Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses. - Stefan Washietl; Frank Eisenhaber (BMC Bioinform., 2003)

Fast and reliable prediction of noncoding RNAs. - Stefan Washietl; Ivo L. Hofacker; Peter F. Stadler (Proc. Natl. Acad. Sci. USA, 2005)

Evolutionary patterns of non-coding RNAs. - Athanasius F. Bompfünewerer; Christoph Flamm; Claudia Fried; Guido Fritzsch; Ivo L. Hofacker; Jörg Lehmann; Kristin Missal; Axel Mosig; Bettina Müller; Sonja J. Prohaska; Bärbel M. R. Stadler; Peter F. Stadler; et al. (Theory Biosci., 2005)

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes. - Paul Wei-Che Hsu; Hsien-Da Huang; Sheng-Da Hsu; Li-Zen Lin; Ann-Ping Tsou; Ching-Ping Tseng; Peter F. Stadler; Stefan Washietl; Ivo L. Hofacker (Nucleic Acids Res., 2006)

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures. - Andreas R. Gruber; Richard Neuböck; Ivo L. Hofacker; Stefan Washietl (Nucleic Acids Res., 2007)

Dinucleotide controlled null models for comparative RNA gene prediction. - Tanja Gesell; Stefan Washietl (BMC Bioinform., 2008)

Strategies for measuring evolutionary conservation of RNA secondary structures. - Andreas R. Gruber; Stephan H. Bernhart; Ivo L. Hofacker; Stefan Washietl (BMC Bioinform., 2008)

RNAz 2.0: Improved Noncoding RNA Detection. - Andreas R. Gruber; Sven Findeiß; Stefan Washietl; Ivo L. Hofacker; Peter F. Stadler (Pacific Symposium on Biocomputing, 2010)

Graph Representations and Algorithms in Computational Biology of RNA Secondary Structure. - Stefan Washietl; Tanja Gesell (Structural Analysis of Complex Networks, 2011)