, 15, 71. http://doi.org/10.1186/s12870-015-0449-x

Bolger, A. M., Lohse, M., Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. http://doi.org/10.1093/bioinformatics/btu170

Lohse, M., Nagel, A., Herter, T., May, P., Schroda, M., Zrenner, R., Tohge, T., Fernie, A. R., Stitt, M., Usadel, B. (2014). Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant Cell Environment, 37(2). doi:10.1111/pce.12231.

Lee, Y. P., Giorgi, F. M., Lohse, M., Kvederaviciute, K., Klages, S., Usadel, B., Meskiene, I., Reinhardt, R., Hincha, D. K. (2013). Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum). BMC Genomics, 14, 793-793. doi:10.1186/1471-2164-14-793.

Lohse, M., Drechsel, O., Kahlau, S., Bock, R. (2013). OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets. Nucleic Acids Res., 41(Web Server issue), W575-W581. doi:10.1093/nar/gkt289.

Araujo, W. L., Tohge, T., Osorio, S., Lohse, M., Balbo, I., Krahnert, I., Sienkiewicz-Porzucek, A., Usadel, B., Nunes-Nesi, A., Fernie, A. R. (2012). Antisense Inhibition of the 2-Oxoglutarate Dehydrogenase Complex in Tomato Demonstrates Its Importance for Plant Respiration and during Leaf Senescence and Fruit Maturation. Plant Cell, 24(6), 2328-2351. doi:10.1105/tpc.112.099002.

Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M., Usadel, B. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40(W1), W622-W627. doi:10.1093/Nar/Gks540.

Gaude, N., Bortfeld, S., Duensing, N., Lohse, M., Krajinski, F. (2012). Arbuscule-containing and non-colonized cortical cells of mycorrhizal roots undergo extensive and specific reprogramming during arbuscular mycorrhizal development. Plant Journal, 69(3), 510-528. doi:10.1111/j.1365-313X.2011.04810.x.

Ryngajllo, M., Childs, L., Lohse, M., Giorgi, F. M., Lude, A., Selbig, J., Usadel, B. (2011). SLocX: predicting subcellular localization of Arabidopsis proteins leveraging gene expression data. Frontiers in Plant Science, 2, 43. doi:10.3389/fpls.2011.00043.

Osorio, S., Alba, R., Damasceno, C. M. B., Lopez-Casado, G., Lohse, M., Zanor, M. I., Tohge, T., Usadel, B., Rose, J. K. C., Fei, Z. J., Giovannoni, J. J., Fernie, A. R. (2011). Systems Biology of Tomato Fruit Development: Combined Transcript, Protein, and Metabolite Analysis of Tomato Transcription Factor (nor, rin) and Ethylene Receptor (Nr) Mutants Reveals Novel Regulatory Interactions. Plant Physiology, 157(1), 405-425. doi:10.1104/pp.111.175463.

Nagel, A., Lohse, M., Bolger, A., Bolger, A. M., Stitt, M., Usadel, B. (2011). Visualizing large, high-throughput datasets based on the cognitive representation of biological pathways. Human Vision and Electronic Imaging Xvi, 7865, 78650h. doi:10.1117/12.881998.

Giorgi, F. M., Bolger, A. M., Lohse, M., Usadel, B. (2010). Algorithm-driven Artifacts in median polish summarization of Microarray data. BMC Bioinformatics, 11, 553. doi:10.1186/1471-2105-11-553.

Lohse, M., Nunes-Nesi, A., Krueger, P., Nagel, A., Hannemann, J., Giorgi, F. M., Childs, L., Osorio, S., Walther, D., Selbig, J., Sreenivasulu, N., Stitt, M., Fernie, A. R., Usadel, B. (2010). Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis. Plant Physiology, 153(2), 642-651. doi:10.1104/pp.109.152553.

Rotter, A., Camps, C., Lohse, M., Kappel, C., Pilati, S., Hren, M., Stitt, M., Coutos-Thevenot, P., Moser, C., Usadel, B., Delrot, S., Gruden, K. (2009). Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: Extending MapMan ontology for grapevine. BMC Plant Biology, 9, 104. doi:10.1186/1471-2229-9-104.

Zanor, M. I., Osorio, S., Nunes-Nesi, A., Carrari, F., Lohse, M., Usadel, B., Kuehn, C., Bleiss, W., Giavalisco, P., Willmitzer, L., Sulpice, R., Zhou, Y. H., Fernie, A. R. (2009). RNA Interference of LIN5 in Tomato Confirms Its Role in Controlling Brix Content, Uncovers the Influence of Sugars on the Levels of Fruit Hormones, and Demonstrates the Importance of Sucrose Cleavage for Normal Fruit Development and Fertility. Plant Physiology, 150(3), 1204-1218. doi:10.1104/pp.109.136598.

Usadel, B., Poree, F., Nagel, A., Lohse, M., Czedik-Eysenberg, A., Stitt, M. (2009). A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell and Environment, 32(9), 1211-1229. doi:10.1111/j.1365-3040.2009.01978.x.

Oey, M., Lohse, M., Scharff, L. B., Kreikemeyer, B., Bock, R. (2009). Plastid production of protein antibiotics against pneumonia via a new strategy for high-level expression of antimicrobial proteins. Proceedings of the National Academy of Sciences of the United States of America, 106(16), 6579-6584. doi:10.1073/pnas.0813146106.

Oey, M., Lohse, M., Kreikemeyer, B., Bock, R. (2009). Exhaustion of the chloroplast protein synthesis capacity by massive expression of a highly stable protein antibiotic. Plant Journal, 57(3), 436-445. doi:10.1111/j.1365-313X.2008.03702.x.

Howell, K. A., Narsai, R., Carroll, A., Ivanova, A., Lohse, M., Usadel, B., Millar, A. H., Whelan, J. (2009). Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process. Plant Physiology, 149(2), 961-980. doi:10.1104/pp.108.129874.

Waadt, R., Schmidt, L. K., Lohse, M., Hashimoto, K., Bock, R., Kudla, J. (2008). Multicolor bimolecular fluorescence complementation reveals simultaneous formation of alternative CBL/CIPK complexes in planta. Plant Journal, 56(3), 505-516. doi:10.1111/j.1365-313X.2008.03612.x.

