Prof. Dr. Peter Florian Stadler

Prof. Dr. Peter Florian Stadler

IZBI BOARD MEMBER

stadler@bioinf.uni-leipzig.de

+49 341 97 16691

Room: 312 - Professorship Bioinformatics

ACADEMIC CAREER

  • Studies of Chemistry, Mathematics, Physics, and Astronomy at the University of Vienna (Austria) Undergratuate degrees (1.Diploma) in Chemistry (1986), Astronomy (1988), Physics (1989), and Mathematics, (1990). Graduate degrees: Mag.rer.nat. (Masters Degree) 1988 in Chemistry, Dr.rer.nat. (PhD Degree) 1990.
  • Postdoctoral assistant with Prof. Manfred Eigen at the Max Planck Insitute for Biophysical Chemistry (Karl Friedrich Bonhoeffer Institute) Göttingen, Germany, 1990-1991.
  • Assistant Professor of Theoretical Chemistry at the University of Vienna since 1991-1997.
  • Research Visitor at the Santa Fe Institute, Santa Fe, New Mexico, in 1993.
  • Habilitation in "Theoretical Chemistry" at the University of Vienna 1994 (Dozent fü Theoretische Chemie).
  • Member of the External Faculty of the Santa Fe Institute, Santa Fe, USA, since 1994.
  • Mandatory Military Service 1997
  • "Ausserordendlicher Universitätsprofessor" (Ao.Univ.-Prof.) at the University of Vienna since 1997-2002.
  • Member of the Board of the Chemisch Physikalische Gesellschaft in Wien (CPG)
  • Professor für Bioinformatik at the University of Leipzig, Germany, since Sept. 2002.

SCIENTIFIC INTERESTS

  • evolutionary bioinformatics and RNA bioinformatics at the genome level (RNomics)
  • contribute to the clarification of the role of RNA in gene regulation

MISCELLANEOUS

  • He is one of the most cited structural and evolutionary biologists in German-speaking countries.
  • Novartis Preis für Chemie 2002
  • Co-head (2005-2006), then Senior Scientific Advisor (since 2007) of the RNomics Group at the Fraunhofer Institute for Cell Therapy and Immunology
  • External Scientific Member of the Max Planck Society, affliated with the MPI Mathematics in the Sciences" in Leipzig since March 2009
  • Corresponding Member Abroad of the Austrian Academy of Sciences since 2010.
for more informtions click here: http://www.bioinf.uni-leipzig.de/~studla/

PUBLICATIONS

Rest (4)

  • Martin Beck, Gil Benkö, Gunther Eble, Christoph Flamm, Stefan Müller, Peter F. Stadler. Graph Grammars as Models for the Evolution of Developmental Pathways. In: The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems, IOS Press, Akademische Verlagsgesellschaft 8-15. Ed: Schaub, H. and Detje, F. and Brüggemann, U.
  • A. R. Gruber, S. Findeiss, S. Washietl, I. L. Hofacker, P. F. Stadler. Rnaz 2.0: Improved Noncoding Rna Detection. In: Pac Symp Biocomput 15: 69-79.
  • D. Langenberger, C. I. Bermudez-Santana, P. F. Stadler, S. Hoffmann. Identification and classification of small rnas in transcriptome sequence data. In: Pac Symp Biocomput 80-7.
  • Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhard, Maribel Hernandez-Rosales, J. Vogel, Peter F. Stadler, Ivo L. Hofacker. Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. In: BioInformatics Research and Development --- BIRD 2008, Springer 13: 114-127. Ed: Elloumi, Mourad and Küng, Josef and Linial, Michal and Murphy, Robert F. and Schneider, Kristan and Toma, Cristian Toma.

2021 (3)

  • D. Hübschmann, K. Kleinheinz, R. Wagener, S. H. Bernhart, C. López, U. H. Toprak, S. Sungalee, N. Ishaque, H. Kretzmer, M. Kreuz, S. M. Waszak, N. Paramasivam, O. Ammerpohl, S. M. Aukema, R. Beekman, A. K. Bergmann, M. Bieg, H. Binder, A. Borkhardt, C. Borst, B. Brors, P. Bruns, E. Carrillo de Santa Pau, A. Claviez, G. Doose, A. Haake, D. Karsch, S. Haas, M. L. Hansmann, J. I. Hoell, V. Hovestadt, B. Huang, M. Hummel, C. Jäger-Schmidt, J. N. A. Kerssemakers, J. O. Korbel, D. Kube, C. Lawerenz, D. Lenze, J. H. A. Martens, G. Ott, B. Radlwimmer, E. Reisinger, J. Richter, D. Rico, P. Rosenstiel, A. Rosenwald, M. Schillhabel, S. Stilgenbauer, P. F. Stadler, J. I. Martín-Subero, M. Szczepanowski, G. Warsow, M. A. Weniger, M. Zapatka, A. Valencia, H. G. Stunnenberg, P. Lichter, P. Möller, M. Loeffler, R. Eils, W. Klapper, S. Hoffmann, L. Trümper, R. Küppers, M. Schlesner, R. Siebert. Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas. Leukemia. 2021.
  • Anat Yaskolka Meir, Maria Keller, Stephan H. Bernhart, Ehud Rinott, Gal Tsaban, Hila Zelicha, Alon Kaplan, Dan Schwarzfuchs, Ilan Shelef, Yftach Gepner, Jun Li, Yifei Lin, Matthias Blüher, Uta Ceglarek, Michael Stumvoll, Peter F. Stadler, Meir J. Stampfer, Peter Kovacs, Liming Liang, Iris Shai. Lifestyle weight-loss intervention may attenuate methylation aging: the CENTRAL MRI randomized controlled trial. Clinical Epigenetics. 2021. 13: 48.
  • Anat Yaskolka Meir, Maria Keller, Luise Müller, Stephan H. Bernhart, Gal Tsaban, Hila Zelicha, Ehud Rinott, Alon Kaplan, Yftach Gepner, Ilan Shelef, Dan Schwarzfuchs, Uta Ceglarek, Peter Stadler, Matthias Blüher, Michael Stumvoll, Peter Kovacs, Iris Shai. Effects of lifestyle interventions on epigenetic signatures of liver fat: Central randomized controlled trial. Liver International. 2021. 41: 2101-2111.

