T Dandekar

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi request reprint Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches
    T Dandekar
    European Molecular Biology Laboratory, Postfach 102209, D 69012 Heidelberg, Germany
    Bioinformatics 14:271-8. 1998
  2. pmc Pathway alignment: application to the comparative analysis of glycolytic enzymes
    T Dandekar
    EMBL, P O Box 102209, D 69012 Heidelberg, Germany
    Biochem J 343:115-24. 1999
  3. ncbi request reprint Medical target prediction from genome sequence: combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches
    T Dandekar
    European Molecular Biology Laboratory, PO Box 102209, Meyerhostrasse 1, D 69012 Heidelberg, Germany
    Comput Chem 26:15-21. 2001
  4. ncbi request reprint Comparative genome analysis and pathway reconstruction
    Thomas Dandekar
    EMBL, Postfach 102209, D 69012 Heidelberg, Germany
    Pharmacogenomics 3:245-56. 2002
  5. ncbi request reprint Predicting function: from genes to genomes and back
    P Bork
    European Molecular Biology Laboratory, Meyerhofstr 1, Heidelberg, PF 10 2209, Germany
    J Mol Biol 283:707-25. 1998
  6. ncbi request reprint Variation and evolution of the citric-acid cycle: a genomic perspective
    M A Huynen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Microbiol 7:281-91. 1999
  7. ncbi request reprint Folding the main chain of small proteins with the genetic algorithm
    T Dandekar
    European Molecular Biology Laboratory, Heidelberg, Germany
    J Mol Biol 236:844-61. 1994
  8. pmc Translational regulation of mammalian and Drosophila citric acid cycle enzymes via iron-responsive elements
    N K Gray
    Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
    Proc Natl Acad Sci U S A 93:4925-30. 1996
  9. ncbi request reprint Solvent entropy-driven searching for protein modeling examined and tested in simplified models
    R Konig
    European Molecular Biology Laboratory, Meyerhofstr 1, Postfach 10 22 09, D 69012 Heidelberg, Germany
    Protein Eng 14:329-35. 2001
  10. ncbi request reprint Metabolites: a helping hand for pathway evolution?
    Steffen Schmidt
    European Molecular Biology Laboratory Heidelberg, Postfach 102209, Germany
    Trends Biochem Sci 28:336-41. 2003

Collaborators

  • P Bork
  • M Huynen
  • S Schmidt
  • B Snel
  • S Schuster
  • F Eisenhaber
  • G Flouriot
  • B A Ackrell
  • Shamil Sunyaev
  • Roland Schwarz
  • Folker Meyer
  • R Giegerich
  • Sven Rahmann
  • Philipp N Seibel
  • Olaf Kaiser
  • Marcus Dittrich
  • Tobias Müller
  • Matthias Wolf
  • Chunguang Liang
  • Daniel Gerlach
  • Tomasz Zemojtel
  • Ingvild Birschmann
  • Albert Sickmann
  • Ulrich Walter
  • Werner Goebel
  • Wolfgang Eisenreich
  • Ali Nowrouzi
  • Rosalia Deeken
  • Torsten Hain
  • Joachim Friedrich
  • Susanne Schmitt
  • Tobias Lohmüller
  • R Konig
  • Silke Mietner
  • Andreas Pokorny
  • Tobias Penzkofer
  • Richard Badge
  • Martin Vingron
  • Jörg Schultz
  • Eugen Domann
  • Werner M Kaiser
  • Som Subhra Chatterjee
  • Markus Krischke
  • Daniela Bartels
  • Julia C Engelmann
  • Rohit Ghai
  • Alexander Goesmann
  • Christof von Kalle
  • Jurgen Wehland
  • Johanna Bussemer
  • Ralf Laupitz
  • Marina Efetova
  • Uwe Karst
  • Carsten Tobias Kuenne
  • Christiane Steinweg
  • Christine Schwarz
  • Chuck Klanke
  • Jochen Stritzker
  • Martin J Mueller
  • Tina Czirjak
  • Matthias Rammling
  • Thomas Bekel
  • Alfred Pühler
  • Andre Billion
  • Adelbert Bacher
  • Olaf Tietz
  • Martin Heinkelein
  • Jürgen Kreft
  • Bernd Weisshaar
  • Trinad Chakraborty
  • Axel Rethwilm
  • Rainer Hedrich
  • Jörg Slaghuis
  • Robert Lampidis
  • Klaus Palme
  • Sabine Herterich
  • Ute Hentschel
  • Christiane Stuhlfelder
  • Sven Zea
  • Bernhard Nieswandt
  • Christoph Peters
  • Daniel Wenzler
  • Thomas Reinheckel
  • Wolfgang Kiess
  • Sascha Hagemann
  • N K Gray
  • M W Hentze
  • K Pantopoulos

