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| 2019 | Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation
Kolora, S.R.R.; Weigert, A.; Saffari, A.; Kehr, S.; Costa, M.B.W.; Spröer, C.; Indrischek, H.; Chintalapati, M.; Lohse, K.; Doose, G.; Overmann, J.; Bunk, B.; Bleidorn, C.; Grimm-Seyfarth, A.; Henle, K.; Nowick, K.; Faria, R.; Stadler, P.F.; Schlegel, M. | Journal Article |
| 2019 | RNAcentral: a hub of information for non-coding RNA sequences
Sweeney, B.A.; Petrov, A.I.; Burkov, B.; Finn, R.D.; Bateman, A.; Szymanski, M.; Karlowski, W.M.; Gorodkin, J.; Seemann, S.E.; Cannone, J.J.; Gutell, R.R.; Fey, P.; Basu, S.; Kay, S.; Cochrane, G.; Billis, K.; Emmert, D.; Marygold, S.J.; Huntley, R.P.; Lovering, R.C.; Frankish, A.; Chan, P.P.; Lowe, T.M.; Bruford, E.; Seal, R.; Vandesompele, J.; Volders, P.J.; Paraskevopoulou, M.; Ma, L.; Zhang, Z.; Griffiths-Jones, S.; Bujnicki, J.M.; Boccaletto, P.; Blake, J.A.; Bult, C.J.; Chen, R.S.; Zhao, Y.; Wood, V.; Rutherford, K.; Rivas, E.; Cole, J.; Laulederkind, S.J.F.; Shimoyama, M.; Gillespie, M.E.; Orlic-Milacic, M.; Kalvari, I.; Nawrocki, E.; Engel, S.R.; Cherry, J.M.; Berardini, T.Z.; Hatzigeorgiou, A.; Karagkouni, D.; Howe, K.; Davis, P.; Dinger, M.; He, S.M.; Yoshihama, M.; Kenmochi, N.; Stadler, P.F.; Williams, K.P. | Journal Article |
| 2018 | Detailed secondary structure models of invertebrate 7SK RNAs
Yazbeck, A.M.; Tout, K.R.; Stadler, P.F. | Journal Article |
| 2018 | Toward a mechanistic explanation of phenotypic evolution
Laubichler, M.D.; Prohaska, S.J.; Stadler, P.F. | Journal Article |
| 2017 | The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis
Kolora, S.R.; Faria, R.; Weigert, A.; Schaffer, S.; Grimm, A.; Henle, K.; Sahyoun, A.H.; Stadler, P.F.; Nowick, K.; Bleidorn, C.; Schlegel, M. | Journal Article |
| 2017 | Evolution of Fungal U3 snoRNAs: Structural Variation and Introns
Canzler, S.; Stadler, P.F.; Hertel, J. | Journal Article |
| 2017 | Evolutionary clues in lncRNAs
Nitsche, A.; Stadler, P.F. | Journal Article |
| 2017 | Recent advances in RNA folding
Fallmann, J.; Will, S.; Engelhardt, J.; Grüning, B.; Backofen, R.; Stadler, P.F. | Journal Article |
| 2017 | RNA-bioinformatics: Tools, services and databases for the analysis of RNA-based regulation
Backofen, R.; Engelhardt, J.; Erxleben, A.; Fallmannc, J.; Grüning, B.; Ohler, U.; Rajewsky, N.; Stadler, P.F. | Journal Article |
| 2017 | STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer
Binder, S.; Hösler, N.; Riedel, D.; Zipfel, I.; Buschmann, T.; Kämpf, C.; Reiche, K.; Burger, R.; Gramatzki, M.; Hackermüller, J.; Stadler, P.F.; Horn, F. | Journal Article |
| 2016 | Algebraic dynamic programming for multiple context-free grammars
Riechert, M.; Höner zu Siederdissen, C.; Stadler, P.F. | Journal Article |
| 2016 | Associativity and non-associativity of some hypergraph products
Hammack, R.H.; Hellmuth, M.; Ostermeier, L.; Stadler, P.F. | Journal Article |
