2011

Ratzka C, Liang C, Dandekar T, Gross R, Feldhaar H. Immune response of the ant Camponotus floridanus against pathogens and its obligate mutualistic endosymbiont. Insect Biochem Mol Biol. 2011 Mar 23. [Epub ahead of print] PubMed PMID: 21440063.
Cecil A, Rikanovic C, Ohlsen K, Liang C, Bernhardt J, Oelschlaeger TA, Gulder T, Bringmann G, Holzgrabe U, Unger M, Dandekar T. Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells. Genome Biol. 2011 Mar 21;12(3):R24. [Epub ahead of print] PubMed PMID: 21418624.
Liebeke M, Dörries K, Zühlke D, Bernhardt J, Fuchs S, Pané-Farré J, Engelmann S, Völker U, Bode R, Dandekar T, Lindequist U, Hecker M, Lalk M. A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Mol Biosyst. 2011 Apr 1;7(4):1241-53. Epub 2011 Feb 16. PubMed PMID: 21327190.
Agarwal S, Kern S, Halbert J, Przyborski JM, Baumeister S, Dandekar T, Doerig C, Pradel G. Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor. J Cell Biochem. 2011 Feb 10. doi: 10.1002/jcb.23034. [Epub ahead of print] PubMed PMID: 21312235.
Förster F, Beisser D, Frohme M, Schill RO und Dandekar T (2011). Tardigrade bioinformatics: Molecular adapations, DNA j-family and dynamical modeling. Journal of Zoological Systematics and Evolutionary Research 49 (1), 120-126.
Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. Staphylococcus aureus physiological growth limitations: Insights from flux calculations built on proteomics and external metabolite data. Proteomics. 2011 May;11(10):1915-35.
Dittrich M, Birschmann I, Dandekar T (2011) Integrated Platelet Networks for the Analysis of Different System States. Current Proteomics 8, in press
Schlatter R, Philippi N, Wangorsch G, Pick R, Sawodny O, Borner C, Timmer J, Ederer M and Dandekar T. Integration of Boolean models exemplified on hepatocyte signal transduction. Briefings in Bioinformatics BIB-11-0103.R1, in press

2010

Fuchs S, Mehlan H, Kusch H, Teumer A, Zühlke D, Berth M, Wolf C, Dandekar T, Hecker M, Engelmann S, Bernhardt J. Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics. 2010 Aug;10(16):2982-3000. PubMed PMID: 20662099.
Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J. 2010 Jul 8. [Epub ahead of print] PubMed PMID: 20613790.
Löhmann C, Schachmann E, Dandekar T, Villmann C, Becker CM. Developmental profiling by mass spectrometry of phosphocholine containing phospholipids in the
rat nervous system reveals temporo-spatial gradients. J Neurochem. 2010
Aug;114(4):1119-34. Epub 2010 May 28. PubMed PMID: 20524967.
Eisenreich W, Dandekar T, Heesemann J, Goebel W. Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nat Rev Microbiol. 2010 Jun;8(6):401-12. Epub 2010 May 10. Review. PubMed PMID: 20453875.
Mischke R, Kühnlein P, Kehl A, Langbein-Detsch I, Steudle F, Schmid A, Dandekar T, Czwalinna A, Müller E. G244E in the canine factor IX gene leads to severe haemophilia B in Rhodesian Ridgebacks. Vet J. 2010 Mar 17. [Epub ahead of print] PubMed PMID: 20303304.
Mali B, Grohme MA, Förster F, Dandekar T, Schnölzer M, Reuter D, We?nicz W, Schill RO, Frohme M. Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer. BMC Genomics. 2010 Mar 12;11:168. PubMed PMID: 20226016; PubMed Central PMCID: PMC2848246.
Schokraie E, Hotz-Wagenblatt A, Warnken U, Mali B, Frohme M, Förster F, Dandekar T, Hengherr S, Schill RO, Schnölzer M. Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms. PLoS One. 2010 Mar 3;5(3):e9502. PubMed PMID: 20224743; PubMed Central PMCID: PMC2835947.
Vainshtein Y, Sanchez M, Brazma A, Hentze MW, Dandekar T, Muckenthaler MU. The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. BMC Bioinformatics. 2010 Mar 1;11:112. PubMed PMID: 20193060; PubMed Central PMCID: PMC2838865.
Beisser D, Klau GW, Dandekar T, Müller T, Dittrich MT. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics. 2010 Apr 15;26(8):1129-30. Epub 2010 Feb 25. PubMed PMID: 20189939.
Dittrich M, Strassberger V, Fackler M, Tas P, Lewandrowski U, Sickmann A, Walter U, Dandekar T, Birschmann I. Characterization of a novel interaction between vasodilator-stimulated phosphoprotein and Abelson interactor 1 in human platelets: a concerted computational and experimental approach. Arterioscler Thromb Vasc Biol. 2010 Apr;30(4):843-50. Epub 2010 Jan 28. PubMed PMID: 20110575.
Schill RO, Förster F, Dandekar T, Wolf M (2010) Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada). Organisms Diversity and Evolution (in press).
Keller A, Wolf M, Dandekar T (2010) Ribosomal RNA phylogenetics: the third dimension. Biologia 3:388-391.
Sorhannus U, Ortiz JD, Wolf M, Fox MG (2010) Microevolution and speciation in Thalassiosira weissflogii. Protist 161:237-249.
Hegewald E, Wolf M, Keller A, Friedl T, Krienitz L (2010) ITS2 sequence-structure phylogeny in Scenedesmaceae with special reference on Coelastrum (Chlorophyta, Chlorophyceae). Phycologia (in press).
Koetschan C, Förster F, Keller A, Schleicher T, Ruderisch B, Schwarz R, Müller T, Wolf M, Schultz J (2010) The ITS2 Database III – sequences and structures for phylogeny. Nucleic Acids Research 38:D275-D279.
Keller A, Förster F, Müller T, Schultz J, Dandekar T, Wolf M (2010) Including RNA secondary structures improve accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct 5:4.
Ruhl M, Wolf M, Jenkins TM (2010) Compensatory base changes illuminate morphologically difficult taxonomy. Molecular Phylogenetics and Evolution 54:664-669.

