Thomas Dandekar

Department of Bioinformatics, University of Würzburg

Affiliated withUniversity of Würzburg University Wuerzburg

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JoVE Journal Publications

ArticleTotal : 2	Year
Publication title Cited by 52	2012
Publication title Cited by 29	2016

Other Publications

Article	Year
A versatile structural domain analysis server using profile weight matrices. Journal of chemical information and computer sciences\| PubMed ID: 11911710	2002
Comparative genome analysis and pathway reconstruction. Pharmacogenomics\| PubMed ID: 11972445	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 gl... Omics : a journal of integrative biology\| PubMed ID: 12427276	2002
A software tool-box for analysis of regulatory RNA elements. Nucleic acids research\| PubMed ID: 12824342	2003
Metabolites: a helping hand for pathway evolution? Trends in biochemical sciences\| PubMed ID: 12826406	2003
Toward computer-based cleavage site prediction of cysteine endopeptidases. Biological chemistry\| PubMed ID: 12887057	2003
A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. Bio Systems\| PubMed ID: 12941488	2003
In search of the prototype of nitric oxide synthase. FEBS letters\| PubMed ID: 14596904	2003
An open source protein gel documentation system for proteome analyses. Journal of chemical information and computer sciences\| PubMed ID: 14741024	2004
NO-bound myoglobin: structural diversity and dynamics of the NO ligand. Journal of the American Chemical Society\| PubMed ID: 14971914	2004
A novel conserved family of nitric oxide synthase? Trends in biochemical sciences\| PubMed ID: 15130557	2004
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\| PubMed ID: 15143038	2004
Pharmacogenomic strategies against resistance development in microbial infections. Pharmacogenomics\| PubMed ID: 15165173	2004
Riboswitch finder--a tool for identification of riboswitch RNAs. Nucleic acids research\| PubMed ID: 15215370	2004
Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta). BMC evolutionary biology\| PubMed ID: 15222898	2004
Shared components of protein complexes--versatile building blocks or biochemical artefacts? BioEssays : news and reviews in molecular, cellular and developmental biology\| PubMed ID: 15551274	2004
Metabolic interdependence of obligate intracellular bacteria and their insect hosts. Microbiology and molecular biology reviews : MMBR\| PubMed ID: 15590782	2004
L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic acids research\| PubMed ID: 15608246	2005
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinformatics (Oxford, England)\| PubMed ID: 15677706	2005
Current efforts in the analysis of RNAi and RNAi target genes. Briefings in bioinformatics\| PubMed ID: 15826358	2005
ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae). Journal of molecular evolution\| PubMed ID: 15871043	2005
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC bioinformatics\| PubMed ID: 15929789	2005
Metabolites and pathway flexibility. In silico biology\| PubMed ID: 15972010	2005
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. In silico biology\| PubMed ID: 15996120	2005
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures. RNA (New York, N.Y.)\| PubMed ID: 16244129	2005
B-Raf and C-Raf signaling investigated in a simplified model of the mitogenic kinase cascade. Biological chemistry\| PubMed ID: 16307482	2005
Understanding platelets. Lessons from proteomics, genomics and promises from network analysis. Thrombosis and haemostasis\| PubMed ID: 16363231	2005
Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus. BMC microbiology\| PubMed ID: 16401340	2006
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\| PubMed ID: 16461909	2006
RIP death domain structural interactions implicated in TNF-mediated proliferation and survival. Proteins\| PubMed ID: 16470584	2006
Analysis of SAGE data in human platelets: features of the transcriptome in an anucleate cell. Thrombosis and haemostasis\| PubMed ID: 16601835	2006
Genome-wide mapping of foamy virus vector integrations into a human cell line. The Journal of general virology\| PubMed ID: 16603537	2006
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\| PubMed ID: 16636100	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 s... The Journal of biological chemistry\| PubMed ID: 16760464	2006
The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses. Nucleic acids research\| PubMed ID: 16845103	2006
Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. Journal of bacteriology\| PubMed ID: 16936040	2006
A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists. The Journal of eukaryotic microbiology\| PubMed ID: 16968448	2006
Modelling interaction sites in protein domains with interaction profile hidden Markov models. Bioinformatics (Oxford, England)\| PubMed ID: 17000753	2006
inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons. BMC bioinformatics\| PubMed ID: 17054788	2006
XML schemas for common bioinformatic data types and their application in workflow systems. BMC bioinformatics\| PubMed ID: 17087823	2006
4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing. BMC bioinformatics\| PubMed ID: 17101042	2006
An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach. The Plant cell\| PubMed ID: 17172353	2006
Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism. Gene\| PubMed ID: 17467928	2007
Distinguishing species. RNA (New York, N.Y.)\| PubMed ID: 17652131	2007
Deep metazoan phylogeny. In silico biology\| PubMed ID: 17688440	2007
Integrated network reconstruction, visualization and analysis using YANAsquare. BMC bioinformatics\| PubMed ID: 17725829	2007
