Thomas Dandekar - Publications

Biozentrum University of Würzburg, Würzburg, Bayern, Germany 

132 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Luther CH, Brandt P, Vylkova S, Dandekar T, Müller T, Dittrich M. Integrated analysis of SR-like protein kinases Sky1 and Sky2 links signaling networks with transcriptional regulation in . Frontiers in Cellular and Infection Microbiology. 13: 1108235. PMID 37082713 DOI: 10.3389/fcimb.2023.1108235  0.446
2023 Vogg N, Müller T, Floren A, Dandekar T, Riester A, Dischinger U, Kurlbaum M, Kroiss M, Fassnacht M. Simplified urinary steroid profiling by LC-MS as diagnostic tool for malignancy in adrenocortical tumors. Clinica Chimica Acta; International Journal of Clinical Chemistry. 543: 117301. PMID 36948238 DOI: 10.1016/j.cca.2023.117301  0.345
2022 Rackevei AS, Borges A, Engstler M, Dandekar T, Wolf M. About the Analysis of 18S rDNA Sequence Data from Trypanosomes in Barcoding and Phylogenetics: Tracing a Continuation Error Occurring in the Literature. Biology. 11. PMID 36358313 DOI: 10.3390/biology11111612  0.363
2022 Vogg N, Müller T, Floren A, Dandekar T, Scherf-Clavel O, Fassnacht M, Kroiss M, Kurlbaum M. Targeted metabolic profiling of urinary steroids with a focus on analytical accuracy and sample stability. Journal of Mass Spectrometry and Advances in the Clinical Lab. 25: 44-52. PMID 35910411 DOI: 10.1016/j.jmsacl.2022.07.006  0.344
2020 Naseem M, Osmanoğlu Ö, Kaltdorf M, Alblooshi AAMA, Iqbal J, Howari FM, Srivastava M, Dandekar T. Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem. International Journal of Molecular Sciences. 21. PMID 32796535 DOI: 10.3390/Ijms21165745  0.306
2020 Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, Göbel M, Döring K, Menegatti J, Antrobus R, Matheson NJ, Künzig FWH, Mastrobuoni G, ... ... Dandekar T, et al. Integrative functional genomics decodes herpes simplex virus 1. Nature Communications. 11: 2038. PMID 32341360 DOI: 10.1038/S41467-020-15992-5  0.339
2020 Shityakov S, Bencurova E, Förster C, Dandekar T. Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches. Bmc Bioinformatics. 21: 132. PMID 32245400 DOI: 10.1186/S12859-020-3461-6  0.31
2020 Gupta SK, Srivastava M, Osmanoglu Ö, Dandekar T. Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs. Scientific Reports. 10: 2334. PMID 32047225 DOI: 10.1038/S41598-020-59344-1  0.328
2019 Yang M, Rajeeve K, Rudel T, Dandekar T. Comprehensive Flux Modeling of Proteome and qRT-PCR Data Indicate Biphasic Metabolic Differences Between Elementary Bodies and Reticulate Bodies During Infection. Frontiers in Microbiology. 10: 2350. PMID 31681215 DOI: 10.3389/Fmicb.2019.02350  0.312
2019 Akhoon BA, Gupta SK, Tiwari S, Rathor L, Pant A, Singh N, Gupta SK, Dandekar T, Pandey R. C. elegans protein interaction network analysis probes RNAi validated pro-longevity effect of nhr-6, a human homolog of tumor suppressor Nr4a1. Scientific Reports. 9: 15711. PMID 31673088 DOI: 10.1038/S41598-019-51649-0  0.33
2019 Kunz M, Wolf B, Fuchs M, Christoph J, Xiao K, Thum T, Atlan D, Prokosch HU, Dandekar T. A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs. Briefings in Bioinformatics. PMID 31578571 DOI: 10.1093/Bib/Bbz066  0.353
2018 Orth MF, Gerke JS, Knösel T, Altendorf-Hofmann A, Musa J, Alba-Rubio R, Stein S, Hölting TLB, Cidrea-Aranaz F, Romero-Pérez L, Dallmayer M, Baldauf MC, Marchetto A, Sannino G, Knott MML, ... ... Dandekar T, et al. Functional genomics identifies AMPD2 as a new prognostic marker for undifferentiated pleomorphic sarcoma. International Journal of Cancer. PMID 30267407 DOI: 10.1002/Ijc.31903  0.316