2009

Krüger,B. Dandekar,T. (2009) Bioinformatical approaches to detect and analyze protein interactions. In: Proteomics: Methods and Protocols (Ed.s: Reinders, J. and Sickmann, A). Humana Press Inc. Totowa, NJ, USA in press.
Wiemers M, Keller A, Wolf M (2009) ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies (Lepidoptera: Lycaenidae: Polyommatus). BMC Evolutionary Biology 9:300.
Keller A, Schleicher T, Schultz J, Müller T, Dandekar T, Wolf M (2009) 5.8S-28S rRNA interaction and HMM based ITS2-annotation. Gene 430:50-57.
Guidetti R, Schill R, Bertolani R, Dandekar T, Wolf M (2009) New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov. Journal of Zoological Systematics and Evolutionary Research 47:315-321.
Engelmann JC, Rahmann S, Wolf M, Schultz J, Fritzilas E, Kneitz S, Dandekar T, Müller T (2009) Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources 9:83-93.
Ahvenniemi P, Wolf M, Lehtonen MJ, Wilson P, German-Kinnari M, Valkonen JPT (2009) Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species, Rhizoctonia solani. Journal of Molecular Evolution 69:150-163.
Schultz J, Wolf M (2009) ITS2 Sequence-Structure Analysis in Phylogenetics: A How-to Manual for Molecular Systematics. Molecular Phylogenetics and Evolution 52:520-523.
Schwarz R, Wolf M, Müller T (2009) A probabilistic model of cell size reduction in Pseudo-nitzschia delicatissima (Bacillariophyta). Journal of Theoretical Biology 258:316-322.
Wolf M, Schultz J (2009) ITS better than its reputation. Science (E-Letter, 10 December 2009) http://www.sciencemag.org/cgi/eletters/325/5941/682#12692.

