Lightweight comparison of RNAs based on exact sequence-structure matches. - Steffen Heyne; Sebastian Will; Michael Beckstette; Rolf Backofen (Bioinform., 2009)

Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA. - Cameron Smith; Steffen Heyne; Andreas S. Richter; Sebastian Will; Rolf Backofen (Nucleic Acids Res., 2010)

Local Exact Pattern Matching for Non-fixed RNA Structures. - Mika Amit; Rolf Backofen; Steffen Heyne; Gad M. Landau; Mathias Möhl; Christina Schmiedl; Sebastian Will (CPM, 2012)

Exact Pattern Matching for RNA Structure Ensembles. - Christina Schmiedl; Mathias Möhl; Steffen Heyne; Mika Amit; Gad M. Landau; Sebastian Will; Rolf Backofen (RECOMB, 2012)

GraphClust: alignment-free structural clustering of local RNA secondary structures. - Steffen Heyne; Fabrizio Costa; Dominic Rose; Rolf Backofen (Bioinform., 2012)

Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. - Nuno D. Mendes; Steffen Heyne; Ana T. Freitas; Marie-France Sagot; Rolf Backofen (Bioinform., 2012)

LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. - Sebastian Will; Michael F. Siebauer; Steffen Heyne; Jan Engelhardt; Peter F. Stadler; Kristin Reiche; Rolf Backofen (Algorithms Mol. Biol., 2013)

Scalable structural clustering of local RNA secondary structures. - Fabrizio Costa; Steffen Heyne; Dominic Rose; Rolf Backofen (CMSR@ECCB, 2014)

ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. - Christina Otto; Mathias Möhl; Steffen Heyne; Mika Amit; Gad M. Landau; Rolf Backofen; Sebastian Will (BMC Bioinform., 2014)

Local Exact Pattern Matching for Non-FixedRNA Structures. - Mika Amit; Rolf Backofen; Steffen Heyne; Gad M. Landau; Mathias Möhl; Christina Otto; Sebastian Will (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Using local RNA secondary structures for computational comparison and clustering of RNA molecules - Steffen Heyne (2014)

deepTools2: a next generation web server for deep-sequencing data analysis. - Fidel Ramírez; Devon Patrick Ryan; Björn A. Grüning; Vivek Bhardwaj 002; Fabian Kilpert; Andreas S. Richter; Steffen Heyne; Friederike Dündar; Thomas Manke (Nucleic Acids Res., 2016)

Freiburg RNA tools: a central online resource for RNA-focused research and teaching. - Martin Raden; Syed M. Ali; Omer S. Alkhnbashi; Anke Busch; Fabrizio Costa; Jason A. Davis; Florian Eggenhofer; Rick Gelhausen; Jens Georg; Steffen Heyne; Michael Hiller; Kousik Kundu; et al. (Nucleic Acids Res., 2018)

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis. - Vivek Bhardwaj 002; Steffen Heyne; Katarzyna Sikora; Leily Rabbani; Michael Rauer; Fabian Kilpert; Andreas S. Richter; Devon Patrick Ryan; Thomas Manke (Bioinform., 2019)