2018 Page L, Weis P, Müller T, Dittrich M, Lazariotou M, Dragan M, Waaga-Gasser AM, Helm J, Dandekar T, Einsele H, Löffler J, Ullmann AJ, Wurster S. Evaluation of Aspergillus and Mucorales specific T-cells and peripheral blood mononuclear cell cytokine signatures as biomarkers of environmental mold exposure. International Journal of Medical Microbiology : Ijmm. PMID 30201279 DOI: 10.1016/J.Ijmm.2018.09.002  0.43
2018 Bencurova E, Gupta SK, Sarukhanyan E, Dandekar T. Identification of Antifungal Targets Based on Computer Modeling. Journal of Fungi (Basel, Switzerland). 4. PMID 29973534 DOI: 10.3390/Jof4030081  0.362
2018 Schmidt H, Vlaic S, Krüger T, Schmidt F, Balkenhohl J, Dandekar T, Guthke R, Kniemeyer O, Heinekamp T, Brakhage AA. Proteomics ofconidia-containing phagolysosomes identifies processes governing immune evasion. Molecular & Cellular Proteomics : McP. PMID 29507050 DOI: 10.1074/Mcp.Ra117.000069  0.335
2017 Ampattu BJ, Hagmann L, Liang C, Dittrich M, Schlüter A, Blom J, Krol E, Goesmann A, Becker A, Dandekar T, Müller T, Schoen C. Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. Bmc Genomics. 18: 282. PMID 28388876 DOI: 10.1186/S12864-017-3616-7  0.457
2017 Ewald J, Bartl M, Dandekar T, Kaleta C. Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism. Plos Computational Biology. 13: e1005371. PMID 28212377 DOI: 10.1371/Journal.Pcbi.1005371  0.302
2016 Czakai K, Dittrich M, Kaltdorf M, Müller T, Krappmann S, Schedler A, Bonin M, Dühring S, Schuster S, Speth C, Rambach G, Einsele H, Dandekar T, Löffler J. Influence of Platelet-rich Plasma on the immune response of human monocyte-derived dendritic cells and macrophages stimulated with Aspergillus fumigatus. International Journal of Medical Microbiology : Ijmm. PMID 27965080 DOI: 10.1016/J.Ijmm.2016.11.010  0.443
2016 Gupta SK, Gross R, Dandekar T. An antibiotic target ranking and prioritization pipeline combining sequence, structure and network-based approaches exemplified for Serratia marcescens. Gene. PMID 27425866 DOI: 10.1016/J.Gene.2016.07.030  0.347
2016 Kaltdorf M, Srivastava M, Gupta SK, Liang C, Binder J, Dietl AM, Meir Z, Haas H, Osherov N, Krappmann S, Dandekar T. Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. Frontiers in Molecular Biosciences. 3: 22. PMID 27379244 DOI: 10.3389/Fmolb.2016.00022  0.322
2015 Shityakov S, Dandekar T, Förster C. Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia. Hiv/Aids (Auckland, N.Z.). 7: 265-276. PMID 26604827 DOI: 10.2147/Hiv.S88438  0.305
2015 Gabed N, Yang M, Bey Baba Hamed M, Drici H, Gross R, Dandekar T, Liang C. Draft Genome Sequence of the Moderately Heat-Tolerant Lactococcus lactis subsp. lactis bv. diacetylactis Strain GL2 from Algerian Dromedary Milk. Genome Announcements. 3. PMID 26586883 DOI: 10.1128/Genomea.01334-15  0.315
2015 Fiedler J, Breckwoldt K, Remmele CW, Hartmann D, Dittrich M, Pfanne A, Just A, Xiao K, Kunz M, Müller T, Hansen A, Geffers R, Dandekar T, Eschenhagen T, Thum T. Development of Long Noncoding RNA-Based Strategies to Modulate Tissue Vascularization. Journal of the American College of Cardiology. 66: 2005-15. PMID 26516004 DOI: 10.1016/J.Jacc.2015.07.081  0.469
2015 Remmele CW, Luther CH, Balkenhol J, Dandekar T, Müller T, Dittrich MT. Integrated inference and evaluation of host-fungi interaction networks. Frontiers in Microbiology. 6: 764. PMID 26300851 DOI: 10.3389/Fmicb.2015.00764  0.487
2015 Gupta SK, Kupper M, Ratzka C, Feldhaar H, Vilcinskas A, Gross R, Dandekar T, Förster F. Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing. Bmc Genomics. 16: 540. PMID 26198742 DOI: 10.1186/S12864-015-1748-1  0.323
2015 Wolf B, Kuonen P, Dandekar T, Atlan D. DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation. Biomed Research International. 2015: 403497. PMID 26137478 DOI: 10.1155/2015/403497  0.326