Detail Information

Publications28

  1. ncbi request reprint Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches
    T Dandekar
    European Molecular Biology Laboratory, Postfach 102209, D 69012 Heidelberg, Germany
    Bioinformatics 14:271-8. 1998
    ..To reveal unidentified regulatory signals, we combine information from experiments with computational approaches. Depending on available knowledge, three different strategies are employed...
  2. pmc Pathway alignment: application to the comparative analysis of glycolytic enzymes
    T Dandekar
    EMBL, P O Box 102209, D 69012 Heidelberg, Germany
    Biochem J 343:115-24. 1999
    ..Archaean, bacterial and parasite specific adaptations are identified and described...
  3. ncbi request reprint Medical target prediction from genome sequence: combining different sequence analysis algorithms with expert knowledge and input from artificial intelligence approaches
    T Dandekar
    European Molecular Biology Laboratory, PO Box 102209, Meyerhostrasse 1, D 69012 Heidelberg, Germany
    Comput Chem 26:15-21. 2001
    ..Fast sequence comparisons, data mining, and genetic algorithms further promote these procedures. Mycobacterium tuberculosis proteins were chosen as applied examples...
  4. ncbi request reprint Comparative genome analysis and pathway reconstruction
    Thomas Dandekar
    EMBL, Postfach 102209, D 69012 Heidelberg, Germany
    Pharmacogenomics 3:245-56. 2002
    ..Target selection, drug development and optimization can all be sped up using these approaches...
  5. ncbi request reprint Predicting function: from genes to genomes and back
    P Bork
    European Molecular Biology Laboratory, Meyerhofstr 1, Heidelberg, PF 10 2209, Germany
    J Mol Biol 283:707-25. 1998
    ..The final goal will be to elucidate the mapping between genotype and phenotype...
  6. ncbi request reprint Variation and evolution of the citric-acid cycle: a genomic perspective
    M A Huynen
    European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
    Trends Microbiol 7:281-91. 1999
    ..Several distinct, incomplete cycles reflect adaptations to different environments. Their distribution over the phylogenetic tree hints at precursors in the evolution of the citric-acid cycle...
  7. ncbi request reprint Folding the main chain of small proteins with the genetic algorithm
    T Dandekar
    European Molecular Biology Laboratory, Heidelberg, Germany
    J Mol Biol 236:844-61. 1994
    ..In addition the backbone topology as predicted by the genetic algorithm for crambin, a mixed helix/strand protein with known structure, is presented and discussed...
  8. pmc Translational regulation of mammalian and Drosophila citric acid cycle enzymes via iron-responsive elements
    N K Gray
    Gene Expression Programme, European Molecular Biology Laboratory, Heidelberg, Germany
    Proc Natl Acad Sci U S A 93:4925-30. 1996
    ..Our results identify a regulatory link between energy and iron metabolism in vertebrates and invertebrates, and suggest biological functions for the IRE/IRP regulatory system in addition to the maintenance of iron homeostasis...
  9. ncbi request reprint Solvent entropy-driven searching for protein modeling examined and tested in simplified models
    R Konig
    European Molecular Biology Laboratory, Meyerhofstr 1, Postfach 10 22 09, D 69012 Heidelberg, Germany
    Protein Eng 14:329-35. 2001
    ..It is compared in detail with the above results, indicating also how this solvent shell model may advantageously be implemented in more complex protein modeling simulations...
  10. ncbi request reprint Metabolites: a helping hand for pathway evolution?
    Steffen Schmidt
    European Molecular Biology Laboratory Heidelberg, Postfach 102209, Germany
    Trends Biochem Sci 28:336-41. 2003
    ..Thus, a picture is emerging in which new pathways are evolving from central metabolites by preference, thereby keeping the overall topology of the metabolic network...
  11. pmc Exonization of active mouse L1s: a driver of transcriptome evolution?
    Tomasz Zemojtel
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, D 14195 Berlin, Germany
    BMC Genomics 8:392. 2007
    ..Long interspersed nuclear elements (LINE-1s, L1s) have been recently implicated in the regulation of mammalian transcriptomes...
  12. pmc Integrated network reconstruction, visualization and analysis using YANAsquare
    Roland Schwarz
    Department of Bioinformatics, Biocenter Am Hubland, D 97074 University of Würzburg, Germany
    BMC Bioinformatics 8:313. 2007
    ..Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network...
  13. ncbi request reprint Deep metazoan phylogeny
    Daniel Gerlach
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    In Silico Biol 7:151-4. 2007
    ....
  14. pmc An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach
    Rosalia Deeken
    Julius von Sachs Institute, Department of Molecular Plant Physiology and Biophysics, University of Wuerzburg, D 97082 Wuerzburg, Germany
    Plant Cell 18:3617-34. 2006
    ..Thus, understanding of gene-to-metabolite networks in plant tumors promotes the identification of mechanisms that control tumor development...
  15. pmc 4SALE--a tool for synchronous RNA sequence and secondary structure alignment and editing