| 2016 | Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate
Velandia-Huerto, C.A.; Gittenberger, A.A.; Brown, F.D.; Stadler, P.F.; Bermúdez-Santana, C.I. | Journal Article |
| 2016 | Generalized Topologies: Hypergraphs, Chemical Reactions, and Biological Evolution
Flamm, C.; Stadler, B.M.R.; Stadler, P.F. | Book Article |
| 2015 | Connectivity Spaces
Stadler, B.M.R.; Stadler, P.F. | Journal Article |
| 2015 | The grid property and product-like hypergraphs
Ostermeier, L.; Stadler, P.F. | Journal Article |
| 2015 | The relaxed square property
Hellmuth, M.; Marc, T.; Ostermeier, L.; Stadler, P.F. | Journal Article |
| 2015 | Spiders can be recognized by counting their legs
Berkemer, S.J.; Chaves, R.R.C.; Fritz, A.; Hellmuth, M.; Hernandez-Rosales, M.; Stadler, P.F. | Journal Article |
| 2015 | Unusual Novel SnoRNA-Like RNAs in Drosophila melanogaster
Agrisani, A.; Tafer, H.; Stadler, P.F.; Furia, M. | Journal Article |
| 2014 | 50 shades of rule composition
Andersen, J.L.; Flamm, C.; Merkle, D.; Stadler, P.F. | Conference Paper |
| 2014 | Atypical RNAs in the coelacanth transcriptome
Nitsche, A.; Doose, G.; Tafer, H.; Robinson, M.; Saha, N.R.; Gerdol, M.; Canapa, A.; Hoffmann, S.; Amemiya, C.T.; Stadler, P.F. | Journal Article |
| 2014 | Biological evidence for the world's smallest tRNAs
Wende, S.; Platzer, E.G.; Jühling, F.; Pütz, J.; Florentz, C.; Stadler, P.F.; Mörl, M. | Journal Article |
| 2014 | Computational methods for the analysis of mitochondrial genome rearrangements
Bernt, M.; Merkle, D.; Middendorf, M.; Schierwater, B.; Schlegel, M.; Stadler, P.F. | Book Article |
| 2014 | Convex cycle bases
Hellmuth, M.; Leydold, J.; Stadler, P.F. | Journal Article |
| 2014 | Deuterostome phylogeny - a molecular perspective
Schlegel, M.; Weidhase, M.; Stadler, P.F. | Book Article |
| 2014 | A first Glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus
Rivarola-Duarte, L.; Otto, C.; Jühling, F.; Schreiber, S.; Bedulina, D.; Jakob, L.; Gurkov, A.; Axenov-Gribanov, D.; Sahyoun, A.H.; Lucassen, M.; Hackermüller, J.; Hoffmann, S.; Sartoris, F.; Pörtner, H.-O.; Timofeyev, M.; Luckenbach, T.; Stadler, P.F. | Journal Article |
| 2014 | Intron positions and near intron pairs
Lehmann, J.; Eisenhardt, C.; Krauss, V.; Stadler, P.F. | Book Article |
| 2014 | Molecular morphology: Higher order characters derivable from sequence information
Donath, A.; Stadler, P.F. | Book Article |
| 2014 | RNA in phylogenetic reconstruction
Stocsits, R.R.; Letsch, H.; Meusemann, K.; Reumont, B.M. von; Misof, B.; Hertel, J.; Tafer, H.; Stadler, P.F. | Book Article |
| 2014 | Rugged and elementary landscapes
Klemm, K.; Stadler, P.F. | Book Article |
| 2014 | Unique square property, equitable partitions, and product-like graphs
Hellmuth, M.; Ostermeier, L.; Stadler, P.F. | Journal Article |
| 2013 | 2D meets 4G: G-quadruplexes in RNA secondary structure prediction
