Seibel, Philipp N, Müller, Tobias, Dandekar, Thomas, Wolf, Matthias
Abstract Background The function of a noncoding RNA sequence is mainly determined by its secondary structure and therefore a family of noncoding RNA sequences is much more conserved on the structural...
ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales) (2008)
Keller, Alexander, Schleicher, Tina, Förster, Frank, Ruderisch, Benjamin, Dandekar, Thomas, Müller, Tobias, ...
Abstract Background Within Chlorophyceae the ITS2 secondary structure shows an unbranched helix I, except for the ' Hydrodictyon ' and the ' Scenedesmus ' clade having a ramified first helix. The...
The linear chromosome of the plant-pathogenic mycoplasma 'CandidatusPhytoplasma mali' (2008)
Kube, Michael, Schneider, Bernd, Kuhl, Heiner, Dandekar, Thomas, Heitmann, Katja, Migdoll, Alexander M, ...
Abstract Background Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. They represent a monophyletic group...
Blenk, Steffen, Engelmann, Julia C, Pinkert, Stefan, Weniger, Markus, Schultz, Jörg, Rosenwald, Andreas, ...
Abstract Background Mantle cell lymphoma (MCL) is an incurable B cell lymphoma and accounts for 6% of all non-Hodgkin's lymphomas. On the genetic level, MCL is characterized by the hallmark...
Julia C. Engelmann, Roland Schwarz, Steffen Blenk, Torben Friedrich, Philipp N. Seibel, Thomas Dandekar, ...
Over the past years, microarray databases have increased rapidly in size. While they offer a wealth of data, it remains challenging to integrate data arising from different studies. Here we propose...
Exonization of active mouse L1s: a driver of transcriptome evolution? (2007)
Zemojtel, Tomasz, Penzkofer, Tobias, Schultz, Jörg, Dandekar, Thomas, Badge, Richard, Vingron, Martin
Abstract Background Long interspersed nuclear elements (LINE-1s, L1s) have been recently implicated in the regulation of mammalian transcriptomes. Results Here, we show that members of the three...
Exonization of active mouse LIs: a driver of transcriptome evolution? (2007)
Zemojtel, Tomasz, Penzkofe, Tobias, Schultz, Jorg, Dandekar, Thomas, Badge, Richard, Vingron, Martin
This is the authors final draft of the paper published in BMC Genomics, 2007, vol. 8(392). The final publsihed version is available at http://www.biomedcentral.com/1471-2164/8/392
Integrated network reconstruction, visualization and analysis using YANAsquare (2007)
Schwarz, Roland, Liang, Chunguang, Kaleta, Christoph, Kühnel, Mark, Hoffmann, Eik, Kuznetsov, Sergei, ...
Abstract Background Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network. Results...
Exonization of active mouse L1s: a driver of transcriptome evolution? (2007)
Zemojtel, Tomasz, Penzkofer, Tobias, Schultz, Jörg, Dandekar, Thomas, Badge, Richard, Vingron, Martin
Background: Long interspersed nuclear elements (LINE-1s, L1s) have been recently implicated in the regulation of mammalian transcriptomes. Results: Here, we show that members of the three active...
4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing (2006)
Seibel, Philipp N, Müller, Tobias, Dandekar, Thomas, Schultz, Jörg, Wolf, Matthias
Abstract Background In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore...
XML schemas for common bioinformatic data types and their application in workflow systems (2006)
Seibel, Philipp N, Krüger, Jan, Hartmeier, Sven, Schwarzer, Knut, Löwenthal, Kai, Mersch, Henning, ...
Abstract Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create...
inGeno – an integrated genome and ortholog viewer for improved genome to genome comparisons (2006)
Liang, Chunguang, Dandekar, Thomas
Abstract Background Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics....
Gaudermann, Peter, Vogl, Ina, Zientz, Evelyn, Silva, Francisco J, Moya, Andres, Gross, Roy, ...
Abstract Background There is an increasing interest to better understand endosymbiont capabilities in insects both from an ecological point of view and for pest control. Blochmannia floridanus...
YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities (2005)
Schwarz, Roland, Musch, Patrick, Von Kamp, Axel, Engels, Bernd, Schirmer, Heiner, Schuster, Stefan, ...
Abstract Background A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA) has proven especially useful....
L1Base: from functional annotation to prediction of active LINE-1 elements (2005)
Penzkofer, Tobias, Dandekar, Thomas, Zemojtel, Tomasz
L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes that are as follows: (i) intact in the two open reading frames (ORFs),...
Müller, Tobias, Rahmann, Sven, Dandekar, Thomas, Wolf, Matthias
Abstract Background In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns...
A novel conserved family of nitric oxide synthase? (2004)
Zemojtel,Tomasz, Penzkofer,Tobias, Dandekar,Thomas, Schultz,Jörg
We describe a novel system for the production of nitric oxide (NO) that is conserved in all eukaryotes and many bacteria. The prediction of candidate functional sites as well as the link to...
A novel conserved family of nitric oxide synthase? (2004)
Zemojtel,Tomasz, Penzkofer,Tobias, Dandekar,Thomas, Schultz,Joerg
We describe a novel system for the production of nitric oxide (NO) that is conserved in all eukaryotes and many bacteria. The prediction of candidate functional sites as well as the link to...
A novel conserved family of nitric oxide synthase? (2004)
Zemojtel, Tomasz, Penzkofer, Tobias, Dandekar, Thomas, Schultz, Jörg
We describe a novel system for the production of nitric oxide (NO) that is conserved in all eukaryotes and many bacteria. The prediction of candidate functional sites as well as the link to...
A novel conserved family of nitric oxide synthase? (2004)
Zemojtel, Tomasz, Penzkofer, Tobias, Dandekar, Thomas, Schultz, Joerg
We describe a novel system for the production of nitric oxide (NO) that is conserved in all eukaryotes and many bacteria. The prediction of candidate functional sites as well as the link to...
Robust estimation of the phylogeny of chlorophyceae (chlorophyta) based on profile distances (2003)
Müller, Tobias, Rahmann, Sven, Dandekar, Thomas, Wolf, Matthias
Z. Biochimica et Biophysica Acta 1343 1997 1--15 (2002)
Contents 1. Introduction ................................................... 1 2. The protein folding problem ......................................... 2 2.1. The minimum of free energy...
Pathway alignment : application to the comparative analysis of glycolytic enzymes (1999)
Dandekar, Thomas, Schuster, Stefan, Snel, Berend, Huynen, Martijn, Bork, Peer
Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on...
München, Univ., Diss., 1986.
Thesis (doctoral)--Ludwig-Maximilians Universität München, 1985.
Wang, Rui, Zheng, Liangbiao, Touré, Yeya T., Dandekar, Thomas, Kafatos, Fotis C.
Genetic distance measurements are an important tool to differentiate field populations of disease vectors such as the mosquito vectors of malaria. Here, we have measured the genetic differentiation...
Processing of the Precursors to Small Nucleolar RNAs and rRNAs Requires Common Components
Petfalski, Elisabeth, Dandekar, Thomas, Henry, Yves, Tollervey, David
The genes encoding the small nucleolar RNA (snoRNA) species snR190 and U14 are located close together in the genome of Saccharomyces cerevisiae. Here we report that these two snoRNAs are synthesized...
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
Dandekar, Thomas, Huynen, Martijn, Regula, Jörg Thomas, Ueberle, Barbara, Zimmermann, Carl Ulrich, Andrade, Miguel A., ...
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10...
A software tool-box for analysis of regulatory RNA elements
Bengert, Peter, Dandekar, Thomas
We describe an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format....
Riboswitch finder—a tool for identification of riboswitch RNAs
Bengert, Peter, Dandekar, Thomas
We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence...
Metabolic Interdependence of Obligate Intracellular Bacteria and Their Insect Hosts†
Zientz, Evelyn, Dandekar, Thomas, Gross, Roy
Mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. However,...
L1Base: from functional annotation to prediction of active LINE-1 elements
Penzkofer, Tobias, Dandekar, Thomas, Zemojtel, Tomasz
L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes that are as follows: (i) intact in the two open reading frames (ORFs),...
YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities
Schwarz, Roland, Musch, Patrick, Von Kamp, Axel, Engels, Bernd, Schirmer, Heiner, Schuster, Stefan, ...
WOLF, MATTHIAS, ACHTZIGER, MARCO, SCHULTZ, JÖRG, DANDEKAR, THOMAS, MÜLLER, TOBIAS
Structural genomics meets phylogenetics and vice versa: Knowing rRNA secondary structures is a prerequisite for constructing rRNA alignments for inferring phylogenies, and inferring phylogenies is a...
Eisenreich, Wolfgang, Slaghuis, Jörg, Laupitz, Ralf, Bussemer, Johanna, Stritzker, Jochen, Schwarz, Christine, ...
The carbon metabolism of Listeria monocytogenes (Lm) EGD and the two isogenic mutant strains LmΔprfA and LmΔprfApPRFA* (showing no or enhanced expression, respectively, of the virulence factor...
Schultz, Jörg, Müller, Tobias, Achtziger, Marco, Seibel, Philipp N., Dandekar, Thomas, Wolf, Matthias
The internal transcribed spacer 2 (ITS2) is a phylogenetic marker which has been of broad use in generic and infrageneric level classifications, as its sequence evolves comparably fast. Only...
4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing
Seibel, Philipp N, Müller, Tobias, Dandekar, Thomas, Schultz, Jörg, Wolf, Matthias
Wang, Rui, Zheng, Liangbiao, Touré, Yeya T., Dandekar, Thomas, Kafatos, Fotis C.
Genetic distance measurements are an important tool to differentiate field populations of disease vectors such as the mosquito vectors of malaria. Here, we have measured the genetic differentiation...
Processing of the Precursors to Small Nucleolar RNAs and rRNAs Requires Common Components
Petfalski, Elisabeth, Dandekar, Thomas, Henry, Yves, Tollervey, David
The genes encoding the small nucleolar RNA (snoRNA) species snR190 and U14 are located close together in the genome of Saccharomyces cerevisiae. Here we report that these two snoRNAs are synthesized...
Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames
Dandekar, Thomas, Huynen, Martijn, Regula, Jörg Thomas, Ueberle, Barbara, Zimmermann, Carl Ulrich, Andrade, Miguel A., ...
Four years after the original sequence submission, we have re-annotated the genome of Mycoplasma pneumoniae to incorporate novel data. The total number of ORFss has been increased from 677 to 688 (10...
A software tool-box for analysis of regulatory RNA elements
Bengert, Peter, Dandekar, Thomas
We describe an integrated tool-box to identify regulatory RNA elements. The RNA analyzer collects general and specific information on any submitted RNA sequence or batch of sequences in FASTA format....
Riboswitch finder—a tool for identification of riboswitch RNAs
Bengert, Peter, Dandekar, Thomas
We describe a dedicated RNA motif search program and web server to identify RNA riboswitches. The Riboswitch finder analyses a given sequence using the web interface, checks specific sequence...
Metabolic Interdependence of Obligate Intracellular Bacteria and Their Insect Hosts†
Zientz, Evelyn, Dandekar, Thomas, Gross, Roy
Mutualistic associations of obligate intracellular bacteria and insects have attracted much interest in the past few years due to the evolutionary consequences for their genome structure. However,...
L1Base: from functional annotation to prediction of active LINE-1 elements
Penzkofer, Tobias, Dandekar, Thomas, Zemojtel, Tomasz
L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes that are as follows: (i) intact in the two open reading frames (ORFs),...
YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities
Schwarz, Roland, Musch, Patrick, Von Kamp, Axel, Engels, Bernd, Schirmer, Heiner, Schuster, Stefan, ...
