Fraunhofer-Gesellschaft

Publica

Hier finden Sie wissenschaftliche Publikationen aus den Fraunhofer-Instituten.
2018Accurate mapping of tRNA reads
Hoffmann, Anne; Fallmann, Jörg; Vilardo, Elisa; Mörl, Mario; Stadler, Peter F.; Amman, Fabian
Journal Article
2018Comparative RNA genomics
Backofen, Rolf; Gorodkin, Jan; Hofacker, Ivo L.; Stadler, Peter F.
Book Article
2018Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem
Prohaska, Sonja J.; Berkemer, Sarah J.; Gärtner, Fabian; Gatter, Thomas; Retzlaff, Nancy; Höner zu Siederdissen, Christian; Stadler, Peter F.
Journal Article
2018Finding the K best synthesis plans
Fagerberg, Rolf; Flamm, Christoph; Kianian, Rojin; Merkle, Daniel; Stadler, Peter F.
Journal Article
2018The fungal snoRNAome
Canzler, Sebastian; Stadler, Peter F.; Schor, Jana
Journal Article
2018Gene phylogenies and orthologous groups
Setubal, João C.; Stadler, Peter F.
Book Article
2018Noncoding RNA transcripts during differentiation of induced pluripotent stem cells into hepatocytes
Skrzypczyk, Aniela; Kehr, Stephanie; Krystel, Ilona; Bernhart, Stephan H.F.; Giri, Shibashish; Bader, Augustinus; Stadler, Peter F.
Journal Article
2018Phylogenetics beyond biology
Retzlaff, Nancy; Stadler, Peter F.
Journal Article
2018Proceedings of the “Mathematics in chemistry meeting”, Leipzig, Germany, October 26 - 28 2016. Foreword
Restrepo, Guillermo; Stadler, Peter F.; Jost, Jürgen
Conference Paper, Journal Article
2018Reachability, connectivity, and proximity in chemical spaces
Stadler, Bärbel M.R.; Stadler, Peter F.
Conference Paper, Journal Article
2018Reconstructing gene trees from Fitch’s xenology relation
Geiß, Manuela; Anders, John; Stadler, Peter F.; Wieseke, Nicolas; Hellmuth, Marc
Journal Article
2018Rule composition in graph transformation models of chemical reactions
Andersen, Jakob L.; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.
Conference Paper, Journal Article
2018The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments
Wiegreffe, Daniel; Müller, Lydia; Steuck, Jens; Zeckzer, Dirk; Stadler, Peter F.
Journal Article
2018Split-inducing indels in phylogenomic analysis
Donath, Alexander; Stadler, Peter F.
Journal Article
2018Superbubbles revisited
Gärtner, Fabian; Müller, Lydia; Stadler, Peter F.
Journal Article
2018Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1
Walter Costa, Maria B.; Höner zu Siederdissen, Christian; Tulpan, Dan C.; Stadler, Peter F.; Nowick, Katja
Journal Article
2018Time-consistent reconciliation maps and forbidden time travel
Nøjgaard, Nikolai; Geiß, Manuela; Merkle, Daniel; Stadler, Peter F.; Wieseke, Nicolas; Hellmuth, Marc
Journal Article
2018Towards mechanistic prediction of mass spectra using graph transformation
Andersen, Jakob L.; Fagerberg, Rolf; Flamm, Christoph; Kianian, Rojin; Merkle, Daniel; Stadler, Peter F.
Conference Paper, Journal Article
2017Accurate annotation of protein-coding genes in mitochondrial genomes
Al-Arab, Marwa; Höner zu Siederdissen, Christian; Tout, Kifah R.; Sahyoun, Abdullah H.; Stadler, Peter F.; Bernt, Matthias
Journal Article
2017Algebraic dynamic programming on trees
Berkemer, Sarah J.; Höner zu Siederdissen, Christian; Stadler, Peter F.
Journal Article
2017Applicability of a computational design approach for synthetic riboswitches
Domin, Gesine; Findeiß, Sven; Wachsmuth, Manja; Will, Sebastian; Stadler, Peter F.; Mörl, Mario
Journal Article
2017Chemical graph transformation with stereo-information
Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.
Conference Paper
2017Design of artificial riboswitches as biosensors
Findeiß, Sven; Etzel, Maja; Will, Sebastian; Mörl, Mario; Stadler, Peter F.
Journal Article
2017An intermediate level of abstraction for computational systems chemistry
Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.
Journal Article
2017Keeping it complicated: Mitochondrial genome plasticity across diplonemids
Valach, Matus; Moreira, Sandrine; Hoffmann, Steve; Stadler, Peter F.; Burger, Gertraud
Journal Article
2017Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements
Al-Arab, Marwa; Bernt, Matthias; Höner zu Siederdissen, Christian; Tout, Kifah R.; Stadler, Peter F.
Journal Article
2017Rare splice variants in long non-coding RNAs
Sen, Rituparno; Doose, Gero; Stadler, Peter F.
Journal Article
2017Similarity-based segmentation of multi-dimensional signals
Machné, Rainer; Murray, Douglas B.; Stadler, Peter F.
Journal Article
2017SMORE: Synteny modulator of repetitive elements
Berkemer, Sarah J.; Hoffmann, Anne; Murray, Cameron R.A.; Stadler, Peter F.
Journal Article
2017Uncovering missing pieces: Duplication and deletion history of arrestins in deuterostomes
Indrischek, Henrike; Prohaska, Sonja J.; Gurevich, Vsevolod V.; Gurevich, Eugenia V.; Stadler, Peter F.
Journal Article
2016Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis
Hezaveh, Kebria; Kloetgen, Andreas; Bernhart, Stephan H.; Mahapatra, Kunal Das; Lenze, Dido; Richter, Julia; Haake, Andrea; Bergmann, Anke K.; Brors, Benedikt; Burkhardt, Birgit; Claviez, Alexander; Drexler, Hans G.; Eils, Roland; Haas, Siegfried; Hoffmann, Steve; Karsch, Dennis; Klapper, Wolfram; Kleinheinz, Kortine; Korbel, Jan; Kretzmer, Helene; Kreuz, Markus; Küppers, Ralf; Lawerenz, Chris; Leich, Ellen; Loeffler, Markus; Mantovani-Loeffler, Luisa; López, Cristina; McHardy, Alice C.; Möller, Peter; Rohde, Marius; Rosenstiel, Philip; Rosenwald, Andreas; Schilhabel, Markus; Schlesner, Matthias; Scholz, Ingrid; Stadler, Peter F.; Stilgenbauer, Stephan; Sungalee, Stéphanie; Szczepanowski, Monika; Trümper, Lorenz; Weniger, Marc A.; Siebert, Reiner; Borkhardt, Arndt; Hummel, Michael; Hoell, Jessica I.
Journal Article
2016Assessing greenness of chemical reactions and synthesis plans through posetic landscapes
Restrepo, Guillermo; Stadler, Peter F.
Journal Article
2016Automatic inference of graph transformation rules using the cyclic nature of chemical reactions
Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.; Thorsen, Uffe
Conference Paper
2016Design specifications for cellular regulation
Krakauer, David C.; Müller, Lydia; Prohaska, Sonja J.; Stadler, Peter F.
Journal Article
2016Metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
Jühling, Frank; Kretzmer, Helene; Bernhart, Stephan H.; Otto, Christian; Stadler, Peter F.; Hoffmann, Steve
Journal Article
2016Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies
Velandia-Huerto, Cristian A.; Berkemer, Sarah J.; Hoffmann, Anne; Retzlaff, Nancy; Romero Marroquín, Liliana C.; Hernandez-Rosales, Maribel; Stadler, Peter F.; Bermúdez-Santana, Clara I.
Journal Article
2016The paralog-to-contig assignment problem
Indrischek, Henrike; Wieseke, Nicolas; Stadler, Peter F.; Prohaska, Sonja J.
Journal Article
2016Phylogenetic distribution of plant snoRNA families
Patra Bhattacharya, Deblina; Canzler, Sebastian; Kehr, Stephanie; Hertel, Jana; Grosse, Ivo; Stadler, Peter F.
Journal Article
2016Pseudoknots in RNA folding landscapes
Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing
Journal Article
2016RNA folding with hard and soft constraints
Lorenz, Ronny; Hofacker, Ivo L.; Stadler, Peter F.
