Thomas Dandekar

A versatile structural domain analysis server using profile weight matrices.

Comparative genome analysis and pathway reconstruction.

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.

A software tool-box for analysis of regulatory RNA elements.

Metabolites: a helping hand for pathway evolution?

Toward computer-based cleavage site prediction of cysteine endopeptidases.

A method for classifying metabolites in topological pathway analyses based on minimization of pathway number.

In search of the prototype of nitric oxide synthase.

An open source protein gel documentation system for proteome analyses.

NO-bound myoglobin: structural diversity and dynamics of the NO ligand.

A novel conserved family of nitric oxide synthase?

Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data.

Pharmacogenomic strategies against resistance development in microbial infections.

Riboswitch finder--a tool for identification of riboswitch RNAs.

Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta).

Shared components of protein complexes--versatile building blocks or biochemical artefacts?

Metabolic interdependence of obligate intracellular bacteria and their insect hosts.

L1Base: from functional annotation to prediction of active LINE-1 elements.

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.

Current efforts in the analysis of RNAi and RNAi target genes.

ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae).

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

Metabolites and pathway flexibility.

CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures.

Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures.

B-Raf and C-Raf signaling investigated in a simplified model of the mitogenic kinase cascade.

Understanding platelets. Lessons from proteomics, genomics and promises from network analysis.

Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus.

13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA.

RIP death domain structural interactions implicated in TNF-mediated proliferation and survival.

Analysis of SAGE data in human platelets: features of the transcriptome in an anucleate cell.

Genome-wide mapping of foamy virus vector integrations into a human cell line.

Lysosomal, cytoskeletal, and metabolic alterations in cardiomyopathy of cathepsin L knockout mice.

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 internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses.

Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes.

A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists.

Modelling interaction sites in protein domains with interaction profile hidden Markov models.

inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons.

XML schemas for common bioinformatic data types and their application in workflow systems.

4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing.

An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach.

Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.

Distinguishing species.

Deep metazoan phylogeny.

Integrated network reconstruction, visualization and analysis using YANAsquare.

Use of functional highly purified human platelets for the identification of new proteins of the IPP signaling pathway.

The ITS2 Database II: homology modelling RNA structure for molecular systematics.

Exonization of active mouse L1s: a driver of transcriptome evolution?

Interactions of methylene blue with human disulfide reductases and their orthologues from Plasmodium falciparum.

Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis.

Platelet protein interactions: map, signaling components, and phosphorylation groundstate.

The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'.

Identifying functional modules in protein-protein interaction networks: an integrated exact approach.

ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales).

ProfDistS: (profile-) distance based phylogeny on sequence--structure alignments.

Synchronous visual analysis and editing of RNA sequence and secondary structure alignments using 4SALE.

New trends in pharmacogenomic strategies against resistance development in microbial infections.

5.8S-28S rRNA interaction and HMM-based ITS2 annotation.

Modelling phagosomal lipid networks that regulate actin assembly.

Molecular mechanisms of tolerance in tardigrades: new perspectives for preservation and stabilization of biological material.

Bioinformatical approaches to detect and analyze protein interactions.

Detecting species-site dependencies in large multiple sequence alignments.

CA/C1 peptidases of the malaria parasites Plasmodium falciparum and P. berghei and their mammalian hosts--a bioinformatical analysis.

The highly attenuated oncolytic recombinant vaccinia virus GLV-1h68: comparative genomic features and the contribution of F14.5L inactivation.

Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection.

Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation.

Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades.

Stress response in tardigrades: differential gene expression of molecular chaperones.

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.

Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees.

Characterization of a novel interaction between vasodilator-stimulated phosphoprotein and Abelson interactor 1 in human platelets: a concerted computational and experimental approach.

BioNet: an R-Package for the functional analysis of biological networks.

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.

Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms.

Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer.

Carbon metabolism of intracellular bacterial pathogens and possible links to virulence.

Developmental profiling by mass spectrometry of phosphocholine containing phospholipids in the rat nervous system reveals temporo-spatial gradients.

Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges.

Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL.

Pharmacogenomic strategies against microbial resistance: from bright to bleak to innovative.

Deciphering the intracellular metabolism of Listeria monocytogenes by mutant screening and modelling.

High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis.

Lead expansion and virtual screening of Indinavir derivate HIV-1 protease inhibitors using pharmacophoric - shape similarity scoring function.

Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor.

A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation.

Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells.

Immune response of the ant Camponotus floridanus against pathogens and its obligate mutualistic endosymbiont.

Staphylococcus aureus physiological growth limitations: insights from flux calculations built on proteomics and external metabolite data.

Modelling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species.

Integration of Boolean models exemplified on hepatocyte signal transduction.

Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation.

PlateletWeb: a systems biologic analysis of signaling networks in human platelets.

Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection.