Decomposition During Search for Propagation-Based Constraint Solvers - Martin Mann; Guido Tack; Sebastian Will (CoRR, 2007)

CPSP-tools - Exact and complete algorithms for high-throughput 3D lattice protein studies. - Martin Mann; Sebastian Will; Rolf Backofen (BMC Bioinform., 2008)

Decomposition Techniques for Subgraph Matching - Stéphane Zampelli; Martin Mann; Yves Deville; Rolf Backofen (CoRR, 2008)

CPSP-web-tools: a server for 3D lattice protein studies. - Martin Mann; Cameron Smith; Mohamad Rabbath; Marlien Edwards; Sebastian Will; Rolf Backofen (Bioinform., 2009)

Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains - Martin Mann; Rolf Backofen; Sebastian Will (CoRR, 2009)

Constraint-based Local Move Definitions for Lattice Protein Models Including Side Chains - Martin Mann; Mohamed Abou Hamra; Kathleen Steinhöfel; Rolf Backofen (CoRR, 2009)

Shape-based Barrier Estimation for RNAs. - Sergiy Bogomolov; Martin Mann; Björn Voß; Andreas Podelski; Rolf Backofen (GCB, 2010)

Lattice model refinement of protein structures. - Martin Mann; Alessandro Dal Palù (WCB@ICLP, 2010)

Producing High-Accuracy Lattice Models from Protein Atomic Coordinates Including Side Chains. - Martin Mann; Rhodri Saunders; Cameron Smith; Rolf Backofen; Charlotte M. Deane (Adv. Bioinformatics, 2012)

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

Atom Mapping with Constraint Programming. - Martin Mann; Feras Nahar; Heinz Ekker; Rolf Backofen; Peter F. Stadler; Christoph Flamm (CP, 2013)

The Graph Grammar Library - A Generic Framework for Chemical Graph Rewrite Systems. - Martin Mann; Heinz Ekker; Christoph Flamm (ICMT, 2013)

Atom mapping with constraint programming. - Martin Mann; Feras Nahar; Norah Schnorr; Rolf Backofen; Peter F. Stadler; Christoph Flamm (Algorithms Mol. Biol., 2014)

Exact methods for lattice protein models. - Martin Mann; Rolf Backofen (Bio Algorithms Med Syst., 2014)

MoDPepInt: an interactive web server for prediction of modular domain-peptide interactions. - Kousik Kundu; Martin Mann; Fabrizio Costa; Rolf Backofen (Bioinform., 2014)

Memory-efficient RNA energy landscape exploration. - Martin Mann; Marcel Kucharík; Christoph Flamm; Michael T. Wolfinger (Bioinform., 2014)

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains. - Patrick R. Wright; Jens Georg; Martin Mann; Dragos Alexandru Sorescu; Andreas S. Richter; Steffen Lott; Robert Kleinkauf; Wolfgang R. Hess; Rolf Backofen (Nucleic Acids Res., 2014)

antaRNA: ant colony-based RNA sequence design. - Robert Kleinkauf; Martin Mann; Rolf Backofen (Bioinform., 2015)

antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization. - Robert Kleinkauf; Torsten Houwaart; Rolf Backofen; Martin Mann (BMC Bioinform., 2015)

IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. - Martin Mann; Patrick R. Wright; Rolf Backofen (Nucleic Acids Res., 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)

MICA: Multiple interval-based curve alignment. - Martin Mann; Hans-Peter Kahle; Matthias Beck; Bela Johannes Bender; Heinrich Spiecker; Rolf Backofen (SoftwareX, 2018)

Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction. - Rick Gelhausen; Sebastian Will; Ivo L. Hofacker; Rolf Backofen; Martin Raden (BIOINFORMATICS, 2019)

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)

IntaRNAhelix-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction. - Rick Gelhausen; Sebastian Will; Ivo L. Hofacker; Rolf Backofen; Martin Raden (J. Bioinform. Comput. Biol., 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)

pourRNA - a time- and memory-efficient approach for the guided exploration of RNA energy landscapes. - Gregor Entzian; Martin Raden (Bioinform., 2020)

The impact of various seed, accessibility and interaction constraints on sRNA target prediction- a systematic assessment. - Martin Raden; Teresa Müller; Stefan Mautner; Rick Gelhausen; Rolf Backofen (BMC 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)

CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. - Omer S. Alkhnbashi; Alexander Mitrofanov; Robson Bonidia; Martin Raden; Van Dinh Tran; Florian Eggenhofer; Shiraz A. Shah; Ekrem Öztürk; Victor Alexandre Padilha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho; Rolf Backofen (Nucleic Acids Res., 2021)