Journal Article
2016SnoReport 2.0. New features and a refined support vector machine to improve snoRNA identification
Araujo Oliviera, João Victor de; Costa, Fabrizio; Backofen, Rolf; Stadler, Peter F.; Machado Telles Walter, Maria Emilía; Hertel, Jana
Journal Article, Conference Paper
2016A software package for chemically inspired graph transformation
Andersen, Jakob L.; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.
Conference Paper
2016The systematic design and application of robust DNA barcodes
Buschmann, Tilo
: Grosse, Ivo (Gutachter); Stadler, Peter F. (Gutachter)
Dissertation
2016Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis
Righetti, Francesco; Nuss, Aaron M.; Twittenhoff, Christian; Beele, Sascha; Urban, Kristina; Will, Sebastian; Bernhart, Stephan H.; Stadler, Peter F.; Dersch, Petra; Narberhaus, Franz
Journal Article
2016U6 snRNA intron insertion occurred multiple times during fungi evolution
Canzler, Sebastian; Stadler, Peter F.; Hertel, Jana
Journal Article
2016An updated human snoRNAome
Jorjani, Hadi; Kehr, Stephanie; Jedlinski, Dominik J.; Gumienny, Rafal; Hertel, Jana; Stadler, Peter F.; Zavolan, Mihaela; Gruber, Andreas R.
Journal Article
2015Algebraic dynamic programming over general data structures
Höner zu Siederdissen, Christian; Prohaska, Sonja J.; Stadler, Peter F.
Journal Article
2015The ancestor of modern Holozoa acquired the CCA-adding enzyme from alphaproteobacteria by horizontal gene transfer
Betat, Heike; Mede, Tobias; Tretbar, Sandy; Steiner, Lydia; Stadler, Peter F.; Mörl, Mario; Prohaska, Sonja J.
Journal Article
2015Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved
Nitsche, Anne; Rose, Dominic; Fasold, Mario; Reiche, Kristin; Stadler, Peter F.
Journal Article
2015Conservation and losses of non-coding RNAs in avian genomes
Gardner, Paul P.; Fasold, Mario; Burge, Sarah W.; Ninova, Maria; Hertel, Jana; Kehr, Stephanie; Steeves, Tammy E.; Griffiths-Jones, Sam; Stadler, Peter F.
Journal Article
2015Design criteria for synthetic riboswitches acting on transcription
Wachsmuth, Manja; Domin, Gesine; Lorenz, Ronny; Serfling, Robert; Findeiß, Sven; Stadler, Peter F.; Mörl, Mario
Journal Article
2015Design of transcription regulating riboswitches
Findeiß, Sven; Wachsmuth, Manja; Mörl, Mario; Stadler, Peter F.
Book Article
2015DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control
Kretzmer, H.; Bernhart, S.H.; Wang, W.; Haake, A.; Weniger, M.A.; Bergmann, A.K.; Betts, M.J.; Carrillo-de-Santa-Pau, E.; Doose, G.; Gutwein, J.; Richter, J.; Hovestadt, V.; Huang, B.D.; Rico, D.; Juhling, F.; Kolarova, J.; Lu, Q.H.; Otto, C.; Wagener, R.; Arnolds, J.; Burkhardt, B.; Claviez, A.; Drexler, H.G.; Eberth, S.; Eils, R.; Flicek, P.; Haas, S.; Hummel, M.; Karsch, D.; Kerstens, H.H.D.; Klapper, W.; Kreuz, M.; Lawerenz, C.; Lenze, D.; Loeffler, M.; Lopez, C.; MacLeod, R.A.F.; Martens, J.H.A.; Kulis, M.; Martin-Subero, J.I.; Moller, P.; Nagel, I.; Picelli, S.; Vater, I.; Rohde, M.; Rosenstiel, P.; Rosolowski, M.; Russell, R.B.; Schilhabel, M.; Schlesner, M.; Stadler, Peter F.; Szczepanowski, M.; Trumper, L.; Stunnenberg, H.G.; Kuppers, R.; Stunnenberg, H.G.; Lichter, P.; Siebert, R.; Hoffmann, S.; Radlwimmer, B.
