Thomas Dandekar Department of Bioinformatics University Wuerzburg Biography Publications Institution JoVE Articles Thomas Dandekar has not added a biography. If you are Thomas Dandekar and would like to personalize this page please email our Author Liaison for assistance. Publications Toward a Systemic Understanding of Listeria Monocytogenes Metabolism During Infection Frontiers in Microbiology. 2012 | Pubmed ID: 22347216 PlateletWeb: a Systems Biologic Analysis of Signaling Networks in Human Platelets Blood. Jan, 2012 | Pubmed ID: 22123846 Time-resolved in Silico Modeling of Fine-tuned CAMP Signaling in Platelets: Feedback Loops, Titrated Phosphorylations and Pharmacological Modulation BMC Systems Biology. 2011 | Pubmed ID: 22034949 Integration of Boolean Models Exemplified on Hepatocyte Signal Transduction Briefings in Bioinformatics. Oct, 2011 | Pubmed ID: 22016404 Staphylococcus Aureus Physiological Growth Limitations: Insights from Flux Calculations Built on Proteomics and External Metabolite Data Proteomics. May, 2011 | Pubmed ID: 21472852 Immune Response of the Ant Camponotus Floridanus Against Pathogens and Its Obligate Mutualistic Endosymbiont Insect Biochemistry and Molecular Biology. Aug, 2011 | Pubmed ID: 21440063 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. 2011 | Pubmed ID: 21418624 A Metabolomics and Proteomics Study of the Adaptation of Staphylococcus Aureus to Glucose Starvation Molecular BioSystems. Apr, 2011 | Pubmed ID: 21327190 Two Nucleus-localized CDK-like Kinases with Crucial Roles for Malaria Parasite Erythrocytic Replication Are Involved in Phosphorylation of Splicing Factor Journal of Cellular Biochemistry. May, 2011 | Pubmed ID: 21312235 Single-cell Genomics Reveals the Lifestyle of Poribacteria, a Candidate Phylum Symbiotically Associated with Marine Sponges The ISME Journal. Jan, 2011 | Pubmed ID: 20613790 Lead Expansion and Virtual Screening of Indinavir Derivate HIV-1 Protease Inhibitors Using Pharmacophoric - Shape Similarity Scoring Function Bioinformation. 2010 | Pubmed ID: 20978602 High-throughput Microarray Technology in Diagnostics of Enterobacteria Based on Genome-wide Probe Selection and Regression Analysis BMC Genomics. 2010 | Pubmed ID: 20964857 Deciphering the Intracellular Metabolism of Listeria Monocytogenes by Mutant Screening and Modelling BMC Genomics. 2010 | Pubmed ID: 20955543 Pharmacogenomic Strategies Against Microbial Resistance: from Bright to Bleak to Innovative Pharmacogenomics. Sep, 2010 | Pubmed ID: 20860457 Protecs, a Comprehensive and Powerful Storage and Analysis System for OMICS Data, Applied for Profiling the Anaerobiosis Response of Staphylococcus Aureus COL Proteomics. Aug, 2010 | Pubmed ID: 20662099 Developmental Profiling by Mass Spectrometry of Phosphocholine Containing Phospholipids in the Rat Nervous System Reveals Temporo-spatial Gradients Journal of Neurochemistry. Aug, 2010 | Pubmed ID: 20524967 Carbon Metabolism of Intracellular Bacterial Pathogens and Possible Links to Virulence Nature Reviews. Microbiology. Jun, 2010 | Pubmed ID: 20453875 Transcriptome Survey of the Anhydrobiotic Tardigrade Milnesium Tardigradum in Comparison with Hypsibius Dujardini and Richtersius Coronifer BMC Genomics. 2010 | Pubmed ID: 20226016 Proteomic Analysis of Tardigrades: Towards a Better Understanding of Molecular Mechanisms by Anhydrobiotic Organisms PloS One. 2010 | Pubmed ID: 20224743 The IronChip Evaluation Package: a Package of Perl Modules for Robust Analysis of Custom Microarrays BMC Bioinformatics. 2010 | Pubmed ID: 20193060 BioNet: an R-Package for the Functional Analysis of Biological Networks Bioinformatics (Oxford, England). Apr, 2010 | Pubmed ID: 20189939 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. Apr, 2010 | Pubmed ID: 20110575 Including RNA Secondary Structures Improves Accuracy and Robustness in Reconstruction of Phylogenetic Trees Biology Direct. 