2008

Christoph Schoen, Jochen Blom, Heike Claus, Anja Schramm-Glück, Petra Brandt, Tobias Müller, Alexander Goesmann, Biju Joseph, Sebastian Konietzny, Oliver Kurzai, Corinna Schmitt, Torben Friedrich, Burkhard Linke, Ulrich Vogel, Matthias Frosch (2008) Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis. Proc Natl Acad Sci U S A 105: 9.3473-3478 Mar
Selig C, Wolf M, Muller T, Dandekar T, Schultz J. (2008) The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res. Nucleic Acids Res. 36(Database issue):D377-80.
Birschmann I, Mietner S, Dittrich M, Pfrang J, Dandekar T, Walter U. (2008) Use of functional highly purified human platelets for the identification of new proteins of the IPP signaling pathway. Thromb Res. 122, 59-68
Buchholz K, Schirmer RH, Eubel JK, Akoachere MB, Dandekar, T., Becker K, Gromer S. (2008) Interactions of methylene blue with human disulfide reductases and their orthologues from Plasmodium falciparum. Antimicrob Agents Chemother. 52, 183-191.
Dandekar, G., Dandekar, T. (2008) From Sanger to ultrafast DNA sequencing. Feature article. Chemtracts ? Biochemistry and Molecular Biology in press
Dittrich,M., Birschmann,I., Mietner,S., Sickmann, A., Walter,U. und Dandekar,T. (2008) Platelet protein interactions: map, signaling components and phosphorylation groundstate, Arteriosclerosis, Thrombosis, and Vascular Biology 28, 1326-1331 (is an Editorial highlight: Cagney G, McRedmond J.; Arterioscler Thromb Vasc Biol. 2008;28:1214-1215) (chosen as faculty of 1000 paper)
Blenk,S., Engelmann, J.C., Pinkert,S., Weniger, M., Schultz, J., Rosenwald, A., Müller-Hermelink, H.-K., Müller,T., und Dandekar,T. (2008) Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis, BMC Cancer 8, 106 (10 pp.).
Dittrich, M., Klau, G., Rosenwald, A., Dandekar, T., Müller, T. (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 24, i223-31. (paper bekam den ISMB best paper award)
Engelmann,J., Schwarz,S., Blenk,S., Friedrich,T., Seibel,P., Dandekar,T., Müller,T. unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation. Bioinformatics and Biological Insights 2, 271-286
Engelmann,J.C., Rahmann,S., Wolf,M., Schultz,J., Fritzilas, E., Kneitz,S., Dandekar,T., Müller,T. (2008) Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources, in press

2007

Gerlach D, Wolf M, Dandekar T, Muller T, Pokorny A, Rahmann S. (2007) Deep metazoan phylogeny. In Silico Biol. 7, 151-154.
Blenk, S., Engelmann, J., Weniger, M., Schultz, J., Dittrich, M., Rosenwald, A., Müller-Hermelink, H. K., Müller, T. und Dandekar, T. (2007) Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): Analysis of molecular predictors, signatures, cell cycle state and patient survival. Cancer Informatics 3, 409-430.
Zemojtel, T., Penzkofer, T., Schultz, J., Dandekar, T., Badge, R. und Vingron, M. (2007) Exonization of active mouse L1s: a driver of transcriptome evolution? BMC Genomics 8, 392.

Matthias Wolf, Christian Selig, Tobias Mueller, Nicole Philippi, Thomas Dandekar & Jörg Schultz. (2007) Placozoa: at least two. Biologia, Section Cellular and Molecular Biology, Bratislava, 62/6: 1?5, 2007
Pachkov, M., Dandekar, T., Korbel, J., Bork, P. und Schuster, S. (2007) Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism. Gene 396, 215-225.
Schwarz,R., Liang,C., Kaleta, C., Kuhnel, M., Hoffmann, E., Kuznetsov, S., Hecker, M., Griffith, G., Schuster, S. und Dandekar, T. (2007) Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinformatics 8, 313 (10 pp.)
Müller T, Philippi N, Dandekar T, Schultz J, Wolf M. Distinguishing species. RNA 13, 1469-1472.

