SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein. - Antje Krause; Stefan A. Haas; Eivind Coward; Martin Vingron (Nucleic Acids Res., 2002)

Genome wide identification and classification of alternative splicing based on EST data. - Shobhit Gupta; Dorothea Zink; Bernhard Korn; Martin Vingron; Stefan A. Haas (Bioinform., 2004)

T-STAG: resource and web-interface for tissue-specific transcripts and genes. - Shobhit Gupta; Martin Vingron; Stefan A. Haas (Nucleic Acids Res., 2005)

PASTAA: identifying transcription factors associated with sets of co-regulated genes. - Helge G. Roider; Thomas Manke; Sean O'Keeffe; Martin Vingron; Stefan A. Haas (Bioinform., 2009)

Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. - Anne-Katrin Emde; Marcel H. Schulz; David Weese; Ruping Sun; Martin Vingron; Vera M. Kalscheuer; Stefan A. Haas; Knut Reinert (Bioinform., 2012)

Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. - Ruping Sun; Michael I. Love; Tomasz Zemojtel; Anne-Katrin Emde; Ho-Ryun Chung; Martin Vingron; Stefan A. Haas (Bioinform., 2012)

Ranbow: A fast and accurate method for polyploid haplotype reconstruction. - M-Hossein Moeinzadeh; Jun Yang 043; Evgeny Muzychenko; Giuseppe Gallone; David Heller; Knut Reinert; Stefan A. Haas; Martin Vingron (PLoS Comput. Biol., 2020)