Lorenz, R.; Bernhart, S.H.; Qin, J.; Höner zu Siederdissen, C.; Tanzer, A.; Amman, F.; Hofacker, I.L.; Stadler, P.F. | Journal Article |
| 2013 | Atom mapping with constraint programming
Mann, M.; Nahar, F.; Ekker, H.; Backofen, R.; Stadler, P.F.; Flamm, C. | Conference Paper |
| 2013 | A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny
Bernt, M.; Bleidorn, C.; Braband, A.; Dambach, J.; Donath, A.; Fritzsch, G.; Golombek, A.; Hadrys, H.; Jühling, F.; Meusemann, K.; Middendorf, M.; Misof, B.; Perseke, M.; Podsiadlowski, L.; Reumont, B. von; Schierwater, B.; Schlegel, M.; Schrödl, M.; Simon, S.; Stadler, P.F.; Stöger, I.; Struck, T.H. | Journal Article |
| 2013 | Computational design of RNAs with complex energy landscapes
Höner zu Siederdissen, C.; Hammer, S.; Abfalter, I.; Hofacker, I.L.; Flamm, C.; Stadler, P.F. | Journal Article |
| 2013 | Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures
Backofen, R.; Fricke, M.; Marz, M.; Qin, J.; Stadler, P.F. | Conference Paper |
| 2013 | Evolution of metabolic networks: A computational frame-work
Flamm, C.; Ullrich, A.; Ekker, H.; Mann, M.; Högerl, D.; Rohrschneider, M.; Sauer, S.; Scheuermann, G.; Klemm, K.; Hofacker, I.L.; Stadler, P.F. | Journal Article |
| 2013 | Navigating the chemical space of hcn polymerization and hydrolysis: Guiding graph grammars by mass spectrometry data
Andersen, J.L.; Andersen, T.; Flamm, C.; Hanczyc, M.M.; Merkle, D.; Stadler, P.F. | Journal Article |
| 2013 | On the complexity of reconstructing chemical reaction networks
Fagerberg, R.; Flamm, C.; Merkle, D.; Peters, P.; Stadler, P.F. | Journal Article |
| 2012 | Armless mitochondrial tRNAs in enoplea (nematoda)
Jühling, F.; Putz, J.; Florentz, C.; Stadler, P.F. | Journal Article |
| 2012 | Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels
Tippmann, S.C.; Ivanek, R.; Gaidatzis, D.; Scholer, A.; Hoerner, L.; Nimwegen, E. van; Stadler, P.F.; Stadler, M.B.; Schubeler, D. | Journal Article |
| 2012 | Clustering Rfam 10.1: Clans, families, and classes
Lessa, F.A.; Raiol, T.; Brigido, M.M.; Martins Neto, D.S.B.; Walter, M.E.M.T.; Stadler, P.F. | Journal Article |
| 2012 | Fast and sensitive mapping of bisulfite-treated sequencing data
Otto, C.; Stadler, P.F.; Hoffmann, S. | Journal Article |
| 2012 | Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements
Jühling, F.; Pütz, J.; Bernt, M.; Donath, A.; Middendorf, M.; Florentz, C.; Stadler, P.F. | Journal Article |
| 2012 | Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete
Andersen, J.L.; Flamm, C.; Merkle, D.; Stadler, P.F. | Journal Article |
| 2012 | Minimum cycle bases of lexicographic products
Hellmuth, M.; Ostermeier, P.-J.; Stadler, P.F. | Journal Article |
| 2011 | "Hypothesis for the Modern RNA World": A pervasive Non-coding RNA-Based Genetic Regulation is a Prerequisite for the Emergence of Multicellular Complexity