Journal Article
2015Evolution of the unspliced transcriptome
Engelhardt, Jan; Stadler, Peter F.
Journal Article
2015The expansion of animal microRNA families revisited
Hertel, Jana; Stadler, Peter F.
Journal Article
2015In silico support for Eschenmoser's glyoxylate scenario
Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.
Journal Article
2015Indications for potential parent-of-origin effects within the FTO gene
Liu, Xuanshi; Hinney, Anke; Scholz, Markus; Scherag, André; Tönjes, Anke; Stumvoll, Michael; Stadler, Peter F.; Hebebrand, Johannes; Böttcher, Yvonne
Journal Article
2015Phylogenomics with paralogs
Hellmuth, Marc; Wieseke, Nicolas; Lechner, Marcus; Lenhof, Hans-Peter; Middendorf, Martin; Stadler, Peter F.
Journal Article
2015Product grammars for alignment and folding
Höner zu Siederdissen, Christian; Hofacker, Ivo L.; Stadler, Peter F.
Journal Article
2015The relativity of biological function
Laubichler, Manfred D.; Stadler, Peter F.; Prohaska, Sonja J.; Nowick, Katja
Journal Article
2015A simple data-adaptive probabilistic variant calling model
Hoffmann, Steve; Stadler, Peter F.; Strimmer, Korbinian
Journal Article
2015Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes
Sahyoun, Abdullah H.; Hölzer, Martin; Jühling, Frank; Höner zu Siederdissen, Christian; Al-Arab, Marwa; Tout, K.; Marz, M.; Middendorf, Martin; Stadler, Peter F.; Bernt, Matthias
Journal Article
2014Atom mapping with constraint programming
Mann, Martin; Nahar, Feras; Schnorr, Norah; Backofen, Rolf; Stadler, Peter F.; Flamm, Christoph
Journal Article
2014Basin hopping graph: A computational framework to characterize RNA folding landscapes
Kucharík, Marcel; Hofacker, Ivo L.; Stadler, Peter F.; Qin, Jing
Journal Article
2014Bioinformatics of prokaryotic RNAs
Backofen, Rolf; Amman, Fabian; Costa, Fabrizio; Findeiß, Sven; Richter, Andreas S.; Stadler, Peter F.
Journal Article
2014Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs
Hackermüller, Jörg; Reiche, Kristin; Otto, Christian; Hösler, Nadine; Blumert, Conny; Brocke-Heidrich, Katja; Böhlig, Levin; Nitsche, Anne; Kasack, Katharina; Ahnert, Peter; Krupp, Wolfgang; Engeland, Kurt; Stadler, Peter F.; Horn, Friedemann
Journal Article
2014GC skew and mitochondrial origins of replication
Sahyoun, Abdullah H.; Bernt, Matthias; Stadler, Peter F.; Tout, Kifah R.
Journal Article
2014Generic strategies for chemical space exploration
Andersen, Jakob Lykke; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F.
Journal Article
2014Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures
Qin, Jing; Fricke, Markus; Marz, Manja; Stadler, Peter F.; Backofen, Rolf
Journal Article
2014Lacking alignments? The next-generation sequencing mapper segemehl revisited
Otto, Christian; Stadler, Peter F.; Hoffmann, Steve
Journal Article
2014Matching of soulmates: Coevolution of snoRNAs and their targets
Kehr, Stephanie; Bartschat, Sebastian; Tafer, Hakim; Stadler, Peter F.; Hertel, Jana
Journal Article
2014A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection
Hoffmann, Steve; Otto, Christian; Doose, Gero; Tanzer, Andrea; Langenberger, David; Christ, Sabina; Kunz, Manfred; Holdt, Lesca M.; Teupser, Daniel; Hackermüller, Jörg; Stadler, Peter F.
Journal Article
2014Orthology detection combining clustering and synteny for very large datasets
Lechner, Marcus; Hernandez-Rosales, Maribel; Doerr, Daniel; Wieseke, Nicolas; Thévenin, Annelyse; Stoye, Jens; Hartmann, Roland K.; Prohaska, Sonja J.; Stadler, Peter F.
Journal Article
2014plantDARIO: Web based quantitative and qualitative analysis of small RNA-seq data in plants
Patra, Deblina; Fasold, Mario; Langenberger, David; Steger, Gerhard; Grosse, Ivo; Stadler, Peter F.
