Extended Cross-Serial Dependencies in Tree Adjoining Grammars. - Marco Kuhlmann; Mathias Möhl (TAG, 2006)

Mildly Context-Sensitive Dependency Languages. - Marco Kuhlmann; Mathias Möhl (ACL, 2007)

Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. - Mathias Möhl; Sebastian Will; Rolf Backofen (CPM, 2008)

Dynamic programming based RNA pseudoknot alignment. - Mathias Möhl (2009)

A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies. - Alessandro Dal Palù; Mathias Möhl; Sebastian Will (CP, 2010)

Alignnment of RNA with Structures of Unlimited Complexity. - Alessandro Dal Palù; Mathias Möhl; Sebastian Will (WCB@ICLP, 2010)

Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. - Raheleh Salari; Mathias Möhl; Sebastian Will; Süleyman Cenk Sahinalp; Rolf Backofen (RECOMB, 2010)

Sparsification of RNA structure prediction including pseudoknots. - Mathias Möhl; Raheleh Salari; Sebastian Will; Rolf Backofen; Süleyman Cenk Sahinalp (Algorithms Mol. Biol., 2010)

Lifting Prediction to Alignment of RNA Pseudoknots. - Mathias Möhl; Sebastian Will; Rolf Backofen (J. Comput. Biol., 2010)

Fast RNA structure alignment for crossing input structures. - Rolf Backofen; Gad M. Landau; Mathias Möhl; Dekel Tsur; Oren Weimann (J. Discrete Algorithms, 2011)

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)

CARNA - alignment of RNA structure ensembles. - Dragos Alexandru Sorescu; Mathias Möhl; Martin Mann; Rolf Backofen; Sebastian Will (Nucleic Acids Res., 2012)

SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. - Sebastian Will; Christina Schmiedl; Milad Miladi; Mathias Möhl; Rolf Backofen (RECOMB, 2013)

Bellman's GAP - a language and compiler for dynamic programming in sequence analysis. - Georg Sauthoff; Mathias Möhl; Stefan Janssen; Robert Giegerich (Bioinform., 2013)

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)

SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. - Sebastian Will; Christina Otto; Milad Miladi; Mathias Möhl; Rolf Backofen (Bioinform., 2015)