Identification and characterization of IL-6-regulated ncRNAs (2009)
Grollmütz, N., Brocke-Heidrich, K., Jahndel, V., Schramedei, K., Hackermüller, J., Kretzschmar, A., ...
Long non-protein coding RNAs in oncogenic pathways (2009)
Hackermüller, J., Brocke-Heidrich, K., Reiche, K., Kretzschmar, A., Schutt, K., Ahnert, P., ...
Non-protein coding RNAs as highly specific biomarkers for cancer (2009)
Schutt, K., Horn, F., Ullmann, K., Kretzschmar, A., Hackermüller, J.
Regulation of non-protein-coding RNA genes by the Stat3 pathway (2009)
Horn, F., Brocke-Heidrich, K., Hackermüller, J., Stadler, P.
Transcriptome profiling reveals many novel p53-regulated human non-coding RNAs (2009)
Böhlig, L., Hackermüller, J., Rose, D., Reiche, K., Kretzschmar, A., Stadler, P.F., ...
Evolution of vault RNAs (2009)
Stadler, P.F., Chen, J.J.-L., Hackermüller, J., Hoffmann, S., Horn, F., Khaitovich, P., ...
Vault RNAs (vtRNAs) are small, about 100 nt long, polymerase III transcripts contained in the vault particles of eukaryotic cells. Presumably due to their enigmatic function, they have received...
Hoffmann, S., Otto, C., Kurtz, S., Sharma, C.M., Khaitovich, P., Vogel, J., ...
With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only...
NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences (2008)
Rose, D., Hertel, J., Reiche, K., Stadler, P.F., Hackermüller, J.
Genome-wide multiple sequence alignments (MSAs) are a necessary prerequisite for an increasingly diverse collection of comparative genomic approaches. Here we present a versatile method that...
Hoffmann, S., Cepok, S., Grummel, V., Lehmann-Horn, K., Hackermüller, J., Stadler, P.F., ...
The formation of antibodies to interferon-beta (IFN-beta), a protein-based disease-modifying agent for multiple sclerosis (MS), is a problem in clinical practice. These antibodies may neutralize the...
Duplicated RNA genes in teleost fish genomes (2008)
Rose, D., Jöris, J., Hackermüller, J., Reiche, K., Li, Q., Stadler, P.F.
Teleost fishes share a duplication of their entire genomes. We report here on a computational survey of structured non-coding RNAs (ncRNAs) in teleost genomes, focusing on the fate of fish-specific...
Sonnleitner, E., Sorger-Domenigg, T., Madej, M.J., Findeiss, S., Hackermüller, J., Hüttenhofer, A., ...
Inactivation of the Pseudomonas aeruginosa (PAO1) hfq gene, encoding the Sm-like Hfq protein, resulted in pleiotropic effects that included an attenuated virulence. As regulation by Hfq often...
RNAs everywhere: Genome-wide annotation of structured RNAs (2007)
Backofen, R., Bernhart, S.H., Flamm, C., Fried, C., Fritzsch, G., Hackermüller, J., ...
Starting with the discovery of microRNAs and the advent of genome-wide transcriptomics, non-protein-coding transcripts have moved from a fringe topic to a central field research in molecular biology....
RNA maps reveal new RNA classes and a possible function for pervasive transcription (2007)
Kapranov, P., Cheng, J., Dike, S., Nix, D.A., Duttagupta, R., Willingham, A.T., ...
Significant fractions of eukaryotic genomes give rise to RNA, much of which is unannotated and has reduced protein-coding potential. The genomic origins and the associations of human nuclear and...
We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genomeas part of the pilot phase of the ENCODE Project. These data...
Structured RNAs in the ENCODE selected regions of the human genome (2007)
Washietl, S., Pedersen, J.S., Korbel, J.O., Stocsits, C., Gruber, A.R., Hackermüller, J., ...
Functional RNA structures play an important role both in the context of noncoding RNA transcripts as well as regulatory elements in mRNAs. Here we present a computational study to detect functional...
Löffler, D., Brocke-Heidrich, K., Pfeifer, G., Stocsits, C., Hackermüller, J., Kretzschmar, A.K., ...
Signal transducer and activator of transcription 3 (Stat3) is implicated in the pathogenesis of many malignancies and essential for IL-6-dependent survival and growth of multiple myeloma cells. Here,...
Computational RNomics of drosophilids (2007)
Rose, D., Hackermüller, J., Washietl, S., Reiche, K., Hertel, J., Findeiß, S., ...
Background: Recent experimental and computational studies have provided overwhelming evidence for a plethora of diverse transcripts that are unrelated to protein-coding genes. One subclass consists...
RNA maps reveal new RNA classes and a possible function for pervasive transcription (2007)
Kapranov, P., Cheng, J., Dike, S., Nix, DA., Duttagupta, R., Willingham, AT., ...
Induction of microRNA-21 contributes to the oncogenic potential of Stat3 (2007)
Löffler, D., Brocke-Heidrich, K., Pfeifer, G., Stocsits, C., Hackermüller, J., Kretzschmar, A., ...
Thermodynamics of RNA-RNA binding (2006)
Mückstein, U., Tafer, H., Hackermüller, J., Bernhart, S.H., Stadler, P.F., Hofacker, I.L.
Background: Reliable prediction of RNA-RNA binding energies is crucial, e.g. for the understanding on RNAi, microRNA-mRNA binding and antisense interactions. The thermodynamics of such RNA-RNA...