2015 Cecil A, Ohlsen K, Menzel T, François P, Schrenzel J, Fischer A, Dörries K, Selle M, Lalk M, Hantzschmann J, Dittrich M, Liang C, Bernhardt J, Ölschläger TA, Bringmann G, ... ... Dandekar T, et al. Modelling antibiotic and cytotoxic isoquinoline effects in Staphylococcus aureus, Staphylococcus epidermidis and mammalian cells. International Journal of Medical Microbiology : Ijmm. 305: 96-109. PMID 25500547 DOI: 10.1016/J.Ijmm.2014.11.006  0.345
2014 Reister M, Hoffmeier K, Krezdorn N, Rotter B, Liang C, Rund S, Dandekar T, Sonnenborn U, Oelschlaeger TA. Complete genome sequence of the gram-negative probiotic Escherichia coli strain Nissle 1917. Journal of Biotechnology. 187: 106-7. PMID 25093936 DOI: 10.1016/J.Jbiotec.2014.07.442  0.305
2014 Boyanova D, Nilla S, Klau GW, Dandekar T, Müller T, Dittrich M. Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data. Molecular & Cellular Proteomics : McP. 13: 1877-89. PMID 24807868 DOI: 10.1074/Mcp.M113.032839  0.515
2014 Dandekar T, Fieselmann A, Majeed S, Ahmed Z. Software applications toward quantitative metabolic flux analysis and modeling. Briefings in Bioinformatics. 15: 91-107. PMID 23142828 DOI: 10.1093/Bib/Bbs065  0.319
2013 Winstel V, Liang C, Sanchez-Carballo P, Steglich M, Munar M, Bröker BM, Penadés JR, Nübel U, Holst O, Dandekar T, Peschel A, Xia G. Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens. Nature Communications. 4: 2345. PMID 23965785 DOI: 10.1038/Ncomms3345  0.303
2013 Liang C, Krüger B, Dandekar T. GoSynthetic database tool to analyse natural and engineered molecular processes. Database : the Journal of Biological Databases and Curation. 2013: bat043. PMID 23813641 DOI: 10.1093/Database/Bat043  0.318
2012 Krüger B, Liang C, Prell F, Fieselmann A, Moya A, Schuster S, Völker U, Dandekar T. Metabolic adaptation and protein complexes in prokaryotes. Metabolites. 2: 940-58. PMID 24957769 DOI: 10.3390/Metabo2040940  0.32
2012 Ratzka C, Förster F, Liang C, Kupper M, Dandekar T, Feldhaar H, Gross R. Molecular characterization of antimicrobial peptide genes of the carpenter ant Camponotus floridanus. Plos One. 7: e43036. PMID 22912782 DOI: 10.1371/Journal.Pone.0043036  0.356
2012 Beisser D, Grohme MA, Kopka J, Frohme M, Schill RO, Hengherr S, Dandekar T, Klau GW, Dittrich M, Müller T. Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. Bmc Systems Biology. 6: 72. PMID 22713133 DOI: 10.1186/1752-0509-6-72  0.502
2012 Krueger B, Friedrich T, Förster F, Bernhardt J, Gross R, Dandekar T. Different evolutionary modifications as a guide to rewire two-component systems. Bioinformatics and Biology Insights. 6: 97-128. PMID 22586357 DOI: 10.4137/Bbi.S9356  0.324
2012 Beisser D, Brunkhorst S, Dandekar T, Klau GW, Dittrich MT, Müller T. Robustness and accuracy of functional modules in integrated network analysis. Bioinformatics (Oxford, England). 28: 1887-94. PMID 22581175 DOI: 10.1093/Bioinformatics/Bts265  0.482
2012 Förster F, Beisser D, Grohme MA, Liang C, Mali B, Siegl AM, Engelmann JC, Shkumatov AV, Schokraie E, Müller T, Schnölzer M, Schill RO, Frohme M, Dandekar T. Transcriptome analysis in tardigrade species reveals specific molecular pathways for stress adaptations. Bioinformatics and Biology Insights. 6: 69-96. PMID 22563243 DOI: 10.4137/Bbi.S9150  0.492
2012 Merget B, Koetschan C, Hackl T, Förster F, Dandekar T, Müller T, Schultz J, Wolf M. The ITS2 Database. Journal of Visualized Experiments : Jove. PMID 22433429 DOI: 10.3791/3806  0.633
2012 Fuchs TM, Eisenreich W, Kern T, Dandekar T. Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection. Frontiers in Microbiology. 3: 23. PMID 22347216 DOI: 10.3389/Fmicb.2012.00023  0.301
2011 Cecil A, Rikanovi? 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 Biology. 12: R24. PMID 21418624 DOI: 10.1186/Gb-2011-12-3-R24  0.33
2011 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. Molecular Biosystems. 7: 1241-53. PMID 21327190 DOI: 10.1039/C0Mb00315H  0.303