2006

Rosalia Deeken, Julia C. Engelmann, Marina Efetova, Tina Czirjak, Tobias Müller, Werner M. Kaiser, Olaf Tietz, Markus Krischke, Martin J. Mueller, Klaus Palme, Thomas Dandekar, and Rainer Hedrich (2006). An Integrated View of Gene Expression and Solute Profiles of Arabidopsis Tumors: A Genome-Wide Approach. The Plant Cell, in press.
Thakar,J., Schleinkofer,K., Borner, C and Dandekar,T. (2006) RIP death domain structural interactions implicated in TNF-mediated proliferation and survival. Proteins, Structure, Function and Bioinformatics 63, 413-423.
Gaudermann, P., Vogl, I., Zientz, E., Silva, F.J., Moya, A., Gross, R. und Dandekar, T. (2006) Function predictions for conserved hypothetical proteins and proteins with putative function in Blochmannia floridanus. BMC Microbiology 6, 1 (15 pp.).
Eisenreich,W., Slaghuis,J., Laupitz,R., Bussemer,J., Stritzker,J., Schwarz,C., Schwarz,R., Dandekar,T., Goebel,W. und Bacher,A. (2006) 13C Isotopolog perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA. Proc. Natl. Acad. Sci. USA 103, 2040-2045.
Dittrich, M., Smolenski, A., Herterich, S., Birschmann, I., Walter, U. and Dandekar, T. (2006) Analysis of SAGE data in the platelet: Features of active translation and regulation. Thromb Haemost. 95, 643-651.
Nowrouzi,A., Dittrich, M., Klanke, C., Heinkelein,M., Rammling,R., Dandekar, T., von Kalle,C. und Rethwilm,A. (2006) Genome-wide mapping of foamy virus vector integrations into a human cell line. J. General Virology 87,1339-1347.
Rahmann, S., Müller, T., Dandekar, T. und Wolf,M. (2006) In: Hui-Huang Hsu (ed.), Efficient and robust analysis of large phylogenetic datasets. Advanced Data Mining Technologies in Bioinformatics. Idea Group, Inc., Hershey, PA. in press
Petermann, I., Mayer, C., Stypmann, J., Biniossek, M.L., Tobin, D.J., Engelen, M.A., Dandekar, T., Grune, T., Schild, L., Peters, C. und Reinheckel, T. (2006) Lysosomal, cytoskeletal, and metabolic alterations in cardiomyopathy of cathepsin L knockout mice. FASEB J. 20, 1266-8.
Sanchez M, Galy B, Dandekar, T., Bengert P, Vainshtein Y, Stollte J, Muckenthaler MU, Hentze MW. (2006) Iron regulation and the cell cycle: Identification of an iron-responsive element in the 3' untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy. J Biol Chem. 2006 Jun 7; [Epub ahead of print]
Schultz, J., Müller, T., Achtziger, M., Seibel, P.N., Dandekar, T., Wolf, M. The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W704-7.
Hain T, Steinweg C, Kuenne CT, Billion A, Ghai R, Chatterjee SS, Domann E, Karst U, Goesmann A, Bekel T, Bartels D, Kaiser O, Meyer F, Puhler A, Weisshaar B, Wehland J, Liang C, Dandekar, T., Lampidis R, Kreft J, Goebel W, Chakraborty T. (2006) Whole genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J Bacteriol. 2006 Aug 25; [Epub ahead of print]
Wolf M, Seibel PN, Dandekar, T. und Lynn DH. (2006) A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol. 53, 315.
Friedrich T, Pils B, Dandekar T, Schultz J, Muller T. Modelling interaction sites in protein domains with interaction profile hidden Markov models. Bioinformatics. 2006 Sep 25;
Liang, C. und Dandekar, T. (2006) inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons. BMC Bioinformatics, in press.

