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)

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)

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs. - Milad Miladi; Alexander Junge; Fabrizio Costa; Stefan E. Seemann; Jakob Hull Havgaard; Jan Gorodkin; Rolf Backofen (Bioinform., 2017)

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)

Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. - Milad Miladi; Martin Raden; Sebastian Will; Rolf Backofen (WABI, 2019)

ShaKer: RNA SHAPE prediction using graph kernel. - Stefan Mautner; Soheila Montaseri; Milad Miladi; Martin Raden; Fabrizio Costa; Rolf Backofen (Bioinform., 2019)

Integration of accessibility data from structure probing into RNA-RNA interaction prediction. - Milad Miladi; Soheila Montaseri; Rolf Backofen; Martin Raden (Bioinform., 2019)

Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains. - Milad Miladi; Martin Raden; Sebastian Will; Rolf Backofen (Algorithms Mol. Biol., 2020)

The locality dilemma of Sankoff-like RNA alignments. - Teresa Müller; Milad Miladi; Frank Hutter; Ivo L. Hofacker; Sebastian Will; Rolf Backofen (Bioinform., 2020)

MutaRNA: analysis and visualization of mutation-induced changes in RNA structure. - Milad Miladi; Martin Raden; Sven Diederichs; Rolf Backofen (Nucleic Acids Res., 2020)