Lozada-Chavez, I.; Stadler, P.F.; Prohaska, S.J. | Journal Article |
| 2011 | Animal snoRNAs and scaRNAs with exceptional structures
Marz, M.; Gruber, A.R.; Siederdissen, C.H.Z.; Amman, F.; Badelt, S.; Bartschat, S.; Bernhart, S.H.; Beyer, W.; Kehr, S.; Lorenz, R.; Tanzer, A.; Yusuf, D.; Tafer, H.; Hofacker, I.L.; Stadler, P.F. | Journal Article |
| 2011 | The challenges and scope of theoretical biology
Krakauer, D.C.; Collins, J.P.; Erwin, D.; Flack, J.C.; Fontana, W.; Laubichler, M.D.; Prohaska, S.J.; West, G.B.; Stadler, P.F. | Journal Article |
| 2011 | Evolution and quantitative comparison of genome-wide protein domain distributions
Parikesit, A.A.; Stadler, P.F.; Prohaska, S.J. | Journal Article |
| 2011 | Fast local fragment chaining using sum-of-pair gap costs
Otto, C.; Hoffmann, S.; Gorodkin, J.; Stadler, P.F. | Journal Article |
| 2011 | In silico evolution of early metabolism
Ullrich, A.; Rohrschneider, M.; Scheuermann, G.; Stadler, P.F.; Flamm, C. | Journal Article |
| 2011 | MicroRNA or not microRNA?
Langenberger, D.; Bartschat, S.; Hertel, J.; Hoffmann, S.; Tafer, H.; Stadler, P.F. | Conference Paper |
| 2011 | Molecular evolution of the non-coding eosinophil granule ontogeny transcript
Rose, D.; Stadler, P.F. | Journal Article |
| 2011 | Phylogenetic footprinting and consistent sets of local aligments
Otto, W.; Stadler, P.F.; Prohaska, S.J. | Conference Paper |
| 2011 | A pipeline for computational historical linguistics
Steiner, L.; Stadler, P.F.; Cysouw, M. | Journal Article |
| 2011 | RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data
Washietl, S.; Findeiß, S.; Müller, S.A.; Kalkhof, S.; Bergen, M. von; Hofacker, I.L.; Stadler, P.F.; Goldman, N. | Journal Article |
| 2011 | Traces of post-transcriptional RNA modifications in deep sequencing data
Findeiß, S.; Langenberger, D.; Stadler, P.F.; Hoffmann, S. | Journal Article |
| 2011 | The use and abuse of -omes
Prohaska, S.J.; Stadler, P.F. | Book Article |
| 2011 | ViennaRNA Package 2.0
Lorenz, R.; Bernhart, S.H.; Höner zu Siederdissen, C.; Tafer, H.; Flamm, C.; Stadler, P.F.; Hofacker, I.L. | Journal Article |
| 2010 | Bcheck: A wrapper tool for detecting RNase P RNA genes
Yusuf, D.; Marz, M.; Stadler, P.F.; Hofacker, I.L. | Journal Article |
| 2010 | Combinatorial vector fields and the valley structure of fitness landscapes
Stadler, B.M.R.; Stadler, P.F. | Journal Article |
| 2010 | Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome
Amemiya, C.T.; Powers, T.P.; Prohaska, S.J.; Grimwood, J.; Schmutz, J.; Dickson, M.; Miyake, T.; Schönborn, M.A.; Myers, R.M.; Ruddle, F.H.; Stadler, P.F. | Journal Article |
| 2010 | Evolution of the long non-coding RNAs MALAT1 and MEN beta/epsilon
Stadler, P.F. | Conference Paper |
| 2010 | In silico evolution of early metabolism
Ullrich, A.; Flamm, C.; Rohrschneider, M.; Stadler, P.F. | Conference Paper |
| 2010 | Innovation in gene regulation: The case of chromatin computation
