Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region. - Thomas Dandekar; Katrin Beyer; Peer Bork; Vera Sonntag-Buck; Gilles Flouriot; Frank Gannon; W. Keller; Sonja Schreiber (German Conference on Bioinformatics, 1997)

Pathway alignment: Application in the comparative analysis of glycolysis. - Thomas Dandekar; Stefan Schuster; Martijn A. Huynen; Peer Bork (German Conference on Bioinformatics, 1998)

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches. - Thomas Dandekar; Katrin Beyer; Peer Bork; Mary-Rose Kenealy; Kostas Pantopoulos; Matthias W. Hentze; Vera Sonntag-Buck; Gilles Flouriot; Frank Gannon; Sonja Schreiber (Bioinform., 1998)

Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae. - Stefan Schuster; Thomas Pfeiffer 004; Ferdinand Moldenhauer; Ina Koch; Thomas Dandekar (German Conference on Bioinformatics, 2000)

Metabolic Pathways. - Steffen Schmidt; Thomas Dandekar (Gene Regulations and Metabolism, 2002)

Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. - Stefan Schuster; Thomas Pfeiffer 004; Ferdinand Moldenhauer; Ina Koch; Thomas Dandekar (Bioinform., 2002)

Medical Target Prediction From Genome Sequence: Combining Different Sequence Analysis Algorithms with Expert Knowledge and Input From Artificial Intelligence Approaches. - Thomas Dandekar; Fuli Du; R. Heiner Schirmer; Steffen Schmidt (Comput. Chem., 2002)

A Versatile Structural Domain Analysis Server Using Profile Weight Matrices. - Steffen Schmidt; Peer Bork; Thomas Dandekar (J. Chem. Inf. Comput. Sci., 2002)

Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances. - Tobias Müller 001; Sven Rahmann; Thomas Dandekar; Matthias Wolf 002 (German Conference on Bioinformatics, 2003)

A software tool-box for analysis of regulatory RNA elements. - Peter Bengert; Thomas Dandekar (Nucleic Acids Res., 2003)

Metabolites, pathway flexibility. - Thomas Dandekar; Steffen Schmidt (Silico Biol., 2004)

Stoffwechselanalyse: Der Weg vom Genom zum metabolischen Netzwerk (Pathway Analysis: On the Route from Genomics to Metabolic Networks). - Helge Bertram; Thomas Dandekar (it Inf. Technol., 2004)

An Open Source Protein Gel Documentation System for Proteome Analyses. - Daniel Faller; Thomas Reinheckel; Daniel Wenzler; Sascha Hagemann; Ke Xiao; Josef Honerkamp; Christoph Peters; Thomas Dandekar; Jens Timmer (J. Chem. Inf. Model., 2004)

Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework. - M. Dünßer; R. Lampidis; Steffen Schmidt; Dietmar Seipel; Thomas Dandekar (J. Integr. Bioinform., 2004)

Riboswitch finder tool for identification of riboswitch RNAs. - Peter Bengert; Thomas Dandekar (Nucleic Acids Res., 2004)

Current efforts in the analysis of RNAi and RNAi target genes. - Peter Bengert; Thomas Dandekar (Briefings Bioinform., 2005)

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances. - Joachim Friedrich; Thomas Dandekar; Matthias Wolf 002; Tobias Müller 001 (Bioinform., 2005)

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. - Roland Schwarz 002; Patrick Musch; Axel von Kamp; Bernd Engels; R. Heiner Schirmer; Stefan Schuster; Thomas Dandekar (BMC Bioinform., 2005)

CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures. - Matthias Wolf 002; Joachim Friedrich; Thomas Dandekar; Tobias Müller 001 (Silico Biol., 2005)

L1Base: from functional annotation to prediction of active LINE-1 elements. - Tobias Penzkofer; Thomas Dandekar; Tomasz Zemojtel (Nucleic Acids Res., 2005)

Modelling interaction sites in protein domains with interaction profile hidden Markov models. - Torben Friedrich; Birgit Pils; Thomas Dandekar; Jörg Schultz; Tobias Müller 001 (Bioinform., 2006)

inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons. - Chunguang Liang; Thomas Dandekar (BMC Bioinform., 2006)

XML schemas for common bioinformatic data types and their application in workflow systems. - Philipp N. Seibel; Jan Krüger; Sven Hartmeier; Knut Schwarzer; Kai Löwenthal; Henning Mersch; Thomas Dandekar; Robert Giegerich (BMC Bioinform., 2006)

