SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics.

Mathias Möhl

Sebastian Will Christina Otto Milad Miladi Mathias Möhl Rolf Backofen SPARSE: quadratic time simultaneous alignment and folding of RNAs without sequence-based heuristics. 2489-2496 2015 31 Bioinform. 15 https://doi.org/10.1093/bioinformatics/btv185 https://www.wikidata.org/entity/Q41972499 db/journals/bioinformatics/bioinformatics31.html#WillOMMB15

Christina Otto Mathias Möhl Steffen Heyne Mika Amit Gad M. Landau Rolf Backofen Sebastian Will ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs. 6602 2014 15 BMC Bioinform. https://doi.org/10.1186/s12859-014-0404-0 https://www.wikidata.org/entity/Q34996184 db/journals/bmcbi/bmcbi15.html#OttoMHALBW14

Mika Amit Rolf Backofen Steffen Heyne Gad M. Landau Mathias Möhl Christina Otto Sebastian Will Local Exact Pattern Matching for Non-FixedRNA Structures. 219-230 2014 11 IEEE ACM Trans. Comput. Biol. Bioinform. 1 https://doi.org/10.1109/TCBB.2013.2297113 https://doi.ieeecomputersociety.org/10.1109/TCBB.2013.2297113 https://dl.acm.org/doi/10.1109/TCBB.2013.2297113 https://www.wikidata.org/entity/Q51128828 db/journals/tcbb/tcbb11.html#AmitBHLMOW14

Georg Sauthoff Mathias Möhl Stefan Janssen Robert Giegerich Bellman's GAP - a language and compiler for dynamic programming in sequence analysis. 551-560 2013 29 Bioinform. 5 https://doi.org/10.1093/bioinformatics/btt022 https://www.wikidata.org/entity/Q41824690 db/journals/bioinformatics/bioinformatics29.html#SauthoffMJG13

Sebastian Will Christina Schmiedl Milad Miladi Mathias Möhl Rolf Backofen SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs without Sequence-Based Heuristics. 289-290 2013 RECOMB https://doi.org/10.1007/978-3-642-37195-0_28 conf/recomb/2013 db/conf/recomb/recomb2013.html#WillSMMB13

Dragos Alexandru Sorescu Mathias Möhl Martin Mann Rolf Backofen Sebastian Will CARNA - alignment of RNA structure ensembles. 49-53 2012 40 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gks491 https://www.wikidata.org/entity/Q42232909 db/journals/nar/nar40.html#SorescuMMBW12

Mika Amit Rolf Backofen Steffen Heyne Gad M. Landau Mathias Möhl Christina Schmiedl Sebastian Will Local Exact Pattern Matching for Non-fixed RNA Structures. 306-320 2012 CPM https://doi.org/10.1007/978-3-642-31265-6_25 conf/cpm/2012 db/conf/cpm/cpm2012.html#AmitBHLMSW12 Christina Schmiedl Mathias Möhl Steffen Heyne Mika Amit Gad M. Landau Sebastian Will Rolf Backofen Exact Pattern Matching for RNA Structure Ensembles. 245-260 2012 RECOMB https://doi.org/10.1007/978-3-642-29627-7_27 conf/recomb/2012 db/conf/recomb/recomb2012.html#SchmiedlMHALWB12

Rolf Backofen Gad M. Landau Mathias Möhl Dekel Tsur Oren Weimann Fast RNA structure alignment for crossing input structures. 2-11 2011 9 J. Discrete Algorithms 1 https://doi.org/10.1016/j.jda.2010.07.004 https://www.wikidata.org/entity/Q56813223 db/journals/jda/jda9.html#BackofenLMTW11

Mathias Möhl Raheleh Salari Sebastian Will Rolf Backofen Süleyman Cenk Sahinalp Sparsification of RNA structure prediction including pseudoknots. 39 2010 5 Algorithms Mol. Biol. https://doi.org/10.1186/1748-7188-5-39 https://www.wikidata.org/entity/Q38259402 db/journals/almob/almob5.html#MohlSWBS10