2005

Schleinkofer, K. und Dandekar, T. (2005) Clues from 3-dimensional structure analysis and molecular modelling: new insights into cytochrome P450 mechanisms/functions. Buchkapitel, pp 1-10. In: Eisenhaber, F. (Hrgb.) Discovering Biomolecular Mechanisms with Computational Biology. Springer Verlag Heidelberg.
Wolf, M., Achtziger, M., Schultz, J., Dandekar, T. & Müller, T. (2005): Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA 11: 1616-1623. [ supplementary material ] [ PubMed ]
Wolf , M., J. Friedrich, T. Dandekar & T. Müller (2005): CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures . In Silico Biology 5: 0027. [ PubMed ]
Friedrich, J., T. Dandekar, M. Wolf & T., Müller (2005): ProfDist: A tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics 21: 2108-2109. [ PubMed ]
Buchheim, M.A., Buchheim, J. A., Carlson, T., Braband, A., Hepperle, D., Krienitz, L., Wolf , M. & Hegewald, E. (2005): Phylogeny of the Hydrodictyaceae (Chlorophyta, Sphaeropleales): Inferrences from rDNA data. J. Phycol. 41: 1039-1054.
Schultz, J., Maisel, S., Gerlach, D., Müller, T. & M. Wolf (2005): A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11: 361-364. [ supplementary material ] [ PubMed ]
Schmitt, S., Hentschel, U., Zea, S., Dandekar, T. & M. Wolf (2005): ITS2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). J. Mol. Evol. 60: 327-336. [ PubMed ]
Schmitt, S., Hentschel, U., Zea, S., Dandekar, T. & M. Wolf (2005): Erratum for: J. Mol. Evol. 60: 327-326 (2005) ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). J. Mol. Evol. 61: 148-150. [ PubMed ]
Rahmann, S., T. Müller, T. Dandekar & M. Wolf (2005): Efficent and robust analysis of large phylogenetic datasets. In: Hui-Huang Hsu (ed.): Advanced Data Mining Technologies in Bioinformatics. Idea Group, Inc., Hershey, PA, USA, pp. (in press).
Dandekar, T. (2005) Modelling cellular networks. (Condensation and Commentary) Chemtracts – Biochemistry and Molecular Biology, in press.
Robubi, A., Mueller. T., Fueller,J., Hekman,M., Rapp,U.R. und Dandekar, T. (2005) B-Raf and C-Raf signaling investigated in a simplified model of the mitogenic kinase cascade. Biol. Chemistry, in press.
Dittrich, M., Birschmann, I., Stuhlfelder, C., Sickmann, A., Herterich, S., Nieswandt, B., Walter, U. und Dandekar, T. (2005) Understanding platelets: Lessons from proteomics and promises from network analysis. Thrombosis & Haemostasis, in press.
Schwarz, R., Musch, P., v.Kamp, A., Engels, B., Schirmer, H., Schuster, S. und Dandekar, T. (2005) YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics 6, 135-146.
P. Bengert und T. Dandekar (2005). Current efforts in the analysis of RNAi and RNAi target genes. Brief. Bioinformatics, in press.
T. Penzkofer, T. Dandekar, T. Zemojtel (2005) L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic Acids Res 33 (Database Issue) D498-500.

