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2016
  • The orientation of transcription factor binding site motifs in gene promoter regions: does it matter? BMC Genomics
  • Spatial proximity statistics suggest a regulatory role of protein phosphorylation on compound binding. Proteins.
  • Limited phosphate: mobile RNAs convey the message. Nature Plants
  • The identification of cis-regulatory sequence motifs in gene promoters based on SNP information. Methods in Mol Biol


2015
  • Endogenous Arabidopsis messenger RNAs transported to distant tissues. Nature Plants
  • The roles of post-translational modifications in the context of protein interaction networks. PLoS Computatational Biology
  • Assessment of drought tolerance and its potential yield penalty in potato. Functional Plant Biol.
  • Computational phosphorylation network reconstruction: methods and resources. Methods in Mol Biol
  • COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics
  • Multiple RNA processing defects and impaired chloroplast function in plants deficient in the organellar protein-only RNase P enzyme. PLoS One
  • Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. Frontiers Mol Biosci
  • Substantial reprogramming of the Eutrema salsugineum (Thellungiella salsuginea) transcriptome in response to UV and silver nitrate challenge. BMC Plant Biol


2014
  • Tabea Mettler, Timo Mühlhaus, Dorothea Hemme, Mark-Aurel Schöttler, Jens Rupprecht, Adam Idoine, Daniel Veyel, Sunil Kumar Pal, Liliya Yaneva-Roder1, Flavia Vischi Winck, Frederik Sommer, Daniel Vosloh, Bettina Seiwert, Alexander Erban, Asdrubal Burgos, Samuel Arvidsson, Stephanie Schönfelder, Anne Arnold, Manuela Günther, Ursula Krause, Marc Lohse, Joachim Kopka, Zoran Nikoloski, Bernd Mueller-Roeber, Lothar Willmitzer, Ralph Bock, Michael Schroda and Mark Stitt (2014) Systems analysis of the response of photosynthesis, metabolism and growth to an increase in irradiance in the photosynthesis model organism Chlamydomonas reinhardtii, Plant Cell (in press)
  • The sucrose–trehalose 6-phosphate (Tre6P) nexus: specificity and mechanisms of sucrose signalling by Tre6P. J Exp Bot
  • Klaas J. van Wijk, Giulia Friso, Dirk Walther, Waltraud X. Schulze (2014) Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs, Plant Cell (in press)
  • Korkuć, P., Schippers, J., Walther, D. (2014) Characterization and identification of cis-regulatory elements in Arabidopsis thaliana based on SNP information. Plant Physiol. pp.113.229716
2013

  • Duan, G., Walther, D., Schulze, W.X. (2013) Reconstruction and analysis of nutrient-induced phosphorylation networks in Arabidopsis thaliana. Front Plant Sci 4, 540
  • Hummel J, Strehmel N, Boelling C, Schmidt S, Walther D, Kopka J (2013) Mass Spectral Search and Analysis Using the Golm Metabolome Database. In: The Handbook of Plant Metabolomics: Metabolite Profiling and Networking, Eds. Weckwerth W, Kahl G
  • Duan G, Christian N, Schwachtje J, Walther D, and Ebenhöh O (2013) The metabolic interplay between plants and phytopathogens. Metabolites (in press)
  • 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 Env DOI: 10.1111/pce.12231
  • Toepel, J., Illmer-Kephalides, M., Jaenicke, S., Straube, J., May, P., Goesmann, A., Kruse O. (2013) New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. Plant Biotechnol 11, 717-733
  • Vischi Winck, F., Arvidsson, S., Riaño-Pachón, D.M., Hempel, S., Koseska, A., Nikoloski, Z., Urbina Gomez, D.A., Rupprecht, J., Mueller-Roeber, B., (2013) Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga Chlamydomonas reinhardtii under carbon deprivation., PLoS One. 8(11):e79909
  • Shao, N., Duan, G.,  Bock, R. (2013) A Mediator of Singlet Oxygen Responses in Chlamydomonas reinhardtii and Arabidopsis Identified by a Luciferase-Based Genetic Screen in Algal Cells. Plant Cell 25: 4209–26