4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing. - Philipp N. Seibel; Tobias Müller 001; Thomas Dandekar; Jörg Schultz; Matthias Wolf 002 (BMC Bioinform., 2006)

The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses. - Jörg Schultz; Tobias Müller 001; Marco Achtziger; Philipp N. Seibel; Thomas Dandekar; Matthias Wolf 002 (Nucleic Acids Res., 2006)

Integrated network reconstruction, visualization and analysis using YANAsquare. - Roland Schwarz 002; Chunguang Liang; Christoph Kaleta; Mark Kühnel; Eik Hoffmann; Sergei Kuznetsov; Michael Hecker; Gareth Griffiths 003; Stefan Schuster; Thomas Dandekar (BMC Bioinform., 2007)

Deep Metazoan Phylogeny. - Daniel Gerlach; Matthias Wolf 002; Thomas Dandekar; Tobias Müller 001; Andreas Pokorny; Sven Rahmann (Silico Biol., 2007)

Identifying functional modules in protein-protein interaction networks: an integrated exact approach. - Marcus T. Dittrich; Gunnar W. Klau; Andreas Rosenwald; Thomas Dandekar; Tobias Müller 001 (ISMB, 2008)

ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments. - Matthias Wolf 002; Benjamin Ruderisch; Thomas Dandekar; Jörg Schultz; Tobias Müller 001 (Bioinform., 2008)

Modelling phagosomal lipid networks that regulate actin assembly. - Mark Kühnel; Luis S. Mayorga; Thomas Dandekar; Juilee Thakar; Roland Schwarz 002; Elsa Anes; Gareth Griffiths 003; Jens G. Reich (BMC Syst. Biol., 2008)

The ITS2 Database II: homology modelling RNA structure for molecular systematics. - Christian Selig; Matthias Wolf 002; Tobias Müller 001; Thomas Dandekar; Jörg Schultz (Nucleic Acids Res., 2008)

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. - Chunguang Liang; Alexander Schmid 001; María José López-Sánchez; Andrés Moya; Roy Gross; Jörg Bernhardt; Thomas Dandekar (BMC Bioinform., 2009)

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection. - Nicole Philippi; Dorothee Walter; Rebekka Schlatter; Karine Ferreira; Michael Ederer; Oliver Sawodny; Jens Timmer; Christoph Borner; Thomas Dandekar (BMC Syst. Biol., 2009)

BioNet: an R-Package for the functional analysis of biological networks. - Daniela Beisser; Gunnar W. Klau; Thomas Dandekar; Tobias Müller 001; Marcus T. Dittrich (Bioinform., 2010)

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. - Yevhen Vainshtein; Mayka Sanchez; Alvis Brazma; Matthias W. Hentze; Thomas Dandekar; Martina U. Muckenthaler (BMC Bioinform., 2010)

Towards Design and Implementation of a Language Technology based Information Processor for PDM Systems - Zeeshan Ahmed 001; Saman Majeed; Thomas Dandekar (CoRR, 2010)

Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation. - Gaby Wangorsch; Elke Butt; Regina Mark; Katharina Hubertus; Jörg Geiger; Thomas Dandekar; Marcus T. Dittrich (BMC Syst. Biol., 2011)

Integration of Boolean models exemplified on hepatocyte signal transduction. - Rebekka Schlatter; Nicole Philippi; Gaby Wangorsch; Robert Pick; Oliver Sawodny; Christoph Borner; Jens Timmer; Michael Ederer; Thomas Dandekar (Briefings Bioinform., 2012)

Robustness and accuracy of functional modules in integrated network analysis. - Daniela Beisser; Stefan Brunkhorst; Thomas Dandekar; Gunnar W. Klau; Marcus T. Dittrich; Tobias Müller 001 (Bioinform., 2012)

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. - Daniela Beisser; Markus A. Grohme; Joachim Kopka; Marcus Frohme; Ralph O. Schill; Steffen Hengherr; Thomas Dandekar; Gunnar W. Klau; Marcus T. Dittrich; Tobias Müller 001 (BMC Syst. Biol., 2012)

Review: Semantic Web; Ontology Specific Languages for Web Application Development. - Zeeshan Ahmed 001; Thomas Dandekar; Saman Majeed (Int. J. Web Appl., 2012)

GoSynthetic database tool to analyse natural and engineered molecular processes. - Chunguang Liang; Beate Krüger; Thomas Dandekar (Database J. Biol. Databases Curation, 2013)