Mathias Möhl Sebastian Will Rolf Backofen Lifting Prediction to Alignment of RNA Pseudoknots. 429-442 2010 17 J. Comput. Biol. 3 https://doi.org/10.1089/cmb.2009.0168 https://www.wikidata.org/entity/Q44192674 db/journals/jcb/jcb17.html#MohlWB10

Alessandro Dal Palù Mathias Möhl Sebastian Will A Propagator for Maximum Weight String Alignment with Arbitrary Pairwise Dependencies. 167-175 2010 CP https://doi.org/10.1007/978-3-642-15396-9_16 conf/cp/2010 db/conf/cp/cp2010.html#PaluMW10 Alessandro Dal Palù Mathias Möhl Sebastian Will Alignnment of RNA with Structures of Unlimited Complexity. 53-58 2010 WCB@ICLP https://doi.org/10.29007/f883 conf/iclp/2010wcb db/conf/iclp/wcb2010.html#PaluMW10 Raheleh Salari Mathias Möhl Sebastian Will Süleyman Cenk Sahinalp Rolf Backofen Time and Space Efficient RNA-RNA Interaction Prediction via Sparse Folding. 473-490 2010 RECOMB https://doi.org/10.1007/978-3-642-12683-3_31 conf/recomb/2010 db/conf/recomb/recomb2010.html#SalariMWSB10 Mathias Möhl Raheleh Salari Sebastian Will Rolf Backofen Süleyman Cenk Sahinalp Sparsification of RNA Structure Prediction Including Pseudoknots. 40-51 2010 WABI https://doi.org/10.1007/978-3-642-15294-8_4 conf/wabi/2010 db/conf/wabi/wabi2010.html#MohlSWBS10 Mathias Möhl Dynamic programming based RNA pseudoknot alignment. 2009 Saarland University http://scidok.sulb.uni-saarland.de/volltexte/2010/2961/ https://nbn-resolving.org/urn:nbn:de:bsz:291-scidok-29611 https://d-nb.info/1002293545 Rolf Backofen Gad M. Landau Mathias Möhl Dekel Tsur Oren Weimann Fast RNA Structure Alignment for Crossing Input Structures. 236-248 2009 CPM https://doi.org/10.1007/978-3-642-02441-2_21 conf/cpm/2009 db/conf/cpm/cpm2009.html#BackofenLMTW09 Mathias Möhl Sebastian Will Rolf Backofen Lifting Prediction to Alignment of RNA Pseudoknots. 285-301 2009 RECOMB https://doi.org/10.1007/978-3-642-02008-7_22 conf/recomb/2009 db/conf/recomb/recomb2009.html#MohlWB09 Mathias Möhl Sebastian Will Rolf Backofen Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots. 69-81 2008 CPM https://doi.org/10.1007/978-3-540-69068-9_9 conf/cpm/2008 db/conf/cpm/cpm2008.html#MohlWB08 Marco Kuhlmann Mathias Möhl Mildly Context-Sensitive Dependency Languages. 2007 ACL https://aclanthology.org/P07-1021/ conf/acl/2007 db/conf/acl/acl2007.html#KuhlmannM07 Marco Kuhlmann Mathias Möhl Extended Cross-Serial Dependencies in Tree Adjoining Grammars. 121-126 2006 TAG https://aclanthology.org/W06-1517/ conf/tag/2006 db/conf/tag/tag2006.html#KuhlmannM06 Mika Amit Rolf Backofen Robert Giegerich Steffen Heyne Stefan Janssen Marco Kuhlmann Gad M. Landau Milad Miladi Christina Otto Alessandro Dal Palù Martin RadenMartin Mann Süleyman Cenk Sahinalp Raheleh Salari Georg Sauthoff Christina Schmiedl Dragos Alexandru Sorescu Dekel Tsur Oren Weimann Sebastian Will