2010 | Pubmed ID: 20078867 Stress Response in Tardigrades: Differential Gene Expression of Molecular Chaperones Cell Stress & Chaperones. Jul, 2010 | Pubmed ID: 19943197 Modelling Cross-hybridization on Phylogenetic DNA Microarrays Increases the Detection Power of Closely Related Species Molecular Ecology Resources. Jan, 2009 | Pubmed ID: 21564570 JANE: Efficient Mapping of Prokaryotic ESTs and Variable Length Sequence Reads on Related Template Genomes BMC Bioinformatics. 2009 | Pubmed ID: 19943962 Tardigrade Workbench: Comparing Stress-related Proteins, Sequence-similar and Functional Protein Clusters As Well As RNA Elements in Tardigrades BMC Genomics. 2009 | Pubmed ID: 19821996 Modeling System States in Liver Cells: Survival, Apoptosis and Their Modifications in Response to Viral Infection BMC Systems Biology. 2009 | Pubmed ID: 19772631 The Highly Attenuated Oncolytic Recombinant Vaccinia Virus GLV-1h68: Comparative Genomic Features and the Contribution of F14.5L Inactivation Molecular Genetics and Genomics : MGG. Oct, 2009 | Pubmed ID: 19701652 CA/C1 Peptidases of the Malaria Parasites Plasmodium Falciparum and P. Berghei and Their Mammalian Hosts--a Bioinformatical Analysis Biological Chemistry. Nov, 2009 | Pubmed ID: 19663681 Detecting Species-site Dependencies in Large Multiple Sequence Alignments Nucleic Acids Research. Oct, 2009 | Pubmed ID: 19661281 Bioinformatical Approaches to Detect and Analyze Protein Interactions Methods in Molecular Biology (Clifton, N.J.). 2009 | Pubmed ID: 19544036 Molecular Mechanisms of Tolerance in Tardigrades: New Perspectives for Preservation and Stabilization of Biological Material Biotechnology Advances. Jul-Aug, 2009 | Pubmed ID: 19472511 5.8S-28S RRNA Interaction and HMM-based ITS2 Annotation Gene. Feb, 2009 | Pubmed ID: 19026726 Unsupervised Meta-analysis on Diverse Gene Expression Datasets Allows Insight into Gene Function and Regulation Bioinformatics and Biology Insights. 2008 | Pubmed ID: 19812781 Modelling Phagosomal Lipid Networks That Regulate Actin Assembly BMC Systems Biology. 2008 | Pubmed ID: 19061496 New Trends in Pharmacogenomic Strategies Against Resistance Development in Microbial Infections Pharmacogenomics. Nov, 2008 | Pubmed ID: 19018725 Synchronous Visual Analysis and Editing of RNA Sequence and Secondary Structure Alignments Using 4SALE BMC Research Notes. 2008 | Pubmed ID: 18854023 ProfDistS: (profile-) Distance Based Phylogeny on Sequence--structure Alignments Bioinformatics (Oxford, England). Oct, 2008 | Pubmed ID: 18723521 ITS2 Data Corroborate a Monophyletic Chlorophycean DO-group (Sphaeropleales) BMC Evolutionary Biology. 2008 | Pubmed ID: 18655698 Identifying Functional Modules in Protein-protein Interaction Networks: an Integrated Exact Approach Bioinformatics (Oxford, England). Jul, 2008 | Pubmed ID: 18586718 The Linear Chromosome of the Plant-pathogenic Mycoplasma 'Candidatus Phytoplasma Mali' BMC Genomics. 2008 | Pubmed ID: 18582369 Platelet Protein Interactions: Map, Signaling Components, and Phosphorylation Groundstate Arteriosclerosis, Thrombosis, and Vascular Biology. Jul, 2008 | Pubmed ID: 18451328 Explorative Data Analysis of MCL Reveals Gene Expression Networks Implicated in Survival and Prognosis Supported by Explorative CGH Analysis BMC Cancer. 2008 | Pubmed ID: 18416826 Interactions of Methylene Blue with Human Disulfide Reductases and Their Orthologues from Plasmodium Falciparum Antimicrobial Agents and Chemotherapy. Jan, 2008 | Pubmed ID: 17967916 The ITS2 Database II: Homology Modelling RNA Structure for Molecular Systematics Nucleic Acids Research. Jan, 2008 | Pubmed ID: 17933769 Use of Functional Highly Purified Human Platelets for the Identification of New Proteins of the IPP Signaling Pathway Thrombosis Research. 2008 | Pubmed ID: 17931695 Exonization of Active Mouse L1s: a Driver of Transcriptome Evolution? BMC Genomics. 2007 | Pubmed ID: 17963496 Integrated Network Reconstruction, Visualization and Analysis Using YANAsquare BMC Bioinformatics. 2007 | Pubmed ID: 17725829 Deep Metazoan Phylogeny In Silico Biology. 