Journal Article
2014A priori assessment of data quality in molecular phylogenetics
Misof, Bernhard; Reumont, Björn von; Kück, Patrick; Meusemann, Karen; Prohaska, Sonja J.; Stadler, Peter F.
Journal Article
2014TSSAR: TSS annotation regime for dRNA-seq data
Amman, Fabian; Wolfinger, Michael T.; Lorenz, Ronny; Hofacker, Ivo L.; Stadler, Peter F.; Findeiß, Sven
Journal Article
2013Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences
Bernt, Matthias; Braband, Anke; Middendorf, Martin; Misof, Bernhard; Rota-Stabelli, Omar; Stadler, Peter F.
Journal Article
2013Chromatin computation: Epigenetic inheritance as a pattern reconstruction problem
Arnold, Christian; Stadler, Peter F.; Prohaska, Sonja J.
Journal Article
2013Computational biology of RNA interactions
Dieterich, Christoph; Stadler, Peter F.
Journal Article
2013The correlation of genome size and DNA methylation rate in metazoans
Lechner, Marcus; Marz, Manja; Ihling, Christian; Sinz, Andrea; Stadler, Peter F.; Krauss, Veiko
Journal Article
2013De novo design of a synthetic riboswitch that regulates transcription termination
Wachsmuth, Manja; Findeiß, Sven; Weissheimer, Nadine; Stadler, Peter F.; Mörl, Mario
Journal Article
2013Dicer-processed small RNAs: Rules and exceptions
Langenberger, David; Cakir, M. Volkan; Hoffmann, Steve; Stadler, Peter F.
Journal Article
2013Genetic aspects of mitochondrial genome evolution
Bernt, Matthias; Braband, Anke; Schierwater, Bernd; Stadler, Peter F.
Journal Article
2013Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics
Müller, Stephan A.; Findeiß, Sven; Pernitzsch, Sandy R.; Wissenbach, Dirk K.; Stadler, Peter F.; Hofacker, Ivo L.; Bergen, Martin von; Kalkhof, Stefan
Journal Article
2013LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search
Will, Sebastian; Siebauer, Michael F.; Heyne, Steffen; Engelhardt, Jan; Stadler, Peter F.; Reiche, Kristin; Backofen, Rolf
Journal Article
2013Mapping the RNA-Seq trash bin: Unusual transcripts in prokaryotic transcriptome sequencing data
Doose, Gero; Alexis, Maria; Kirsch, Rebecca; Findeiß, Sven; Langenberger, David; Machné, Rainer; Mörl, Mario; Hoffmann, Steve; Stadler, Peter F.
Journal Article
2013MITOS: Improved de novo metazoan mitochondrial genome annotation
Bernt, Matthias; Donath, Alexander; Jühling, Frank; Externbrink, Fabian; Florentz, Catherine; Fritzsch, Guido; Pütz, Joern; Middendorf, Martin; Stadler, Peter F.
Journal Article
2013Near intron pairs and the metazoan tree
Lehmann, Jörg; Stadler, Peter F.; Krauss, Veiko
Journal Article
2013Relations between graphs
Hubicka, Jan; Jost, Jürgen; Long, Yangjing; Stadler, Peter F.; Yang, Ling
Journal Article
2013The RNAsnp web server: Predicting SNP effects on local RNA secondary structure
Sabarinathan, Radhakrishnan; Tafer, Hakim; Seemann, Stefan E.; Hofacker, Ivo L.; Stadler, Peter F.; Gorodkin, Jan
Journal Article
2013RNAsnp: Efficient detection of local RNA secondary structure changes induced by SNPs
Sabarinathan, Radhakrishnan; Tafer, Hakim; Seemann, Stefan E.; Hofacker, Ivo L.; Stadler, Peter F.; Gorodkin, Jan
Journal Article
2012The Cartesian product of hypergraphs
Ostermeier, Lydia; Hellmuth, Marc; Stadler, Peter F.