2020 (6)

  • Sarah J Berkemer, Lisa-Katharina Maier, Fabian Amman, Stephan H Bernhart, Julia Wörtz, Pascal Märkle, Friedhelm Pfeiffer, Peter F Stadler, Anita Marchfelder. Identification of RNA 3´ ends and termination sites in Haloferax volcanii. RNA biology. 2020. 1-14.
  • Campbell PJ, Getz G, Korbel JO, Stuart JM, Jennings JL, Stein LD, Perry MD, Nahal-Bose HK, Ouellette BFF, Li CH, H. Binder, S. Bernhardt, P. Stadler. Pan-cancer analysis of whole genomes. Nature. 2020. 578: 82-93.
  • Simon M. Hoser, Anne Hoffmann, Andreas Meindl, Maximilian Gamper, Jörg Fallmann, Stephan H. Bernhart, Lisa Müller, Melanie Ploner, Matthias Misslinger, Leopold Kremser, Herbert Lindner, Stephan Geley, Heiner Schaal, Peter F. Stadler, Alexander Huettenhofer. Intronic tRNAs of mitochondrial origin regulate constitutive and alternative splicing. Genome Biology. 2020. 21: 299.
  • M. Keller, A. Yaskolka Meir, S. H. Bernhart, Y. Gepner, I. Shelef, D. Schwarzfuchs, G. Tsaban, H. Zelicha, L. Hopp, L. Müller, K. Rohde, Y. Böttcher, P. F. Stadler, M. Stumvoll, M. Blüher, P. Kovacs, I. Shai. DNA methylation signature in blood mirrors successful weight-loss during lifestyle interventions: the CENTRAL trial. Genome Med. 2020. 12: 97.
  • Iwona Nowak, Elżbieta Boratyn, Sebastian Student, Stephan F. Bernhart, Jörg Fallmann, Małgorzata Durbas, Peter F. Stadler, Hanna Rokita. MCPIP1 ribonuclease can bind and cleave AURKA mRNA in MYCN-amplified neuroblastoma cells. RNA biology. 2020. 1-13.
  • Thandi S. Schwarz, Sarah J. Berkemer, Stephan H. Bernhart, Matthias Weiß, Sébastien Ferreira-Cerca, Peter F. Stadler, Anita Marchfelder. Splicing Endonuclease Is an Important Player in rRNA and tRNA Maturation in Archaea. Frontiers in Microbiology. 2020. 11: 2856.

2019 (3)

  • Alexander Donath, Frank Jühling, Marwa Al-Arab, Stephan H Bernhart, Franziska Reinhardt, Peter F Stadler, Martin Middendorf, Matthias Bernt. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic acids research. 2019. 47: 10543-10552.
  • C. Lopez, K. Kleinheinz, S. M. Aukema, M. Rohde, S. H. Bernhart, D. Hubschmann, R. Wagener, U. H. Toprak, F. Raimondi, M. Kreuz, H. Binder, G. Doose, L. Hopp, P. F. Stadler, M. Loeffler, et al. Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma. Nat Commun. 2019. 10: 019-08578.
  • Sigrid Uxa, Stephan H Bernhart, Christina FS Mages, Martin Fischer, Robin Kohler, Steve Hoffmann, Peter F Stadler, Kurt Engeland, Gerd A Müller. DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation. Nucleic acids research. 2019. 47: 9087-9103.

2018 (3)

  • M. D. Laubichler, S. J. Prohaska, P. F. Stadler. Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration. J Exp Zool B Mol Dev Evol. 2018. 330: 5-14.
  • Aniela Skrzypczyk, Stephanie Kehr, Ilona Krystel, Stephan H Bernhart, Shibashish Giri, Augustinus Bader, Peter F Stadler. Noncoding RNA transcripts during differentiation of induced pluripotent stem cells into hepatocytes. Stem cells international. 2018. 2018:
  • Melanie von Brandenstein, Stephan H Bernhart, Andreas Pansky, Claudia Richter, Tobias Kohl, Martina Deckert, Axel Heidenreich, Peter F Stadler, Manuel Montesinos-Rongen, Jochen WU Fries. Beyond the 3′ UTR binding–microRNA-induced protein truncation via DNA binding. Oncotarget. 2018. 9: 32855.

2017 (3)

  • H. Indrischek, S. J. Prohaska, V. V. Gurevich, E. V. Gurevich, P. F. Stadler. Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes. BMC Evol Biol. 2017. 17: 163.
  • S. J. Prohaska, S. J. Berkemer, F. Gartner, T. Gatter, N. Retzlaff, C. Honer Zu Siederdissen, P. F. Stadler. Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem. J Math Biol. 2017.
  • C. L. Richards, C. Alonso, C. Becker, O. Bossdorf, E. Bucher, M. Colome-Tatche, W. Durka, J. Engelhardt, B. Gaspar, A. Gogol-Doring, I. Grosse, T. P. van Gurp, K. Heer, I. Kronholm, C. Lampei, V. Latzel, M. Mirouze, L. Opgenoorth, O. Paun, S. J. Prohaska, S. A. Rensing, P. F. Stadler, E. Trucchi, K. Ullrich, K. J. F. Verhoeven. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecol Lett. 2017. 20: 1576-1590.

2016 (16)

