Schudoma, C.; Larhlimi, A.; Walther, D.: The influence of the local sequence environment on RNA loop structures. Rna-a Publication of the Rna Society 17 (7), pp. 1247 - 1257 (2011)

Childs, L. H.; Witucka-Wall, H.; Gunther, T.; Sulpice, R.; Korff, M. V.; Stitt, M.; Walther, D.; Schmid, K. J.; Altmann, T.: Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana. BMC Genomics 11, p. 188 (2010)

Hummel, J.; Strehmel, N.; Selbig, J.; Walther, D.; Kopka, J.: Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics 6 (2), pp. 322 - 333 (2010)

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

Riano-Pachon, D. M.; Kleessen, S.; Neigenfind; Durek, P.; Weber, E.; Engelsberger, W. R.; Walther, D.; Selbig, J.; Schulze, W. X.; Kersten, B.: Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics 11, p. 411 (2010)

Schudoma, C.; May, P.; Nikiforova, V.; Walther, D.: Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Research 38 (3), pp. 970 - 980 (2010)

Schudoma, C.; May, P.; Walther, D.: Modeling RNA loops using sequence homology and geometric constraints. Bioinformatics 26 (13), pp. 1671 - 1672 (2010)

Strassburg, K.; Walther, D.; Takahashi, H.; Kanaya, S.; Kopka, J.: Dynamic Transcriptional and Metabolic Responses in Yeast Adapting to Temperature Stress. Omics-a Journal of Integrative Biology 14 (3), pp. 249 - 259 (2010)

Sun, X.; Zou, Y.; Nikiforova, V.; Kurths, J.; Walther, D.: The complexity of gene expression dynamics revealed by permutation entropy. BMC Bioinformatics 11, p. 607 (2010)

Walther, D.; Strassburg, K.; Durek, P.; Kopka, J.: Metabolic Pathway Relationships Revealed by an Integrative Analysis of the Transcriptional and Metabolic Temperature Stress-Response Dynamics in Yeast. OMICS: A Journal of Integrative Biology 14 (3), pp. 261 - 274 (2010)

Childs, L.; Nikoloski, Z.; May, P.; Walther, D.: Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Research 37 (9), p. e66 (2009)

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

Durek, P.; Schudoma, C.; Weckwerth, W.; Selbig, J.; Walther, D.: Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. BMC Bioinformatics 10, p. 117 (2009)

Kersten, B.; Agrawal, G. K.; Durek, P.; Neigenfind, J.; Schulze, W. X.; Walther, D.; Rakwal, R.: Plant phosphoproteomics: An update. Proteomics 9 (4), pp. 964 - 988 (2009)

Kierszniowska, S.; Walther, D.; Schulze, W. X.: Ratio-dependent significance thresholds in reciprocal N-15-labeling experiments as a robust tool in detection of candidate proteins responding to biological treatment. Proteomics 9 (7), pp. 1916 - 1924 (2009)

May, P.; Christian, J. O.; Kempa, S.; Walther, D.: ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 10, p. 209 (2009)

Pant, B. D.; Musialak-Lange, M.; Nuc, P.; May, P.; Buhtz, A.; Kehr, J.; Walther, D.; Scheible, W.-R.: Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing. Plant Physiology 150 (3), pp. 1541 - 1555 (2009)

Durek, P.; Walther, D.: The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. BMC Systems Biology 2, p. 100 (2008)

Fait, A.; Fromm, H.; Walther, D.; Galili, G.; Fernie, A. R.: Highway or byway: the metabolic role of the GABA shunt in plants. Trends in Plant Science 13 (1), pp. 14 - 19 (2008)

Heazlewood, J. L.; Durek, P.; Hummel, J.; Selbig, J.; Weckwerth, W.; Walther, D.; Schulze, W. X.: PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Research 36 (Database issue), pp. D1015 - D1021 (2008)

Koehl, K. I.; Basler, G.; Lüdemann, A.; Selbig, J.; Walther, D.: A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research. Plant Methods 4, p. 11 (2008)

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

May, P.; Wienkoop, S.; Kempa, S.; Usadel, B.; Christian, N.; Rupprecht, J.; Weiss, J.; Recuenco-Munoz, L.; Ebenhoeh, O.; Weckwerth, W. et al.; Walther, D.: Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics 179 (1), pp. 157 - 166 (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)

Deng, M. C.; Eisen, H. J.; Mehra, M. R.; Billingham, M.; Marboe, C. C.; Berry, G.; Kobashigawa, J.; Johnson, F. L.; Starling, R. C.; Murali, S. et al.; Pauly, D. F.; Baron, H.; Wohlgemuth, J. G.; Woodward, R. N.; Klingler, T. M.; Walther, D.; Lal, P. G.; Rosenberg, S.; Hunt, S.: Noninvasive discrimination of rejection in cardiac allograft recipients using gene expression profiling. American Journal of Transplantation 6 (1), pp. 150 - 160 (2006)

Mehra, M. R.; Uber, P. A.; Walther, D.; Vesely, M.; Wohlgemuth, J. G.; Prentice, J.; Tayama, D.; Billingham, M.: Gene expression profiles and B-type natriuretic peptide elevation in heart transplantation more than a hemodynamic marker. Circulation 114 (1 Suppl), pp. I21 - I26 (2006)

Jin, P.; Walther, D.; Zhang, J.; Rowe-Teeter, C.; Fu, G. K.: Serine 171, a conserved residue in the gamma-aminobutyric acid type A (GABA(A)) receptor gamma 2 subunit, mediates subunit interaction and cell surface localization. Journal of Biological Chemistry 279 (14), pp. 14179 - 14183 (2004)

Gabdoulline, R. R.; Wade, R. C.; Walther, D.: MolSurfer: a macromolecular interface navigator. Nucleic Acids Research 31 (13), pp. 3349 - 3351 (2003)

Meyer, A. S.; Gillespie, J. R.; Walther, D.; Millet, I. S.; Doniach, S.; Frydman, J.: Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis. Cell 113 (3), pp. 369 - 381 (2003)

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)

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)

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)

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)