2004

P. Bengert und T. Dandekar (2004). Riboswitch finder - a tool for identification of riboswitch RNAs. Nucleic Acids Research 31, 3441-3445.
F. Breinig , K. Schleinkofer, MJ. Schmitt (2004) Related Articles, Links Yeast Kre1p is GPI-anchored and involved in both cell wall assembly and architecture. Microbiology. 150(Pt 10):3209-18. PMID: 15470101 [PubMed - in process]
T. Crass, I. Antes, R. Basekow, et al. (2004) The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. BIOINFORMATICS 20 (2): 268-270
T. Dandekar (2004) Molekular- und Evolutionsbiologische Aspekte des Alterns. In: „Enzyklopädie der Gerontologie“ (Herausgeber: A.Kruse, M.Martin), Seiten 151-166, Hans Huber Verlag, Bern, Göttingen, Toronto.
T. Dandekar und S. Schmidt (2004) Metabolites and Pathway flexibility. In Silico Biology, 5 (No. 0012), pp. 1-13.
M. Dittrich und T. Dandekar (2004) Targets of the cyclin-dependent kinase Cdk1. (Condensation and Commentary) Chemtracts – Biochemistry and Molecular Biology 17, 1-5.
M. Dünßer, R. Lampidis, S. Schmidt, D. Seipel and T. Dandekar (2004) Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework. J. of Integrative Bioinformatics, in press.
O. Hecht, N.A. Van Nuland, K. Schleinkofer, A.J. Dingley, H. Bruhn, M. Leippe, Grotzinger J. (2004) Related Articles, Links Solution structure of the pore-forming protein of Entamoeba histolytica. J Biol Chem. 23;279(17):17834-41. Epub 2004 Feb 17. PMID: 14970207 [PubMed - indexed for MEDLINE]
R. Krause, C. v.Mering, P. Bork und T. Dandekar (2004) Shared components of protein complexes—versatile building blocks or biochemical artefacts? BioEssays 26, 1333-1343
Krienitz, L., E. Hegewald, D. Hepperle, V.A.R. Huss, T. Rohr & M. Wolf (2004): Phylogenetic relationship of Chlorella and Parachlorella nov. gen. (Chlorophyta, Trebouxiophyceae). Phycologia 43: 529-542.
I. Letunic, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP and P. Bork (2004) SMART 4.0: towards genomic data integration. Nucleic Acids Res. (2004), 32, D142-4
T. Müller, S. Rahmann, T. Dandekar und M. Wolf (2004) Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta) BMC Evolutionary Biology 4, 20-26.
T. Müller, S. Rahmann, T. Dandekar und M. Wolf (2004): Robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC Evolutionary Biology 4: 20.
B. Pils, Schultz J. (2004) Inactive Enzyme-Homologues find new Function in Regulatory Processes. J Mol Biol, 340, 399-404
B. Pils and J. Schultz Evolution of the multifunctional protein tyrosine phosphatase family. Mol Biol Evol (2004), Epub ahead of print
S. Rahmann, T. Müller, and M. Vingron (2004) Non-unique probe selection by matrix condition optimization. In Currents in Computational Molecular Biology. San Diego, USA, 2004.
S. Rahmann and T. Müller (2004) The embedding problem for evolutionary Markov processes. In Proceedings of the Karlsruher Stochastik-Tage.
K. Rateitschak, T. Müller and M. Vingron (2004) Annotating significant pairs of transcription factor binding sites in regulatory DNA.
In Silico Biology 4, 0040.
K. Schleinkofer, U. Wiedemann, L. Otte, T. Wang, G. Krause, H. Oschkinat, R.C. Wade (2004) Related Articles, Links Comparative Structural and Energetic Analysis of WW Domain-Peptide Interactions. J Mol Biol.;344(3):865-81. PMID: 15533451 [PubMed - in process]
S. Schmitt, U. Hentschel, S. Zea, T. Dandekar & M. Wolf (2004): ITS2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). J. Mol. Evol. (in press).
J. Schultz. HTTM, a horizontally transferred transmembrane domain. Trends Biochem Sci (2004),29, 4-7.
B. Schuster-Boeckler, J. Schultz, S. Rahmann (2004) HMM Logos for Visualization of Protein Families, BMC Bioinformatics, 5, 7
M. Wolf, T. Müller, T. Dandekar & J.D. Pollack (2004): Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int. J. Syst. Evol. Microbiol. (IJSEM) 54: 871-875.
M. Wolf (2004): The secondary structure of the ITS2 transcript in Cyclotella and Stephanodiscus (Thalassiosiraceae, Bacillariophyta). Diatom Res. 19: 135-142.
M. Wolf (2004): Verweisstichwort: Sphaeroplea. In: Lexikon der Biologie, Spektrum Akademischer Verlag, Heidelberg, Bd. 14: 79.
M. Wolf (2004): Stichwort: Sphaeropleales. In: Lexikon der Biologie, Spektrum Akademischer Verlag, Heidelberg, Bd. 14: 79.
M. Wolf (2004): Stichwort: Sphaeropleaceae. In: Lexikon der Biologie, Spektrum Akademischer Verlag, Heidelberg, Bd. 14: 79.
T. Zemojtel, T. Penzkofer, T. Dandekar, J. Schultz (2004) A novel conserved family of nitric oxide synthase? Trends Biochem Sci, 29, 224-6
T. Zemojtel, M. Rini, K. Heyne, T. Dandekar, E. T. J. Nibbering, P.M. Kozlowski (2004) NO bound Myoglobin: Structural diversity and dynamics of the NO ligand. J.Am.Chem.Soc. 126, 1930-1931.
R. W. Ziebuhr, K. Xiao, B. Coulibaly, R. Schwarz und T. Dandekar (2004) Pharmacogenomic strategies against resistance development in microbial infections. Pharmacogenomics 5, 361-379.
E. Zientz, T. Dandekar and R. Gross (2004) Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbial and Molecular Biology Reviews 68, 745-777.

Book:

T. Dandekar (2004) Genetik des Alterns. Book chapter in „Lehrbuch der Gerontologie“ (Herausgeber: A.Kruse, M.Martin) Huber Verlag, in press