2007 | Pubmed ID: 17688440 Distinguishing Species RNA (New York, N.Y.). Sep, 2007 | Pubmed ID: 17652131 Use of Pathway Analysis and Genome Context Methods for Functional Genomics of Mycoplasma Pneumoniae Nucleotide Metabolism Gene. Jul, 2007 | Pubmed ID: 17467928 An Integrated View of Gene Expression and Solute Profiles of Arabidopsis Tumors: a Genome-wide Approach The Plant Cell. Dec, 2006 | Pubmed ID: 17172353 4SALE--a Tool for Synchronous RNA Sequence and Secondary Structure Alignment and Editing BMC Bioinformatics. 2006 | Pubmed ID: 17101042 XML Schemas for Common Bioinformatic Data Types and Their Application in Workflow Systems BMC Bioinformatics. 2006 | Pubmed ID: 17087823 InGeno--an Integrated Genome and Ortholog Viewer for Improved Genome to Genome Comparisons BMC Bioinformatics. 2006 | Pubmed ID: 17054788 Modelling Interaction Sites in Protein Domains with Interaction Profile Hidden Markov Models Bioinformatics (Oxford, England). Dec, 2006 | Pubmed ID: 17000753 A Java Applet for Exploring the New Higher Level Classification of Eukaryotes with Emphasis on the Taxonomy of Protists The Journal of Eukaryotic Microbiology. Sep-Oct, 2006 | Pubmed ID: 16968448 Whole-genome Sequence of Listeria Welshimeri Reveals Common Steps in Genome Reduction with Listeria Innocua As Compared to Listeria Monocytogenes Journal of Bacteriology. Nov, 2006 | Pubmed ID: 16936040 The Internal Transcribed Spacer 2 Database--a Web Server for (not Only) Low Level Phylogenetic Analyses Nucleic Acids Research. Jul, 2006 | Pubmed ID: 16845103 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 The Journal of Biological Chemistry. Aug, 2006 | Pubmed ID: 16760464 Lysosomal, Cytoskeletal, and Metabolic Alterations in Cardiomyopathy of Cathepsin L Knockout Mice FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology. Jun, 2006 | Pubmed ID: 16636100 Genome-wide Mapping of Foamy Virus Vector Integrations into a Human Cell Line The Journal of General Virology. May, 2006 | Pubmed ID: 16603537 Analysis of SAGE Data in Human Platelets: Features of the Transcriptome in an Anucleate Cell Thrombosis and Haemostasis. Apr, 2006 | Pubmed ID: 16601835 RIP Death Domain Structural Interactions Implicated in TNF-mediated Proliferation and Survival Proteins. May, 2006 | Pubmed ID: 16470584 13C Isotopologue Perturbation Studies of Listeria Monocytogenes Carbon Metabolism and Its Modulation by the Virulence Regulator PrfA Proceedings of the National Academy of Sciences of the United States of America. Feb, 2006 | Pubmed ID: 16461909 Analysis of and Function Predictions for Previously Conserved Hypothetical or Putative Proteins in Blochmannia Floridanus BMC Microbiology. 2006 | Pubmed ID: 16401340 Understanding Platelets. Lessons from Proteomics, Genomics and Promises from Network Analysis Thrombosis and Haemostasis. Nov, 2005 | Pubmed ID: 16363231 B-Raf and C-Raf Signaling Investigated in a Simplified Model of the Mitogenic Kinase Cascade Biological Chemistry. Nov, 2005 | Pubmed ID: 16307482 Homology Modeling Revealed More Than 20,000 RRNA Internal Transcribed Spacer 2 (ITS2) Secondary Structures RNA (New York, N.Y.). Nov, 2005 | Pubmed ID: 16244129 CBCAnalyzer: Inferring Phylogenies Based on Compensatory Base Changes in RNA Secondary Structures In Silico Biology. 2005 | Pubmed ID: 15996120 Metabolites and Pathway Flexibility In Silico Biology. 2005 | Pubmed ID: 15972010 YANA - a Software Tool for Analyzing Flux Modes, Gene-expression and Enzyme Activities BMC Bioinformatics. 