2012

  • Thieme CJ, Schudoma C, May P and Walther D (2012) Give it AGO: the search for miRNA-Argonaute sorting signals in Arabidopsis thaliana indicates a relevance of sequence positions other than the 5′-position alone. Front. Plant Sci. 3:272. doi: 10.3389/fpls.2012.00272
  • Christian J-O, Braginets R, Schulze WX and Walther D (2012) Characterization and prediction of protein phosphorylation hotspots in Arabidopsis thaliana. Front. Plant Sci. 3:207. doi: 10.3389/fpls.2012.00207
  • Billiau K, Sprenger H, Schudoma C, Walther D, Köhl K (2012) Data management pipeline for plant phenotyping. Funct Plant Biol. 39(11) 948-957
  • Bringmann M, Landrein B, Schudoma C, Hamant O, Hauser MT, Persson S (2012) Cracking the elusive alignment hypothesis: the microtubule-cellulose synthase nexus unraveled. Trends in Plant Science 17: 666–674
  • Zhang J, Ruf S, Hasse C, Childs LH, Scharff LB and Bock R (2012) Identification of cis-elements conferring high levels of gene expression in non-green plastids. Plant J 72: 115-128
  • Zuther E, Schulz E, Childs LH and Hincha DK (2012) Clinal variation in the nonacclimated and cold acclimated freezing tolerance of Arabidopsis thaliana accessions. Plant Cell & Environment 35: 1860–1878
  • Draffehn AM, Durek P, Nunes-Nesi A, Stich B, Fernie AR, Gebhardt C (2012) Tapping natural variantion at functional level revelas allele specific molecular characteristics of potato invertase Pain-1. Plant Cell & Environment 35: 2143–2154,
  • Childs L, Lisec J, and Walther D (2012) Matapax: An online high-throughput genome-wide association study pipeline. Plant Phys 158(4):1534-4
  • Walther D (2012) 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. Eds. Berendzen K, Wanke D
  • Schudoma C, Steinfath M, Sprenger H, van Dongen JT, Hincha D, Zuther E, Geigenberger P, Kopka J, Köhl K,Walther D(2012) Conducting biomarker discovery studies in plants. Methods Mol Biol 918: 127-150
2011
  • Giavalisco P., Li Y., Matthes A., Eckhardt A., Hubberten H-M., Hesse H., Segu S., Hummel J., Köhl K., Willmitzer L.: 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.: 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.
  • Toepel J, Albaum SP, Arvidsson S, Goesmann A, La Russa M, Rogge K and Kruse O (2011) Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics 12:579
  • Lenz D, May P, Walther D(2011) Comparative analysis of miRNAs and their targets across four plant species. BMC Res Notes 4:483
  • Hoehenwarter W, Larhlimi A, Hummel J, Egelhofer V, Selbig J, van Dongen JT, Wienkoop S, Weckwerth W. (2011) MAPA distinguishes genotype-specific variability of highly similar regulatory protein isoforms in potato tuber. J Proteome Res 10 (7), pp 2979–2991
  • Devers, E.A., Branscheid, A., May, P., Krajinski, F. (2011) Stars and symbiosis: microRNA- and microRNA*- mediated transcript cleavage involved in arbuscular mycorrhizal symbiossis.Plant Physiology. 156 no. 4 1990-2010
  • Scharff LB, Childs L, Walther D, Bock R (2011) Local absence of secondary structure permits translation of mRNAs that lack ribosome-binding sites. PLoS Genet7(6): e1002155. doi:10.1371/journal.pgen.100215
  • Janssen S, Schudoma C, Steger G, Giegerich R (2011) Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. BMC Bioinformatics 12: 429
  • Schudoma C, Larhlimi A, Walther D (2011) The influence of local sequence environment on RNA loop structures. RNA. 17: 1247-1257
  • Schudoma C (2011) It's a loop world - Single strands in RNA as structural and functional elements. Biomol Concepts 2: 171–181, DOI: 10.1515/BMC.2011.016
  • Hädrich N, Gibon Y, Schudoma C, Altmann T, Lunn JE, Stitt M (2011) Use of TILLING and robotised enzyme assays to generate an allelic series of Arabidopsis thaliana mutants with altered ADP-glucose pyrophosphorylase activity. Plant Phys 12 :1395–1405

