Thomas Dandekar

67 papers A 1Journal 58Unranked 7
YearRankTypeTitle / Venue / Authors
2026 J jnl
A screening pipeline for human proteins interacting with dyes and toxins applied to the melanin virulence determinant 1,8-dihydroxynaphthalene of Aspergillus fumigatus.
Comput. Biol. Medicine
Mahshid Danesh, Özge Osmanoglu, Shishir K. Gupta, Isabel Heineking, Axel A. Brakhage, Olaf Kniemeyer, Thomas Dandekar
2025 J jnl
Adaptive sampling methods facilitate the determination of reliable dataset sizes for evidence-based modeling.
Frontiers Bioinform.
Tim Breitenbach, Thomas Dandekar
2023 — book
Bioinformatics - An Introductory Textbook
Thomas Dandekar, Meik Kunz
2022 J jnl
Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing.
Bioinform.
Tim Breitenbach, Matthias Jürgen Schmitt, Thomas Dandekar
2021 J jnl
A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2.
Bioinform.
Juan Pablo Prada, Gaby Wangorsch, Kirstin Kucka, Isabell Lang, Thomas Dandekar, Harald Wajant
2020 J jnl
A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs.
Briefings Bioinform.
Meik Kunz, Beat Wolf, Maximilian Fuchs, Jan Christoph, Ke Xiao, Thomas Thum, David Atlan, Hans-Ulrich Prokosch, Thomas Dandekar
2020 J jnl
In silico signaling modeling to understand cancer pathways and treatment responses.
Briefings Bioinform.
Meik Kunz, Julian Jeromin, Maximilian Fuchs, Jan Christoph, Giulia Veronesi, Michael Flentje, Sarah Nietzer, Gudrun Dandekar, Thomas Dandekar
2020 J jnl
Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches.
BMC Bioinform.
Sergey Shityakov, Elena Bencurova, Carola Förster, Thomas Dandekar
2019 J jnl
Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks.
PLoS Comput. Biol.
Tim Breitenbach, Chunguang Liang, Niklas Beyersdorf, Thomas Dandekar
2018 J jnl
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.
Juan Prada, Manju Sasi, Corinna Martin, Sibylle Jablonka, Thomas Dandekar, Robert Blum
2018 — conf
Meta-Alignment: Combining Sequence Aligners for Better Results.
IWBBIO (1)
Beat Wolf, Pierre Kuonen, Thomas Dandekar
2017 J jnl
FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms.
PLoS Comput. Biol.
Kristin Verena Kaltdorf, Katja Schulze, Frederik Helmprobst, Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher
2017 J jnl
Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism.
PLoS Comput. Biol.
Jan Ewald, Martin Bartl, Thomas Dandekar, Christoph Kaleta
2016 — conf
GNATY: Optimized NGS Variant Calling and Coverage Analysis.
IWBBIO
Beat Wolf, Pierre Kuonen, Thomas Dandekar
2016 J jnl
Mining biomedical images towards valuable information retrieval in biomedical and life sciences.
Database J. Biol. Databases Curation
Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
2016 J jnl
Mining biomedical images towards valuable information retrieval in biomedical and life sciences.
Database J. Biol. Databases Curation
Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
2016 J jnl
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development.
Database J. Biol. Databases Curation
Meik Kunz, Chunguang Liang, Santosh Nilla, Alexander Cecil, Thomas Dandekar
2015 J jnl
MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format.
F1000Research
Zeeshan Ahmed, Thomas Dandekar
2014 J jnl
'Isotopo' a database application for facile analysis and management of mass isotopomer data.
Database J. Biol. Databases Curation
Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Eva Eylert, Wolfgang Eisenreich, Thomas Dandekar
2014 J jnl
Developing sustainable software solutions for bioinformatics by the "
F1000Research
Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
2014 J jnl
Software applications toward quantitative metabolic flux analysis and modeling.
Briefings Bioinform.
Thomas Dandekar, Astrid Fieselmann, Saman Majeed, Zeeshan Ahmed
2013 J jnl
Analysing molecular polar surface descriptors to predict blood-brain barrier permeation.
Int. J. Comput. Biol. Drug Des.
Sergey Shityakov, Winfried Neuhaus, Thomas Dandekar, Carola Förster
2013 J jnl
GoSynthetic database tool to analyse natural and engineered molecular processes.