    Philipp N Seibel
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, Wurzburg, Germany
    BMC Bioinformatics 7:498. 2006
    ..g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously...
  16. pmc XML schemas for common bioinformatic data types and their application in workflow systems
    Philipp N Seibel
    Department of Bioinformatics, Biocenter, University of Wurzburg, Wurzburg, Germany
    BMC Bioinformatics 7:490. 2006
    ..Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats...
  17. pmc inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons
    Chunguang Liang
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    BMC Bioinformatics 7:461. 2006
    ..All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in Java with Biojava subroutines...
  18. pmc Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes
    Torsten Hain
    Institute for Medical Microbiology, Justus Liebig University, Frankfurter Strasse 107, D 35392 Giessen, Germany
    J Bacteriol 188:7405-15. 2006
    ..The species L. welshimeri appears to have been derived from early evolutionary events and an ancestor more compact than L. monocytogenes that led to the emergence of nonpathogenic Listeria spp...
  19. ncbi request reprint Genome-wide mapping of foamy virus vector integrations into a human cell line
    Ali Nowrouzi
    Institut fur Virologie und Immunbiologie, Universitat Wurzburg, Germany
    J Gen Virol 87:1339-47. 2006
    ..In summary, it is shown that the integration pattern of FVs appears to be unique compared with those of other retroviral genera...
  20. pmc 13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA
    Wolfgang Eisenreich
    Lehrstuhl fur Organische Chemie und Biochemie, Lichtenbergstrasse 4, D 85747 Garching, Germany
    Proc Natl Acad Sci U S A 103:2040-5. 2006
    ..Bioinformatical steady-state network analyses and flux distribution predictions confirmed the experimental data and predicted metabolite fluxes through the enzymes of the pathways under study...
  21. ncbi request reprint Understanding platelets. Lessons from proteomics, genomics and promises from network analysis
    Marcus Dittrich
    Department of Bioinformatics, Biocenter, University of Wurzburg, Wurzburg, Germany
    Thromb Haemost 94:916-25. 2005
    ..Understanding the surprisingly complex platelet regarding compartmentalization, key cascades, and pathways including clinical implications will remain an exciting and hopefully fruitful challenge for the future...
  22. ncbi request reprint Metabolites and pathway flexibility
    Thomas Dandekar
    Dept of Bioinformatics, Biocenter, Am Hubland, D 97074 Wuerzburg, Germany
    In Silico Biol 5:103-10. 2005
    ..Both effects provide a strong source for resistance in parasites and pathogens. Specific adaptations scenarios and some counter strategies are discussed...
  23. pmc YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
    Roland Schwarz
    Dept of Bioinformatics, Biocenter, University of Wurzburg, Germany
    BMC Bioinformatics 6:135. 2005
    ..Analysis routines for expression levels and the most central, well connected metabolites and their metabolic connections are of particular interest...
  24. ncbi request reprint ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae)
    Susanne Schmitt
    Research Center for Infectious Diseases, University of Wurzburg, Germany
    J Mol Evol 60:327-36. 2005
    ..The species concept for Aplysina sponges as well as a phylogenetic history with a possibly Tethyan origin is discussed...
  25. ncbi request reprint ProfDist: a tool for the construction of large phylogenetic trees based on profile distances
    Joachim Friedrich
    Department of Bioinformatics, Biocenter, University of Wurzburg, Germany
    Bioinformatics 21:2108-9. 2005
    ..It is a tool for reconstructing and visualizing large phylogenetic trees providing new and standard features with a special focus on time efficency, robustness and accuracy...
  26. pmc Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)
    Tobias Müller
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, D 97074 Wurzburg, Germany
    BMC Evol Biol 4:20. 2004
    ..We represent each subclade by a sequence profile and estimate evolutionary distances between profiles to obtain a matrix of distances between subclades...
  27. ncbi request reprint Toward computer-based cleavage site prediction of cysteine endopeptidases
    Tobias Lohmüller
    Institut für Molekulare Medizin und Zellforschung, Albert Ludwigs Universitat, Breisacherstr 66, D 79106 Freiburg, Germany
    Biol Chem 384:899-909. 2003
    ..These results indicate that CSSM/PEPS can correctly predict relevant peptidase substrates...
  28. doi request reprint Platelet protein interactions: map, signaling components, and phosphorylation groundstate
    Marcus Dittrich
    Department of Bioinformatics, Biocenter, University of Wurzburg, Am Hubland, Wurzburg D 97074, Germany
    Arterioscler Thromb Vasc Biol 28:1326-31. 2008
    ..Assembly of a comprehensive proteome and transcriptome database of human platelets, derivation of a model of the platelet-specific interactome, and generation of a functional interaction map of platelet phosphorylations and kinases...