2011 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. The Isme Journal. 5: 61-70. PMID 20613790 DOI: 10.1038/Ismej.2010.95  0.363
2011 Förster F, Beisser D, Frohme M, Schill RO, Dandekar T. Bioinformatics identifies tardigrade molecular adaptations including the DNA-j family and first steps towards dynamical modelling Journal of Zoological Systematics and Evolutionary Research. 49: 120-126. DOI: 10.1111/J.1439-0469.2010.00609.X  0.333
2010 Friedrich T, Rahmann S, Weigel W, Rabsch W, Fruth A, Ron E, Gunzer F, Dandekar T, Hacker J, Müller T, Dobrindt U. High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis. Bmc Genomics. 11: 591. PMID 20964857 DOI: 10.1186/1471-2164-11-591  0.501
2010 Schauer K, Geginat G, Liang C, Goebel W, Dandekar T, Fuchs TM. Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling. Bmc Genomics. 11: 573. PMID 20955543 DOI: 10.1186/1471-2164-11-573  0.345
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. 10: 2982-3000. PMID 20662099 DOI: 10.1002/Pmic.200900388  0.353
2010 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. 11: 168. PMID 20226016 DOI: 10.1186/1471-2164-11-168  0.389
2010 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. 5: e9502. PMID 20224743 DOI: 10.1371/Journal.Pone.0009502  0.357
2010 Beisser D, Klau GW, Dandekar T, Müller T, Dittrich MT. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics (Oxford, England). 26: 1129-30. PMID 20189939 DOI: 10.1093/Bioinformatics/Btq089  0.462
2010 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. Arteriosclerosis, Thrombosis, and Vascular Biology. 30: 843-50. PMID 20110575 DOI: 10.1161/Atvbaha.109.200683  0.307
2010 Keller A, Förster F, Müller T, Dandekar T, Schultz J, Wolf M. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct. 5: 4. PMID 20078867 DOI: 10.1186/1745-6150-5-4  0.62
2010 Keller A, Wolf M, Dandekar T. Ribosomal RNA phylogenetics: The third dimension Biologia. 65: 388-391. DOI: 10.2478/S11756-010-0045-3  0.54
2010 Schill RO, Förster F, Dandekar T, Wolf M. Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada) Organisms Diversity and Evolution. 10: 287-296. DOI: 10.1007/S13127-010-0025-Z  0.515
2009 Engelmann JC, Rahmann S, Wolf M, Schultz J, Fritzilas E, Kneitz S, Dandekar T, Müller T. Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular Ecology Resources. 9: 83-93. PMID 21564570 DOI: 10.1111/J.1755-0998.2008.02199.X  0.579
2009 Liang C, Schmid A, López-Sánchez MJ, Moya A, Gross R, Bernhardt J, Dandekar T. JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. Bmc Bioinformatics. 10: 391. PMID 19943962 DOI: 10.1186/1471-2105-10-391  0.347
2009 Förster F, Liang C, Shkumatov A, Beisser D, Engelmann JC, Schnölzer M, Frohme M, Müller T, Schill RO, Dandekar T. Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. Bmc Genomics. 10: 469. PMID 19821996 DOI: 10.1186/1471-2164-10-469  0.326
2009 Schwarz R, Seibel PN, Rahmann S, Schoen C, Huenerberg M, Müller-Reible C, Dandekar T, Karchin R, Schultz J, Müller T. Detecting species-site dependencies in large multiple sequence alignments. Nucleic Acids Research. 37: 5959-68. PMID 19661281 DOI: 10.1093/Nar/Gkp634  0.507
2009 Krüger B, Dandekar T. Bioinformatical approaches to detect and analyze protein interactions. Methods in Molecular Biology (Clifton, N.J.). 564: 401-31. PMID 19544036 DOI: 10.1007/978-1-60761-157-8_23  0.372
2009 Schill RO, Mali B, Dandekar T, Schnölzer M, Reuter D, Frohme M. Molecular mechanisms of tolerance in tardigrades: new perspectives for preservation and stabilization of biological material. Biotechnology Advances. 27: 348-52. PMID 19472511 DOI: 10.1016/J.Biotechadv.2009.01.011  0.302
2009 Keller A, Schleicher T, Schultz J, Müller T, Dandekar T, Wolf M. 5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene. 430: 50-7. PMID 19026726 DOI: 10.1016/J.Gene.2008.10.012  0.64
