Thomas Dandekar

Orcid: 0000-0003-1886-7625

  • University of Würzburg, Germany

According to our database1, Thomas Dandekar authored at least 65 papers between 1997 and 2023.

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In proceedings 
PhD thesis 


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Bioinformatics - An Introductory Textbook
Springer, ISBN: 978-3-662-65035-6, 2023

Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing.
Bioinform., 2022

A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2.
Bioinform., 2021

Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches.
BMC Bioinform., 2020

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs.
Briefings Bioinform., 2020

In silico signaling modeling to understand cancer pathways and treatment responses.
Briefings Bioinform., 2020

Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks.
PLoS Comput. Biol., 2019

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., 2018

Meta-Alignment: Combining Sequence Aligners for Better Results.
Proceedings of the Bioinformatics and Biomedical Engineering, 2018

FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms.
PLoS Comput. Biol., 2017

Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism.
PLoS Comput. Biol., 2017

The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development.
Database J. Biol. Databases Curation, 2016

Mining biomedical images towards valuable information retrieval in biomedical and life sciences.
Database J. Biol. Databases Curation, 2016

GNATY: Optimized NGS Variant Calling and Coverage Analysis.
Proceedings of the Bioinformatics and Biomedical Engineering, 2016

MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format.
F1000Research, 2015

<i>Lipid-Pro: </i> a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms.
Bioinform., 2015

Developing sustainable software solutions for bioinformatics by the "<i>Butterfly</i>" paradigm.
F1000Research, 2014

'Isotopo' a database application for facile analysis and management of mass isotopomer data.
Database J. Biol. Databases Curation, 2014

Software applications toward quantitative metabolic flux analysis and modeling.
Briefings Bioinform., 2014

Analysing molecular polar surface descriptors to predict blood-brain barrier permeation.
Int. J. Comput. Biol. Drug Des., 2013

PlanktoVision - an automated analysis system for the identification of phytoplankton.
BMC Bioinform., 2013

Jimena: efficient computing and system state identification for genetic regulatory networks.
BMC Bioinform., 2013

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.
BMC Bioinform., 2013

GoSynthetic database tool to analyse natural and engineered molecular processes.
Database J. Biol. Databases Curation, 2013

Review: Semantic Web; Ontology Specific Languages for Web Application Development.
Int. J. Web Appl., 2012

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum.
BMC Syst. Biol., 2012

Robustness and accuracy of functional modules in integrated network analysis.
Bioinform., 2012

Integration of Boolean models exemplified on hepatocyte signal transduction.
Briefings Bioinform., 2012

Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation.
BMC Syst. Biol., 2011

Towards Design and Implementation of a Language Technology based Information Processor for PDM Systems
CoRR, 2010

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays.
BMC Bioinform., 2010

BioNet: an R-Package for the functional analysis of biological networks.
Bioinform., 2010

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection.
BMC Syst. Biol., 2009

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes.
BMC Bioinform., 2009

The ITS2 Database II: homology modelling RNA structure for molecular systematics.
Nucleic Acids Res., 2008

Modelling phagosomal lipid networks that regulate actin assembly.
BMC Syst. Biol., 2008

ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments.
Bioinform., 2008

Identifying functional modules in protein-protein interaction networks: an integrated exact approach.
Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

Deep Metazoan Phylogeny.
Silico Biol., 2007

Integrated network reconstruction, visualization and analysis using YANAsquare.
BMC Bioinform., 2007

The internal transcribed spacer 2 database - a web server for (not only) low level phylogenetic analyses.
Nucleic Acids Res., 2006

4SALE - A tool for synchronous RNA sequence and secondary structure alignment and editing.
BMC Bioinform., 2006

XML schemas for common bioinformatic data types and their application in workflow systems.
BMC Bioinform., 2006

inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons.
BMC Bioinform., 2006

Modelling interaction sites in protein domains with interaction profile hidden Markov models.
Bioinform., 2006

L1Base: from functional annotation to prediction of active LINE-1 elements.
Nucleic Acids Res., 2005

CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures.
Silico Biol., 2005

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
BMC Bioinform., 2005

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.
Bioinform., 2005

Current efforts in the analysis of RNAi and RNAi target genes.
Briefings Bioinform., 2005

Riboswitch finder tool for identification of riboswitch RNAs.
Nucleic Acids Res., 2004

Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework.
J. Integr. Bioinform., 2004

An Open Source Protein Gel Documentation System for Proteome Analyses.
J. Chem. Inf. Model., 2004

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

Metabolites, pathway flexibility.
Silico Biol., 2004

A software tool-box for analysis of regulatory RNA elements.
Nucleic Acids Res., 2003

Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances.
Proceedings of the German Conference on Bioinformatics, 2003

A Versatile Structural Domain Analysis Server Using Profile Weight Matrices.
J. Chem. Inf. Comput. Sci., 2002

Medical Target Prediction From Genome Sequence: Combining Different Sequence Analysis Algorithms with Expert Knowledge and Input From Artificial Intelligence Approaches.
Comput. Chem., 2002

Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae.
Bioinform., 2002

Metabolic Pathways.
Proceedings of the Gene Regulations and Metabolism - Postgenomic Computational Approaches, 2002

Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae.
Proceedings of the German Conference on Bioinformatics (GCB 2000), 2000

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Bioinform., 1998

Pathway alignment: Application in the comparative analysis of glycolysis.
Proceedings of the German Conference on Bioinformatics, 1998

Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region.
Proceedings of the German Conference on Bioinformatics, 1997