Strehmel, N.; Hummel, J.; Erban, A.; Strassburg, K.; Kopka, J.: Retention index thresholds for compound matching in GC-MS metabolite profiling. Journal of Chromatography B-Analytical Technologies in the Biomedical and Life Sciences 871 (2), pp. 182 - 190 (2008)

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

Stacklies, W.; Redestig, H.; Scholz, M.; Walther, D.; Selbig, J.: pcaMethods - a bioconductor package providing PCA methods for incomplete data. Bioinformatics 23 (9), pp. 1164 - 1167 (2007)

Walther, D.; Brunnemann, R.; Selbig, J.: The Regulatory Code for Transcriptional Response Diversity and Its Relation to Genome Structural Properties in A. thaliana. PLoS Genetics 3 (2), p. e11 (2007)

Hummel, J.; Keshvari, N.; Weckwerth, W.; Selbig, J.: Species-specific analysis of protein sequence motifs using mutual information. BMC Bioinformatics 6, p. 164 (2005)

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

Walther, D.: Specifics of Metabolite-Protein Interactions and Their Computational Analysis and Prediction. In: Methods in Molecular Biology (Ed. Walker, J. M.) (2023)

Kleessen, S.; Nikoloski, Z.: Computational Approaches to Dissect and Understand Mechanisms of Adaptation. In: Molecular Mechanisms in Plant Adaptation, pp. 193 - 215. Wiley-Blackwell, Malden (2015)

Groth, D.; Hartmann, S.; Klie, S.; Selbig, J.: Principal components analysis. In: Methods in Molecular Biology, Vol. 930, pp. 527 - 547 (2013)

Walther, D.: The combinatorics of cis-regulatory elements: from cooperatively acting motifs to gene regulatory networks. In: The analysis of cis-elements: Current developments, knowledge and applications to gene networking, pp. 176 - 188 (Eds. Berendzen, K.; Wanke, D.). Bentham Books, AG Bussum (2013)

Hummel, J.; Strehmel, N.; Boelling, C.; Schmidt, S.; Walther, D.; Kopka, J.: Mass spectral search and analysis using the Golm Metabolome Database. In: The Handbook of Plant Metabolomics, pp. 321 - 343 (Ed. Weckwerth, W.) (2012)

Schudoma, C.; Steinfath, M.; Sprenger, H.; van Dongen, J.; Hincha, D. K.; Zuther, E.; Geigenberger, P.; Kopka, J.; Koehl, K. I.; Walther, D.: Conducting molecular biomarker discovery studies in plants. In: High Throughput Phenotyping in Plants, 10 (Ed. Normanly, J.). Humana Press Inc., Totowa, NJ, USA (2012)

Kopka, J.; Walther, D.; Allwood, J. W.; Goodacre, R.: Progress in chemometrics and biostatistics for plant applications: Or a good red wine is a bad white wine. In: The biology of plant metabolomics, 10, 2011/05/03 Ed., pp. 317 - 342 (Ed. Hall, R. D.). Blackwell-Wiley, London, UK (2011)

May, P.; Christian, N.; Ebenhoeh, O.; Weckwerth, W.; Walther, D.: Integration of proteomic and metabolomic profiling as well as metabolic modeling for the functional analysis of metabolic networks. In: Bioinformatics for Comparative Proteomics, 21, 2010/12/01 Ed., pp. 341 - 363 (Eds. Wu, C. H.; Chen, C.). Humana Press Inc., Totowa, NJ, USA (2011)

Kempa, S.; Walther, D.; Ebenhoeh, O.; Weckwerth, W.: Metabolic Engineering. In: Molecular Biology and Biotechnology, pp. 194 - 217 (Eds. Walker, J.; Rapley, R.). Royal Society of Chemistry (2009)

Kersten, B.; Feilner, T.: Protein microarrays for phosphorylation studies. In: The Protein Protocols Handbook, Vol. 162, pp. 1567 - 1578 (Ed. Walker, J. M.). Humana Press Inc., Totowa, NJ, USA (2009)