Prohaska, S.J.; Stadler, P.F.; Krakauer, D.C. | Journal Article |
| 2010 | Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata
Perseke, M.; Bernhard, D.; Fritzsch, G.; Brümmer, F.; Stadler, P.F.; Schlegel, M. | Journal Article |
| 2010 | Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): Genome assembly and analysis
Dalloul, R.A.; Long, J.A.; Zimin, A.V.; Stadler, P.F. et al. | Journal Article |
| 2010 | Nematode sbRNAs: Homologs of vertebrate Y RNAs
Boria, I.; Gruber, A.R.; Tanzer, A.; Bernhart, S.H.; Lorenz, R.; Mueller, M.M.; Hofacker, I.L.; Stadler, P.F. | Journal Article |
| 2010 | Optimization of parameters for coverage of low molecular weight proteins
Müller, S.A.; Kohajda, T.; Findei, S.; Stadler, P.F.; Washietl, S.; Kellis, M.; Bergen, M. von; Kalkhof, S. | Journal Article |
| 2010 | The primary transcriptome of the major human pathogen Helicobacter pylori
Sharma, C.M.; Hoffmann, S.; Darfeuille, F.; Reignier, J.; Findeiß, S.; Sittka, A.; Chabas, S.; Reiche, K.; Hackermüller, J.; Reinhardt, R.; Stadler, P.F.; Vogel, J. | Journal Article |
| 2010 | Quantitative comparison of genomic-wide protein domain distributions
Parikesit, A.A.; Stadler, P.F.; Prohaska, S.J. | Conference Paper |
| 2010 | RNAsnoop: Efficient target prediction for H/ACA snoRNAs
Tafer, H.; Kehr, S.; Hertel, J.; Hofacker, I.L.; Stadler, P.F. | Journal Article |
| 2010 | Target prediction and a statistical sampling algorithm for RNA-RNA interaction
Huang, F.W.D.; Qin, J.; Reidys, C.M.; Stadler, P.F. | Journal Article |
| 2010 | Visualization of graph products
Jänicke, S.; Heine, C.; Hellmuth, M.; Stadler, P.F.; Scheuermann, G. | Journal Article |
| 2009 | Accurate and efficient reconstruction of deep phylogenies from structured RNAs
Stocsits, R.R.; Letsch, H.; Hertel, J.; Misof, B.; Stadler, P.F. | Journal Article |
| 2009 | Automatic classification of embryonic fruit fly gene expression patterns
Heffel, A.; Prohaska, S.J.; Stadler, P.F.; Kauer, G.; Kuska, J.-P. | Conference Paper |
| 2009 | Biomarker: Die Neue Welt der ncRNAs und ihre medizinische Relevanz
Hackermüller, J.; Horn, F.; Stadler, P.F.; Buller, B. | Journal Article |
| 2009 | Comparative analysis of eukaryotic U3 snoRNA
Marz, M.; Stadler, P.F. | Journal Article |
| 2009 | Conserved introns reveal novel transcripts in Drosophila melanogaster
Hiller, M.; Findeiß, S.; Lein, S.; Marz, M.; Nickel, C.; Rose, D.; Schulz, C.; Backofen, R.; Prohaska, S.J.; Reuter, G.; Stadler, P.F. | Journal Article |
| 2009 | Defining genes: A computational framework
Stadler, P.F.; Prohaska, S.J.; Forst, C.V.; Krakauer, D.C. | Journal Article |
| 2009 | Discovering cis-regulatory modules by optimizing barbecues
Mosig, A.; Biyikoglu, T.; Prohaska, S.J.; Stadler, P.F. | Conference Paper, Journal Article |
| 2009 | Evidence for human microRNA-offset RNAs in small RNA sequencing data
