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ORCIDThomas Dandekar
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- affiliation: University of Würzburg, Germany
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2020 – today
- 2023
[b1]Thomas Dandekar, Meik Kunz:
Bioinformatics - An Introductory Textbook. Springer 2023, ISBN 978-3-662-65035-6, pp. 3-351- 2022
- [j54]Tim Breitenbach
, Matthias Jürgen Schmitt, Thomas Dandekar:
Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing. Bioinform. 38(17): 4162-4171 (2022) - 2021
- [j53]Juan Pablo Prada, Gaby Wangorsch, Kirstin Kucka, Isabell Lang, Thomas Dandekar, Harald Wajant:
A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2. Bioinform. 37(5): 669-676 (2021) - 2020
- [j52]Meik Kunz, Julian Jeromin, Maximilian Fuchs, Jan Christoph, Giulia Veronesi, Michael Flentje, Sarah Nietzer, Gudrun Dandekar, Thomas Dandekar:
In silico signaling modeling to understand cancer pathways and treatment responses. Briefings Bioinform. 21(3): 1115-1117 (2020) - [j51]Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Ke Xiao, Thomas Thum, David Atlan, Hans-Ulrich Prokosch, Thomas Dandekar:
A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs. Briefings Bioinform. 21(4): 1391-1396 (2020) - [j50]Sergey Shityakov, Elena Bencurova, Carola Förster, Thomas Dandekar:
Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches. BMC Bioinform. 21(1): 132 (2020)
2010 – 2019
- 2019
- [j49]Tim Breitenbach, Chunguang Liang, Niklas Beyersdorf, Thomas Dandekar:
Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks. PLoS Comput. Biol. 15(7) (2019) - 2018
- [j48]Juan Prada, Manju Sasi, Corinna Martin, Sibylle Jablonka, Thomas Dandekar, Robert Blum:
An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data. PLoS Comput. Biol. 14(3) (2018) - [c8]Beat Wolf, Pierre Kuonen, Thomas Dandekar:
Meta-Alignment: Combining Sequence Aligners for Better Results. IWBBIO (1) 2018: 395-404 - 2017
- [j47]Kristin Verena Kaltdorf, Katja Schulze, Frederik Helmprobst, Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher:
FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. PLoS Comput. Biol. 13(1) (2017) - [j46]Jan Ewald, Martin Bartl, Thomas Dandekar, Christoph Kaleta:
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism. PLoS Comput. Biol. 13(2) (2017) - 2016
- [j45]Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar:
Mining biomedical images towards valuable information retrieval in biomedical and life sciences. Database J. Biol. Databases Curation 2016 (2016) - [j44]Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar:
Mining biomedical images towards valuable information retrieval in biomedical and life sciences. Database J. Biol. Databases Curation 2016 (2016) - [j43]Meik Kunz, Chunguang Liang, Santosh Nilla, Alexander Cecil, Thomas Dandekar:
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development. Database J. Biol. Databases Curation 2016 (2016) - [c7]Beat Wolf, Pierre Kuonen, Thomas Dandekar:
GNATY: Optimized NGS Variant Calling and Coverage Analysis. IWBBIO 2016: 446-454 - 2015
- [j42]Zeeshan Ahmed, Michel Mayr, Saman Zeeshan, Thomas Dandekar, Martin J. Mueller, Agnes Fekete:
Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinform. 31(7): 1150-1153 (2015) - [i3]Zeeshan Ahmed, Thomas Dandekar:
MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format. F1000Research 4: 1453 (2015) - 2014
- [j41]Thomas Dandekar, Astrid Fieselmann, Saman Majeed, Zeeshan Ahmed:
Software applications toward quantitative metabolic flux analysis and modeling. Briefings Bioinform. 15(1): 91-107 (2014) - [j40]Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Eva Eylert, Wolfgang Eisenreich, Thomas Dandekar:
'Isotopo' a database application for facile analysis and management of mass isotopomer data. Database J. Biol. Databases Curation 2014 (2014) - [i2]Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar:
Developing sustainable software solutions for bioinformatics by the "Butterfly" paradigm. F1000Research 3: 71 (2014) - 2013
- [j39]Chunguang Liang, Beate Krüger, Thomas Dandekar:
GoSynthetic database tool to analyse natural and engineered molecular processes. Database J. Biol. Databases Curation 2013 (2013) - [j38]Katja Schulze, Ulrich M. Tillich, Thomas Dandekar, Marcus Frohme:
PlanktoVision - an automated analysis system for the identification of phytoplankton. BMC Bioinform. 14: 115 (2013) - [j37]Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Wolfgang Eisenreich, Thomas Dandekar:
Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. BMC Bioinform. 14: 218 (2013) - [j36]Stefan Karl, Thomas Dandekar:
Jimena: efficient computing and system state identification for genetic regulatory networks. BMC Bioinform. 14: 306 (2013) - [j35]Sergey Shityakov, Winfried Neuhaus, Thomas Dandekar, Carola Förster:
Analysing molecular polar surface descriptors to predict blood-brain barrier permeation. Int. J. Comput. Biol. Drug Des. 6(1/2): 146-156 (2013) - 2012
- [j34]Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch, Robert Pick, Oliver Sawodny, Christoph Borner, Jens Timmer, Michael Ederer, Thomas Dandekar:
Integration of Boolean models exemplified on hepatocyte signal transduction. Briefings Bioinform. 13(3): 365-376 (2012) - [j33]Daniela Beisser, Stefan Brunkhorst, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller:
Robustness and accuracy of functional modules in integrated network analysis. Bioinform. 28(14): 1887-1894 (2012) - [j32]Daniela Beisser, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller:
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Syst. Biol. 6: 72 (2012) - [j31]Zeeshan Ahmed, Thomas Dandekar, Saman Majeed:
Review: Semantic Web; Ontology Specific Languages for Web Application Development. Int. J. Web Appl. 4(1): 33-41 (2012) - 2011
- [j30]Gaby Wangorsch, Elke Butt, Regina Mark, Katharina Hubertus, Jörg Geiger, Thomas Dandekar, Marcus T. Dittrich:
Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation. BMC Syst. Biol. 5: 178 (2011) - 2010
- [j29]Daniela Beisser, Gunnar W. Klau, Thomas Dandekar, Tobias Müller, Marcus T. Dittrich:
BioNet: an R-Package for the functional analysis of biological networks. Bioinform. 26(8): 1129-1130 (2010) - [j28]Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W. Hentze, Thomas Dandekar, Martina U. Muckenthaler:
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. BMC Bioinform. 11: 112 (2010) - [i1]Zeeshan Ahmed, Saman Majeed, Thomas Dandekar:
Towards Design and Implementation of a Language Technology based Information Processor for PDM Systems. CoRR abs/1008.1394 (2010)
2000 – 2009
- 2009
- [j27]Chunguang Liang, Alexander Schmid, María José López-Sánchez, Andrés Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar:
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. BMC Bioinform. 10: 391 (2009) - [j26]Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar:
Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection. BMC Syst. Biol. 3: 97 (2009) - 2008
- [j25]Matthias Wolf, Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, Tobias Müller:
ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments. Bioinform. 24(20): 2401-2402 (2008) - [j24]Mark Kühnel, Luis S. Mayorga, Thomas Dandekar, Juilee Thakar, Roland Schwarz, Elsa Anes, Gareth Griffiths, Jens G. Reich:
Modelling phagosomal lipid networks that regulate actin assembly. BMC Syst. Biol. 2: 107 (2008) - [j23]Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, Jörg Schultz:
The ITS2 Database II: homology modelling RNA structure for molecular systematics. Nucleic Acids Res. 36(Database-Issue): 377-380 (2008) - [c6]Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller:
Identifying functional modules in protein-protein interaction networks: an integrated exact approach. ISMB 2008: 223-231 - 2007
- [j22]Roland Schwarz, Chunguang Liang, Christoph Kaleta, Mark Kühnel, Eik Hoffmann, Sergei Kuznetsov, Michael Hecker, Gareth Griffiths, Stefan Schuster, Thomas Dandekar:
Integrated network reconstruction, visualization and analysis using YANAsquare. BMC Bioinform. 8 (2007) - [j21]Daniel Gerlach, Matthias Wolf, Thomas Dandekar, Tobias Müller, Andreas Pokorny, Sven Rahmann:
Deep Metazoan Phylogeny. Silico Biol. 7(2): 151-154 (2007) - 2006
- [j20]Torben Friedrich, Birgit Pils, Thomas Dandekar, Jörg Schultz, Tobias Müller:
Modelling interaction sites in protein domains with interaction profile hidden Markov models. Bioinform. 22(23): 2851-2857 (2006) - [j19]Chunguang Liang, Thomas Dandekar:
inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons. BMC Bioinform. 7: 461 (2006) - [j18]Philipp N. Seibel, Jan Krüger, Sven Hartmeier, Knut Schwarzer, Kai Löwenthal, Henning Mersch, Thomas Dandekar, Robert Giegerich:
XML schemas for common bioinformatic data types and their application in workflow systems. BMC Bioinform. 7: 490 (2006) - [j17]Philipp N. Seibel, Tobias Müller, Thomas Dandekar, Jörg Schultz, Matthias Wolf:
4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing. BMC Bioinform. 7: 498 (2006) - [j16]Jörg Schultz, Tobias Müller, Marco Achtziger, Philipp N. Seibel, Thomas Dandekar, Matthias Wolf:
The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses. Nucleic Acids Res. 34(Web-Server-Issue): 704-707 (2006) - 2005
- [j15]Peter Bengert, Thomas Dandekar:
Current efforts in the analysis of RNAi and RNAi target genes. Briefings Bioinform. 6(1): 72-85 (2005) - [j14]Joachim Friedrich, Thomas Dandekar, Matthias Wolf, Tobias Müller:
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. Bioinform. 21(9): 2108-2109 (2005) - [j13]Roland Schwarz, Patrick Musch, Axel von Kamp, Bernd Engels, R. Heiner Schirmer, Stefan Schuster, Thomas Dandekar:
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinform. 6: 135 (2005) - [j12]Matthias Wolf, Joachim Friedrich, Thomas Dandekar, Tobias Müller:
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. Silico Biol. 5(3): 291-294 (2005) - [j11]Tobias Penzkofer, Thomas Dandekar, Tomasz Zemojtel:
L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic Acids Res. 33(Database-Issue): 498-500 (2005) - 2004
- [j10]Thomas Dandekar, Steffen Schmidt:
Metabolites, pathway flexibility. Silico Biol. 5(2): 103-110 (2004) - [j9]Helge Bertram, Thomas Dandekar:
Stoffwechselanalyse: Der Weg vom Genom zum metabolischen Netzwerk (Pathway Analysis: On the Route from Genomics to Metabolic Networks). it Inf. Technol. 46(1): 5-11 (2004) - [j8]Daniel Faller, Thomas Reinheckel, Daniel Wenzler, Sascha Hagemann, Ke Xiao, Josef Honerkamp, Christoph Peters, Thomas Dandekar, Jens Timmer:
An Open Source Protein Gel Documentation System for Proteome Analyses. J. Chem. Inf. Model. 44(1): 168-169 (2004) - [j7]M. Dünßer, R. Lampidis, Steffen Schmidt, Dietmar Seipel, Thomas Dandekar:
Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework. J. Integr. Bioinform. 1(1) (2004) - [j6]Peter Bengert, Thomas Dandekar:
Riboswitch finder tool for identification of riboswitch RNAs. Nucleic Acids Res. 32(Web-Server-Issue): 154-159 (2004) - 2003
- [j5]Peter Bengert, Thomas Dandekar:
A software tool-box for analysis of regulatory RNA elements. Nucleic Acids Res. 31(13): 3441-3445 (2003) - [c5]Tobias Müller, Sven Rahmann, Thomas Dandekar, Matthias Wolf:
Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances. German Conference on Bioinformatics 2003: 97-101 - 2002
- [j4]Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar:
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinform. 18(2): 351-361 (2002) - [j3]Thomas Dandekar, Fuli Du, R. Heiner Schirmer, Steffen Schmidt:
Medical Target Prediction From Genome Sequence: Combining Different Sequence Analysis Algorithms with Expert Knowledge and Input From Artificial Intelligence Approaches. Comput. Chem. 26(1): 15-21 (2002) - [j2]Steffen Schmidt, Peer Bork, Thomas Dandekar:
A Versatile Structural Domain Analysis Server Using Profile Weight Matrices. J. Chem. Inf. Comput. Sci. 42(2): 405-407 (2002) - [c4]Steffen Schmidt, Thomas Dandekar:
Metabolic Pathways. Gene Regulations and Metabolism 2002: 251-272 - 2000
- [c3]Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar:
Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae. German Conference on Bioinformatics 2000: 115-120
1990 – 1999
- 1998
- [j1]Thomas Dandekar, Katrin Beyer, Peer Bork, Mary-Rose Kenealy, Kostas Pantopoulos, Matthias W. Hentze, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon, Sonja Schreiber:
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches. Bioinform. 14(3): 271-278 (1998) - [c2]Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork:
Pathway alignment: Application in the comparative analysis of glycolysis. German Conference on Bioinformatics 1998 - 1997
- [c1]Thomas Dandekar, Katrin Beyer, Peer Bork, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon, W. Keller, Sonja Schreiber:
Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region. German Conference on Bioinformatics 1997: 31-32
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