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...
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...
Weniger, Markus, Engelmann, Julia C, Schultz, Jörg
Abstract Background Regulation of gene expression is relevant to many areas of biology and medicine, in the study of treatments, diseases, and developmental stages. Microarrays can be used to measure...
Context-Specific Independence Mixture Modelling for Protein Families. (2007)
Georgi, Benjamin, Schultz, Jörg, Schliep, Alexander
Protein families can be divided into subgroups with functional differences. The analysis of these subgroups and the determination of which residues convey substrate specificity is a central question...
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...
Büssow, Konrad, Scheich, Christoph, Sievert, Volker, Harttig, Ulrich, Schultz, Jörg, Simon, Bernd, ...
Background The availability of suitable recombinant protein is still a major bottleneck in protein structure analysis. The Protein Structure Factory, part of the international structural genomics...
SMART 4.0: towards genomic data integration (2004)
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
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...
Developing a protein-interactions ontology (2003)
Ratsch, Esther, Schultz, Jörg, Saric, Jasmin, Lavin, Philipp Cimiano, Wittig, Ulrike, Reyle, Uwe, ...
SMART: a web-based tool for the study of genetically mobile domains (2000)
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de )....
Ponting, Chris P., Schultz, Jörg, Milpetz, Frank, Bork, Peer
SMART is a simple modular architecture research tool and database that provides domain identification and annotation on the WWW (http://coot.embl-heidelberg.de/SMART ). The tool compares query...
4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing
Seibel, Philipp N, Müller, Tobias, Dandekar, Thomas, Schultz, Jörg, Wolf, Matthias
Dimopoulos, George, Casavant, Thomas L., Chang, Shereen, Scheetz, Todd, Roberts, Chad, Donohue, Micca, ...
Together with AIDS and tuberculosis, malaria is at the top of the list of devastating infectious diseases. However, molecular genetic studies of its major vector, Anopheles gambiae, are still quite...
SMART, a simple modular architecture research tool: Identification of signaling domains
Schultz, Jörg, Milpetz, Frank, Bork, Peer, Ponting, Chris P.
Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows...
SMART: a web-based tool for the study of genetically mobile domains
Schultz, Jörg, Copley, Richard R., Doerks, Tobias, Ponting, Chris P., Bork, Peer
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de )....
Dimopoulos, George, Christophides, George K., Meister, Stephan, Schultz, Jörg, White, Kevin P., Barillas-Mury, Carolina, ...
The complex gene expression responses of Anopheles gambiae to microbial and malaria challenges, injury, and oxidative stress (in the mosquito and/or a cultured cell line) were surveyed by using cDNA...
Systematic Identification of Novel Protein Domain Families Associated with Nuclear Functions
Doerks, Tobias, Copley, Richard R., Schultz, Jörg, Ponting, Chris P., Bork, Peer
A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of...
Predicting Protein Cellular Localization Using a Domain Projection Method
Mott, Richard, Schultz, Jörg, Bork, Peer, Ponting, Chris P.
We investigate the co-occurrence of domain families in eukaryotic proteins to predict protein cellular localization. Approximately half (300) of SMART domains form a “small-world network”, linked...
SMART 4.0: towards genomic data integration
Letunic, Ivica, Copley, Richard R., Schmidt, Steffen, Ciccarelli, Francesca D., Doerks, Tobias, Schultz, Jörg, ...
SMART (Simple Modular Architecture Research Tool) is a web tool (http://smart.embl.de/) for the identification and annotation of protein domains, and provides a platform for the comparative study of...
Büssow, Konrad, Scheich, Christoph, Sievert, Volker, Harttig, Ulrich, Schultz, Jörg, Simon, Bernd, ...
SMART 5: domains in the context of genomes and networks
Letunic, Ivica, Copley, Richard R., Pils, Birgit, Pinkert, Stefan, Schultz, Jörg, Bork, Peer
The Simple Modular Architecture Research Tool (SMART) is an online resource () used for protein domain identification and the analysis of protein domain architectures. Many new features were...
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
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...