 

2010

  • Branscheid, A., Sieh, D., Pant, B. D., May, P., Devers, E. A., Elkrog, A., Schauser, L., Scheible, W. R. and Krajinski, F. (2010) Expression Pattern Suggests a Role of MiR399 in the Regulation of the Cellular Response to Local Pi Increase During Arbuscular Mycorrhizal Symbiosis. Mol. Plant-Microbe Interact. 23, 7, 915-926
  • Childs, L. H., Witucka-Wall, H., Gunther, T., Sulpice, R., Korff, M. V., Stitt, M., Walther, D., Schmid, K. J. and Altmann, T. (2010) Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana.BMC Genomics 11,
  • Cuadros-Inostroza, A., Giavalisco, P., Hummel, J., Eckardt, A., Willmitzer, L. and Pena-Cortes, H. (2010) Discrimination of Wine Attributes by Metabolome Analysis. Anal. Chem. 82, 9, 3573-3580
  • Durek, P., Schmidt, R., Heazlewood, J. L., Jones, A., MacLean, D., Nagel, A., Kersten, B. and Schulze, W. X. (2010) PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update. Nucleic Acids Res. 38, D828-D834
  • Hummel, J., Strehmel, N., Selbig, J., Walther, D. and Kopka, J. (2010) Decision tree supported substructure prediction of metabolites from GC-MS profiles. Metabolomics 6, 2, 322-333
  • 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. and Usadel, B. (2010) Robin: An Intuitive Wizard Application for R-Based Expression Microarray Quality Assessment and Analysis.Plant Physiol. 153, 2, 642-651
  • May, P., Kreuchwig, A., Steinke, T. and Koch, I. (2010) PTGL: a database for secondary structure-based protein topologies. Nucleic Acids Res. 38, D326-D330
  • Riano-Pachon, D. M., Kleessen, S., Neigenfind, J., Durek, P., Weber, E., Engelsberger, W. R., Walther, D., Selbig, J., Schulze, W. X. and Kersten, B. (2010) Proteome-wide survey of phosphorylation patterns affected by nuclear DNA polymorphisms in Arabidopsis thaliana. BMC Genomics 11,
  • Schudoma, C., May, P., Nikiforova, V. and Walther, D. (2010) Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. Nucleic Acids Res. 38, 3, 970-980
  • Schudoma, C., May, P. and Walther, D. (2010) Modeling RNA loops using sequence homology and geometric constraints. Bioinformatics 26, 13, 1671-1672
  • Steinfath, M., Strehmel, N., Peters, R., Schauer, N., Groth, D., Hummel, J., Steup, M., Selbig, J., Kopka, J., Geigenberger, P. and van Dongen, J. T. (2010) Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach. Plant Biotechnol. J. 8, 8, 900-911
  • Strassburg, K., Walther, D., Takahashi, H., Kanaya, S. and Kopka, J. (2010) Dynamic Transcriptional and Metabolic Responses in Yeast Adapting to Temperature Stress. OMICS 14, 3, 249-259
  • Sulpice, R., Trenkamp, S., Steinfath, M., Usadel, B., Gibon, Y., Witucka-Wall, H., Pyl, E. T., Tschoep, H., Steinhauser, M. C., Guenther, M., Hoehne, M., Rohwer, J. M., Altmann, T., Fernie, A. R. and Stitt, M. (2010) Network analysis of enzyme activities and metabolite levels and their relationship to biomass in a large panel of Arabidopsis accessions. Plant Cell 22, 8, 2872-2893
  • Sun, X., Zou, Y., Nikiforova, V., Kurths, J. and Walther, D. (2010) The complexity of gene expression dynamics revealed by permutation entropy.BMC Bioinformatics 11, 607
  • Walther, D., Strassburg, K., Durek, P. and Kopka, J. (2010) Metabolic Pathway Relationships Revealed by an Integrative Analysis of the Transcriptional and Metabolic Temperature Stress-Response Dynamics in Yeast. OMICS 14, 3, 261-274
  • Wienkoop, S., Weiss, J., May, P., Kempa, S., Irgang, S., Recuenco-Munoz, L., Pietzke, M., Schwemmer, T., Rupprecht, J. and Weckwerth, W. (2010) Targeted proteomics for Chlamydomonas reinhardtii combined with rapid subcellular protein fractionation, metabolomics and metabolic flux analyses. Mol. Biosyst. 6, 1018-1031