2009 Guidetti R, Schill RO, Bertolani R, Dandekar T, Wolf M. New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov Journal of Zoological Systematics and Evolutionary Research. 47: 315-321. DOI: 10.1111/J.1439-0469.2009.00526.X  0.503
2008 Engelmann JC, Schwarz R, Blenk S, Friedrich T, Seibel PN, Dandekar T, Müller T. Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation. Bioinformatics and Biology Insights. 2: 265-80. PMID 19812781 DOI: 10.4137/Bbi.S665  0.501
2008 Kühnel M, Mayorga LS, Dandekar T, Thakar J, Schwarz R, Anes E, Griffiths G, Reich J. Modelling phagosomal lipid networks that regulate actin assembly. Bmc Systems Biology. 2: 107. PMID 19061496 DOI: 10.1186/1752-0509-2-107  0.518
2008 Seibel PN, Müller T, Dandekar T, Wolf M. Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. Bmc Research Notes. 1: 91. PMID 18854023 DOI: 10.1186/1756-0500-1-91  0.61
2008 Wolf M, Ruderisch B, Dandekar T, Schultz J, Müller T. ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments. Bioinformatics (Oxford, England). 24: 2401-2. PMID 18723521 DOI: 10.1093/Bioinformatics/Btn453  0.623
2008 Keller A, Schleicher T, Förster F, Ruderisch B, Dandekar T, Müller T, Wolf M. ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). Bmc Evolutionary Biology. 8: 218. PMID 18655698 DOI: 10.1186/1471-2148-8-218  0.606
2008 Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics (Oxford, England). 24: i223-31. PMID 18586718 DOI: 10.1093/bioinformatics/btn161  0.421
2008 Blenk S, Engelmann JC, Pinkert S, Weniger M, Schultz J, Rosenwald A, Müller-Hermelink HK, Müller T, Dandekar T. Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis. Bmc Cancer. 8: 106. PMID 18416826 DOI: 10.1186/1471-2407-8-106  0.318
2008 Selig C, Wolf M, Müller T, Dandekar T, Schultz J. The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Research. 36: D377-80. PMID 17933769 DOI: 10.1093/Nar/Gkm827  0.627
2007 Blenk S, Engelmann J, Weniger M, Schultz J, Dittrich M, Rosenwald A, Müller-Hermelink HK, Müller T, Dandekar T. 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: 399-420. PMID 19455257 DOI: 10.4137/Cin.S0  0.468
2007 Gerlach D, Wolf M, Dandekar T, Müller T, Pokorny A, Rahmann S. Deep metazoan phylogeny. In Silico Biology. 7: 151-4. PMID 17688440  0.527
2007 Müller T, Philippi N, Dandekar T, Schultz J, Wolf M. Distinguishing species. Rna (New York, N.Y.). 13: 1469-72. PMID 17652131 DOI: 10.1261/rna.617107  0.538
2007 Pachkov M, Dandekar T, Korbel J, Bork P, Schuster S. Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism. Gene. 396: 215-25. PMID 17467928 DOI: 10.1016/J.Gene.2007.02.033  0.689
2007 Wolf M, Selig C, Müller T, Philippi N, Dandekar T, Schultz J. Placozoa: At least two Biologia - Section Botany. 62: 641-645. DOI: 10.2478/S11756-007-0143-Z  0.537
2006 Deeken R, Engelmann JC, Efetova M, Czirjak T, Müller T, Kaiser WM, Tietz O, Krischke M, Mueller MJ, Palme K, Dandekar T, Hedrich R. An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach. The Plant Cell. 18: 3617-34. PMID 17172353 DOI: 10.1105/Tpc.106.044743  0.302
2006 Seibel PN, Müller T, Dandekar T, Schultz J, Wolf M. 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. Bmc Bioinformatics. 7: 498. PMID 17101042 DOI: 10.1186/1471-2105-7-498  0.623
2006 Seibel PN, Krüger J, Hartmeier S, Schwarzer K, Löwenthal K, Mersch H, Dandekar T, Giegerich R. XML schemas for common bioinformatic data types and their application in workflow systems. Bmc Bioinformatics. 7: 490. PMID 17087823 DOI: 10.1186/1471-2105-7-490  0.348
2006 Liang C, Dandekar T. inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons. Bmc Bioinformatics. 7: 461. PMID 17054788 DOI: 10.1186/1471-2105-7-461  0.375
2006 Friedrich T, Pils B, Dandekar T, Schultz J, Müller T. Modelling interaction sites in protein domains with interaction profile hidden Markov models. Bioinformatics (Oxford, England). 22: 2851-7. PMID 17000753 DOI: 10.1093/Bioinformatics/Btl486  0.517