Langenberger, D.; Bermudez-Santana, C.; Hertel, J.; Hoffmann, S.; Khaitovich, P.; Stadler, P.F. | Journal Article |
| 2009 | Evolution of 7SK RNA and Its Protein Partners in Metazoa
Marz, M.; Donath, A.; Verstraete, N.; Nguyen, V.T.; Stadler, P.F.; Bensaude, O. | Journal Article |
| 2009 | FRANz: Reconstruction of wild multi-generation pedigrees
Riester, M.; Stadler, P.F.; Klemm, K. | Journal Article |
| 2009 | HLA-alleles determine the risk to develop antibodies against interferon-beta therapy in multiple sclerosis
Buck, D.; Cepok, S.; Hoffmann, S.; Grummel, V.; Lehmann-Horn, K.; Hackermüller, J.; Stadler, P.F.; Hartung, H.-P.; Berthele, A.; Deisenhammer, F.; Wassmuth, R.; Hemmer, B. | Abstract |
| 2009 | Homology- based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum
Copeland, C.C.; Marz, M.; Rose, D.; Hertel, J.; Brindley, P.J.; Santana, C.B.; Kehr, S.; Attolini, C.S.O.; Stadler, P.F. | Journal Article |
| 2009 | Hox cluster duplication in the basal teleost Hiodon alosoides (Osteoglossomorpha)
Chambers, K.E.; McDaniell, R.; Raincrow, J.D.; Deshmukh, M.; Stadler, P.F.; Chiu, C.-H. | Journal Article |
| 2009 | Local algorithms for the prime factorization of strong product graphs
Hellmuth, M.; Imrich, W.; Klöckl, W.; Stadler, P.F. | Journal Article |
| 2009 | Long non-protein coding RNAs in oncogenic pathways
Hackermüller, J.; Brocke-Heidrich, K.; Reiche, K.; Kretzschmar, A.; Schutt, K.; Ahnert, P.; Böhlig, L.; Stadler, P.F.; Engeland, K.; Horn, F. | Abstract |
| 2009 | Maximum likelihood estimation of weight matrices for targeted homology search
Menzel, P.; Gorodkin, J.; Stadler, P.F. | Conference Paper |
| 2009 | Mutate now, die later
Munteanu, A.; Stadler, P.F. | Journal Article |
| 2009 | Non-coding RNA annotation of the genome of Trichoplax adhaerens
Hertel, J.; Jong, D. de; Marz, M.; Rose, D.; Tafer, H.; Tanzer, A.; Schierwater, B.; Stadler, P.F. | Journal Article |
| 2009 | A note on fundamental, non-fundamental, and robust cycle bases
Klemm, K.; Stadler, P.F. | Conference Paper, Journal Article |
| 2009 | A note on quasi-robust cycle bases
Ostermeier, P.-J.; Hellmuth, M.; Klemm, K.; Leydold, J.; Stadler, P.F. | Journal Article |
| 2009 | Partition function and base pairing probabilities for RNA-RNA interaction prediction
Huang, F.W.D.; Qin, J.; Reidys, C.M.; Stadler, P.F. | Journal Article |
| 2009 | Sequence assembly. Review
Scheibye-Alsing, K.; Hoffmann, S.; Frankel, A.; Jensen, P.; Stadler, P.F.; Mang, Y.; Tommerup, N.; Gilchrist, M.J.; Nygard, A.B.; Cirera, S.; Jorgensen, C.B.; Fredholm, M.; Gorodkin, J. | Journal Article |
| 2009 | Solvent exposure imparts similar selective pressures across a range of yeast proteins
Conant, G.C.; Stadler, P.F. | Journal Article |
| 2009 | A survey of nematode SmY RNAs. Editorial
Jones, T.A.; Otto, W.; Marz, M.; Eddy, S.R.; Stadler, P.F. | Journal Article |
| 2009 | The tedious task of finding homologous noncoding RNA genes