 

2009

  • Childs, L., Nikoloski, Z., May, P. and Walther, D. (2009) Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Res. 37, 9, e66
  • Christian, N., May, P., Kempa, S., Handorf, T. and Ebenhoeh, O. (2009) An integrative approach towards completing genome-scale metabolic networks. Mol. Biosyst. 5, 12, 1889-1903
  • Degenkolbe, T., Do, P. T., Zuther, E., Repsilber, D., Walther, D., Hincha, D. K. and Koehl, K. I. (2009) Expression profiling of rice cultivars differing in their tolerance to long-term drought stress. Plant Mol. Biol. 69, 1-2, 133-153
  • Durek, P., Schudoma, C., Weckwerth, W., Selbig, J. and Walther, D. (2009) Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. BMC Bioinformatics 10, 117,
  • Giavalisco, P., Koehl, K. I., Hummel, J., Seiwert, B. and Willmitzer, L. (2009) C-13 Isotope-Labeled Metabolomes Allowing for Improved Compound Annotation and Relative Quantification in Liquid Chromatography-Mass Spectrometry-based Metabolomic Research. Anal. Chem. 81, 15, 6546-6551
  • Guenther, S., von Eichborn, J., May, P. and Preissner, R. (2009) JAIL: a structure-based interface library for macromolecules. Nucleic Acids Res.37, 338-341
  • Kempa, S., Hummel, J., Schwemmer, T., Pietzke, M., Strehmel, N., Wienkoop, S., Kopka, J. and Weckwerth, W. (2009) An automated GCxGC-TOF-MS protocol for batch-wise extraction and alignment of mass isotopomer matrixes from differential C-13-labelling experiments: a case study for photoautotrophic-mixotrophic grown Chlamydomonas reinhardtii cells. J. Basic Microbiol. 49, 1, 82-91
  • Kierszniowska, S., Walther, D. and Schulze, W. X. (2009) 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, 1916-1924
  • Kim, J. A., Cho, K., Singh, R., Jung, Y. H., Jeong, S. H., Kim, S. H., Lee, J. E., Cho, Y. S., Agrawal, G. K., Rakwal, R., Tamogami, S., Kersten, B., Jeon, J. S., An, G. and Jwa, N. S. (2009) Rice OsACDR1 (Oryza sativa accelerated cell death and resistance 1) is a potential positive regulator of fungal disease resistance. Mol. Cells 28, 5, 431-439
  • May, P., Christian, J. O., Kempa, S. and Walther, D. (2009) ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii. BMC Genomics 10, 209,
  • Pajerowska-Mukhtar, K., Stich, B., Achenbach, U., Ballvora, A., Lubeck, J., Strahwald, J., Tacke, E., Hofferbert, H. R., Ilarionova, E., Bellin, D., Walkemeier, B., Basekow, R., Kersten, B. and Gebhardt, C. (2009) Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars. 181, 3, 1115-1127
  • Pant, B. D., Musialak-Lange, M., Nuc, P., May, P., Buhtz, A., Kehr, J., Walther, D. and Scheible, W. R. (2009) Identification of Nutrient-Responsive Arabidopsis and Rapeseed MicroRNAs by Comprehensive Real-Time Polymerase Chain Reaction Profiling and Small RNA Sequencing. Plant Physiol. 150, 3, 1541-1555
  • Perez-Rodriguez, P., Riano-Pachon, D. M., Correa, L. G., Rensing, S. A., Kersten, B. and Mueller-Roeber, B. (2009) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res. 38, Database issue, D822-D827
  • Riano-Pachon, D. M., Nagel, A., Neigenfind, J., Wagner, R., Basekow, R., Weber, E., Mueller-Roeber, B., Diehl, S. and Kersten, B. (2009) GabiPD: the GABI primary database-a plant integrative 'omics' database. Nucleic Acids Res. 37, 954-959