2006 Wolf M, Seibel PN, Dandekar T, Lynn DH. A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists. The Journal of Eukaryotic Microbiology. 53: 315. PMID 16968448 DOI: 10.1111/J.1550-7408.2006.00123.X  0.448
2006 Hain T, Steinweg C, Kuenne CT, Billion A, Ghai R, Chatterjee SS, Domann E, Kärst U, Goesmann A, Bekel T, Bartels D, Kaiser O, Meyer F, Pühler A, Weisshaar B, ... ... Dandekar T, et al. Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. Journal of Bacteriology. 188: 7405-15. PMID 16936040 DOI: 10.1128/Jb.00758-06  0.309
2006 Schultz J, Müller T, Achtziger M, Seibel PN, Dandekar T, Wolf M. The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses. Nucleic Acids Research. 34: W704-7. PMID 16845103 DOI: 10.1093/Nar/Gkl129  0.631
2006 Nowrouzi A, Dittrich M, Klanke C, Heinkelein M, Rammling M, Dandekar T, von Kalle C, Rethwilm A. Genome-wide mapping of foamy virus vector integrations into a human cell line. The Journal of General Virology. 87: 1339-47. PMID 16603537 DOI: 10.1099/Vir.0.81554-0  0.3
2006 Dittrich M, Birschmann I, Pfrang J, Herterich S, Smolenski A, Walter U, Dandekar T. Analysis of SAGE data in human platelets: features of the transcriptome in an anucleate cell. Thrombosis and Haemostasis. 95: 643-51. PMID 16601835 DOI: 10.1160/Th05-11-0764  0.308
2006 Gaudermann P, Vogl I, Zientz E, Silva FJ, Moya A, Gross R, Dandekar T. Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus. Bmc Microbiology. 6: 1. PMID 16401340 DOI: 10.1186/1471-2180-6-1  0.412
2006 Rahmann S, Müller T, Dandekar T, Wolf M. Efficient and robust analysis of large phylogenetic datasets Advanced Data Mining Technologies in Bioinformatics. 104-117. DOI: 10.4018/978-1-59140-863-5.ch006  0.392
2005 Wolf M, Achtziger M, Schultz J, Dandekar T, Müller T. Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. Rna (New York, N.Y.). 11: 1616-23. PMID 16244129 DOI: 10.1261/Rna.2144205  0.62
2005 Wolf M, Friedrich J, Dandekar T, Müller T. CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. In Silico Biology. 5: 291-4. PMID 15996120  0.564
2005 Schwarz R, Musch P, von Kamp A, Engels B, Schirmer H, Schuster S, Dandekar T. YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. Bmc Bioinformatics. 6: 135. PMID 15929789 DOI: 10.1186/1471-2105-6-135  0.32
2005 Schmitt S, Hentschel U, Zea S, Dandekar T, Wolf M. ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). Journal of Molecular Evolution. 60: 327-36. PMID 15871043 DOI: 10.1007/S00239-004-0162-0  0.516
2005 Friedrich J, Dandekar T, Wolf M, Müller T. ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics (Oxford, England). 21: 2108-9. PMID 15677706 DOI: 10.1093/Bioinformatics/Bti289  0.594
2004 Krause R, von Mering C, Bork P, Dandekar T. Shared components of protein complexes--versatile building blocks or biochemical artefacts? Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 26: 1333-43. PMID 15551274 DOI: 10.1002/Bies.20141  0.686
2004 Müller T, Rahmann S, Dandekar T, Wolf M. Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). Bmc Evolutionary Biology. 4: 20. PMID 15222898 DOI: 10.1186/1471-2148-4-20  0.57
2004 Bengert P, Dandekar T. Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic Acids Research. 32: W154-9. PMID 15215370 DOI: 10.1093/Nar/Gkh352  0.335
2004 Wolf M, Müller T, Dandekar T, Pollack JD. Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. International Journal of Systematic and Evolutionary Microbiology. 54: 871-5. PMID 15143038 DOI: 10.1099/Ijs.0.02868-0  0.613
2004 Bertram H, Dandekar T. Stoffwechselanalyse: Der Weg vom Genom zum metabolischen Netzwerk (Pathway Analysis: On the Route from Genomics to Metabolic Networks) Information Technology. 46: 5-11. DOI: 10.1524/Itit.  0.317
