Thomas Dandekar

发表

Efficient and Robust Analysis of Large Phylogenetic Datasets

Sven Rahmann, Matthias Wolf, Tobias Müller, 2006 .

Mining biomedical images towards valuable information retrieval in biomedical and life sciences

Zeeshan Ahmed, Thomas Dandekar, Saman Zeeshan, 2016, Database J. Biol. Databases Curation.

Review: Semantic Web; Ontology Specific Languages for Web Application Development

Zeeshan Ahmed, Thomas Dandekar, Saman Majeed, 2012, Int. J. Web Appl..

A software tool-box for analysis of regulatory RNA elements

Thomas Dandekar, Peter Bengert, T. Dandekar, 2003, Nucleic Acids Res..

The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays

Alvis Brazma, Thomas Dandekar, Yevhen Vainshtein, 2010, BMC Bioinformatics.

PlanktoVision – an automated analysis system for the identification of phytoplankton

Thomas Dandekar, Marcus Frohme, Katja Schulze, 2013, BMC Bioinformatics.

Robustness and accuracy of functional modules in integrated network analysis

Tobias Müller, Gunnar W. Klau, Thomas Dandekar, 2012, Bioinform..

‘Isotopo’ a database application for facile analysis and management of mass isotopomer data

Zeeshan Ahmed, Dietmar Schomburg, Thomas Dandekar, 2014, Database J. Biol. Databases Curation.

Software applications toward quantitative metabolic flux analysis and modeling

Zeeshan Ahmed, Thomas Dandekar, Saman Majeed, 2014, Briefings Bioinform..

Pathway alignment: Application in the comparative analysis of glycolysis

Peer Bork, Stefan Schuster, Martijn A. Huynen, 1998, German Conference on Bioinformatics.

Playing with pesticides.

Jan Krüger, Robert Giegerich, Henning Mersch, 1998, BMC Bioinformatics.

GoSynthetic database tool to analyse natural and engineered molecular processes

Thomas Dandekar, Chunguang Liang, Beate Krüger, 2013, Database J. Biol. Databases Curation.

Structural Analysis of Metabolic Networks: Elementary Flux Modes, Analogy to Petri Nets, and Application to Mycoplasma Pneumoniae

Thomas Pfeiffer, Ina Koch, Stefan Schuster, 2000, German Conference on Bioinformatics.

Current efforts in the analysis of RNAi and RNAi target genes

Thomas Dandekar, Peter Bengert, T. Dandekar, 2005, Briefings Bioinform..

The internal transcribed spacer 2 database—a web server for (not only) low level phylogenetic analyses

Tobias Müller, Matthias Wolf, Thomas Dandekar, 2006, Nucleic Acids Res..

The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development

Thomas Dandekar, Chunguang Liang, Meik Kunz, 2016, Database J. Biol. Databases Curation.

YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities

Stefan Schuster, Axel von Kamp, Thomas Dandekar, 2005, BMC Bioinformatics.

Towards Design and Implementation of a Language Technology based Information Processor for PDM Systems pdf

Zeeshan Ahmed, Thomas Dandekar, Saman Majeed, 2010, ArXiv.

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum

Tobias Müller, Gunnar W. Klau, Thomas Dandekar, 2012, BMC Systems Biology.

Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches

Thomas Dandekar, Sergey Shityakov, Elena Bencurova, 2020, BMC Bioinformatics.

IntelliEppi: Intelligent reaction monitoring and holistic data management system for the molecular biology lab

Zeeshan Ahmed, Thomas Dandekar, Arthur Neuberger, 2017 .

A Versatile Structural Domain Analysis Server Using Profile Weight Matrices

Peer Bork, Thomas Dandekar, Steffen Schmidt, 2002, J. Chem. Inf. Comput. Sci..

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes

Alexander Schmid, Andrés Moya, Jörg Bernhardt, 2009, BMC Bioinformatics.

FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms

Philip Kollmannsberger, Thomas Dandekar, Christian Stigloher, 2017, PLoS Comput. Biol..

A system for non-contact monitoring of reaction vessels with electronic storage support, manufacture of suitable vessels and monitoring technology

Zeeshan Ahmed, Thomas Dandekar, Arthur Neuberger, 2014 .

inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons

Thomas Dandekar, Chunguang Liang, T. Dandekar, 2006, BMC Bioinformatics.

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

Tobias Müller, Matthias Wolf, Thomas Dandekar, 2006, BMC Bioinformatics.

Metabolic Pathways

Thomas Dandekar, Steffen Schmidt, T. Dandekar, 1961, Gene Regulations and Metabolism.

Medical Target Prediction From Genome Sequence: Combining Different Sequence Analysis Algorithms with Expert Knowledge and Input From Artificial Intelligence Approaches

Thomas Dandekar, Steffen Schmidt, R. Heiner Schirmer, 2001, Comput. Chem..

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

Thomas Dandekar, Marcus T. Dittrich, Jörg Geiger, 2011, BMC Systems Biology.

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances

Tobias Müller, Matthias Wolf, Thomas Dandekar, 2005, Bioinform..

Metabolites, pathway flexibility

Thomas Dandekar, Steffen Schmidt, 2004, Silico Biol..

Jimena: efficient computing and system state identification for genetic regulatory networks

Thomas Dandekar, Stefan Karl, T. Dandekar, 2013, BMC Bioinformatics.

Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms

Zeeshan Ahmed, Thomas Dandekar, Saman Zeeshan, 2015, Bioinform..

ProfDistS: (profile-) distance based phylogeny on sequence - structure alignments

Tobias Müller, Matthias Wolf, Thomas Dandekar, 2008, Bioinform..

Meta-Alignment: Combining Sequence Aligners for Better Results

Pierre Kuonen, Thomas Dandekar, Beat Wolf, 2018, IWBBIO.

Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework

Dietmar Seipel, Thomas Dandekar, Steffen Schmidt, 2004, J. Integr. Bioinform..

Integrated network reconstruction, visualization and analysis using YANAsquare

Michael Hecker, Christoph Kaleta, Stefan Schuster, 2007, BMC Bioinformatics.

The ITS2 Database II: homology modelling RNA structure for molecular systematics

Tobias Müller, Matthias Wolf, Thomas Dandekar, 2007, Nucleic Acids Res..

Systematic genomic screening and analysis of mRNA in the 5' and 3' untranslated region

Katrin Beyer, Peer Bork, Thomas Dandekar, 1997, German Conference on Bioinformatics.

Nanocellulose: A New Multifunctional Tool for RNA Systems Biology Research

Thomas Dandekar, Meik Kunz, Elena Bencurova, 2018 .

GNATY: Optimized NGS Variant Calling and Coverage Analysis

Pierre Kuonen, Thomas Dandekar, Beat Wolf, 2016, IWBBIO.

Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection

Oliver Sawodny, Jens Timmer, Michael Ederer, 2009, BMC Systems Biology.

Analysing molecular polar surface descriptors to predict blood-brain barrier permeation

Thomas Dandekar, Sergey Shityakov, Carola Förster, 2013, Int. J. Comput. Biol. Drug Des..

CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures

Tobias Müller, Matthias Wolf, Thomas Dandekar, 2005, Silico Biol..

Modelling interaction sites in protein domains with interaction profile hidden Markov models

Tobias Müller, Thomas Dandekar, Jörg Schultz, 2006, Bioinform..

Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework

Dietmar Seipel, Thomas Dandekar, Steffen Schmidt, 2004, J. Integr. Bioinform..

Bioinformatics Applications Note Systems Biology Bionet: an R-package for the Functional Analysis of Biological Networks

Tobias Müller, Gunnar W. Klau, Thomas Dandekar, 2022 .

An open source tool for automatic spatiotemporal assessment of calcium transients and local ‘signal-close-to-noise’ activity in calcium imaging data

Robert Blum, Thomas Dandekar, Juan Prada, 2018, PLoS Comput. Biol..

Robust estimation of the phylogeny of Chlorophyceae(Chlorophyta)based on profile distances

Sven Rahmann, Tobias Müller, Matthias Wolf, 2003, German Conference on Bioinformatics.

Modelling phagosomal lipid networks that regulate actin assembly

Thomas Dandekar, Jens G. Reich, Luis S. Mayorga, 2008, BMC Systems Biology.

Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism

Christoph Kaleta, Thomas Dandekar, Jan Ewald, 2017, PLoS Comput. Biol..

Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae

Thomas Pfeiffer, Ina Koch, Stefan Schuster, 2002, Bioinform..

Unified Modeling and HCI Mockup Designing towards MIDA

Zeeshan Ahmed, Thomas Dandekar, Saman Majeed, 2012 .

Integrating Formal UML Designs and HCI Patterns with Spiral SDLC in DroLIGHT Implementation

Zeeshan Ahmed, Thomas Dandekar, Charlotte Helfrich-Förster, 2013 .

Deep Metazoan Phylogeny

Sven Rahmann, Tobias Müller, Matthias Wolf, 2007, Silico Biol..

An Open Source Protein Gel Documentation System for Proteome Analyses

Ke Xiao, Jens Timmer, Christoph Peters, 2004, J. Chem. Inf. Model..

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

Katrin Beyer, Peer Bork, Thomas Dandekar, 1998, Bioinform..

Integration of Boolean models exemplified on hepatocyte signal transduction

Oliver Sawodny, Jens Timmer, Michael Ederer, 2012, Briefings Bioinform..

Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling

Zeeshan Ahmed, Dietmar Schomburg, Thomas Dandekar, 2013, BMC Bioinformatics.

Riboswitch finder tool for identification of riboswitch RNAs

Thomas Dandekar, Peter Bengert, T. Dandekar, 2004, Nucleic Acids Res..

IntelliEppi: Intelligent Reaction Monitoring and Holistic Data Management System for the Molecular Biology Lab

Zeeshan Ahmed, Thomas Dandekar, Arthur Neuberger, 2019 .

Identifying functional modules in protein–protein interaction networks: an integrated exact approach

Tobias Müller, Gunnar W. Klau, Thomas Dandekar, 2008, ISMB.

Stoffwechselanalyse: Der Weg vom Genom zum metabolischen Netzwerk (Pathway Analysis: On the Route from Genomics to Metabolic Networks)

Thomas Dandekar, Helge Bertram, 2004, it Inf. Technol..

Computational Feature Performance and Domain Specific Architecture Evaluation of Software Applications Towards Metabolic Flux Analysis

Zeeshan Ahmed, Thomas Dandekar, Saman Majeed, 2012 .

L1Base: from functional annotation to prediction of active LINE-1 elements

Thomas Dandekar, Tobias Penzkofer, Tomasz Zemojtel, 2004, Nucleic Acids Res..