  • S. H. Bernhart, H. Kretzmer, L. M. Holdt, F. Juehling, O. Ammerpohl, A. K. Bergmann, B. H. Northoff, G. Doose, R. Siebert, P. F. Stadler, S. Hoffmann. Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. Sci Rep. 2016. 6: 37393.
  • Stephan H Bernhart, Helene Kretzmer, Lesca M Holdt, Frank Jühling, Ole Ammerpohl, Anke K Bergmann, Bernd H Northoff, Gero Doose, Reiner Siebert, Peter F Stadler. Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer. Scientific reports. 2016. 6: 37393.
  • D. E. Blasi, S. Wichmann, H. Hammarstrom, P. F. Stadler, M. H. Christiansen. Sound-meaning association biases evidenced across thousands of languages. Proc Natl Acad Sci U S A. 2016. 113: 10818-23.
  • S. Canzler, P. F. Stadler, J. Hertel. U6 snRNA intron insertion occurred multiple times during fungi evolution. RNA Biol. 2016. 13: 119-27.
  • G. Domin, S. Findeiss, M. Wachsmuth, S. Will, P. F. Stadler, M. Moerl. Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res. 2016.
  • J. Gu, J. Jost, S. Liu, P. F. Stadler. Spectral classes of regular, random, and empirical graphs. Linear Algebra and its Applications. 2016. 489: 30-49.
  • K. Hezaveh, A. Kloetgen, S. H. Bernhart, K. D. Mahapatra, D. Lenze, J. Richter, A. Haake, A. K. Bergmann, B. Brors, B. Burkhardt, A. Claviez, H. G. Drexler, R. Eils, S. Haas, S. Hoffmann, D. Karsch, W. Klapper, K. Kleinheinz, J. Korbel, H. Kretzmer, M. Kreuz, R. Kuppers, C. Lawerenz, E. Leich, M. Loeffler, L. Mantovani-Loeffler, C. Lopez, A. C. McHardy, P. Moller, M. Rohde, P. Rosenstiel, A. Rosenwald, M. Schilhabel, M. Schlesner, I. Scholz, P. F. Stadler, S. Stilgenbauer, S. Sungalee, M. Szczepanowski, L. Trumper, M. A. Weniger, R. Siebert, A. Borkhardt, M. Hummel, J. I. Hoell. Alterations of microRNA and microRNA-regulated messenger RNA expression in germinal center B-cell lymphomas determined by integrative sequencing analysis. Haematologica. 2016. 101: 1380-1389.
  • M. Hoelzer, V. Krahling, F. Amman, E. Barth, S. H. Bernhart, V. A. Carmelo, M. Collatz, G. Doose, F. Eggenhofer, J. Ewald, J. Fallmann, L. M. Feldhahn, M. Fricke, J. Gebauer, A. J. Gruber, F. Hufsky, H. Indrischek, S. Kanton, J. Linde, N. Mostajo, R. Ochsenreiter, K. Riege, L. Rivarola-Duarte, A. H. Sahyoun, S. J. Saunders, S. E. Seemann, A. Tanzer, B. Vogel, S. Wehner, M. T. Wolfinger, R. Backofen, J. Gorodkin, I. Grosse, I. Hofacker, S. Hoffmann, C. Kaleta, P. F. Stadler, S. Becker, M. Marz. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Sci Rep. 2016. 6: 34589.
  • H. Indrischek, N. Wieseke, P. F. Stadler, S. J. Prohaska. The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. Algorithms Mol Biol. 2016. 11: 1.
  • H. Jorjani, S. Kehr, D. J. Jedlinski, R. Gumienny, J. Hertel, P. F. Stadler, M. Zavolan, A. R. Gruber. An updated human snoRNAome. Nucleic Acids Res. 2016. 44: 5068-82.
  • F. Juehling, H. Kretzmer, S. H. Bernhart, C. Otto, P. F. Stadler, S. Hoffmann. metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 2016. 26: 256-62.
  • Frank Jühling, Helene Kretzmer, Stephan H Bernhart, Christian Otto, Peter F Stadler, Steve Hoffmann. metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome research. 2016. 26: 256-262.
  • D. C. Krakauer, L. Mueller, S. J. Prohaska, P. F. Stadler. Design specifications for cellular regulation. Theory Biosci. 2016. 135: 231-240.
  • D. Patra Bhattacharya, S. Canzler, S. Kehr, J. Hertel, I. Grosse, P. F. Stadler. Phylogenetic distribution of plant snoRNA families. BMC Genomics. 2016. 17: 969.
  • F. Righetti, A. M. Nuss, C. Twittenhoff, S. Beele, K. Urban, S. Will, S. H. Bernhart, P. F. Stadler, P. Dersch, F. Narberhaus. Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A. 2016. 113: 7237-42.
  • Francesco Righetti, Aaron M Nuss, Christian Twittenhoff, Sascha Beele, Kristina Urban, Sebastian Will, Stephan H Bernhart, Peter F Stadler, Petra Dersch, Franz Narberhaus. Temperature-responsive in vitro RNA structurome of Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences. 2016. 113: 7237-7242.

2015 (9)

  • H. Betat, T. Mede, S. Tretbar, L. Steiner, P. F. Stadler, M. Mörl, S. J. Prohaska. The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer. Nucleic Acids Res. 2015. 43: 6739-46.
  • P. P. Gardner, M. Fasold, S. W. Burge, M. Ninova, J. Hertel, S. Kehr, T. E. Steeves, S. Griffiths-Jones, P. F. Stadler. Conservation and losses of non-coding RNAs in avian genomes. PLoS One. 2015. 10: e0121797.
  • S. Hoffmann, P. F. Stadler, K. Strimmer. A simple data-adaptive probabilistic variant calling model. Algorithms Mol Biol. 2015. 10: 10.
  • F. Jühling, H. Kretzmer, S. H. Bernhart, C. Otto, P. F. Stadler, S. Hoffmann. metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 2015.
  • S. R. Kolora, R. Faria, A. Weigert, S. Schaffer, A. Grimm, K. Henle, A. H. Sahyoun, P. F. Stadler, K. Nowick, C. Bleidorn, M. Schlegel. The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis. Mitochondrial DNA. 2015. 1-3.
  • H. Kretzmer, S. H. Bernhart, W. Wang, A. Haake, M. A. Weniger, A. K. Bergmann, M. J. Betts, E. Carrillo-de-Santa-Pau, G. Doose, J. Gutwein, J. Richter, V. Hovestadt, B. Huang, D. Rico, F. Juhling, J. Kolarova, Q. Lu, C. Otto, R. Wagener, J. Arnolds, B. Burkhardt, A. Claviez, H. G. Drexler, S. Eberth, R. Eils, P. Flicek, S. Haas, M. Hummel, D. Karsch, H. H. Kerstens, W. Klapper, M. Kreuz, C. Lawerenz, D. Lenze, M. Loeffler, C. Lopez, R. A. MacLeod, J. H. Martens, M. Kulis, J. I. Martin-Subero, P. Moller, I. Nagel, S. Picelli, I. Vater, M. Rohde, P. Rosenstiel, M. Rosolowski, R. B. Russell, M. Schilhabel, M. Schlesner, P. F. Stadler, M. Szczepanowski, L. Trumper, H. G. Stunnenberg, R. Kuppers, O. Ammerpohl, P. Lichter, R. Siebert, S. Hoffmann, B. Radlwimmer. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nat Genet. 2015. 47: 1316-25.
  • M. D. Laubichler, P. F. Stadler, S. J. Prohaska, K. Nowick. The relativity of biological function. Theory Biosci. 2015. 134: 143-7.
  • M. Schmid, J. Smith, D. W. Burt, B. L. Aken, P. B. Antin, A. L. Archibald, C. Ashwell, P. J. Blackshear, C. Boschiero, C. T. Brown, S. C. Burgess, H. H. Cheng, W. Chow, D. J. Coble, A. Cooksey, R. P. Crooijmans, J. Damas, R. V. Davis, D. J. de Koning, M. E. Delany, T. Derrien, T. T. Desta, I. C. Dunn, M. Dunn, H. Ellegren, L. Eory, I. Erb, M. Farre, M. Fasold, D. Fleming, P. Flicek, K. E. Fowler, L. Fresard, D. P. Froman, V. Garceau, P. P. Gardner, A. A. Gheyas, D. K. Griffin, M. A. Groenen, T. Haaf, O. Hanotte, A. Hart, J. Hasler, S. B. Hedges, J. Hertel, K. Howe, A. Hubbard, D. A. Hume, P. Kaiser, D. Kedra, S. J. Kemp, C. Klopp, K. E. Kniel, R. Kuo, S. Lagarrigue, S. J. Lamont, D. M. Larkin, R. A. Lawal, S. M. Markland, F. McCarthy, H. A. McCormack, M. C. McPherson, A. Motegi, S. A. Muljo, A. Munsterberg, R. Nag, I. Nanda, M. Neuberger, A. Nitsche, C. Notredame, H. Noyes, R. O'Connor, E. A. O'Hare, A. J. Oler, S. C. Ommeh, H. Pais, M. Persia, F. Pitel, L. Preeyanon, P. Prieto Barja, E. M. Pritchett, D. D. Rhoads, C. M. Robinson, M. N. Romanov, M. Rothschild, P. F. Roux, C. J. Schmidt, A. S. Schneider, M. G. Schwartz, S. M. Searle, M. A. Skinner, C. A. Smith, P. F. Stadler, T. E. Steeves, C. Steinlein, L. Sun, M. Takata, I. Ulitsky, Q. Wang, Y. Wang, others. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res. 2015. 145: 78-179.
  • C. Zu Siederdissen, S. J. Prohaska, P. F. Stadler. Algebraic Dynamic Programming over general data structures. BMC Bioinformatics. 2015. 16 Suppl 19: S2.