2003

H Arndt, K. Hausmann, M. Wolf (2003): Deep-sea heterotrophic nanofauna of the Eastern Mediterranean Sea: qualitative and quantitative aspects of their pelalgic and benthic occurence. Mar. Ecol. Prog. Ser. (MEPS) 256: 45-56.
P. Bengert and T. Dandekar (2003). A software tool-box for analysis of regulatory RNA elements. Nucleic Acids Research 31, 3441-3445.
H. Bertram, S.Balthasar and T.Dandekar (2003) On the Track of Pathogenicity and Bacteria. BIOforum Europe 3, 2-4.
G. Dandekar and T. Dandekar (2003) A single motif responsible for ubiquitin recognition and monoubiquitination in endocytic proteins (Condensation and Commentary) Chemtracts – Biochemistry and Molecular Biology 16, 632-637.
T. Dandekar, F. Moldenhauer, S. Bulik, H. Bertram and S. Schuster (2003). A method or classifying metabolites in topological pathway analyses based on minimization of pathway number. BioSystems 70, 255-270.
D. Faller, T. Reinheckel, D. Wenzler, S. Hagemann, K. Xiao, J. Honerkamp, C. Peters, T. Dandekar und J. Timmer (2003) A protein gel documentation system for the analysis of gene knockouts. J.Chem.Inf. and Comp.Sci. 44, 168-169.
E. Hegewald, M. Wolf (2003) Phylogenetic relationships of Scenedesmus and Acutodesmus (Chlorophyta, Chlorophyceae) as inferred from 18S rDNA and ITS-2 sequence comparisons. Plant Syst. Evol., in press
S. Kneitz und T.Dandekar (2003) Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network. (Condensation and Commentary) Chemtracts – Biochemistry and Molecular Biology 16, 806-809.
L. Krienitz, E. Hegewald, D. Hepperle, M. Wolf (2003) Systematics of coccoid green algae: morphology versus 18S rRNA gene phylogeny Biologia 58., 437-446
T. Lohmüller, D.Wenzler, S. Hagemann, W. Kieß, C. Peters, T. Dandekar and T. Reinheckel (2003) Toward Computer Based Cleavage Site Prediction of Cysteine Endopeptidases. Biological Chemistry 384, 899-909.
T. Müller, S. Rahmann, T. Dandekar, and M. Wolf. (2003) Robust estimation of the phylogeny of Chlorophyceae (Chlorophyta) based on profile distances. In H.-W. Mewes, D. Frishman, V. Heun, and S. Kramer, editors, Proceedings of the German Conference on Bioinformatics (GCB'03), volume 1, pages 97-101, Munich, . belleville.
S. Rahmann, T. Müller, and M. Vingron. (2003) On the power of profiles for transcription factor binding site detection. Statistical Applications in Genetics and Molecular Biology, 2(1):Article 7.
S. Rahmann, T. Müller, and M. Vingron (2003) Measuring the quality of profiles for transcription factor binding site detection. In Rainer Spang, Patricia Béziat, and Martin Vingron, editors, Currents in Computational Molecular Biology. Berlin, Germany
S. Rahmann, H. Luz, and T. Müller. (2003) The SLIMSEARCH world wide web server for the detection of transmembrane proteins. http://slimsearch.molgen.mpg.de.
E. Ratsch, Schultz J, Saric J, Lavin PC, Wittig U, Reyle U and Rojas I. Developing a protein-interactions ontology. Comparative and Functional Genomics (2003), 4, 85-89
S. Schmidt, S. Sunyaev, P. Bork and T. Dandekar (2003). Metabolites: A key for enzyme flexibility and pathway evolution? Trends in Biochemical Sciences 28, 336-341.
C. Steinhoff*, T. Müller* (*equal contribution), U. A. Nuber and M. Vingron. (2003) Gaussian Mixture Density Estimation Applied to Microarray Data Lect. Notes Comp. Sci. 2810, 418-429
M. Wolf, L. Krienitz & D. Hepperle (2003): On the phylogeny of Radiococcus, Planktosphaeria and Schizochlamydella (Radiococcaceae, Chlorophyta). Biologia 58: 759-765.
M. Wolf., E. Hegewald, D. Hepperle & L. Krienitz (2003): Phylogenetic position of the Golenkiniaceae (Chlorophyta) as inferred from 18S rDNA sequence data. Biologia 58: 433-436.
T. Zemojtel, R. Wade and T. Dandekar (2003). In search for the prototype of Nitric Oxide Synthase. FEBS, in press