Lohse, M., Krueger, P., Hannemann, J., Nagel, A., Stitt, M., Walther, D., Usadel, B. (2008). Robin – Microarray Experimentanalyse leicht gemacht. GenomXPress: Informationen aus der Deutschen Genomforschung, 3, 16-17.

Lohse, M., Drechsel, O., Bock, R. (2007). OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes. Current Genetics, 52(5-6), 267-274. doi:10.1007/s00294-007-0161-y.

Lothar Willmitzer: http://www.mpimp-golm.mpg.de/5852/1Willmitzer

Ko, D., Kang , J., Kiba, T., Park, J., Kojima, M., Do, J., Kim, K.Y., Kwon, M., Endler, A., Song, W.Y., Martinoia, E., Sakakibara, H., Lee, Y. (2014). Arabidopsis ABCG14 is essential for root-to-shoot translocation of cytokinin. Proceedings of the National Academy of Sciences of the United States of America, 111(19), 7150–7155. http://doi.org/10.1073/pnas.1321519111

Henrichs, S., Wang, B., Fukao, Y., Zhu, J., Charrier, L., Bailly, A., Oehring, S.C., Linnert, M., Weiwad, M., Endler, A., Nanni, P., Pollmann, S., Mancuso, S., Schulz, A., Geisler, M. (2012). Regulation of ABCB1/PGP1-catalysed auxin transport by linker phosphorylation. EMBO J, 31(13), 2965-2980. doi: 10.1038/emboj.120.

Endler, A., Persson, S. (2011). Cellulose Synthases and Synthesis in Arabidopsis. Molecular Plant, 4(2), 199-211. doi:10.1093/mp/ssq079.

Reiland, S., Finazzi, G., Endler, A., Willig, A., Baerenfaller, K., Grossmann, J., Gerrits, B., Rutishauser, D., Gruissem, W., Rochaix, J.D., Baginsky, S. (2011). Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF). PNAS, 108(31), 12955-1260. doi: 10.1073/pnas.1104734108.

Endler, A., Baginsky, S., (2011). Use of phosphoproteomics to study posttranslational protein modifications in Arabidopsis chloroplasts. Methods Mol Biol, 775, 283-296. doi: 10.1007/978-1-61779-237-3_15.

Endler, A., Sanchez-Rodriguez, C., Persson, S. (2010). GLYCOBIOLOGY Cellulose squeezes through. Nature Chemical Biology, 6(12), 883-884. doi:10.1038/Nchembio.480.

Meyer, S., Mumm, P., Imes, D., Endler, A., Weder, B., Al-Rasheid, K.A., Geiger, D., Marten, I., Martinoia, E., Hedrich, R. (2010) AtALMT12 represents an R-type anion channel required for stomatal movement in Arabidopsis guard cells. Plant J, 63(6), 1054-1062. doi: 10.1111/j.1365-313X.2010.04302.x.

Reiland, S., Messerli, G., Baerenfaller, K., Gerrits, B., Endler, A., Grossmann, J., Gruissem, W., Baginsky, S. (2009). Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks. Plant Physiol, 150(2), 889-903. doi: 10.1104/pp.109.138677.

Endler, A., Reiland, S., Gerrits, B., Schmidt, U.G., Baginsky, S., Martinoia, E. (2009) In vivo phosphorylation sites of tonoplast proteins from Hordeum vulgare identified by a phosphoproteomic approach, Proteomics, 9(2), 310-321. doi: 10.1002/pmic.200800323.

Schmidt, U.G., Endler, A., Schelbert, S., Brunner, A., Schnell, M., Neuhaus, H.E., Marty-Mazars, D., Marty, F., Baginsky, S., Martinoia, E. (2007). Novel tonoplast transporters identified using a proteomic approach with vacuoles isolated from cauliflower buds. Plant Physiol, 145(1), 216-229.

Endler, A., Meyer, S., Schelbert, S., Schneider, T., Weschke, W., Peters, S.W., Keller, F., Baginsky, S., Martinoia, E., Schmidt, U.G. (2006). Identification of a vacuolar sucrose transporter in barley and Arabidopsis mesophyll cells by a tonoplast proteomic approach. Plant Physiol, 141(1), 196-207.

Kleessen, S., Laitinen, R., Fusari, C. M., Antonio, C., Sulpice, R., Fernie, A. R., Stitt, M., Nikoloski, Z. (2014). Metabolic efficiency underpins performance trade-offs in growth of Arabidopsis thaliana. Nature Communications, 5, 3537. doi:10.1038/ncomms4537.

Angelesca, A., Kleessen, S., Nikoloski, Z. (2014). The Sequence Reconstruction Problem. In N. Jonoska, M. Saito (Eds.), Discrete and Topological Models in Molecular Biology (pp. 23-43). Berlin, Heidelberg: Springer-Verlag.

Kleessen, S., Klie, S., Nikoloski, Z. (2013). Data integration through proximity-based networks provides biological principles of organization across scales. Plant Cell, 25(6), 1917-1927. doi:10.1105/tpc.113.111039.

Sulpice, R., Nikoloski, Z., Tschoep, H., Antonio, C., Kleessen, S., Lahrlimi, A., Selbig, J., Hirofumi, I., Gibon, Y., Fernie, A. R., Stitt, M. (2013). Impact of the carbon and nitrogen supply on relationships and connectivity between metabolism and biomass in a broad panel of Arabidopsis accessions. Plant Physiology, 162(1), 347-363. doi:10.1104/pp.112.210104.

Kleessen, S., Antonio, C., Sulpice, R., Laitinen, R., Fernie, A. R., Stitt, M., Nikoloski, Z. (2012). Structured patterns in geographic variability of metabolic phenotypes in Arabidopsis thaliana. Nature Communications, 3, 1319. doi:10.1038/ncomms2333.