2014 (21)

  • F. Amman, M. T. Wolfinger, R. Lorenz, I. L. Hofacker, P. F. Stadler, S. Findeiss. TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinformatics. 2014. 15: 89.
  • Martin Machyna, Stephanie Kehr, Korinna Straube, Dennis Kappei, Frank Buchholz, Falk Butter, Jernej Ule, Jana Hertel, Peter F Stadler, Karla M Neugebauer. The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies. Molecular Cell. 2014. 56: 389-399.
  • H. Schneider, S. Bartschat, G. Doose, L. Maciel, E. Pizani, M. Bassani, F. A. Torres, S. Will, T. Raiol, M. Brigido, M. E. Walter, P. F. Stadler. Advances in bioinformatics and computational biology : 9th Brazilian Symposium on Bioinformatics, BSB 2014, Belo Horizonte, Brazil, October 28-30, 2014 : proceedings. 2014.
  • A. H. Sahyoun, M. Bernt, P. F. Stadler, K. Tout. GC skew and mitochondrial origins of replication. Mitochondrion. 2014. 17C: 56-66.
  • L. Rivarola-Duarte, C. Otto, F. Jühling, S. Schreiber, D. Bedulina, L. Jakob, A. Gurkov, D. Axenov-Gribanov, A. H. Sahyoun, M. Lucassen, J. Hackermüller, S. Hoffmann, F. Sartoris, H. O. Portner, M. Timofeyev, T. Luckenbach, P. F. Stadler. A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus. J Exp Zool B Mol Dev Evol. 2014. 322: 177-89.
  • A.A. Parikesit, L. Steiner, P.F. Stadler, S.J. Prohaska. Pitfalls of Ascertainment Biases in Genome Annotations —Computing Comparable Protein Domain Distributions in Eukarya. Malaysian Journal of Fundamental and Applied Sciences. 2014. 10, No. 2: 13-033.
  • C. Otto, P. F. Stadler, S. Hoffmann. Lacking alignments? The next generation sequencing mapper segemehl revisited. Bioinformatics. 2014.
  • A. Nitsche, G. Doose, H. Tafer, M. Robinson, N. R. Saha, M. Gerdol, A. Canapa, S. Hoffmann, C. T. Amemiya, P. F. Stadler. Atypical RNAs in the coelacanth transcriptome. J Exp Zool B Mol Dev Evol. 2014. 322: 342-51.
  • G. A. Müller, A. Wintsche, K. Stangner, S. J. Prohaska, P. F. Stadler, K. Engeland. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Res. 2014. 42: 10331-50.
  • G. A. Müller, A. Wintsche, K. Stangner, S. J. Prohaska, P. F. Stadler, K. Engeland. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Res. 2014. 42: 10331-50.
  • M. Lechner, M. Hernandez-Rosales, D. Dörr, N. Wieseke, A. Thevenin, J. Stoye, R. K. Hartmann, S. J. Prohaska, P. F. Stadler. Orthology detection combining clustering and synteny for very large datasets. PLoS One. 2014. 9: e105015.
  • R. Backofen, F. Amman, F. Costa, S. Findeiss, A. S. Richter, P. F. Stadler. Bioinformatics of prokaryotic RNAs. RNA Biol. 2014. 11:
  • Konstantin Klemm, PeterF Stadler. Rugged and Elementary Landscapes. In: Theory and Principled Methods for the Design of Metaheuristics, Springer Berlin Heidelberg 2014. 41-61. Ed: Borenstein, Yossi and Moraglio, Alberto.
  • Konstantin Klemm, Jing Qin, PeterF Stadler. Geometry and Coarse-Grained Representations of Landscapes. In: Recent Advances in the Theory and Application of Fitness Landscapes, Springer Berlin Heidelberg 2014. 6: 153-176. Ed: Richter, Hendrik and Engelbrecht, Andries.
  • S. Kehr, S. Bartschat, H. Tafer, P. F. Stadler, J. Hertel. Matching of Soulmates: coevolution of snoRNAs and their targets. Mol Biol Evol. 2014. 31: 455-67.
  • Christian Höner zu Siederdissen, SonjaJ Prohaska, PeterF Stadler. Dynamic Programming for Set Data Types. In: Advances in Bioinformatics and Computational Biology, Springer International Publishing 2014. 8826: 57-64. Ed: Campos, Sérgio.
  • S. Hoffmann, C. Otto, G. Doose, A. Tanzer, D. Langenberger, S. Christ, M. Kunz, L. Holdt, D. Teupser, J. Hackermueller, P. F. Stadler. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection. Genome Biol. 2014. 15: R34.
  • Jana Hertel, David Langenberger, PeterF Stadler. Computational Prediction of MicroRNA Genes. In: RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods, Humana Press 2014. 1097: 437-456. Ed: Gorodkin, Jan and Ruzzo, Walter L.
  • J. C. Dohm, A. E. Minoche, D. Holtgrawe, S. Capella-Gutierrez, F. Zakrzewski, H. Tafer, O. Rupp, T. R. Sorensen, R. Stracke, R. Reinhardt, A. Goesmann, T. Kraft, B. Schulz, P. F. Stadler, T. Schmidt, T. Gabaldon, H. Lehrach, B. Weisshaar, H. Himmelbauer. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature. 2014. 505: 546-9.
  • S. Bartschat, S. Kehr, H. Tafer, P. F. Stadler, J. Hertel. snoStrip: a snoRNA annotation pipeline. Bioinformatics. 2014. 30: 115-6.
  • S. Wende, E. G. Platzer, F. Jühling, J. Putz, C. Florentz, P. F. Stadler, M. Morl. Biological evidence for the world's smallest tRNAs. Biochimie. 2014. 100: 151-8.