Database J. Biol. Databases Curation
Chunguang Liang, Beate Krüger, Thomas Dandekar
2013 J jnl
Jimena: efficient computing and system state identification for genetic regulatory networks.
BMC Bioinform.
Stefan Karl, Thomas Dandekar
2013 J jnl
PlanktoVision - an automated analysis system for the identification of phytoplankton.
BMC Bioinform.
Katja Schulze, Ulrich M. Tillich, Thomas Dandekar, Marcus Frohme
2013 J jnl
Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.
BMC Bioinform.
Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Wolfgang Eisenreich, Thomas Dandekar
2012 J jnl
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum.
BMC Syst. Biol.
Daniela Beisser, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller
2012 J jnl
Integration of Boolean models exemplified on hepatocyte signal transduction.
Briefings Bioinform.
Rebekka Schlatter, Nicole Philippi, Gaby Wangorsch, Robert Pick, Oliver Sawodny, Christoph Borner, Jens Timmer, Michael Ederer, Thomas Dandekar
2012 J jnl
Review: Semantic Web; Ontology Specific Languages for Web Application Development.
Int. J. Web Appl.
Zeeshan Ahmed, Thomas Dandekar, Saman Majeed
2012 J jnl
Robustness and accuracy of functional modules in integrated network analysis.
Bioinform.
Daniela Beisser, Stefan Brunkhorst, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller
2011 J jnl
Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation.
BMC Syst. Biol.
Gaby Wangorsch, Elke Butt, Regina Mark, Katharina Hubertus, Jörg Geiger, Thomas Dandekar, Marcus T. Dittrich
2010 J jnl
BioNet: an R-Package for the functional analysis of biological networks.
Bioinform.
Daniela Beisser, Gunnar W. Klau, Thomas Dandekar, Tobias Müller, Marcus T. Dittrich
2010 J jnl
The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
BMC Bioinform.
Yevhen Vainshtein, Mayka Sanchez, Alvis Brazma, Matthias W. Hentze, Thomas Dandekar, Martina U. Muckenthaler
2010 J jnl
Towards Design and Implementation of a Language Technology based Information Processor for PDM Systems
CoRR
Zeeshan Ahmed, Saman Majeed, Thomas Dandekar
2009 J jnl
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.
BMC Bioinform.
Chunguang Liang, Alexander Schmid, María José López-Sánchez, Andrés Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar
2009 J jnl
Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection.
BMC Syst. Biol.
Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar
2008 A conf
Identifying functional modules in protein-protein interaction networks: an integrated exact approach.
ISMB
Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller
2008 J jnl
Modelling phagosomal lipid networks that regulate actin assembly.
BMC Syst. Biol.
Mark Kühnel, Luis S. Mayorga, Thomas Dandekar, Juilee Thakar, Roland Schwarz, Elsa Anes, Gareth Griffiths, Jens G. Reich
2008 J jnl
ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments.
Bioinform.
Matthias Wolf, Benjamin Ruderisch, Thomas Dandekar, Jörg Schultz, Tobias Müller
2008 J jnl
The ITS2 Database II: homology modelling RNA structure for molecular systematics.
Nucleic Acids Res.
Christian Selig, Matthias Wolf, Tobias Müller, Thomas Dandekar, Jörg Schultz
2007 J jnl
Deep Metazoan Phylogeny.
Silico Biol.
Daniel Gerlach, Matthias Wolf, Thomas Dandekar, Tobias Müller, Andreas Pokorny, Sven Rahmann
2007 J jnl
Integrated network reconstruction, visualization and analysis using YANAsquare.
BMC Bioinform.
Roland Schwarz, Chunguang Liang, Christoph Kaleta, Mark Kühnel, Eik Hoffmann, Sergei Kuznetsov, Michael Hecker, Gareth Griffiths, Stefan Schuster, Thomas Dandekar
2006 J jnl
4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing.
BMC Bioinform.
Philipp N. Seibel, Tobias Müller, Thomas Dandekar, Jörg Schultz, Matthias Wolf
2006 J jnl
Modelling interaction sites in protein domains with interaction profile hidden Markov models.
Bioinform.
Torben Friedrich, Birgit Pils, Thomas Dandekar, Jörg Schultz, Tobias Müller
2006 J jnl
The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses.