Kersten, B.: Time to search for kinase substrates. In: Plant Proteomics: Technologies, Strategies, and Applications, 33, pp. 485 - 498 (Eds. Rakwal, R.; Agrawal, G.K.). Wiley-Interscience, Hoboken, NY, USA (2008)

Hummel, J.; Selbig, J.; Walther, D.; Kopka, J.: The Golm Metabolome Database: a database for GC-MS based metabolite profiling. In: Metabolomics: A Powerful Tool in Systems Biology, pp. 75 - 95 (Eds. Nielsen, J.; Jewett, M.). Springer-Verlag, Berlin, Heidelberg, New York (2007)

Kersten, B.; Wanker, E.E.: Klinische Proteomik. In: Grundlagen der Molekularen Medizin, 3.1, p. 397 (Eds. Ganten, D.; Ruckpaul, K.). Springer-Verlag, Berlin, Heidelberg, New York (2007)

Steinfath, M.; Repsilber, D.; Scholz, M.; Walther, D.; Selbig, J.: Integrated data analysis for genome-wide research. In: Plant Systems Biology, pp. 309 - 329 (Eds. Baginski, S.; Fernie, A.). Birkhäuser Verlag, Basel, Boston, Berlin (2007)

Kloska, S.; Krueger, P.; Selbig, J.: Lotus japonicus expression database. In: Lotus japonicus handbook, pp. 149 - 154 (Ed. Marques, A. J.). Springer-Verlag, Dordrecht, NED (2005)

Skeffington, A. W.; Fischer, A.; Gorka, M.; Graf, A.; Scheffel, A.: Identifying Proteins important for Coccolith formation in Emiliana huxleyi. In Phycologia, 56 (4 - Supplement), pp. 173 - 174. International Phycological Society, Odense (2017)

Meyer, R. C.; Lisec, J.; Sulpice, R.; Steinfath, M.; Gaertner, T.; Becher, M.; Witucka-Wall, H.; von Korff, M.; Gunther, T.; Childs, L. et al.; Scharr, H.; Walter, A.; Torjek, O.; Fiehn, O.; Schurr, U.; Schmid, K.; Walther, D.; Gibon, Y.; Selbig, J.; Stitt, M.; Willmitzer, L.; Altmann, T.: Analysis of Arabidopsis natural variation in biomass accumulation and metabolism. In New Biotechnology, 25, p. S307 - S307. (2009)

Carroll, A. J.; Salek, R. M.; Arita, M.; Kopka, J.; Walther, D.: Metabolome Informatics and Statistics: Current State and Emerging Trends. Frontiers in Bioengineering and Biotechnology 4, p. 63 - 63 (2016)

Bringmann, M.; Landrein, B.; Schudoma, C.; Hamant, O.; Hauser, M. T.; Persson, S.: Cracking the elusive alignment hypothesis: the microtubule-cellulose synthase nexus unraveled. (2012)

Kryvych, S.; Kleessen, S.; Ebert, B.; Kersten, B.; Fisahn, J.: Proteomics - The key to understanding systems biology of Arabidopsis trichomes. (2011)

Schudoma, C.: It's a loop world – single strands in RNA as structural and functional elements. (2011)

Kersten, B.; Agrawal, G. K.; Durek, P.; Neigenfind, J.; Schulze, W. X.; Walther, D.; Rakwal, R.: Plant phosphoproteomics: An update. (2009)

May, P.; Christian, J. O.; Kempa, S.; Walther, D.: ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. (2009)

Fait, A.; Fromm, H.; Walther, D.; Galili, G.; Fernie, A. R.: Highway or byway: the metabolic role of the GABA shunt in plants. (2008)

Steinfath, M.; Groth, D.; Lisec, J.; Selbig, J.: Metabolite profile analysis: from raw data to regression and classification. (2008)

Usadel, B.; Nagel, A.; Steinhauser, D.; Gibon, Y.; Blaesing, O. E.; Redestig, H.; Sreenivasulu, N.; Krall, L.; Hannah, M. A.; Poree, F. et al.; Fernie, A. R.; Stitt, M.: PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. (2006)

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