2008

  • Arvidsson, S., Kwasniewski, M., Riano-Pachon, D. M. and Mueller-Roeber, B. (2008) QuantPrime - a flexible tool for reliable high-throughput primer design for quantitative PCR. BMC Bioinformatics 9,
  • Correa, L. G., Riano-Pachon, D. M., Schrago, C. G., dos Santos, R. V., Mueller-Roeber, B. and Vincentz, M. (2008) The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PLoS One 3, 8, e2944
  • Durek, P. and Walther, D. (2008) The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. BMC Syst. Biol. 2,
  • Giavalisco, P., Hummel, J., Lisec, J., Inostroza, A. C., Catchpole, G. and Willmitzer, L. (2008) High-resolution direct infusion-based mass spectrometry in combination with whole 13C metabolome isotope labeling allows unambiguous assignment of chemical sum formulas. Anal. Chem. 80, 24, 9417-9425
  • Heazlewood, J. L., Durek, P., Hummel, J., Selbig, J., Weckwerth, W., Walther, D. and Schulze, W. X. (2008) PhosPhAt: a database of phosphorylation sites in Arabidopsis thaliana and a plant-specific phosphorylation site predictor. Nucleic Acids Res. 36, D1015-D1021
  • Hoehenwarter, W., van Dongen, J. T., Wienkoop, S., Steinfath, M., Hummel, J., Erban, A., Sulpice, R., Regierer, B., Kopka, J., Geigenberger, P. and Weckwerth, W. (2008) A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment. Proteomics 8, 20, 4214-4225
  • Kersten, B., Nagel, A., Riano-Pachon, D. M., Neigenfind, J., Weber, E., Wagner, R. and Diehl, S. (2008) Die GABI-Primaerdatenbank GabiPD - Komplexe Integration von GABI-Daten aus Modell- und Nutzpflanzen. GenomXPress 1, 17-19
  • Koehl, K. I., Basler, G., Ludemann, A., Selbig, J. and Walther, D. (2008) A plant resource and experiment management system based on the Golm Plant Database as a basic tool for omics research. Plant Methods 4,
  • May, P., Wienkoop, S., Kempa, S., Usadel, B., Christian, N., Rupprecht, J., Weiss, J., Recuenco-Munoz, L., Ebenhoeh, O., Weckwerth, W. and Walther, D. (2008) Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics 179, 1, 157-166
  • Nikoloski, Z., Grimbs, S., May, P. and Selbig, J. (2008) Metabolic networks are NP-hard to reconstruct. J. Theor. Biol. 254, 4, 807-816
  • Riano-Pachon, D. M., Correa, L. G. G., Trejos-Espinosa, R. and Mueller-Roeber, B. (2008) Green transcription factors: A Chlamydomonas overview. Genetics 179, 1, 31-39
  • Strehmel, N., Hummel, J., Erban, A., Strassburg, K. and Kopka, J. (2008) Retention index thresholds for compound matching in GC-MS metabolite profiling. J. Chromatogr. B 871, 2, 182-190

 

Invited reviews

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

 

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

Lohse, M., Krueger, P., Hannemann, J., Nagel, A., Stitt, M., Walther, D. and Usadel, B. (2008) Robin - Microarray Experimentanalyse leicht gemacht. GenomXPress 3, 16-17

 

Proceedings, Book chapters etc.