Journal Article
2012deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns
Langenberger, D.; Pundhir, Sachin; Ekstrom, Claus T.; Stadler, Peter F.; Hoffmann, Steve; Gorodkin, Jan
Journal Article
2012Diagonalized Cartesian products of S-prime graphs are S-prime
Hellmuth, Marc; Ostermeier, Lydia; Stadler, Peter F.
Journal Article
2012Evolution of the let-7 microRNA Family
Hertel, Jana; Bartschat, Sebastian; Wintsche, Axel; Otto, Christian; Stadler, Peter F.
Journal Article
2012Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
Schmidtke, Cornelius; Findeiß, Sven; Sharma, Cynthia M.; Kuhfuß, Juliane; Hoffmann, Steve; Vogel, Jörg; Stadler, Peter F.; Bonas, Ulla
Journal Article
2012Hidden treasures in unspliced EST data
Engelhardt, Jan; Stadler, Peter F.
Journal Article
2012Landscape encodings enhance optimization
Klemm, Konstantin; Metha, Anita; Stadler, Peter F.
Journal Article
2012LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
Will, Sebastian; Joshi, Tejal; Hofacker, Ivo L.; Stadler, Peter F.; Backofen, Rolf
Journal Article
2012A survey on hypergraph products
Hellmuth, Marc; Ostermeier, Lydia; Stadler, Peter F.
Journal Article
2012Symmetric circular matchings and RNA folding
Hofacker, Ivo L.; Reidys, Christian M.; Stadler, Peter F.
Journal Article
2011Computational discovery of human coding and non-coding transcripts with conserved splice sites
Rose, Dominic; Hiller, Michael; Schutt, Katharina; Hackermüller, Jörg; Backofen, Rolf; Stadler, Peter F.
Journal Article
2011DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments
Fasold, Mario; Langenberger, David; Binder, Hans; Stadler, Peter F.; Hoffmann, Steve
Journal Article
2011Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer
Tramontano, Andrea; Donath, Alexander; Bernhart, Stephan H.; Reiche, Kristin; Böhmdorfer, Gudrun; Stadler, Peter F.; Bachmair, Andreas
Journal Article
2011The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
Perseke, Marleen; Hetmank, Jörg; Bernt, Matthias; Stadler, Peter F.; Schlegel, Martin; Bernhard, Detlef
Journal Article
2011Fast accessibility-based prediction of RNA-RNA interactions
Tafer, Hakim; Amman, Fabian; Eggenhofer, Florian; Stadler, Peter F.; Hofacker, Ivo L.
Journal Article
2011A folding algorithm for extended RNA secondary structures
Höner zu Siederdissen, Christian; Bernhart, Stephan H.; Stadler, Peter F.; Hofacker, Ivo L.
Journal Article, Conference Paper
2011Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny
Raincrow, Jeremy D.; Dewar, Ken; Stocsits, Claudia; Prohaska, Sonja J.; Amemiya, Chris T.; Stadler, Peter F.; Chiu, Chi-Hua
Journal Article
2011maxAlike: Maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
Menzel, Peter; Stadler, Peter F.; Gorodkin, Jan
Journal Article
2011PLEXY: Efficient target prediction for box C/D snoRNAs
Kehr, Stephanie; Bartschat, Sebastian; Stadler, Peter F.; Tafer, Hakim
Journal Article
2011Protein-coding structured RNAs: a computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids
Findeiß, Sven; Engelhardt, Jan; Prohaska, Sonja J.; Stadler, Peter F.
Journal Article
2011Proteinortho: Detection of (Co-)orthologs in large-scale analysis
Lechner, Marcus; Findeiß, Sven; Steiner, Lydia; Marz, Manja; Stadler, Peter F.; Prohaska, Sonja J.
Journal Article
2011The reality of pervasive transcription
Clark, Michael B.; Amaral, Paulo P.; Schlesinger, Felix J.; Dinger, Marcel E.; Taft, Ryan J.; Rinn, John L.; Ponting, Chris P.; Stadler, Peter F.; Morris, Kevin V.; Morillon, Antonin; Rozowsky, Joel S.; Gerstein, Mark B.; Wahlestedt, Claes; Hayashizaki, Yoshihide; Carninci, Piero; Gingeras, Thomas R.; Mattick, John S.
Journal Article
2011RNA interactions
Marz, Manja; Stadler, Peter F.