Use of functional highly purified human platelets for the identification of new proteins of the IPP signaling pathway. Thrombosis research\| PubMed ID: 17931695	2008
The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic acids research\| PubMed ID: 17933769	2008
Exonization of active mouse L1s: a driver of transcriptome evolution? BMC genomics\| PubMed ID: 17963496	2007
Interactions of methylene blue with human disulfide reductases and their orthologues from Plasmodium falciparum. Antimicrobial agents and chemotherapy\| PubMed ID: 17967916	2008
Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis. BMC cancer\| PubMed ID: 18416826	2008
Platelet protein interactions: map, signaling components, and phosphorylation groundstate. Arteriosclerosis, thrombosis, and vascular biology\| PubMed ID: 18451328	2008
The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'. BMC genomics\| PubMed ID: 18582369	2008
Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics (Oxford, England)\| PubMed ID: 18586718	2008
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales). BMC evolutionary biology\| PubMed ID: 18655698	2008
ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments. Bioinformatics (Oxford, England)\| PubMed ID: 18723521	2008
Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE. BMC research notes\| PubMed ID: 18854023	2008
New trends in pharmacogenomic strategies against resistance development in microbial infections. Pharmacogenomics\| PubMed ID: 19018725	2008
5.8S-28S rRNA interaction and HMM-based ITS2 annotation. Gene\| PubMed ID: 19026726	2009
Modelling phagosomal lipid networks that regulate actin assembly. BMC systems biology\| PubMed ID: 19061496	2008
Molecular mechanisms of tolerance in tardigrades: new perspectives for preservation and stabilization of biological material. Biotechnology advances\| PubMed ID: 19472511	2009
Bioinformatical approaches to detect and analyze protein interactions. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 19544036	2009
Detecting species-site dependencies in large multiple sequence alignments. Nucleic acids research\| PubMed ID: 19661281	2009
CA/C1 peptidases of the malaria parasites Plasmodium falciparum and P. berghei and their mammalian hosts--a bioinformatical analysis. Biological chemistry\| PubMed ID: 19663681	2009
The highly attenuated oncolytic recombinant vaccinia virus GLV-1h68: comparative genomic features and the contribution of F14.5L inactivation. Molecular genetics and genomics : MGG\| PubMed ID: 19701652	2009
Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection. BMC systems biology\| PubMed ID: 19772631	2009
Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation. Bioinformatics and biology insights\| PubMed ID: 19812781	2008
Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. BMC genomics\| PubMed ID: 19821996	2009
Stress response in tardigrades: differential gene expression of molecular chaperones. Cell stress & chaperones\| PubMed ID: 19943197	2010
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. BMC bioinformatics\| PubMed ID: 19943962	2009
Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology direct\| PubMed ID: 20078867	2010
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\| PubMed ID: 20110575	2010
BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics (Oxford, England)\| PubMed ID: 20189939	2010
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. BMC bioinformatics\| PubMed ID: 20193060	2010
Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms. PloS one\| PubMed ID: 20224743	2010
Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer. BMC genomics\| PubMed ID: 20226016	2010
Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nature reviews. Microbiology\| PubMed ID: 20453875	2010
Developmental profiling by mass spectrometry of phosphocholine containing phospholipids in the rat nervous system reveals temporo-spatial gradients. Journal of neurochemistry\| PubMed ID: 20524967	2010
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. The ISME journal\| PubMed ID: 20613790	2011
Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics\| PubMed ID: 20662099	2010
Pharmacogenomic strategies against microbial resistance: from bright to bleak to innovative. Pharmacogenomics\| PubMed ID: 20860457	2010
Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling. BMC genomics\| PubMed ID: 20955543	2010
High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis. BMC genomics\| PubMed ID: 20964857	2010
Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function. Bioinformation\| PubMed ID: 20978602	2010
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\| PubMed ID: 21312235	2011
A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Molecular bioSystems\| PubMed ID: 21327190	2011
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\| PubMed ID: 21418624	2011
Immune response of the ant Camponotus floridanus against pathogens and its obligate mutualistic endosymbiont. Insect biochemistry and molecular biology\| PubMed ID: 21440063	2011
Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data. Proteomics\| PubMed ID: 21472852	2011
Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species. Molecular ecology resources\| PubMed ID: 21564570	2009
Integration of Boolean models exemplified on hepatocyte signal transduction. Briefings in bioinformatics\| PubMed ID: 22016404	2011
Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation. BMC systems biology\| PubMed ID: 22034949	2011
PlateletWeb: a systems biologic analysis of signaling networks in human platelets. Blood\| PubMed ID: 22123846	2012
Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection. Frontiers in microbiology\| PubMed ID: 22347216	2012