Kopka, J., Walther, D., Allwood, J. W. and Goodacre, R. (2011) Progress in chemometrics and biostatistics for plant applications: Or a good red wine is a bad white wine. In: Annual Plant Reviews: The biology of plant metabolomics. Blackwell-Wiley, London, in press,

 

May, P., Christian, N., Ebenhoeh, O., Weckwerth, W. and Walther, D. (2010) Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks In: Bioinformatics for Comparative Proteomics Springer, 694, 341-363

 

Kempa, S., Walther, D., Ebenhoeh, O. and Weckwerth, W. (2009) Metabolic Engineering. In: Molecular Biology and Biotechnology. Royal Society of Chemistry, 194–217

Kersten, B. and Feilner, T. (2009) Protein microarrays for phosphorylation studies. In: The Protein Protocols Handbook. Humana Press, Totowa, 162, 1567-1578

Kersten, B. and Wanker, E. E. (2008) Klinische Proteomik. In: Grundlagen der Molekularen Medizin. Springer Berlin, Heidelberg, New York,

Kersten, B. (2008) Time to search for kinase substrates. In: Plant Proteomics: Technologies, Strategies, and Applications. Wiley-Interscience, Hoboken, USA, 485-498

 

2007

Kersten B and Feilner T (2007) High-throughput identification of plant protein kinase substrates. In: Šamaj J, Thelen J (eds) Plant proteomics: 53-70, Springer, Berlin, Heidelberg, New York.Springer

Redestig H, Weicht D, Selbig J, and Hannah M (2007) Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana. BMC Bioinformatics. 8: 454

Heazlewood JL, 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 Acid Res. doi: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 phophorylation sites. BMC Bioinformatics 8: 216.

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.

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

Steinfath M, Repsilber D, Scholz M, Walther D, Selbig J (2007) Integrated data analysis for genome-wide research. In "Plant Systems Biology", Eds. S. Baginsky & A. Fernie, Birkhäuser, Basel p309-329

Walther D, Brunnemann R, Selbig J (2007) The regulatory code for transcriptional response diversity and its relation to genome structural properties in Arabidopsis thaliana.PLoS Genetics 3(2) e11

 

2006

Cordes F, Kaiser R, Selbig J (2006) A bioinformatics approach to predicting HIV drug resistance. Expert Review of Molecular Diagnostics, 6: 207-215.

Roomp K, Beerenwinkel N, Sing T, Schülter E, Büch J, Sierra-Aragon S, Däumer M, Hoffmann D, Kaiser R, Lengauer T, Selbig J (2006) Arevir: a secure platform for designeing personalized antiretroviral therapies against HIV. In Leser, U., Naumann, F., Eckman, B. (Eds.) Data Integration in the Life Sciences, Lecture Notes in Bioinformatics. Springer, Berlin, Heidelberg, New York., 185 - 194.

Steuer R, Humburg P, Selbig J (2006) Validation and functional annotation of expression-based clusters based on gene ontology. BMC Bioinformatics 7: 380.

Steuer R, Gross T, Selbig J, Blasius B (2006) Structural kinetic modeling of metabolic networks. PNAS 103: 11868-11873.

Scholz M, Selbig J (2006) Visualizing and analyzing biological data: Data normalization, feature extraction and dimensionaltiy reduction. In Weckwerth, W. (Ed.) Methods in Molecular Biology. The Humana Press Inc., Totowa, New Jersey, 87-104.

Steuer R, Morgenthal K, Weckwerth W, Selbig J (2006) A gentle guide to the analysis of metabolic data. In Weckwerth, W. (Ed.) Methods in Molecular Biology. The Humana Press Inc., Totowa, New Jersey, 105-128.

Grell S, Schaub T, Selbig J (2006) Modelling biological networks by action languages via answer set programming. Twenty Second International Conference on Logic Programming (ICLP), Seattle, Washington, USA, August 17-20, Lecture Notes in Computer Science, Springer, Heidelberg, Berlin,  285-299.

Redestig H, Repsilber D, Sohler F, Selbig J (2006) Integrating functional knowledge during sample clustering for microarray data using unsupervised decision trees. Biometrical Journal 48:1-16.

Möhlig M, Flöter A, Spranger J, Schill T, Schlösser HW, Brabant G, Pfeiffer AFH, Selbig J, Schöfl C (2006) A screening procedure for daily use to detect abnomal glucose metabolism in women with polycystic ovary. Diabetoligia 49:2572-2579.

Steinfath M, Repsilber D, Hische M, Schauer N, Fernie AR, Selbig J (2006) Metabolite profiles as a reflection of physiological status - a methodological validation. Journal of Integrative Bioinformatics 3:2.

 

 

Publications 2005 and earlier

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