2013 (15)

  • F. Amman, S. H. Bernhart, G. Doose, I. L. Hofacker, J. Qin, P. F. Stadler, S. Will. The Trouble with Long-Range Base Pairs in RNA Folding. In: Advances in Bioinformatics and Computational Biology: 8th Brazilian Symposium on Bioinformatics, BSB 2013, Recife, Brazil, November 3-7, 2013, Proceedings, Springer International Publishing , Cham. 2013. 1-11. Ed: Setubal, João C. and Almeida, Nalvo F.
  • Fabian Amman, Stephan H Bernhart, Gero Doose, Ivo L Hofacker, Jing Qin, Peter F Stadler, Sebastian Will. The trouble with long-range base pairs in RNA folding. In: Brazilian Symposium on Bioinformatics, Springer, Cham 2013. 1-11.
  • C. Arnold, P. F. Stadler, S. J. Prohaska. Chromatin computation: epigenetic inheritance as a pattern reconstruction problem. J Theor Biol. 2013. 336: 61-74.
  • M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Putz, M. Middendorf, P. F. Stadler. MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2013. 69: 313-9.
  • G. Doose, M. Alexis, R. Kirsch, S. Findeiss, D. Langenberger, R. Machne, M. Morl, S. Hoffmann, P. F. Stadler. Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data. RNA Biol. 2013. 10: 1204-10.
  • M. Hellmuth, M. Hernandez-Rosales, K. T. Huber, V. Moulton, P. F. Stadler, N. Wieseke. Orthology relations, symbolic ultrametrics, and cographs. J Math Biol. 2013. 66: 399-420.
  • L. M. Holdt, S. Hoffmann, K. Sass, D. Langenberger, M. Scholz, K. Krohn, K. Finstermeier, A. Stahringer, W. Wilfert, F. Beutner, S. Gielen, G. Schuler, G. Gabel, H. Bergert, I. Bechmann, P. F. Stadler, J. Thiery, D. Teupser. Alu elements in ANRIL non-coding RNA at chromosome 9p21 modulate atherogenic cell functions through trans-regulation of gene networks. PLoS Genet. 2013. 9: e1003588.
  • S. Kehr, S. Bartschat, H. Tafer, P. F. Stadler, J. Hertel. Matching of Soulmates: Coevolution of snoRNAs and Their Targets. Mol Biol Evol. 2013.
  • D. Langenberger, M. V. Cakir, S. Hoffmann, P. F. Stadler. Dicer-Processed Small RNAs: Rules and Exceptions. J Exp Zool B Mol Dev Evol. 2013. 320: 35-46.
  • J. Lehmann, P. F. Stadler, V. Krauss. Near intron pairs and the metazoan tree. Mol Phylogenet Evol. 2013. 66: 811-23.
  • R. Lorenz, S. H. Bernhart, J. Qin, C. Höner zu Siederdissen, A. Tanzer, F. Amman, I. L. Hofacker, P. F. Stadler. 2D meets 4G: G-quadruplexes in RNA secondary structure prediction. IEEE/ACM Trans Comput Biol Bioinform. 2013. 10: 832-44.
  • Ronny Lorenz, Stephan H Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L Hofacker, Peter F Stadler. 2D meets 4G: G-quadruplexes in RNA secondary structure prediction. IEEE/ACM transactions on computational biology and bioinformatics. 2013. 10: 832-844.
  • S. A. Müller, S. Findeiss, S. R. Pernitzsch, D. K. Wissenbach, P. F. Stadler, I. L. Hofacker, M. von Bergen, S. Kalkhof. Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. J Proteomics. 2013. 86: 27-42.
  • M. Wachsmuth, S. Findeiss, N. Weissheimer, P. F. Stadler, M. Morl. De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res. 2013. 41: 2541-51.
  • S. Will, M. F. Siebauer, S. Heyne, J. Engelhardt, P. F. Stadler, Reiche, R. Backofen. LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search. Algorithms Mol Biol. 2013. 8: 14.

2012 (10)

  • J. Engelhardt, P. F. Stadler. Hidden treasures in unspliced EST data. Theory Biosci. 2012. 131: 49-57.
  • J. Hertel, S. Bartschat, A. Wintsche, C. Otto, P. F. Stadler. Evolution of the let-7 microRNA family. RNA Biol. 2012. 9: 231-41.
  • F. Jühling, J. Putz, M. Bernt, A. Donath, M. Middendorf, C. Florentz, P. F. Stadler. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res. 2012. 40: 2833-45.
  • F. Jühling, J. Putz, C. Florentz, P. F. Stadler. Armless mitochondrial tRNAs in Enoplea (Nematoda). RNA Biol. 2012. 9: 1161-6.
  • K. Klemm, A. Mehta, P. F. Stadler. Landscape encodings enhance optimization. PLoS One. 2012. 7: e34780.
  • D. Langenberger, S. Pundhir, C. T. Ekstrom, P. F. Stadler, S. Hoffmann, J. Gorodkin. deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics. 2012. 28: 17-24.
  • Ronny Lorenz, Stephan H Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L Hofacker, Peter F Stadler. RNA folding algorithms with G-quadruplexes. In: Brazilian Symposium on Bioinformatics, Springer, Berlin, Heidelberg 2012. 49-60.
  • C. Otto, P. F. Stadler, S. Hoffmann. Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics. 2012. 28: 1698-704.
  • J. Richter, M. Schlesner, S. Hoffmann, M. Kreuz, E. Leich, B. Burkhardt, M. Rosolowski, O. Ammerpohl, R. Wagener, S. H. Bernhart, D. Lenze, M. Szczepanowski, M. Paulsen, S. Lipinski, R. B. Russell, S. Adam-Klages, G. Apic, A. Claviez, D. Hasenclever, V. Hovestadt, N. Hornig, J. O. Korbel, D. Kube, D. Langenberger, C. Lawerenz, J. Lisfeld, K. Meyer, S. Picelli, J. Pischimarov, B. Radlwimmer, T. Rausch, M. Rohde, M. Schilhabel, R. Scholtysik, R. Spang, H. Trautmann, T. Zenz, A. Borkhardt, H. G. Drexler, P. Moller, R. A. Macleod, C. Pott, S. Schreiber, L. Trumper, M. Loeffler, P. F. Stadler, P. Lichter, R. Eils, R. Kuppers, M. Hummel, W. Klapper, P. Rosenstiel, A. Rosenwald, B. Brors, R. Siebert. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet. 2012. 44: 1316-1320.
  • C. Schmidtke, S. Findeiss, C. M. Sharma, J. Kuhfuss, S. Hoffmann, J. Vogel, P. F. Stadler, U. Bonas. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res. 2012. 40: 2020-31.