Kleessen, S., Fernie, A. R., Nikoloski, Z. (2012). A computational framework for evaluating the efficiency of Arabidopsis accessions in response to nitrogen stress reveals important metabolic mechanisms. Frontiers in Plant Science, 3, 217. doi:10.3389/fpls.2012.00217.

Kleessen, S., Araujo, W. L., Fernie, A. R., Nikoloski, Z. (2012). Model-based confirmation of alternative substrates of mitochondrial electron transport chain. Journal of Biological Chemistry, 287(14), 11122-11131. doi:10.1074/jbc.M111.310383.

Kleessen, S., Nikoloski, Z. (2012). Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology, 6(1), 16. doi:10.1186/1752-0509-6-16.

Riano-Pachon, D. M.*, Kleessen, S.*, Neigenfind, Durek, P., Weber, E., Engelsberger, W. R., Walther, D., Selbig, J., Schulze, W. X., Kersten, B. (2010). Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics, 11, 411. doi:10.1186/1471-2164-11-411. *These authors contributed equally to this work

Kryvych, S., Kleessen, S., Ebert, B., Kersten, B., Fisahn, J. (2011). Proteomics – The key to understanding systems biology of Arabidopsis trichomes. Phytochemistry, 72(10), 1061-1070. doi:10.1016/j.phytochem.2010.09.003.

Klie, S., Osorio, S., Tohge, T., Drincovich, M.F., Fait, A., Giovannoni, J.J., Fernie, A.R. and Nikoloski, Z. (2013) Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species., Plant Physiol., DOI=10.1104/pp.113.226142

Kleessen, S., Klie, S. and Nikoloski, Z. (2013) Data Integration through Proximity-Based Networks Provides Biological Principles of Organization across Scales., The Plant cell, DOI=10.1105/tpc.113.111039

Omranian, N., Klie, S., Mueller-Roeber, B. and Nikoloski, Z. (2013) Network-based segmentation of biological multivariate time series., PloS one, DOI=10.1371/journal.pone.0062974

Klie, S., Caldana, C. and Nikoloski, Z. (2012) Compromise of multiple time-resolved transcriptomics experiments identifies tightly regulated functions, Frontiers in Plant Science 3(249), DOI=10.3389/fpls.2012.00249

Klie, S. and Nikoloski, Z. (2012) The choice between MapMan and Gene Ontology for automated gene function prediction in plant science, Frontiers in Genetics 3(115), DOI:10.3389/fgene.2012.00115

Klie, S., Mutwil, M., Persson, S. and Nikoloski, Z. (2012) Inferring gene functions through dissection of relevance networks: Interleaving the intra- and inter-species views, Molecular Biosystems, 8(9), pp. 2233-2241

Groth, D., Hartmann, S., Klie, S. and Joachim Selbig (2012) Principal Components Analysis, Methods in Molecular Biology -Computational Toxicology, Springer, Heidelberg

Hubberten, H.M., Klie, S., Caldana, C., Degenkolbe, T., Willmitzer, L. and Hoefgen, R. (2012) An additional role of O-acetylserine as a sulphur status independent regulator during plant growth. The Plant Journal, DOI: 10.1111/j.1365-313X.2012.04905.x

Klie, S., Krueger, S., Krall L., Giavalisco, P., Flgge U.I., Willmitzer, L. and Steinhauser, D. (2011) Analysis of the compartmentalized metabolome a validation of the non-aqueous fractionation technique. Frontiers in Plant Science, 2(55), DOI:10.3389/fpls.2011.00055.

Caldana, C., Degenkolbe, T. Cuadros-Inostroza, A., Klie, S., Sulpice, R., Leisse, A., Steinhauser, D., Fernie, A. R., Willmitzer, L. and Hannah, M. A. (2011) High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions, The Plant Journal, doi: 10.1111/j.1365-313X.2011.04640.x

Mutwil, M., Klie, S., Tohge, T., Giorgi, F.M., Wilkins, O., Campbell, M.M., Fernie, A.R., Usadel, B., Nikoloski, Z., Persson, S. (2011) PlaNet: Combined sequence and expression comparisons across plant networks derived from seven species. Plant Cell, 23 (3), pp. 895-910

Nikoloski, Z., Grimbs, S., Klie, S. Selbig, J. (2011) Complexity of automated gene annotation. Biosystems, 104(1), pp. 1-8

Jozefczuk, S., Klie, S., Catchpole, G., Szymanski, J., Cuadros-Inostroza, A., Steinhauser, D., Selbig, J. Willmitzer, L. (2010) Metabolomic and transcriptomic stress response of Escherichia coli. Molecular Systems Biology, 6

Klie, S., Nikoloski, Z. Selbig, J. (2010) Biological Cluster Evaluation for Gene Function Prediction. Journal of Computational Biology, 17, pp. 1-18

Jones, P., Cote, R.G., Cho, S.Y., Klie, S., Martens, L., Quinn, A.F., Thorneycroft, D. Hermjakob, H. (2008), PRIDE: new developments and new datasets. Nucleic Acids Research, 36(1), pp. 878-883

Klie, S., Martens, L., Vizcaino, J.A., Cote, R.G., Jones, P., Apweiler, R., Hinneburg, A. Hermjakob, H. (2008) Analyzing large-scale proteomics projects with latent semantic indexing. Journal of Proteome Research, 7(1), pp. 182-91

Klie, S., Martens, L., Vizcaino, J.A., Cote, R.G., Jones, P., Apweiler, R., Hinneburg, A. Hermjakob, H. (2007) An Application of Latent Topic Document Analysis to Large-Scale Proteomics Databases. Proceedings of the German Conference on Bioinformatics (GCB’07), pp. 174{184

Klie, S. Neumann, S. (2006) Storage and Processing of Mass Spectrometry Data. 17th International Conference on Database and Expert Systems Applications (DEXA2006), pp. 211-215

Neigenfind, J., Gyetvai, G., Basekow, R., Diehl, S., Achenbach, U., Gebhardt, C., et al. (2008). Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT. BMC Genomics, 9, 356. doi:10.1186/1471-2164-9-356.