2004 Dünßer M, Lampidis R, Schmidt S, Seipel D, Dandekar T. Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework Journal of Integrative Bioinformatics. 1: 52-63. DOI: 10.1515/Jib-2004-5  0.382
2003 Zemojtel T, Wade RC, Dandekar T. In search of the prototype of nitric oxide synthase Febs Letters. 554: 1-5. PMID 14596904 DOI: 10.1016/S0014-5793(03)01081-0  0.316
2003 Dandekar T, Moldenhauer F, Bulik S, Bertram H, Schuster S. A method for classifying metabolites in topological pathway analyses based on minimization of pathway number Biosystems. 70: 255-270. PMID 12941488 DOI: 10.1016/S0303-2647(03)00067-4  0.308
2003 Lohmüller T, Wenzler D, Hagemann S, Kieß W, Peters C, Dandekar T, Reinheckel T. Toward computer-based cleavage site prediction of cysteine endopeptidases Biological Chemistry. 384: 899-909. PMID 12887057 DOI: 10.1515/Bc.2003.101  0.326
2003 Schmidt S, Sunyaev S, Bork P, Dandekar T. Metabolites: a helping hand for pathway evolution? Trends in Biochemical Sciences. 28: 336-41. PMID 12826406 DOI: 10.1016/S0968-0004(03)00114-2  0.669
2002 Dandekar T, Sauerborn R. Comparative genome analysis and pathway reconstruction Pharmacogenomics. 3: 245-256. PMID 11972445 DOI: 10.1517/14622416.3.2.245  0.342
2002 Schmidt S, Bork P, Dandekar T. A versatile structural domain analysis server using profile weight matrices. Journal of Chemical Information and Computer Sciences. 42: 405-7. PMID 11911710 DOI: 10.1021/Ci010374R  0.602
2001 Dandekar T, Du F, Schirmer RH, Schmidt S. Medical target prediction from genome sequence: Combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches Computers and Chemistry. 26: 15-21. PMID 11765847 DOI: 10.1016/S0097-8485(01)00095-X  0.364
2001 Saxena IM, Brown RM, Dandekar T. Structure - Function characterization of cellulose synthase: Relationship to other glycosyltransferases Phytochemistry. 57: 1135-1148. PMID 11430986 DOI: 10.1016/S0031-9422(01)00048-6  0.311
2001 Dandekar T. Trends in biochemical systems Trends in Biochemical Sciences. 26: 637. DOI: 10.1016/S0968-0004(01)01871-0  0.308
2000 Dandekar T, Huynen M, Regula JT, Ueberle B, Zimmermann CU, Andrade MA, Doerks T, Sánchez-Pulido L, Snel B, Suyama M, Yuan YP, Herrmann R, Bork P. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Research. 28: 3278-88. PMID 10954595 DOI: 10.1093/Nar/28.17.3278  0.781
2000 Kenealy MR, Flouriot G, Sonntag-Buck V, Dandekar T, Brand H, Gannon F. The 3′-untranslated region of the human estrogen receptor α gene mediates rapid messenger ribonucleic acid turnover Endocrinology. 141: 2805-2813. PMID 10919266 DOI: 10.1210/Endo.141.8.7613  0.303
2000 Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnology. 18: 326-32. PMID 10700151 DOI: 10.1038/73786  0.309
1999 Dandekar T, Schuster S, Snel B, Huynen M, Bork P. Pathway alignment: application to the comparative analysis of glycolytic enzymes. The Biochemical Journal. 343: 115-24. PMID 10493919 DOI: 10.1042/Bj3430115  0.762
1999 Huynen MA, Dandekar T, Bork P. Variation and evolution of the citric-acid cycle: a genomic perspective. Trends in Microbiology. 7: 281-91. PMID 10390638 DOI: 10.1016/S0966-842X(99)01539-5  0.673
1999 Schuster S, Dandekar T, Fell DA. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends in Biotechnology. 17: 53-60. PMID 10087604 DOI: 10.1016/S0167-7799(98)01290-6  0.303
1999 König R, Dandekar T. Refined genetic algorithm simulations to model proteins Journal of Molecular Modeling. 5: 317-324. DOI: 10.1007/Pl00010719  0.352
1998 Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y. Predicting function: from genes to genomes and back. Journal of Molecular Biology. 283: 707-25. PMID 9790834 DOI: 10.1006/Jmbi.1998.2144  0.707
1998 Dandekar T, Snel B, Huynen M, Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends in Biochemical Sciences. 23: 324-8. PMID 9787636 DOI: 10.1016/S0968-0004(98)01274-2  0.744