2011 (27)

  • A. Bateman, S. Agrawal, E. Birney, E. A. Bruford, J. M. Bujnicki, G. Cochrane, J. R. Cole, M. E. Dinger, A. J. Enright, P. P. Gardner, D. Gautheret, S. Griffiths-Jones, J. Harrow, J. Herrero, I. H. Holmes, H. D. Huang, K. A. Kelly, P. Kersey, A. Kozomara, T. M. Lowe, M. Marz, S. Moxon, K. D. Pruitt, T. Samuelsson, P. F. Stadler, A. J. Vilella, J. H. Vogel, K. P. Williams, M. W. Wright, C. Zwieb. RNAcentral: A vision for an international database of RNA sequences. Rna. 2011. 17: 1941-6.
  • P. Menzel, P. F. Stadler, J. Gorodkin. maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinformatics. 2011. 27: 317-25.
  • S. Washietl, S. Findeiss, S. A. Müller, S. Kalkhof, M. von Bergen, I. L. Hofacker, P. F. Stadler, N. Goldman. RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data. Rna. 2011. 17: 578-94.
  • A. Tramontano, A. Donath, S. H. Bernhart, K. Reiche, G. Bohmdorfer, P. F. Stadler, A. Bachmair. Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer. Virology. 2011. 412: 75-82.
  • H. Tafer, F. Amman, F. Eggenhofer, P. F. Stadler, I. L. Hofacker. Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics. 2011. 27: 1934-40.
  • L. Steiner, P.F. Stadler, M. Cysouw. A Pipeline for Computational Historical Linguistics. Language Dynamics and Change. 2011. 1: 89-127.
  • D. Rose, P. F. Stadler. Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript EGOT. Frontiers in Genetics. 2011. 2: 69.
  • D. Rose, M. Hiller, K. Schutt, J. Hackermüller, R. Backofen, P. F. Stadler. Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinformatics. 2011. 27: 1894-900.
  • J. D. Raincrow, K. Dewar, C. Stocsits, S. J. Prohaska, C. T. Amemiya, P. F. Stadler, C. H. Chiu. Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny. J Exp Zool B Mol Dev Evol. 2011. 316: 451-64.
  • S. J. Prohaska, P. F. Stadler. The use and abuse of -omes. Methods Mol Biol. 2011. 719: 173-96.
  • M. Perseke, J. Hetmank, M. Bernt, P. F. Stadler, M. Schlegel, D. Bernhard. The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria. BMC Evol Biol. 2011. 11: 134.
  • A. A. Parikesit, P. F. Stadler, S. J. Prohaska. Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions. Genes. 2011. 2: 912-924.
  • C. Otto, S. Hoffmann, J. Gorodkin, P. F. Stadler. Fast local fragment chaining using sum-of-pair gap costs. Algorithms Mol Biol. 2011. 6: 4.
  • M. Marz, P. F. Stadler. RNA interactions. Adv Exp Med Biol. 2011. 722: 20-38.
  • F. Eggenhofer, H. Tafer, P. F. Stadler, I. L. Hofacker. RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Res. 2011. 39: W149-54.
  • M. Marz, A. R. Gruber, C. Höner Zu Siederdissen, F. Amman, S. Badelt, S. Bartschat, S. H. Bernhart, W. Beyer, S. Kehr, R. Lorenz, A. Tanzer, D. Yusuf, H. Tafer, I. L. Hofacker, P. F. Stadler. Animal snoRNAs and scaRNAs with exceptional structures. RNA Biol. 2011. 8: 938-46.
  • I. Lozada-Chavez, P. F. Stadler, S. J. Prohaska. "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity. Orig Life Evol Biosph. 2011. 41: 587-607.
  • Ronny Lorenz, Stephan H Bernhart, Christian Höner Zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker. ViennaRNA Package 2.0. Algorithms for molecular biology. 2011. 6: 26.
  • R. Lorenz, S. H. Bernhart, C. Höner Zu Siederdissen, H. Tafer, C. Flamm, P. F. Stadler, I. L. Hofacker. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011. 6: 26.
  • M. Lechner, S. Findeiss, L. Steiner, M. Marz, P. F. Stadler, S. J. Prohaska. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics. 2011. 12: 124.
  • D. Langenberger, S. Pundhir, C. T. Ekstrom, P. F. Stadler, S. Hoffmann, J. Gorodkin. deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. Bioinformatics. 2011. 28: 17-24.
  • David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer, Peter Stadler. MicroRNA or Not MicroRNA? Advances in Bioinformatics and Computational Biology. 2011. 6832: 1-9. Ed: Norberto de Souza, Osmar and Telles, Guilherme and Palakal, Mathew.
  • S. Kehr, S. Bartschat, P. F. Stadler, H. Tafer. PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics. 2011. 27: 279-80.
  • S. Findeiss, D. Langenberger, P. F. Stadler, S. Hoffmann. Traces of post-transcriptional RNA modifications in deep sequencing data. Biol Chem. 2011. 392: 305-13.
  • S. Findeiss, J. Engelhardt, S. J. Prohaska, P. F. Stadler. Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids. Biochimie. 2011. 93: 2019-23.
  • M. Fasold, D. Langenberger, H. Binder, P. F. Stadler, S. Hoffmann. DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 2011. 39: W112-7.
  • C. H. zu Siederdissen, S. H. Bernhart, P. F. Stadler, I. L. Hofacker. A folding algorithm for extended RNA secondary structures. Bioinformatics. 2011. 27: i129-36.

2010 (16)