Kersten, B., Nagel, A., Riano-Pachon, D., Neigenfind, J., Weber, E., Wagner, R., et al. (2008). Die GABI-Primaerdatenbank GabiPD – Komplexe Integration von GABI-Daten aus Modell- und Nutzpflanzen. GenomXpress, 1, 17-19.

Riano-Pachon, D. M., Nagel, A., Neigenfind, J., Wagner, R., Basekow, R., Weber, E., et al. (2009). GabiPD: the GABI primary database-a plant integrative ‘omics’ database. Nucleic Acids Research, 37(Database issue), 954-959. doi:10.1093/Nar/Gkn611.

Kersten, B., Agrawal, G. K., Durek, P., Neigenfind, J., Schulze, W. X., Walther, D., et al. (2009). Plant phosphoproteomics: An update. Proteomics, 9(4), 964-988. doi:10.1002/pmic.200800548.

Riano-Pachon, D. M., Kleessen, S., Neigenfind, Durek, P., Weber, E., Engelsberger, W. R., et al. (2010). Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics, 11, 411. doi:10.1186/1471-2164-11-411.

Neigenfind, J., Grimbs, S., Nikoloski, Z. (2013). On the relation between reactions and complexes of (bio)chemical reaction networks. Journal of Theoretical Biology, 317, 359-365. doi:10.1016/j.jtbi.2012.10.016.

Lisso, J., Schröder, F., Müssig, C. (2013). EXO modifies sucrose and trehalose responses and connects the extracellular carbon status to growth. Frontiers in plant science, 4. doi:10.3389/fpls.2013.00219.

Lisso, J., Schröder, F., Schippers, J. und Müssig, C. (2012). NFXL2 modifies cuticle properties in Arabidopsis. Plant Signaling Behavior, 7(5):551-5. doi:10.4161/psb.19838.

Schröder, F., Lisso, J., Müssig, C. (2012). Expression pattern and putative function of EXL1 and homologous genes in Arabidopsis. Plant Signaling Behavior, 7(1), 22-27. doi:10.4161/psb.7.1.18369.

Lisso, J., Schröder, F., Fisahn, J., Müssig, C. (2011). NFX1-LIKE2 (NFXL2) Suppresses Abscisic Acid Accumulation and Stomatal Closure in Arabidopsis thaliana. PLoS One, 6(11), e26982. doi:10.1371/journal.pone.0026982.

Schröder, F., Lisso, J., Müssig, C. (2011). EXORDIUM-LIKE1 Promotes Growth during Low Carbon Availability in Arabidopsis. Plant Physiology, 156(3), 1620-1630. doi:10.1104/pp.111.177204.

Müssig, C., Schröder, F., Usadel, B., Lisso, J. (2010). Structure and putative function of NFX1-like proteins in plants. Plant Biology, 12(3), 381-394. doi:10.1111/j.1438-8677.2009.00303.x.

Schröder, F., Lisso, J., Lange, P., Müssig, C. (2009). The extracellular EXO protein mediates cell expansion in Arabidopsis leaves. BMC Plant Biology, 9, 20. doi:10.1186/1471-2229-9-20.

Evrard A, Kumar M, Lecourieux D, Lucks J, von KoskullDöring P, Hirt H. (2013) Regulation of the heat stress response in Arabidopsis by MPK6-targeted phosphorylation of the heat stress factor HsfA2. PeerJ. 2013 Apr 2;1:e59. doi: 10.7717/peerj.59. Print 2013. PubMed PMID: 23638397; PubMed Central PMCID: PMC3628891.

Siddique M, Gernhard S, von KoskullDöring P, Vierling E, Scharf KD. (2008) The plant sHSP superfamily: five new members in Arabidopsis thaliana with unexpected properties. Cell Stress Chaperones. 2008 Summer;13(2):183-97. doi: 10.1007/s12192-008-0032-6. Epub 2008 Mar 28. PubMed PMID: 18369739; PubMed Central PMCID: PMC2673886.

Schramm F, Larkindale J, Kiehlmann E, Ganguli A, Englich G, Vierling E, von KoskullDöring P. (2008) A cascade of transcription factor DREB2A and heat stress transcription factor HsfA3 regulates the heat stress response of Arabidopsis. Plant J. 2008 Jan;53(2):264-74. Epub 2007 Nov 12. PubMed PMID: 17999647.

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Kotak S, Larkindale J, Lee U, von KoskullDöring P, Vierling E, Scharf KD. (2007) Complexity of the heat stress response in plants. Curr Opin Plant Biol. 2007 Jun;10(3):310-6. Epub 2007 May 4. Review. PubMed PMID: 17482504.

Kotak S, Vierling E, Bäumlein H, von KoskullDöring P. (2007) A novel transcriptional cascade regulating expression of heat stress proteins during seed development of Arabidopsis. Plant Cell. 2007 Jan;19(1):182-95. Epub 2007 Jan 12. PubMed PMID: 17220197; PubMed Central PMCID: PMC1820961.

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Kotak S, Port M, Ganguli A, Bicker F, von KoskullDöring P. (2004) Characterization of C-terminal domains of Arabidopsis heat stress transcription factors (Hsfs) and identification of a new signature combination of plant class A Hsfs with AHA and NES motifs essential for activator function and intracellular localization. Plant J. 2004 Jul;39(1):98-112. PubMed PMID: 15200645.

Bharti K, Von KoskullDöring P, Bharti S, Kumar P, Tintschl-Körbitzer A, Treuter E, Nover L. (2004) Tomato heat stress transcription factor HsfB1 represents a novel type of general transcription coactivator with a histone-like motif interacting with the plant CREB binding protein ortholog HAC1. Plant Cell. 2004 Jun;16(6):1521-35. Epub 2004 May 6. PubMed PMID: 15131252; PubMed Central PMCID: PMC490043.

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Fristedt R, Martins NF, Strenkert D, Clarke CA, Suchoszek M, Thiele W, Schöttler MA, Merchant S. (2015) The Thylakoid Membrane Protein CGL 160 Supports CF1 CF0 ATP Synthase Accumulation in Arabidopsis thaliana. PLoS ONE 10 (4): doi:10.1371/ journal.pone.0121658 [linkout]

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Usadel, B., Schwacke, R., Nagel, A., Kersten, B. (2012). GabiPD – The GABI Primary Database integrates plant proteomic data with gene-centric information. Frontiers in Plant Science, 3: 154. doi:10.3389/fpls.2012.00154.