1998 Dandekar T, Beyer K, Bork P, Kenealy MR, Pantopoulos K, Hentze M, Sonntag-Buck V, Flouriot G, Gannon F, Schreiber S. Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches. Bioinformatics (Oxford, England). 14: 271-8. PMID 9614270 DOI: 10.1093/BIOINFORMATICS/14.3.271  0.533
1998 Huynen M, Dandekar T, Bork P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. Febs Letters. 426: 1-5. PMID 9598967 DOI: 10.1016/S0014-5793(98)00276-2  0.689
1998 Bork P, Dandekar T, Eisenhaber F, Huynen M. Characterization of targeting domains by sequence analysis: glycogen-binding domains in protein phosphatases. Journal of Molecular Medicine (Berlin, Germany). 76: 77-9. PMID 9500672 DOI: 10.1007/s001090050194  0.501
1998 Petfalski E, Dandekar T, Henry Y, Tollervey D. Processing of the precursors to small nucleolar RNAs and rRNAs requires common components Molecular and Cellular Biology. 18: 1181-1189. PMID 9488433 DOI: 10.1128/Mcb.18.3.1181  0.312
1998 Jacobs T, Bruchhaus I, Dandekar T, Tannich E, Leippe M. Isolation and molecular characterization of a surface-bound proteinase of Entamoeba histolytica. Molecular Microbiology. 27: 269-76. PMID 9484883 DOI: 10.1046/J.1365-2958.1998.00662.X  0.31
1998 Dandekar T, Argos P. Applying experimental data to protein fold prediction with the genetic algorithm. Protein Engineering. 10: 877-93. PMID 9415438 DOI: 10.1093/Protein/10.8.877  0.323
1997 Beyer K, Dandekar T, Keller W. RNA Ligands Selected by Cleavage Stimulation Factor Contain Distinct Sequence Motifs That Function as Downstream Elements in 3′-End Processing of Pre-mRNA Journal of Biological Chemistry. 272: 26769-26779. PMID 9334264 DOI: 10.1074/Jbc.272.42.26769  0.309
1996 Dandekar T, Argos P. Ab initio tertiary-fold prediction of helical and non-helical protein chains using a genetic algorithm. International Journal of Biological Macromolecules. 18: 1-4. PMID 8852746 DOI: 10.1016/0141-8130(95)01036-X  0.302
1996 Dandekar T, Argos P. Identifying the tertiary fold of small proteins with different topologies from sequence and secondary structure using the genetic algorithm and extended criteria specific for strand regions. Journal of Molecular Biology. 256: 645-60. PMID 8604145 DOI: 10.1006/Jmbi.1996.0115  0.344
1995 Dandekar T, Hentze MW. Finding the hairpin in the haystack: searching for RNA motifs. Trends in Genetics : Tig. 11: 45-50. PMID 7536364 DOI: 10.1016/S0168-9525(00)88996-9  0.311
1994 Dandekar T, Argos P. Folding the main chain of small proteins with the genetic algorithm. Journal of Molecular Biology. 236: 844-61. PMID 8114098 DOI: 10.1006/Jmbi.1994.1193  0.304
1993 Dandekar T, Argos P. Potential of genetic algorithms in protein folding and protein engineering simulations. Protein Engineering. 5: 637-45. PMID 1480618 DOI: 10.1093/Protein/5.7.637  0.306
1993 Dandekar T, Tollervey D. Identification and functional analysis of a novel yeast small nucleolar RNA Nucleic Acids Research. 21: 5386-5390. DOI: 10.1093/Nar/21.23.5386  0.32
1992 Dandekar T. Yeast U3 localization and correct sequence (snR17a) and promotor activity (snR17b) identified by homology search. Dna Sequence : the Journal of Dna Sequencing and Mapping. 1: 217-8. PMID 1773061 DOI: 10.3109/10425179109020774  0.308
1990 Dandekar T, Sibbald PR. Trans-splicing of pre-mRNA is predicted to occur in a wide range of organisms including vertebrates. Nucleic Acids Research. 18: 4719-25. PMID 2395638 DOI: 10.1093/Nar/18.16.4719  0.304
1989 Dandekar T, Ribes V, Tollervey D. Schizosaccharomyces pombe U4 small nuclear RNA closely resembles vertebrate U4 and is required for growth Journal of Molecular Biology. 208: 371-379. DOI: 10.1016/0022-2836(89)90502-0  0.317
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