  • C. T. Amemiya, T. P. Powers, S. J. Prohaska, J. Grimwood, J. Schmutz, M. Dickson, T. Miyake, M. A. Schoenborn, R. M. Myers, F. H. Ruddle, P. F. Stadler. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci U S A. 2010. 107: 3622-7.
  • C. Arnold, P. F. Stadler. Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. Algorithms Mol Biol. 2010. 5: 25.
  • C. Bermudez-Santana, C. S. Attolini, T. Kirsten, J. Engelhardt, S. J. Prohaska, S. Steigele, P. F. Stadler. Genomic organization of eukaryotic tRNAs. BMC Genomics. 2010. 11: 270.
  • R. A. Dalloul, J. A. Long, A. V. Zimin, L. Aslam, K. Beal, L. Ann Blomberg, P. Bouffard, D. W. Burt, O. Crasta, R. P. Crooijmans, K. Cooper, R. A. Coulombe, S. De, M. E. Delany, J. B. Dodgson, J. J. Dong, C. Evans, K. M. Frederickson, P. Flicek, L. Florea, O. Folkerts, M. A. Groenen, T. T. Harkins, J. Herrero, S. Hoffmann, H. J. Megens, A. Jiang, P. de Jong, P. Kaiser, H. Kim, K. W. Kim, S. Kim, D. Langenberger, M. K. Lee, T. Lee, S. Mane, G. Marcais, M. Marz, A. P. McElroy, T. Modise, M. Nefedov, C. Notredame, I. R. Paton, W. S. Payne, G. Pertea, D. Prickett, D. Puiu, D. Qioa, E. Raineri, M. Ruffier, S. L. Salzberg, M. C. Schatz, C. Scheuring, C. J. Schmidt, S. Schroeder, S. M. Searle, E. J. Smith, J. Smith, T. S. Sonstegard, P. F. Stadler, H. Tafer, Z. J. Tu, C. P. Van Tassell, A. J. Vilella, K. P. Williams, J. A. Yorke, L. Zhang, H. B. Zhang, X. Zhang, Y. Zhang, K. M. Reed. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 2010. 8:
  • A. Donath, S. Findeiss, J. Hertel, M. Marz, W. Otto, C. Schulz, P. F. Stadler, S. Wirth. Non-coding RNAs. 2010. 251-293.
  • M. Fasold, P. F. Stadler, H. Binder. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinformatics. 2010. 11: 207.
  • S. Findeiss, C. Schmidtke, P. F. Stadler, U. Bonas. A novel family of plasmid-transferred anti-sense ncRNAs. RNA Biol. 2010. 7: 120-4.
  • S. Jänicke, C. Heine, M. Hellmuth, P. F. Stadler, G. Scheuermann. Visualization of graph products. IEEE Trans Vis Comput Graph. 2010. 16: 1082-9.
  • S. Kehr, S. Bartschat, P. F. Stadler, H. Tafer. PLEXY: efficient target prediction for box C/D snoRNAs. Bioinformatics. 2010. 27: 279-280.
  • J. Lehmann, C. Eisenhardt, P. F. Stadler, V. Krauss. Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication. BMC Evol Biol. 2010. 10: 156.
  • S. A. Müller, T. Kohajda, S. Findeiss, P. F. Stadler, S. Washietl, M. Kellis, M. von Bergen, S. Kalkhof. Optimization of parameters for coverage of low molecular weight proteins. Anal Bioanal Chem. 2010. 398: 2867-81.
  • A. A. Parikesit, P. F. Stadler, S. J. Prohaska. Quantitative Comparison of Genomic-Wide Protein Domain Distributions. In: German Conference on Bioinformatics, Gesellschaft für Informatik 2010. P-173: 93-102. Ed: Schomburg, D. and Grote, A.
  • S. J. Prohaska, P. F. Stadler, D. C. Krakauer. Innovation in gene regulation: the case of chromatin computation. J Theor Biol. 2010. 265: 27-44.
  • M. Riester, P. F. Stadler, K. Klemm. Reconstruction of pedigrees in clonal plant populations. Theor Popul Biol. 2010. 78: 109-17.
  • C. M. Sharma, S. Hoffmann, F. Darfeuille, J. Reignier, S. Findeiss, A. Sittka, S. Chabas, K. Reiche, J. Hackermüller, R. Reinhardt, P. F. Stadler, J. Vogel. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010. 464: 250-5.
  • H. Tafer, S. Kehr, J. Hertel, I. L. Hofacker, P. F. Stadler. RNAsnoop: efficient target prediction for H/ACA snoRNAs. Bioinformatics. 2010. 26: 610-6.

2009 (11)

  • J. Hertel, d.D. Jong, M. Marz, D. Rose, H. Tafer, A. Tanzer, B. Schierwater, Peter F. Stadler. Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens. Nucleic Acids Res. 2009. 37: 1602-1615.
  • M. Hiller, S. Findeiss, S. Lein, M. Marz, C. Nickel, D. Rose, C. Schulz, R. Backofen, S. J. Prohaska, G. Reuter, P. F. Stadler. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res. 2009. 19: 1289-300.
  • S. Hoffmann, C. Otto, S. Kurtz, C. M. Sharma, P. Khaitovich, J. Vogel, P. F. Stadler, J. Hackermüller. Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol. 2009. 5: e1000502.
  • T. A. Jones, W. Otto, M. Marz, S. R. Eddy, P. F. Stadler. A survey of nematode SmY RNAs. RNA Biol. 2009. 6: 5-8.
  • B. Kaczkowski, E. Torarinsson, K. Reiche, J.H. Havgaard, P.F. Stadler, J. Gorodkin. Structural profiles of human miRNA families from pairwise clustering. Bioinformatics. 2009. 25: 291-4.
  • D. Langenberger, C. Bermudez-Santana, J. Hertel, S. Hoffmann, P. Khaitovich, P. F. Stadler. Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics. 2009. 25: 2298-301.
  • A. Mosig, T. BIyIkoglu, S.J. Prohaska, P.F. Stadler. Discovering cis-regulatory modules by optimizing barbecues. Discrete Applied Mathematics Networks in Computational Biology. 2009. 157: 2458-2468.
  • M. Riester, P. F. Stadler, K. Klemm. FRANz: reconstruction of wild multi-generation pedigrees. Bioinformatics. 2009. 25: 2134-9.
  • K. Scheibye-Alsing, S. Hoffmann, A. Frankel, P. Jensen, P. F. Stadler, Y. Mang, N. Tommerup, M. J. Gilchrist, A. B. Nygard, S. Cirera, C. B. Jorgensen, M. Fredholm, J. Gorodkin. Sequence assembly. Comput Biol Chem. 2009. 33: 121-36.
  • P. F. Stadler, J. J. Chen, J. Hackermüller, S. Hoffmann, F. Horn, P. Khaitovich, A. K. Kretzschmar, A. Mosig, S. J. Prohaska, X. Qi, K. Schutt, K. Ullmann. Evolution of vault RNAs. Mol Biol Evol. 2009. 26: 1975-91.
  • P. F. Stadler, S. J. Prohaska, C. V. Forst, D. C. Krakauer. Defining genes: a computational framework. Theory Biosci. 2009. 128: 165-70.