Nucleic Acids Res.
Jörg Schultz, Tobias Müller, Marco Achtziger, Philipp N. Seibel, Thomas Dandekar, Matthias Wolf
2006 J jnl
XML schemas for common bioinformatic data types and their application in workflow systems.
BMC Bioinform.
Philipp N. Seibel, Jan Krüger, Sven Hartmeier, Knut Schwarzer, Kai Löwenthal, Henning Mersch, Thomas Dandekar, Robert Giegerich
2006 J jnl
inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons.
BMC Bioinform.
Chunguang Liang, Thomas Dandekar
2005 J jnl
CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures.
Silico Biol.
Matthias Wolf, Joachim Friedrich, Thomas Dandekar, Tobias Müller
2005 J jnl
Current efforts in the analysis of RNAi and RNAi target genes.
Briefings Bioinform.
Peter Bengert, Thomas Dandekar
2005 J jnl
L1Base: from functional annotation to prediction of active LINE-1 elements.
Nucleic Acids Res.
Tobias Penzkofer, Thomas Dandekar, Tomasz Zemojtel
2005 J jnl
ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.
Bioinform.
Joachim Friedrich, Thomas Dandekar, Matthias Wolf, Tobias Müller
2005 J jnl
YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
BMC Bioinform.
Roland Schwarz, Patrick Musch, Axel von Kamp, Bernd Engels, R. Heiner Schirmer, Stefan Schuster, Thomas Dandekar
2004 J jnl
An Open Source Protein Gel Documentation System for Proteome Analyses.
J. Chem. Inf. Model.
Daniel Faller, Thomas Reinheckel, Daniel Wenzler, Sascha Hagemann, Ke Xiao, Josef Honerkamp, Christoph Peters, Thomas Dandekar, Jens Timmer
2004 J jnl
Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework.
J. Integr. Bioinform.
M. Dünßer, R. Lampidis, Steffen Schmidt, Dietmar Seipel, Thomas Dandekar
2004 J jnl
Metabolites, pathway flexibility.
Silico Biol.
Thomas Dandekar, Steffen Schmidt
2004 J jnl
Riboswitch finder tool for identification of riboswitch RNAs.
Nucleic Acids Res.
Peter Bengert, Thomas Dandekar
2004 J jnl
Stoffwechselanalyse: Der Weg vom Genom zum metabolischen Netzwerk (Pathway Analysis: On the Route from Genomics to Metabolic Networks).
it Inf. Technol.
Helge Bertram, Thomas Dandekar
2003 J jnl
A software tool-box for analysis of regulatory RNA elements.
Nucleic Acids Res.
Peter Bengert, Thomas Dandekar
2003 — conf
Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances.
German Conference on Bioinformatics
Tobias Müller, Sven Rahmann, Thomas Dandekar, Matthias Wolf
2002 J jnl
A Versatile Structural Domain Analysis Server Using Profile Weight Matrices.
J. Chem. Inf. Comput. Sci.
Steffen Schmidt, Peer Bork, Thomas Dandekar
2002 J jnl
Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae.
Bioinform.
Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar
2002 J jnl
Medical Target Prediction From Genome Sequence: Combining Different Sequence Analysis Algorithms with Expert Knowledge and Input From Artificial Intelligence Approaches.
Comput. Chem.
Thomas Dandekar, Fuli Du, R. Heiner Schirmer, Steffen Schmidt
2002 — conf
Metabolic Pathways.
Gene Regulations and Metabolism
Steffen Schmidt, Thomas Dandekar
2000 — conf
Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae.
German Conference on Bioinformatics
Stefan Schuster, Thomas Pfeiffer, Ferdinand Moldenhauer, Ina Koch, Thomas Dandekar
1998 — conf
Pathway alignment: Application in the comparative analysis of glycolysis.
German Conference on Bioinformatics
Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork
1998 J jnl
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Bioinform.
Thomas Dandekar, Katrin Beyer, Peer Bork, Mary-Rose Kenealy, Kostas Pantopoulos, Matthias W. Hentze, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon, Sonja Schreiber
1997 — conf
Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region.
German Conference on Bioinformatics
Thomas Dandekar, Katrin Beyer, Peer Bork, Vera Sonntag-Buck, Gilles Flouriot, Frank Gannon, W. Keller, Sonja Schreiber