Menzel, P.; Gorodkin, J.; Stadler, P.F. | Journal Article |
| 2009 | Transcriptome profiling reveals many novel p53-regulated human non-coding RNAs
Böhlig, L.; Hackermüller, J.; Rose, D.; Reiche, K.; Kretzschmar, A.; Stadler, P.F.; Horn, F.; Engeland, K. | Abstract |
| 2009 | tRNAdb 2009: Compilation of tRNA sequences and tRNA genes
Jühling, F.; Mörl, M.; Hartmann, R.K.; Sprinzl, M.; Stadler, P.F.; Pütz, J. | Journal Article |
| 2008 | The amphioxus Hox cluster: Characterization, comparative genomics, and evolution
Amemiya, C.T.; Prohaska, S.J.; Hill-Force, A.; Cook, A.; Wasserscheid, J.; Ferrier, D.E.K.; Pascual-Anaya, J.; Garcia-Fernandez, J.; Dewar, K.; Stadler, P.F. | Journal Article |
| 2008 | Arthropod 7SK RNA
Gruber, A.R.; Kilgus, C.; Mosig, A.; Hofacker, I.L.; Hennig, W.; Stadler, P.F. | Journal Article |
| 2008 | Evolution of mitochondrial gene orders in echinoderms
Perseke, M.; Fritzsch, G.; Ramsch, K.; Bernt, M.; Merkle, D.; Middendorf, M.; Bernhard, D.; Stadler, P.F.; Schlegel, M. | Journal Article |
| 2008 | Evolution of spliceosomal snRNA genes in metazoan animals
Marz, M.; Kirsten, T.; Stadler, P.F. | Journal Article |
| 2008 | Folding kinetics of large RNAs
Geis, M.; Flamm, C.; Wolfinger, M.T.; Tanzer, A.; Hofacker, I.L.; Middendorf, M.; Mandl, C.; Stadler, P.F.; Thurner, C. | Journal Article |
| 2008 | FRANz: Fast reconstruction of wild pedigrees
Riester, M.; Stadler, P.F.; Klemm, K. | Conference Paper |
| 2008 | Funnels in energy landscapes
Klemm, K.; Flamm, C.; Stadler, P.F. | Journal Article |
| 2008 | Genes
Prohaska, S.J.; Stadler, P.F. | Journal Article |
| 2008 | HLA-DRB1 0401 and HLA-DRB1 0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis
Cepok, S.; Hoffmann, S.; Grummel, V.; Lehmann-Horn, K.; Hackermüller, J.; Stadler, P.F.; Hartung, H.-P.; Berthele, A.; Deisenhammer, F.; Wasmuth, R.; Hemmer, B. | Journal Article, Conference Paper |
| 2008 | HLA-DRBI*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis
Hoffmann, S.; Cepok, S.; Grummel, V.; Lehmann-Horn, K.; Hackermüller, J.; Stadler, P.F.; Hartung, H.-P.; Berthele, A.; Deisenhammer, F.; Wasmuth, R.; Hemmer, B. | Journal Article |
| 2008 | Invertebrate 7SK snRNAs
Gruber, A.R.; Koper-Emde, D.; Marz, M.; Tafer, H.; Bernhart, S.; Obernosterer, G.; Mosig, A.; Hofacker, I.L.; Stadler, P.F.; Benecke, B.-J. | Journal Article |
| 2008 | NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences
Rose, D.; Hertel, J.; Reiche, K.; Stadler, P.F.; Hackermüller, J. | Journal Article |
| 2008 | Near intron positions are reliable phylogenetic markers
Krauss, V.; Thummler, C.; Georgi, F.; Lehmann, J.; Stadler, P.F.; Eisenhardt, C. | Journal Article |
| 2008 | Noisy: Identification of problematic columns in multiple sequence alignments
Dress, A.W.M.; Flamm, C.; Fritzsch, G.; Grünewald, S.; Kruspe, M.; Prohaska, S.J.; Stadler, P.F. | Journal Article |
| 2008 | Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis
Jochl, C.; Rederstorff, M.; Hertel, J.; Stadler, P.F.; Hofacker, I.L.; Schrettl, M.; Haas, H.; Hüttenhofer, A. | Journal Article |
| 2008 | SnoReport: Computational identification of snoRNAs with unknown targets
Hertel, J.; Hofacker, I.L.; Stadler, P.F. | Journal Article |
| 2008 | A story of growing confusion: Genes and their regulation
Prohaska, S.J.; Stadler, P.F. | Journal Article |
| 2008 | Translational control by RNA-RNA interaction: Improved computation of RNA-RNA binding thermodynamics
Mückstein, U.; Tafer, H.; Bernhart, S.H.; Hernandez-Rosales, M.; Vogel, J.; Stadler, P.F.; Hofacker, I.L. | Conference Paper |
| 2007 | Computational RNomics of drosophilids
Rose, D.; Hackermüller, J.; Washietl, S.; Reiche, K.; Hertel, J.; Findeiß, S.; Stadler, P.F.; Prohaska, S.J. | Journal Article |
| 2007 | CREx: inferring genomic rearrangements based on common intervals
Bernt, M.; Merkle, D.; Ramsch, K.; Fritzsch, G.; Perseke, M.; Bernhard, D.; Schlegel, M.; Stadler, P.F.; Middendorf, M. | Journal Article |
| 2007 | Evolution of the vertebrate Y RNA cluster
Mosig, A.; Guofeng, M.; Stadler, B.M.R.; Stadler, P.F. | Journal Article |
| 2007 | Homology search with fragmented nucleic acid sequence patterns
Mosig, A.; Chen, J.J.-L.; Stadler, P.F. | Conference Paper |
| 2007 | Inerleukin-6-dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer
Löffler, D.; Brocke-Heidrich, K.; Pfeifer, G.; Stocsits, C.; Hackermüller, J.; Kretzschmar, A.K.; Burger, R.; Gramatzki, M.; Blumert, C.; Bauer, K.; Cvijic, H.; Ullmann, A.K.; Stadler, P.F.; Horn, F. | Journal Article |
| 2007 | Progressive multiple sequence alignments from triplets
Kruspe, M.; Stadler, P.F. | Journal Article |
| 2007 | RNA maps reveal new RNA classes and a possible function for pervasive transcription
Kapranov, P.; Cheng, J.; Dike, S.; Nix, D.A.; Duttagupta, R.; Willingham, A.T.; Stadler, P.F.; Hertel, J.; Hackermüller, J.; Hofacker, I.L.; Bell, I.; Cheung, E.; Drenkow, J.; Dumais, E.; Patel, S.; Helt, G.; Ganesh, M.; Ghosh, S.; Piccolboni, A.; Sementchenko, V.; Tammana, H.; Gingeras, T.R. | Journal Article |
| 2007 | Structured RNAs in the ENCODE selected regions of the human genome
Washietl, S.; Pedersen, J.S.; Korbel, J.O.; Stocsits, C.; Gruber, A.R.; Hackermüller, J.; Hertel, J.; Lindemeyer, M.; Reiche, K.; Tanzer, A.; Ucla, C.; Wyss, C.; Antonarakis, S.E.; Denoeud, F.; Lagarde, J.; Drenkow, J.; Kapranov, P.; Gingeras, T.R.; Guigo, R.; Snyder, M.; Gerstein, M.B.; Reymond, A.; Hofacker, I.L.; Stadler, P.F. | Journal Article |
| 2007 | U7 snRNAs: A Computational Survey
Marz, M.; Mosig, A.; Stadler, B.M.R.; Stadler, P.F. | Journal Article |
| 2006 | Thermodynamics of RNA-RNA binding
Mückstein, U.; Tafer, H.; Hackermüller, J.; Bernhart, S.H.; Stadler, P.F.; Hofacker, I.L. | Journal Article |
| 2002 | Evolution in systems of ligation-based replicators
Stadler, B.M.R.; Stadler, P.F.; Wills, P.R. | Journal Article |