Publications (2017)
McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes
Dina Hafez, Aslihan Karabacak, Sabrina Krueger, Yih-Chii Hwang, Li-San Wang, Robert Zinzen, Uwe OhlerGenome Biology 2017;
DOI
RNA localization is a key determinant of neurite-enriched proteome
A. Zappulo, D. Bruck, C. Ciolli, V. Franke, K. Imami, E. McShane, M. Moreno-Estelles, Lorenzo Calviello, A. Filipchyk, E. Peguero-Sanchez, T. Muller, A. Woehler, C. Birchmeier, E. Merino, N. Rajewsky, Uwe Ohler, E. Mazzoni, M. Selbach, A. Akalin, M. ChekulaevaNat Commun 2017;
DOI
Beyond Read-Counts: Ribo-seq Data Analysis to Understand the Functions of the Transcriptome
Lorenzo Calviello, Uwe OhlerTrends Genet. 2017;
DOI
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data
D. Heller, R. Krestel, Uwe Ohler, M. Vingron, A. MarsicoNucleic Acids Res. 2017;
DOI
PubMed
DDX54 regulates transcriptome dynamics during DNA damage response
M. Milek, K. Imami, Neelanjan Mukherjee, F. Bortoli, U. Zinnall, O. Hazapis, C. Trahan, M. Oeffinger, F. Heyd, Uwe Ohler, M. Selbach, M. LandthalerGenome Res. 2017;
DOI
PubMed
RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation
R. Backofen, J. Engelhardt, A. Erxleben, J. Fallmann, B. Gruning, Uwe Ohler, N. Rajewsky, P. StadlerJ. Biotechnol. 2017;
DOI
PubMed
RCAS: an RNA centric annotation system for transcriptome-wide regions of interest
B. Uyar, D. Yusuf, R. Wurmus, N. Rajewsky, Uwe Ohler, A. AkalinNucleic Acids Res. 2017;
DOI
PubMed
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
B. Gruning, J. Fallmann, D. Yusuf, S. Will, A. Erxleben, F. Eggenhofer, T. Houwaart, B. Batut, P. Videm, A. Bagnacani, M. Wolfien, S. Lott, Y. Hoogstrate, W. Hess, O. Wolkenhauer, S. Hoffmann, A. Akalin, Uwe Ohler, P. Stadler, R. BackofenNucleic Acids Res. 2017;
DOI
PubMed
A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells
Silvia Velasco, Mahmoud Ibrahim, Akshay Kakumanu, Gorkem Garipler, Begum Aydin, Mohamed Al-Sayegh, Antje Hirsekorn, Farah Abdul-Rahman, Rahul Satija, Uwe Ohler, Shaun Mahony, Esteban MazzoniCell Stem Cell 2017;
DOI
PubMed
Integrative classification of human coding and noncoding genes through RNA metabolism profiles
Neelanjan Mukherjee, Lorenzo Calviello, Antje Hirsekorn, S. Pretis, M. Pelizzola, Uwe OhlerNat. Struct. Mol. Biol. 2017;
DOI
PubMed
Genome-wide identification of regulatory elements in Sertoli cells
D. Maatouk, A. Natarajan, Y. Shibata, L. Song, G. Crawford, Uwe Ohler, B. CapelDevelopment 2017;
DOI
PubMed
JACUSA: site-specific identification of RNA editing events from replicate sequencing data
M. Piechotta, E. Wyler, Uwe Ohler, M. Landthaler, C. DieterichBMC Bioinformatics 2017;
DOI
PubMed