Book Article
2011RNApredator: fast accessibility-based prediction of sRNA targets
Eggenhofer, Florian; Tafer, Hakim; Stadler, Peter F.; Hofacker, Ivo L.
Journal Article
2011Topology and prediction of RNA pseudoknots
Reidys, Christian M.; Huang, Fenix W.D.; Andersen, Jörgen E.; Penner, Robert C.; Stadler, Peter F.; Nebel, Markus E.
Journal Article
2010BarMap: RNA folding on dynamic energy landscapes
Hofacker, Ivo L.; Flamm, Christoph; Heine, Christian; Wolfinger, Michael T.; Scheuermann, Gerik; Stadler, Peter F.
Journal Article
2010Computational studies on non-coding RNAS - session introduction
Backofen, Rolf; Chitsaz, Hamidreza; Hofacker, Ivo L.; Sahinalp, S. Cenk; Stadler, Peter F.
Conference Paper
2010G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
Fasold, Mario; Stadler, Peter F.; Binder, Hans
Journal Article
2010Genomic organization of eukaryotic tRNAs
Bermudez-Santana, Clara; Attolini, Camille Stephan-Otto; Kirsten, Toralf; Engelhardt, Jan; Prohaska, Sonja J.; Steigele, Stephan; Stadler, Peter F.
Journal Article
2010Identification and classification of small RNAs in transcriptome sequence data
Langenberger, D.; Bermudez-Santana, Clara; Stadler, Peter F.; Hoffmann, Steve
Conference Paper
2010A novel family of plasmid-transferred anti-sense ncRNAs
Findeiß, Sven; Schmidtke, Cornelius; Stadler, Peter F.; Bonas, Ulla
Journal Article
2010Polynomial algorithms for the Maximal Pairing Problem. Efficient phylogenetic targeting on arbitrary trees
Arnold, Christian; Stadler, Peter F.
Journal Article
2010Reconstruction of pedigrees in clonal plant populations
Riester, Markus; Stadler, Peter F.; Klemm, Konstantin
Journal Article
2010RNAZ 2.0. Improved noncoding RNA detection
Gruber, Andreas R.; Findeiß, Sven; Washietl, Stefan; Hofacker, Ivo L.; Stadler, Peter F.
Conference Paper
2010Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication
Lehmann, Jörg; Stadler, Peter F.; Eisenhardt, Carina; Krauss, Veiko
Journal Article
2010Temperature-dependent structural variability of RNAs: Spliced leader RNAs and their evolutionary history
Marz, Manja; Vanzo, Nathalie; Stadler, Peter F.
Journal Article
2009Approximate graph products
Hellmuth, Marc; Imrich, Wilfried; Klöckl, Werner; Stadler, Peter F.
Journal Article
2009Evolution of vault RNAs
Stadler, Peter F.; Chen, Julian J.-L.; Hackermüller, Jörg; Hoffmann, Steve; Horn, Friedemann; Khaitovich, Phillip; Kretzschmar, Antje K.; Mosig, Axel; Prohaska, Sonja J.; Qi, Xiaodong; Schutt, Katharina; Ullmann, Kerstin
Journal Article
2009Fast mapping of short sequences with mismatches, insertions and deletions using index structures
Hoffmann, Steve; Otto, Christian; Kurtz, Stefan; Sharma, Cynthia M.; Khaitovich, Philipp; Vogel, Jörg; Stadler, Peter F.; Hackermüller, Jörg
Journal Article
2009Structural profiles of human miRNA families from pairwise clustering
Kaczkowski, Bogumil; Torarinsson, Elfar; Reiche, Kristin; Havgaard, Jakob Hull; Stadler, Peter F.; Gorodkin, Jan
Journal Article
2008Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools
Sonnleitner, Elisabeth; Sorger-Domenigg, Theresa; Madej, Monika J.; Findeiß, Sven; Hackermüller, Jörg; Hüttenhofer, Alexander; Stadler, Peter F.; Bläsi, Udo; Moll, Isabella
Journal Article
2008Duplicated RNA genes in teleost fish genomes
Rose, Dominic; Jöris, Julian; Hackermüller, Jörg; Reiche, Kristin; Li,; Stadler, Peter F.
Journal Article
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