Lohse, M., Bolger, A. M., Nagel, A., Fernie, A. R., Lunn, J. E., Stitt, M., Usadel, B. (2012). RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Research, 40(W1), W622-W627. doi:10.1093/Nar/Gks540.

Nagel, A., Lohse, M., Bolger, A., Bolger, A. M., Stitt, M., Usadel, B. (2011). Visualizing large, high-throughput datasets based on the cognitive representation of biological pathways. Human Vision and Electronic Imaging Xvi, 7865, 78650h. doi:10.1117/12.881998.

Lohse, M., Nunes-Nesi, A., Krueger, P., Nagel, A., Hannemann, J., Giorgi, F. M., Childs, L., Osorio, S., Walther, D., Selbig, J., Sreenivasulu, N., Stitt, M., Fernie, A. R., Usadel, B. (2010). Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis. Plant Physiology, 153(2), 642-651. doi:10.1104/pp.109.152553.

Durek, P., Schmidt, R., Heazlewood, J. L., Jones, A., MacLean, D., Nagel, A., Kersten, B., Schulze, W. X. (2010). PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Research, 38(Database issue), D828-D834. doi:10.1093/nar/gkp810.

Usadel, B., Poree, F., Nagel, A., Lohse, M., Czedik-Eysenberg, A., Stitt, M. (2009). A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell and Environment, 32(9), 1211-1229. doi:10.1111/j.1365-3040.2009.01978.x.

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Kersten, B., Nagel, A., Riano-Pachon, D., Neigenfind, J., Weber, E., Wagner, R., Diehl, S. (2008). Die GABI-Primaerdatenbank GabiPD – Komplexe Integration von GABI-Daten aus Modell- und Nutzpflanzen. GenomXpress, 1, 17-19.

Lohse, M., Krueger, P., Hannemann, J., Nagel, A., Stitt, M., Walther, D., Usadel, B. (2008). Robin – Microarray Experimentanalyse leicht gemacht. GenomXPress: Informationen aus der Deutschen Genomforschung, 3, 16-17.

Usadel, B., Nagel, A., Steinhauser, D., Gibon, Y., Blaesing, O. E., Redestig, H., Sreenivasulu, N., Krall, L., Hannah, M. A., Poree, F., Fernie, A. R., Stitt, M. (2006). PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics, 7, 535. doi:10.1186/1471-2105-7-535.

Usadel, B., Nagel, A., Thimm, O., Redestig, H., Bläsing, O. E., Palacios-Rojas, N., Selbig, J., Hannemann, J., Piques, M. C., Steinhauser, D., Scheible, W.-R., Gibon, Y., Morcuende, R., Weicht, D., Meyer, S., Stitt, M. (2005). Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of coresponding genes, and comparison with known responses. Plant Physiology, 138(3), 1195-1204. doi:10.1104/pp.105.060459.

Thimm, O., Blaesing, O., Gibon, Y., Nagel, A., Meyer, S., Krueger, P., Selbig, J., Mueller, L. A., Rhee, S. Y., Stitt, M. (2004). MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant Journal, 37(6), 914-939. doi:10.1111/j.1365-313X.2004.02016.x.

McFarlane, H. E., Doering, A., (2014). The Cell Biology of Cellulose Synthesis. Annual Reviews, in press.

Doering, A., Lathe, R., Persson, S. (2012). An Update on Xylan Synthesis. Molecular Plant,(4), 769-771. doi:10.1093/Mp/Sss049.

Hummel J., Strehmel N., Bölling C., Schmidt S., Walther D., Kopka J. (2013) Mass Spectral Search and Analysis Using the Golm Metabolome Database. In: The Handbook of Plant Metabolomics. Wiley-VCH Verlag GmbH Co. KGaA; 2013: 321-343; http://dx.doi.org/10.1002/9783527669882.ch18.

Giavalisco P., Li Y., Matthes A., Eckhardt A., Hubberten H-M., Hesse H., Segu S., Hummel J., Köhl K., Willmitzer L. (2011) Elemental formula annotation of polar and lipophilic metabolites using 13C, 15N and 34S isotope labelling, in combination with high-resolution mass spectrometry. The Plant Journal 2011, 68(2):364-376; http://dx.doi.org/10.1111/j.1365-313X.2011.04682.x.

Hummel J., Segu S., Li Y., Irgang S., Jueppner J., Giavalisco P. (2011) Ultra performance liquid chromatography and high resolution mass spectrometry for the analysis of plant lipids. Frontiers in Plant Science 2011, 2; http://dx.doi.org/10.3389/fpls.2011.00054.

Hoehenwarter W., Larhlimi A., Hummel J., Egelhofer V., Selbig J., van Dongen J.T., Wienkoop S. Weckwerth W. (2011) MAPA Distinguishes Genotype-Specific Variability of Highly Similar Regulatory Protein Isoforms in Potato Tuber,Journal of Proteome Research; http://dx.doi.org/10.1021/pr101109a.

Steinfath M., Strehmel N., Peters R., Schauer N., Groth D.,Hummel J., Steup M., Selbig J., Kopka J., Geigenberger P. van Dongen J.T. (2010) Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach, Plant Biotechnology Journal; http://dx.doi.org/10.1111/j.1467-7652.2010.00516.x.

Cuadros-Inostroza A., Giavalisco P., Hummel J., Eckardt A., Willmitzer L. Pena-Cortes H. (2010) Discrimination of Wine Attributes by Metabolome Analysis, Analytical Chemistry; http://dx.doi.org/10.1021/ac902678t.

Hummel J., Strehmel N., Selbig J., Walther D. Kopka J. (2010) Decision tree supported substructure prediction of metabolites from GC-MS profiles, Metabolomics, 6, 322-333; http://dx.doi.org/10.1007/s11306-010-0198-7.