WOLF, MATTHIAS, ACHTZIGER, MARCO, SCHULTZ, JÖRG, DANDEKAR, THOMAS, MÜLLER, TOBIAS
Structural genomics meets phylogenetics and vice versa: Knowing rRNA secondary structures is a prerequisite for constructing rRNA alignments for inferring phylogenies, and inferring phylogenies is a...
Eisenreich, Wolfgang, Slaghuis, Jörg, Laupitz, Ralf, Bussemer, Johanna, Stritzker, Jochen, Schwarz, Christine, ...
The carbon metabolism of Listeria monocytogenes (Lm) EGD and the two isogenic mutant strains LmΔprfA and LmΔprfApPRFA* (showing no or enhanced expression, respectively, of the virulence factor...
Schultz, Jörg, Müller, Tobias, Achtziger, Marco, Seibel, Philipp N., Dandekar, Thomas, Wolf, Matthias
The internal transcribed spacer 2 (ITS2) is a phylogenetic marker which has been of broad use in generic and infrageneric level classifications, as its sequence evolves comparably fast. Only...
4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing
Seibel, Philipp N, Müller, Tobias, Dandekar, Thomas, Schultz, Jörg, Wolf, Matthias
Hain, Torsten, Steinweg, Christiane, Kuenne, Carsten Tobias, Billion, André, Ghai, Rohit, Chatterjee, Som Subhra, ...
We present the complete genome sequence of Listeria welshimeri, a nonpathogenic member of the genus Listeria. Listeria welshimeri harbors a circular chromosome of 2,814,130 bp with 2,780 open reading...
XML schemas for common bioinformatic data types and their application in workflow systems
Seibel, Philipp N, Krüger, Jan, Hartmeier, Sven, Schwarzer, Knut, Löwenthal, Kai, Mersch, Henning, ...
Integrated network reconstruction, visualization and analysis using YANAsquare
Schwarz, Roland, Liang, Chunguang, Kaleta, Christoph, Kühnel, Mark, Hoffmann, Eik, Kuznetsov, Sergei, ...
Deeken, Rosalia, Engelmann, Julia C., Efetova, Marina, Czirjak, Tina, Müller, Tobias, Kaiser, Werner M., ...
Transformation of plant cells with T-DNA of virulent agrobacteria is one of the most extreme triggers of developmental changes in higher plants. For rapid growth and development of resulting tumors,...
Exonization of active mouse L1s: a driver of transcriptome evolution?
Zemojtel, Tomasz, Penzkofer, Tobias, Schultz, Jörg, Dandekar, Thomas, Badge, Richard, Vingron, Martin
The ITS2 Database II: homology modelling RNA structure for molecular systematics
Selig, Christian, Wolf, Matthias, Müller, Tobias, Dandekar, Thomas, Schultz, Jörg
An increasing number of phylogenetic analyses are based on the internal transcribed spacer 2 (ITS2). They mainly use the fast evolving sequence for low-level analyses. When considering the highly...
Müller, Tobias, Philippi, Nicole, Dandekar, Thomas, Schultz, Jörg, Wolf, Matthias
Given two organisms, how can one distinguish whether they belong to the same species or not? This might be straightforward for two divergent organisms, but can be extremely difficult and laborious...
Buchholz, Kathrin, Schirmer, R. Heiner, Eubel, Jana K., Akoachere, Monique B., Dandekar, Thomas, Becker, Katja, ...
Methylene blue (MB) has experienced a renaissance mainly as a component of drug combinations against Plasmodium falciparum malaria. Here, we report biochemically relevant pharmacological data on MB...
Blenk, Steffen, Engelmann, Julia C, Pinkert, Stefan, Weniger, Markus, Schultz, Jörg, Rosenwald, Andreas, ...
The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali'
Kube, Michael, Schneider, Bernd, Kuhl, Heiner, Dandekar, Thomas, Heitmann, Katja, Migdoll, Alexander M, ...