2008 (20)

  • Stephan Bernhart, Ivo L. Hofacker, Sebastian Will, Andreas R. Gruber, Peter F. Stadler. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 2008. 9: 474.
  • Veiko Krauss, Christian Thümmler, Franziska Georgi, Jörg Lehmann, Peter F. Stadler, Carina Eisenhardt. Near intron positions are reliable phylogenetic markers: An application to Holometabolous Insects. Mol. Biol. Evol. 2008. 25: 821-830.
  • Elisabeth Sonnleitner, Theresa Sorger-Domenigg, Monika J. Madej, Sven Findeiss, Jörg Hackermüller, Alexander Hüttenhofer, Peter F. Stadler, Udo Bäsi, Isabella Moll. Detection of small non-coding RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatics tools. Microbiology. 2008. 154: 3175-3187.
  • Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang Li, Peter F. Stadler. Duplicated RNA Genes in Teleost Fish Genomes. J. Bioinf. Comp. Biol. 2008. 6: 1157-1175.
  • Dominic Rose, Jana Hertel, Kristin Reiche, Peter F. Stadler, Jörg Hackermüller. NcDNAlign: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences. Genomics. 2008. 92: 65-74.
  • Sonja J. Prohaska, Peter F. Stadler. Genes. Th. Biosci. 2008. 127: 215-221.
  • Sonja J. Prohaska, Guido Fritzsch, Peter F. Stadler. Rate Variations, Phylogenetics, and Partial Orders. In: Fifth International Workshop on Computational Systems Biology, WCSB 2008, TU Tampere 2008. 133-136. Ed: Ahdesmäki, Miika and Strimmer, Korbinian and Radde, Nicole and Rahnenführer, Jörg and Klemm, Konstantin and Lähdesmäki, Harri and Yli-Harja, Olli.
  • Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter F. Stadler, Martin Schlegel. Evolution of Mitochondrial Gene Orders in Echinoderms. Mol. Phylog. Evol. 2008. 47: 855-864.
  • Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska. SynBlast: Assisting the Analysis of Conserved Synteny Information. BMC Bioinformatics. 2008. 9: 351.
  • Christoph Joechl, Mathieu Rederstorff, Jana Hertel, Peter F. Stadler, Ivo L. Hofacker, Markus Schrettl, Hubertus Haas, Alexander Hüttenhofer. Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein-synthesis. Nucleic Acids Res. 2008. 36: 2677-2689.
  • Stephan H Bernhart, Ivo L Hofacker, Sebastian Will, Andreas R Gruber, Peter F Stadler. RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics. 2008. 9: 474.
  • S. Hoffmann, S. Cepok, V. Grummel, K. Lehmann-Horn, J. Hackermüller, P. F. Stadler, H. P. Hartung, A. Berthele, F. Deisenhammer, R. Wassmuth, B. Hemmer. HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis. Am J Hum Genet. 2008. 83: 219-27.
  • Jana Hertel, Ivo L. Hofacker, Peter F. Stadler. snoReport: Computational identification of snoRNAs with unknown targets. Bioinformatics. 2008. 24: 158-164.
  • A. Heffel, P. F. Stadler, S. J. Prohaska, G. Kauer, J. P. Kuska. Process Flow for Classification and Clustering of Fruit Fly Gene Expression Patterns. In: Proc Int Conf Image Proc 2008. 1: 721-724.
  • Andreas R. Gruber, Dorota Koper-Emde, Manja Marz, Hakim Tafer, Stephan Bernhart, Gregor Obernosterer, Axel Mosig, Ivo L. Hofacker, Peter F. Stadler, Bernd-Joachim Benecke. Invertebrate 7SK snRNAs. J. Mol. Evol. 2008. 107-115: 66.
  • Michael Geis, Christian Flamm, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker, Martin Middendorf, Christian Mandl, Peter F. Stadler, Caroline Thurner. Folding kinetics of large RNAs. J. Mol. Biol. 2008. 379: 160-173.
  • Guido Fritzsch, Manja U. Böhme, Mike Thorndyke, Hiroaki Nakano, Olle Israelsson, Thomas Stach, Martin Schlegel, Thomas Hankeln, Peter F. Stadler. A PCR Survey of Xenoturbella bocki Hox Genes. J. Exp. Zool: Mol. Dev. Evol. 2008. 310B: 278-284.
  • Andreas W.M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grunewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler. Noisy: identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol. 2008. 3: 7.
  • Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Berhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, Sebastian Will. Variations on RNA Folding and Alignment: Lessons from Benasque. J. Math. Biol. 2008. 56: 129-144.
  • Mingyi Xie, Axel Mosig, Xiaodong Qi, Yang Li, Peter F. Stadler, Julian J.-L. Chen. Size Variation and Structural Conservation of Vertebrate Telomerase RNA. J. Biol. Chem. 2008. 283: 2049-2059.

2007 (5)

  • Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf. CREx: inferring genomic rearrangements based on common intervals. Bioinformatics. 2007. 23: 2957-2958.
  • Athanasius F. Bompfünewerer, Rolf Backofen, Christoph Flamm, Claudia Fried, Guido Fritzsch, Joerg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Domininc Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will. RNAs Everywhere: Genome-Wide Annotation of Structured RNAs. J. Exp.Zool.B: Mol. Dev. Evol. 2007. 308B: 1-25.
  • The Athanasius F. Bompfünewerer RNA Consortium, Rolf Backofen, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Will Sebastian. RNAs Everywhere: Genome-Wide Annotation of Structured RNAs. J. Exp. Zool. B: Mol. Dev. Evol. 2007. 308B: 1-25.
  • Dennis Loffler, Katja Brocke-Heidrich, Gabriele Pfeifer, Claudia Stocsits, Jorg Hackermüller, Antje K. Kretzschmar, Renate Burger, Martin Gramatzki, Conny Blumert, Kay Bauer, Helena Cvijic, A. Kerstin Ullmann, Peter F. Stadler, Friedemann Horn. Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood. 2007. 110: 1330-1333.
  • Madleen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Detlef Bernhard, Martin Schlegel. The Mitochondrial DNA of Xenoturbella bocki: Genomic Architecture and Phylogenetic Analysis. Th. Biosci. 2007. 126: 35-42.

2006 (2)

  • Guido Fritzsch, Martin Schlegel, Peter F. Stadler. Alignments of mitochondrial genome arrangements: applications to metazoan phylogeny. J Theor Biol. 2006. 240: 511-520.
  • Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbo, Runsheng Chen, Peter F. Stadler. Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Exp Zoolog B Mol Dev Evol. 2006. 306: 379-392.

2005 (1)

  • Athanasius F. Bompfuenewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M. R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Christina Witwer. Evolutionary Patterns of Non-Coding RNAs. Th. Biosci. 2005. 123: 301-369.

2004 (2)

  • H Binder, T Kirsten, I.L Hofacker, P Stadler, M. Löffler. Interactions in oligonucleotide hybrid duplexes on microarrays. Journal of Physical Chemistry. 2004. eingereicht.
  • H Binder, T Kirsten, M Löffler, P. Stadler. The sensitivity of microarray oligonucleotide probes - variability and the effect of base composition. Journal of Physical Chemistry. 2004. eingereicht.

2003 (1)

  • Hans Binder, Toralf Kirsten, Markus Loeffler, Peter Stadler. Sequence specific sensitivity of oligonucleotide probes. In: Proceedings of the German Bioinformatics Conference 2003 . 2: 145-147.