Giavalisco P., Koehl K., Hummel J., Seiwert B. Willmitzer L. (2009) 13C Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research, Analytical Chemistry, 81, 6546-6551; http://dx.doi.org/10.1021/ac900979e.

Kempa S., Hummel J., Strehmel N., Pietzke M. Schwemmer T., Kopka J., Wienkoop S. (2009) An automated GCxGC-TOF-MS protocol for batch-wise extraction and alignment of mass isotopomer matrixes from differential 13C-labelling experiments: a case study for photoautotrophic-mixotrophic grown Chlamydomonas reinhardtii cells. JMB 49(1):82-91; http://dx.doi.org/10.1002/jobm.200800337.

Giavalisco P., Hummel J., Lisec J., Inostroza A. C., Catchpole G., Willmitzer L. (2008) High-Resolution Direct Infusion-Based Mass Spectrometry in Combination with Whole 13C Metabolome Isotope Labeling Allowing Unambiguous Assignment of Chemical Sum Formulas. Analytical Chemistry, 2008, 80 (24), pp 9417–9425; http://dx.doi.org/10.1021/ac8014627.

Hoehenwarter W., van Dongen J. T., Wienkoop S., Steinfath M., Hummel J., Erban A., Sulpice R., Regierer B., Kopka J., Geigenberger P., Weckwerth W. (2008) A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment (p 4214-4225) Proteomics, Wiley-VCH; http://dx.doi.org/10.1002/pmic.200701047.

Strehmel N., Hummel J., Erban A., Strassburg K., Kopka J. (2008) Retention Index Thresholds for Compound Matching in GC-MS Metabolite Profiling. Journal of Chromatography B, 871, 182-190; http://dx.doi.org/10.1016/j.jchromb.2008.04.042.

Hummel J., Selbig J., Walther D., Kopka J. (2007) The Golm Metabolome Database: a database for GC-MS based metabolite profiling. In: Hohmann, S. (ed) Topics in Current Genetics: Nielsen, J., Jewett, M. (eds) Metabolomics. Springer-Verlag, Berlin Heidelberg New York; http://dx.doi.org/10.1007/4735_2007_0229.

Heazlewood J., Durek P., Hummel J., Selbig J., Weckwerth W., Walther D., Schulze W. (2007) PhosPhAt: A database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Research 2007; http://dx.doi.org/10.1093/nar/gkm812.

Hummel J., Niemann M., Wienkoop S., Schulze W., Steinhaeuser D., Selbig J., Walther D., Weckwerth W. (2007). ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites. BMC Bioinformatics 2007, 8:216; http://dx.doi.org/10.1186/1471-2105-8-216.

Hummel J., Keshvari N., Weckwerth W., Selbig J. (2005). Species-specific analysis of protein sequence motifs using mutual information. BMC Bioinformatics 2005, 6:164; http://dx.doi.org/10.1186/1471-2105-6-164.

Stech, M., Hust, M., Schulze, C., Dübel, S., Kubick, S., (2014). Cell-free eukaryotic systems for the production, engineering, and modification of scFv antibody fragments. Eng. Life Sci. 14, 387–398.

Stech, M., Quast, R.B., Sachse, R., Schulze, C., Wüstenhagen, D.A., Kubick, S., (2014). A Continuous-Exchange Cell-Free Protein Synthesis System Based on Extracts from Cultured Insect Cells. PLoS ONE 9, e96635.

Bendix, I., Schulze, C., Haefen, C. von, Gellhaus, A., Endesfelder, S., Heumann, R., Felderhoff-Mueser, U., Sifringer, M., (2012). Erythropoietin modulates autophagy signaling in the developing rat brain in an in vivo model of oxygen-toxicity. Int J Mol Sci 13, 12939–12951.

Kahlau S, Aspinall S, Gray JC, Bock R. (2006) Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J Mol Evol. 2006 Aug; 63(2):194-207.

Karcher D, Kahlau S, Bock R. (2008). Faithful editing of a tomato-specific mRNA editing site in transgenic tobacco chloroplasts. RNA. 2008 Feb; 14(2):217-24.

Kahlau S, Bock R. (2008). Plastid transcriptomics and translatomics of tomato fruit development and chloroplast-to-chromoplast differentiation: chromoplast gene expression largely serves the production of a single protein. Plant Cell. 2008 Apr; 20(4):8 56-74.

Valkov VT, Scotti N, Kahlau S, Maclean D, Grillo S, Gray JC, Bock R, Cardi T. (2009). Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control. Plant Physiol. 2009 Aug; 150(4):2030-44.

Ahlert D, Stegemann S, Kahlau S, Ruf S, Bock R. (2009). Insensitivity of chloroplast gene expression to DNA methylation. Mol Genet Genomics. 2009 Jul; 282(1):17-24.

Chateigner-Boutin AL, des Francs-Small CC, Delannoy E, Kahlau S, Tanz SK, de Longevialle AF, Fujii S, Small I. (2011). OTP70 is a pentatricopeptide repeat protein of the E subgroup involved in splicing of the plastid transcript rpoC1. Plant J. 2011 Feb; 65(4):532-42.

Cardi T, Giegé P, Kahlau S, Scotti N. (2012). Expression profiling of organellar genes. Advances in Photosynthesis and Respiration. 2012 35:323-355 (review)

Baerenfaller K, Massonnet C, Walsh S, Baginsky S, Bühlmann P, Hennig L, Hirsch-Hoffmann M, Howell KA, Kahlau S, Radziejwoski A, Russenberger D, Rutishauser D, Small I, Stekhoven D, Sulpice R, Svozil J, Wuyts N, Stitt M, Hilson P, Granier C, Gruissem W. (2012). Systems-based analysis of Arabidopsis leaf growth reveals adaptation to water deficit. Mol Syst Biol. 2012; 8:606

Albus CA, Salinas A, Czarnecki O, Kahlau S, Rothbart M, Thiele W, Lein W, Bock R, Grimm B, Schöttler MA. (2012). LCAA, a novel factor required for magnesium protoporphyrin monomethylester cyclase accumulation and feedback control of aminolevulinic acid biosynthesis in tobacco. Plant Physiol. 2012; 160(4):1923-39.

Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Sherwood CC, Hof PR, Ely JJ, Steinhauser D, Willmitzer L, Giavalisco P, Khaitovich P (2015). Large-scale lipidome analysis of human, chimpanzee, macaque and mouse tissues reveals the unique features of human brain evolution. Neuron 85:695-702.

Meissner S*, Steinhauser D*, Dittmann E (2015). Metabolomic analysis indicates a pivotal role of the hepatotoxin microcystin towards high light adaptation of the bloom-forming Microcystis aeruginosa PCC7806. Environ Microbiol 17: 1497-509. *co-first author

Bozek K, Wei Y, Yan Z, Liu X, Xiong J, Sugimoto M, Tomita M, Pääbo S, Pieszek R, Sherwood CC, Hof PR, Ely JJ, Steinhauser D, Willmitzer L, Bangsbo J, Hansson O, Call J, Giavalisco P, Khaitovich P (2014). Exceptional Evolutionary Divergence of Human Muscle and Brain Metabolomes Parallels Human Cognitive and Physical Uniqueness. PLoS Biol 12(5): e1001871.

Krueger S, Steinhauser D, Lisec J, Giavalisco P (2014). Analysis of Subcellular Metabolite Distributions within Arabidopsis thaliana leaf tissue: A primer for subcellular Metabolomics. Methods Mol Biol 1062:575-96.

Araújo WL, Trofimova L, Graf A, Steinhauser D, Krall L, Fernie AR, Bunik VI (2013). On the role of the mitochondrial 2-oxoglutarate dehydrogenase complex in the amino acid metabolism. Amino Acids 44(2):683-700.

Caldana C, Fernie AR, Willmitzer L, Steinhauser D (2012). Unraveling retrograde signaling pathways: finding candidate signaling molecules via metabolomics and systems biology driven approaches. Front Plant Sci 3:267.

Steinhauser D, Fernie AR, Araújo WL (2012). Unusual cyanobacterial TCA cycles: not broken just different. Trends Plant Sci 17(9):503-9.

Krueger S, Steinhauser D, Willmitzer L, Giavalisco P (2012). High Resolution Plant Metabolomics: From metabolic features to compounds and from whole-cell-analysis to sub-cellular metabolic distributions. Plant J 70(1):39-50.

Tohge T, Ramos MS, Nunes-Nesi A, Mutwil M, Giavalisco P, Steinhauser D, Schellenberg M, Willmitzer L, Persson S, Martinoia E, Fernie AR (2011). Towards the storage metabolome: profiling the barley vacuole. Plant Physiol 157(3):1469-82.

Klie S*, Krueger S*, Krall L, Giavalisco P, Flügge UI, Willmitzer L, Steinhauser D* (2011). Analysis of the compartmentalized metabolome – a validation of the non-aqueous fractionation technique. Front Plant Sci 2:55. *co-first author

Steinhauser MC, Steinhauser D, Gibon Y, Bolger M, Arrivault S, Usadel B, Zamir D, Fernie AR, Stitt M (2011). Identification of Enzyme Activity Quantitative Trait Loci in a Solanum lycopersicum x Solanum pennellii introgression line population. Plant Physiol 157(3):998-1014.

Caldana C, Degenkolbe T, Cuadros-Inostroza A, Klie S, Sulpice R, Leisse A, Steinhauser D, Fernie AR, Willmitzer L, Hannah MA (2011). High-density kinetic analysis of the metabolomic and transcriptomic response of Arabidopsis to eight environmental conditions. Plant J 67(5):869-84.

Krueger S*, Giavalisco P*, Krall L, Steinhauser MC, Büssis D, Usadel B, Flügge UI, Fernie AR, Willmitzer L, Steinhauser D* (2011) A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome. PLoS One 6(3):e17806. *co-first author

Huege J, Krall L, Steinhauser MC, Giavalisco P, Rippka R, Tandeau de Marsac N, Steinhauser D (2011). Sample amount alternatives for data adjustment in comparative cyanobacterial metabolomics. Anal Bioanal Chem 399(10):3503-17.

Jozefczuk S, Klie S, Catchpole G, Szymanski J, Cuadros-Inostroza A, Steinhauser D, Selbig J, Willmitzer L (2010). Metabolomic and transcriptomic stress response of Escherichia coli. Mol Syst Biol 6:364.

Steinhauser MC, Steinhauser D, Koehl K, Carrari F, Gibon Y, Fernie AR, Stitt M (2010). Enzyme Activity Profiles during Fruit Development in Tomato Cultivars and Solanum pennellii. Plant Physiol 153(1):80-98.

Hannah MA*, Caldana C*, Steinhauser D*, Balbo I, Fernie AR, Willmitzer L. (2010). Combined transcript and metabolite profiling of Arabidopsis thaliana grown under widely variant growth conditions facilitates the identification of novel metabolite mediated regulation of gene expression. Plant Physiol 152(4):2120-9. *co-first author

Krall L*, Huege J*, Catchpole G, Steinhauser D*, Willmitzer L (2009). Assessment of sampling strategies for gas chromatography-mass spectrometry (GC-MS) based metabolomics of cyanobacteria. J Chromatogr B 877(27):2952-60. *co-first author

Krueger S, Niehl A, Lopez-Martin CM, Steinhauser D, Donath A, Hildebrandt T, Romero LC, Gotor C, Hoefgen R, Hesse H (2009). Analysis of Cytosolic and Plastidic Serine Acetyltransferase Mutants and Subcellular Metabolite Distributions Suggests Interplay of the Cellular Compartments for Cysteine Biosynthesis in Arabidopsis. Plant Cell Environ 32(4):349-67.

Usadel B, Obayashi T, Mutwil M, Giorgi FM, Bassel GW, Tanimoto M, Chow A, Steinhauser D, Persson S, Provart NJ (2009). Co-expression tools for plant biology: opportunities for hypothesis generation and caveats. Plant Cell Environ 32(12):1633-51.