2002

H. Bertram and T. Dandekar (2002). A 'periodic table' for protein structure. Chemtracts – Biochemistry and Molecular Biology 15, 735-739.
T. Dandekar and R. Sauerborn (2002) Comparative genome analysis and pathway reconstruction. Pharmacogenomics 3, 245-256.
T. Dandekar, B. Snel, S. Schmidt, W. Lathe, M. Suyama, M. Huynen and P. Bork (2002). Comparative genome analysis of the Mollicutes, pp.255-278. In: The Mollicutes (Hgb.: S.Razin and R.Herrmann; Kluver Academic / Plenum Publishers, New York, 2002.
Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature (2002), 420, 520-562
J.D. Pollack, M.A.. Myers, T. Dandekar and R Herrmann (2002). Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: The replacement of the missing “household” nucleoside diphosphate kinase gene and activity by glycolytic kinases. Omics (a journal of integrative biology) 6, 247-258.
S. Schmidt and T.Dandekar (2002) Metabolic Pathways (bookchapter, pp. 251-272 in: ”gene regulation and metabolism: post genomic computational approaches”, (ed. J.Collado-Vides and R.Hofestädt) MIT Press, Massachusettes ISBN 0-262-03297-X
S. Schuster, T. Pfeiffer, F. Moldenhauer, I. Koch and T. Dandekar (2002). Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 18, 351-361.
S. Schmidt, P. Bork and T. Dandekar (2002). A versatile structural domain server using profile weight matrices. Journal of Chemical Information and Computer Sciences 42, 405-407.
T. Müller, R. Spang and M. Vingron (2002) Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method. Mol Biol Evol 19(1): 8-13.
S. Rahmann and T. Müller (2002) A new formulation of evolutionary models. In Liliana Florea, Brian Walenz, and Sridhar Hannenhalli, editors, Currents in Computational Molecular Biology 2002, pages 156-157. Washington D.C., USA
E. Roeb, K. Schleinkofer, T. Kernebeck, S. Potsch, B. Jansen, I. Behrmann, S. Matern, J. Grotzinger (2002) Related Articles, Links The matrix metalloproteinase 9 (mmp-9) hemopexin domain is a novel gelatin binding domain and acts as an antagonist. J Biol Chem. 2002 Dec 27;277(52):50326-32. Epub. PMID: 12384502 [PubMed - indexed for MEDLINE]
J. Schultz and B. Pils (2002) Prediction of structure and functional residues for O-GlcNAcase, a divergent homologue of Acetyltransferases. FEBS Letters 529, 179-182.

Book:

T.Dandekar (2002; Editor) RNA motifs and regulatory elements. Monographie. Springer Verlag, Berlin, Heidelberg, New York (new, completely revised edition, 233pp.). ISBN 3-540-41701-X

T. Dandekar, F. Du, R.H. Schirmer and S. Schmidt (2001) Medical target prediction from genome sequence: Combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches. Computation and Chemistry 26, 15-21.
T. Dandekar, F. Du and H. Bertram (2001) Identification of cellular interactions in RNA and protein molecules. Journal of non-linear analysis 47, 225-234.
T. Dandekar and S.Schuster (2001) The large-scale organization of metabolic networks. Chemtracts - Biochemistry and Molecular Biology 14, 137-141.
R. König and T. Dandekar (2001) Solvent entropy driven searching for protein modeling examined and tested in simplified models. Protein Eng. 14, 329-335.
T. Dandekar (2001) Computational analysis of biochemical systems. (book-review) Trends in Biochemical Sciences 26, 637.
T. Dandekar (2001). Warum müssen wir altern? Biochemische Aspekte des Alterns. In: M.Friedenthal-Haase, G. Meinhold, K. Schneider, U. Zwiener (Hrsg.) Alt werden als sein. Peter Lang, Europäischer Verlag der Wissenschaften.
T. Dandekar (2001). The structural basis of ribosome activity in peptide bond synthesis. Condensation and commentary. Chemtracts – Biochemistry and Molecular Biology 14, 746-750.
I.M. Saxena, R.M. Brown, jr. and T. Dandekar (2001) Structure-function characterization of cellulose synthases: relationship to other glycosyltransferases. Phytochemistry 57, 1135-1148.
R. Wang, L. Zheng, Y.T. Toure, T. Dandekar (corresponding author) and F.C. Kafatos (contributing author) (2001). When genetic distance matters: Measuring genetic differentiation at microsatellite loci in whole-genome scans of recent and incipient mosquito species. Proc. Natl. Acad. Sci. U.S.A. 98, 10769-10774.
T. Müller, S. Rahmann and M. Rehmsmeier (2001) Non-symmetric Score Matrices and the Detection of Homologous Transmembrane Proteins
In: Sören Brunak et al. (eds), Proceedings of the 9th International Conference on Intelligent Systems for Molecular Biology (ISMB 2001)
Bioinformatics 17 Supplement 1, pp. S182-189.

The department exists only since 2001. For previous publications please look in Medline or at the respective personal homepages.