2005 | Pubmed ID: 15929789 ITS-2 and 18S RRNA Gene Phylogeny of Aplysinidae (Verongida, Demospongiae) Journal of Molecular Evolution. Mar, 2005 | Pubmed ID: 15871043 Current Efforts in the Analysis of RNAi and RNAi Target Genes Briefings in Bioinformatics. Mar, 2005 | Pubmed ID: 15826358 ProfDist: a Tool for the Construction of Large Phylogenetic Trees Based on Profile Distances Bioinformatics (Oxford, England). May, 2005 | Pubmed ID: 15677706 L1Base: from Functional Annotation to Prediction of Active LINE-1 Elements Nucleic Acids Research. Jan, 2005 | Pubmed ID: 15608246 Metabolic Interdependence of Obligate Intracellular Bacteria and Their Insect Hosts Microbiology and Molecular Biology Reviews : MMBR. Dec, 2004 | Pubmed ID: 15590782 Shared Components of Protein Complexes--versatile Building Blocks or Biochemical Artefacts? BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology. Dec, 2004 | Pubmed ID: 15551274 Accurate and Robust Phylogeny Estimation Based on Profile Distances: a Study of the Chlorophyceae (Chlorophyta) BMC Evolutionary Biology. Jun, 2004 | Pubmed ID: 15222898 Riboswitch Finder--a Tool for Identification of Riboswitch RNAs Nucleic Acids Research. Jul, 2004 | Pubmed ID: 15215370 Pharmacogenomic Strategies Against Resistance Development in Microbial Infections Pharmacogenomics. Jun, 2004 | Pubmed ID: 15165173 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. May, 2004 | Pubmed ID: 15143038 A Novel Conserved Family of Nitric Oxide Synthase? Trends in Biochemical Sciences. May, 2004 | Pubmed ID: 15130557 NO-bound Myoglobin: Structural Diversity and Dynamics of the NO Ligand Journal of the American Chemical Society. Feb, 2004 | Pubmed ID: 14971914 An Open Source Protein Gel Documentation System for Proteome Analyses Journal of Chemical Information and Computer Sciences. Jan-Feb, 2004 | Pubmed ID: 14741024 In Search of the Prototype of Nitric Oxide Synthase FEBS Letters. Nov, 2003 | Pubmed ID: 14596904 A Method for Classifying Metabolites in Topological Pathway Analyses Based on Minimization of Pathway Number Bio Systems. Aug, 2003 | Pubmed ID: 12941488 Toward Computer-based Cleavage Site Prediction of Cysteine Endopeptidases Biological Chemistry. Jun, 2003 | Pubmed ID: 12887057 Metabolites: a Helping Hand for Pathway Evolution? Trends in Biochemical Sciences. Jun, 2003 | Pubmed ID: 12826406 A Software Tool-box for Analysis of Regulatory RNA Elements Nucleic Acids Research. Jul, 2003 | Pubmed ID: 12824342 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. 2002 | Pubmed ID: 12427276 Comparative Genome Analysis and Pathway Reconstruction Pharmacogenomics. Mar, 2002 | Pubmed ID: 11972445 A Versatile Structural Domain Analysis Server Using Profile Weight Matrices Journal of Chemical Information and Computer Sciences. Mar-Apr, 2002 | Pubmed ID: 11911710 En kombineret 3D manipuleret væv Claudia Göttlich*1, Lena C. Müller*1, Meik Kunz*3, Franziska Schmitt1, Heike Walles1,4, Thorsten Walles2, Thomas Dandekar3, Gudrun Dandekar1,4, Sarah L. Nietzer1 1Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, 2Department of Cardiothoracic Surgery, University Hospital Wuerzburg, 3Department of Bioinformatics, University Wuerzburg, 4Translational Center Wuerzburg, Fraunhofer Institute Interfacial Engineering and Biotechnology IGB Bioengineering Den ITS2 Database Benjamin Merget1,2, Christian Koetschan1, Thomas Hackl1, Frank Förster1, Thomas Dandekar1, Tobias Müller1, Jörg Schultz1, Matthias Wolf1 1Department of Bioinformatics, Biocenter, University of Würzburg, 2Institute of Pharmacy and Food Chemistry, University of Würzburg JoVE 3806 Biology
En kombineret 3D manipuleret væv Claudia Göttlich*1, Lena C. Müller*1, Meik Kunz*3, Franziska Schmitt1, Heike Walles1,4, Thorsten Walles2, Thomas Dandekar3, Gudrun Dandekar1,4, Sarah L. Nietzer1 1Department of Tissue Engineering and Regenerative Medicine (TERM), University Hospital Wuerzburg, 2Department of Cardiothoracic Surgery, University Hospital Wuerzburg, 3Department of Bioinformatics, University Wuerzburg, 4Translational Center Wuerzburg, Fraunhofer Institute Interfacial Engineering and Biotechnology IGB Bioengineering
Den ITS2 Database Benjamin Merget1,2, Christian Koetschan1, Thomas Hackl1, Frank Förster1, Thomas Dandekar1, Tobias Müller1, Jörg Schultz1, Matthias Wolf1 1Department of Bioinformatics, Biocenter, University of Würzburg, 2Institute of Pharmacy and Food Chemistry, University of Würzburg JoVE 3806 Biology