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling. - Zeeshan Ahmed 001; Saman Zeeshan; Claudia Huber; Michael Hensel; Dietmar Schomburg; Richard Münch; Wolfgang Eisenreich; Thomas Dandekar (BMC Bioinform., 2013)

Jimena: efficient computing and system state identification for genetic regulatory networks. - Stefan Karl; Thomas Dandekar (BMC Bioinform., 2013)

PlanktoVision - an automated analysis system for the identification of phytoplankton. - Katja Schulze; Ulrich M. Tillich; Thomas Dandekar; Marcus Frohme (BMC Bioinform., 2013)

Analysing molecular polar surface descriptors to predict blood-brain barrier permeation. - Sergey Shityakov; Winfried Neuhaus; Thomas Dandekar; Carola Förster (Int. J. Comput. Biol. Drug Des., 2013)

Software applications toward quantitative metabolic flux analysis and modeling. - Thomas Dandekar; Astrid Fieselmann; Saman Majeed; Zeeshan Ahmed 001 (Briefings Bioinform., 2014)

'Isotopo' a database application for facile analysis and management of mass isotopomer data. - Zeeshan Ahmed 001; Saman Zeeshan; Claudia Huber; Michael Hensel; Dietmar Schomburg; Richard Münch; Eva Eylert; Wolfgang Eisenreich; Thomas Dandekar (Database J. Biol. Databases Curation, 2014)

Developing sustainable software solutions for bioinformatics by the "Butterfly" paradigm. - Zeeshan Ahmed 001; Saman Zeeshan; Thomas Dandekar (F1000Research, 2014)

Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. - Zeeshan Ahmed 001; Michel Mayr; Saman Zeeshan; Thomas Dandekar; Martin J. Mueller; Agnes Fekete (Bioinform., 2015)

MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format. - Zeeshan Ahmed 001; Thomas Dandekar (F1000Research, 2015)

GNATY: Optimized NGS Variant Calling and Coverage Analysis. - Beat Wolf; Pierre Kuonen; Thomas Dandekar (IWBBIO, 2016)

Mining biomedical images towards valuable information retrieval in biomedical and life sciences. - Zeeshan Ahmed 001; Saman Zeeshan; Thomas Dandekar (Database J. Biol. Databases Curation, 2016)

The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development. - Meik Kunz; Chunguang Liang; Santosh Nilla; Alexander Cecil; Thomas Dandekar (Database J. Biol. Databases Curation, 2016)

Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism. - Jan Ewald; Martin Bartl; Thomas Dandekar; Christoph Kaleta (PLoS Comput. Biol., 2017)

FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. - Kristin Verena Kaltdorf; Katja Schulze; Frederik Helmprobst; Philip Kollmannsberger; Thomas Dandekar; Christian Stigloher (PLoS Comput. Biol., 2017)

Meta-Alignment: Combining Sequence Aligners for Better Results. - Beat Wolf; Pierre Kuonen; Thomas Dandekar (IWBBIO (1), 2018)

An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data. - Juan Prada; Manju Sasi; Corinna Martin; Sibylle Jablonka; Thomas Dandekar; Robert Blum (PLoS Comput. Biol., 2018)

Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks. - Tim Breitenbach; Chunguang Liang; Niklas Beyersdorf; Thomas Dandekar (PLoS Comput. Biol., 2019)

In silico signaling modeling to understand cancer pathways and treatment responses. - Meik Kunz; Julian Jeromin; Maximilian Fuchs; Jan Christoph; Giulia Veronesi; Michael Flentje; Sarah Nietzer; Gudrun Dandekar; Thomas Dandekar (Briefings Bioinform., 2020)

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs. - Meik Kunz; Beat Wolf; Maximilian Fuchs; Jan Christoph; Ke Xiao; Thomas Thum; David Atlan; Hans-Ulrich Prokosch; Thomas Dandekar (Briefings Bioinform., 2020)

Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches. - Sergey Shityakov; Elena Bencurova; Carola Förster; Thomas Dandekar (BMC Bioinform., 2020)

A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2. - Juan Pablo Prada; Gaby Wangorsch; Kirstin Kucka; Isabell Lang; Thomas Dandekar; Harald Wajant (Bioinform., 2021)

Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing. - Tim Breitenbach; Matthias Jürgen Schmitt; Thomas Dandekar (Bioinform., 2022)

Bioinformatics - An Introductory Textbook - Thomas Dandekar; Meik Kunz (Springer, 2023)