Falkenberg B, Witt I, Zanor MI, Steinhauser D, Mueller-Roeber B, Hesse H, Hoefgen R (2008). Transcription factors relevant to auxin signalling coordinate broad-spectrum metabolic shifts including sulphur metabolism. J Exp Bot 59(10):2831-46.

Ogata Y, Sakurai N, Provart NJ, Steinhauser D, Krall L (2008). Bioinformatics Tools to Discover Co-Expressed Genes in Plants: Concepts and Protocols. In The Handbook of Plant Functional Genomics, G. Kahl and K. Meksem (eds.), Wiley. pp. 307 – 335

Steinhauser D, Krall L, Müssig C, Büssis D, Usadel B (2008). Correlation Networks. In Biological Network Analysis, B.H. Junker and F. Schreiber (eds.), Book Series on Bioinformatics (Series Editors: Y. Pan and A.Y. Zomaya), Wiley. pp. 305 – 334.

Dolch D*, Batsaikhan N*, Thiele K*, Burger F, Scheffler I, Kiefer A, Mayer F, Samjaa R, Stubbe A, Stubbe M, Krall L, Steinhauser D* (2007). Contributions to the Chiroptera of Mongolia with first evidences on species communities and ecological niches. Exploration into the Biological Resources of Mongolia (Martin-Luther-University Halle-Wittenberg, Halle) 10:407-58. *co-first author

Hummel J, Niemann M, Wienkoop S, Schulze W, Steinhauser D, Selbig J, Walther D, Weckwerth W (2007). ProMEX: a mass spectral reference database for proteins and protein phosphorylation sites. BMC Bioinformatics 8:216.

Steinhauser D, Kopka J (2007) Methods, applications and concepts of metabolite profiling: primary metabolism. In Plant Systems Biology, S. Baginsky, A. R. Fernie (eds), Basel, Verlag Birkhäuser, pp. 171-194.

Usadel B, Nagel A, Steinhauser D, Gibon Y, Bläsing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M (2006) PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. BMC Bioinformatics 7:535.

Junker BH, Wuttke R, Nunes-Nesi A, Steinhauser D, Schauer N, Büssis D, Willmitzer L, Fernie AR (2006) Enhancing vacuolar sucrose cleavage within the developing potato tuber has only minor effects on metabolism. Plant Cell Physiol 47(2):277-89.

Steinhauser D, Usadel B (2006) CSB.DB – A Comprehensive Systems-Biology Database: Overview and Transcriptional Co-Response (Correlation) Analyses. Plant Genomics and Bioinformatics Expression Micro Arrays and Beyond – a course book, J. Freitag, (ed.), MPI-MPP 2006, Potsdam-Golm, pp. 190-92.

Rautengarten C*, Steinhauser D*, Büssis D, Stintzi A, Schaller A, Kopka J, Altmann T (2005) Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family. PLoS Comp Biol 1(4):e40. *co-first author

Lisso J*, Steinhauser D*, Altmann T, Kopka J, Müssig C (2005) Identification of brassinosteroid-related genes by means of transcript co-response analyses. Nucleic Acids Res 33(8):2685-96. *co-first author

Usadel B, Nagel A, Thimm O, Redestig H, Blaesing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S, Stitt M (2005) Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Corresponding Genes, and Comparison with Known Responses. Plant Physiol 138(3):1195-204.

Kopka J, Schauer N, Krueger S, Birkemeyer C, Usadel B, Bergmüller E, Doermann P, Gibon Y, Stitt M, Willmitzer L, Fernie AR, Steinhauser D (2005) GMD@CSB.DB: The Golm Metabolome Database. Bioinformatics 21(8):1635-38.

Schauer N, Steinhauser D, Strelkov S, Schomburg D, Allison G, Moritz T, Lundgren K, Roessner-Tunali U, Forbes MG, Willmitzer L, Fernie AR, Kopka J (2005) GC–MS libraries for the rapid identification of metabolites in complex biological samples. FEBS Lett 579(6):1332-37.

Usadel B, Kuschinsky AM, Steinhauser D, Pauly M (2005) Transcriptional co-response analysis as a tool to identify new components of the wall biosynthetic machinery. Plant Biosystems 139(1):69-73.

Desbrosses G, Steinhauser D, Kopka J, Udvardi MK (2005) Lotus metabolome analysis using GC-MS. In Lotus japonicus handbook, A.J.Márquez; J.Stougaard; M.Udvardi; M.Parniske; H.Spaink; G.Saalbach; J.Webb; M.Chiurazzi (Eds.) (Dordrecht: Kluwer), pp. 165-74.

Steinhauser D*, Usadel B*, Luedemann A, Thimm O, Kopka J (2004) CSB.DB – a Comprehensive Systems-Biology Database. Bioinformatics 20(18):3647-51. *co-first author

Steinhauser D, Junker BH, Luedemann A, Selbig J, Kopka J (2004) Hypothesis-driven approach to predict transcriptional units from gene expression data. Bioinformatics 20(12):1928-39.

Jakobi AJ*, Passon DM.*, Knoops K, Stellato F, Liang M, White TA, Seine T, Messerschmidt M, Chapman, HN. Wilmanns M. (2016). In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells. IUCrJ 3, doi:10.1107/S2052252515022927. *Equal contribution.

Knott GJ, Lee M, Passon DM, Fox AH, Bond CS. (2015). Caenorhabditis elegans NONO-1: Insights into DBHS protein structure, architecture, and function. Protein Sci. Dec;24(12):2033-43. doi: 10.1002/pro.2816.

Hagen S, Drepper F, Fischer S, Fodor K, Passon D, Platta HW, Zenn M, Schliebs W, Girzalsky W, Wilmanns M, Warscheid B, Erdmann R. (2015). Structural insights into cargo recognition by the yeast PTS1 receptor. J Biol Chem. Oct 30;290(44):26610-26. doi: 10.1074/jbc.M115.657973

Emmanouilidis L, Gopalswamy M, Passon DM, Wilmanns M, Sattler M. (2015). Structural biology of the import pathways of peroxisomal matrix proteins. Biochim Biophys Acta. Oct 9. pii: S0167-4889(15)00346-8. doi: 10.1016/j.bbamcr.2015.09.034.

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