Thomas Dandekar

Publication Activity (10 Years)

Years Active: 1997-2022
Publications (10 Years): 16

Top Topics

Regulatory Networks

Biomedical Images

Top Venues

Database J. Biol. Databases Curation

PLoS Comput. Biol.

Publications

Tim Breitenbach, Matthias Jürgen Schmitt, Thomas Dandekar
Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing. Bioinform. 38 (17) (2022)
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) (2021)
Sergey Shityakov, Elena Bencurova, Carola Förster, Thomas Dandekar
Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches. BMC Bioinform. 21 (1) (2020)
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) (2020)
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) (2020)
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)
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)
Beat Wolf, Pierre Kuonen, Thomas Dandekar
Meta-Alignment: Combining Sequence Aligners for Better Results. IWBBIO (1) (2018)
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)
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)
Beat Wolf, Pierre Kuonen, Thomas Dandekar
GNATY: Optimized NGS Variant Calling and Coverage Analysis. IWBBIO (2016)
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)
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)
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)
Zeeshan Ahmed, Michel Mayr, Saman Zeeshan, Thomas Dandekar, Martin J. Mueller, Agnes Fekete
a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinform. 31 (7) (2015)
Zeeshan Ahmed, Thomas Dandekar
MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format. F1000Research 4 (2015)
Thomas Dandekar, Astrid Fieselmann, Saman Majeed, Zeeshan Ahmed
Software applications toward quantitative metabolic flux analysis and modeling. Briefings Bioinform. 15 (1) (2014)
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)
Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
" paradigm. F1000Research 3 (2014)
Stefan Karl, Thomas Dandekar
Jimena: efficient computing and system state identification for genetic regulatory networks. BMC Bioinform. 14 (2013)
Chunguang Liang, Beate Krüger, Thomas Dandekar
GoSynthetic database tool to analyse natural and engineered molecular processes. Database J. Biol. Databases Curation 2013 (2013)
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) (2013)
Katja Schulze, Ulrich M. Tillich, Thomas Dandekar, Marcus Frohme
PlanktoVision - an automated analysis system for the identification of phytoplankton. BMC Bioinform. 14 (2013)
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 (2013)
Zeeshan Ahmed, Thomas Dandekar, Saman Majeed
Review: Semantic Web; Ontology Specific Languages for Web Application Development. Int. J. Web Appl. 4 (1) (2012)
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) (2012)
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 (2012)
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) (2012)
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 (2011)
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 (2010)
Zeeshan Ahmed, Saman Majeed, Thomas Dandekar
Towards Design and Implementation of a Language Technology based Information Processor for PDM Systems CoRR (2010)
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) (2010)
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 (2009)
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 (2009)
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) (2008)
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 (2008)
Matthias Wolf, Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, Tobias Müller
ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments. Bioinform. 24 (20) (2008)
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)
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)
Daniel Gerlach, Matthias Wolf, Thomas Dandekar, Tobias Müller, Andreas Pokorny, Sven Rahmann
Deep Metazoan Phylogeny. Silico Biol. 7 (2) (2007)
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 (2006)
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) (2006)
Chunguang Liang, Thomas Dandekar
inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons. BMC Bioinform. 7 (2006)
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) (2006)
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 (2006)
Peter Bengert, Thomas Dandekar
Current efforts in the analysis of RNAi and RNAi target genes. Briefings Bioinform. 6 (1) (2005)
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) (2005)
Matthias Wolf, Joachim Friedrich, Thomas Dandekar, Tobias Müller
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. Silico Biol. 5 (3) (2005)
Tobias Penzkofer, Thomas Dandekar, Tomasz Zemojtel
L1Base: from functional annotation to prediction of active LINE-1 elements. Nucleic Acids Res. 33 (Database-Issue) (2005)
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 (2005)
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)
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) (2004)
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) (2004)
Peter Bengert, Thomas Dandekar
Riboswitch finder tool for identification of riboswitch RNAs. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Thomas Dandekar, Steffen Schmidt
Metabolites, pathway flexibility. Silico Biol. 5 (2) (2004)
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)
Peter Bengert, Thomas Dandekar
A software tool-box for analysis of regulatory RNA elements. Nucleic Acids Res. 31 (13) (2003)
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) (2002)
Steffen Schmidt, Peer Bork, Thomas Dandekar
A Versatile Structural Domain Analysis Server Using Profile Weight Matrices. J. Chem. Inf. Comput. Sci. 42 (2) (2002)
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) (2002)
Steffen Schmidt, Thomas Dandekar
Metabolic Pathways. Gene Regulations and Metabolism (2002)
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)
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) (1998)
Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork
Pathway alignment: Application in the comparative analysis of glycolysis. German Conference on Bioinformatics (1998)
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)