Dr. rer. nat. Stephan Bernhart

ACADEMIC CAREER

• Diploma and phD (Doktor) in Chemistry, University of Vienna, specializing in theoretical biochemistry and the prediction of structures of protein and RNA sequences.
• Post-Doc at the theoretical biochemmistry group at the University of Vienna
• transcriptome bioinformatics group since 2011
• commissary Managing Director at IZBI since 2021

SCIENTIFIC INTERESTS

• Transcriptome analysis
• RNA structure prediction
• Cancer epigenomics and transcriptomics

PUBLICATIONS

2023 (4)

• Steffen Fuchs, Clara Danßmann, Filippos Klironomos, Annika Winkler, Jörg Fallmann, Louisa-Marie Kruetzfeldt, Annabell Szymansky, Julian Naderi, Stephan H Bernhart, Laura Grunewald. Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN. Nature communications. 2023. 14: 3936.
• Cristina Lopez, Nikolai Schleussner, Stephan H Bernhart, Kortine Kleinheinz, Stephanie Sungalee, Henrike L Sczakiel, Helene Kretzmer, Umut H Toprak, Selina Glaser, Rabea Wagener. Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B-cell lymphomas. Haematologica. 2023. 108: 543.
• Paula Reichelt, Stephan Bernhart, Franziska Wilke, Sebastian Schwind, Michael Cross, Uwe Platzbecker, Gerhard Behre. MicroRNA Expression Patterns Reveal a Role of the TGF-β Family Signaling in AML Chemo-Resistance. Cancers. 2023. 15: 5086.
• Adam Ustaszewski, Julia Paczkowska, Joanna Janiszewska, Stephan H Bernhart, Julia Bein, Núria Russiñol, Martin-Leo Hansmann, Vicente Chapaprieta, José I Martín-Subero, Reiner Siebert. Identification of two unannotated miRNAs in classic Hodgkin lymphoma cell lines. PLoS One. 2023. 18: e0283186.

2022 (4)

• S. Khamse, S. Alizadeh, S. H. Bernhart, H. Afshar, A. Delbari, M. Ohadi. A (GCC) repeat in SBF1 reveals a novel biological phenomenon in human and links to late onset neurocognitive disorder. Sci Rep. 2022. 12: 15480.
• P. Patil, S. Hillebrecht, E. Chteinberg, C. López, U. H. Toprak, J. Seufert, S. H. Bernhart, H. Kretzmer, A. K. Bergmann, S. Bens, J. Högel, A. Müller, B. M. Jebaraj, A. Schrader, P. Johansson, D. Costa, M. Schlesner, J. Dürig, M. Herling, E. Campo, S. Stilgenbauer, L. Wiehle, R. Siebert. T-cell prolymphocytic leukemia is associated with deregulation of oncogenic microRNAs on transcriptional and epigenetic level. Genes Chromosomes Cancer. 2022. 61: 432-436.
• P. Patil, U. H. Toprak, J. Seufert, T. Braun, S. H. Bernhart, L. Wiehle, A. Müller, M. Schlesner, M. Herling, P. Lichter, S. Stilgenbauer, R. Siebert, M. Zapatka. Exploration of whole genome and transcriptome sequencing data lacks evidence for oncogenic viral elements to drive the pathogenesis of T-cell prolymphocytic leukemia. Leuk Lymphoma. 2022. 63: 3253-3256.
• Josefine Radke, Naveed Ishaque, Randi Koll, Zuguang Gu, Elisa Schumann, Lina Sieverling, Sebastian Uhrig, Daniel Hübschmann, Umut H. Toprak, Cristina López, Xavier Pastor Hostench, Simone Borgoni, Dilafruz Juraeva, Fabienne Pritsch, Nagarajan Paramasivam, Gnana Prakash Balasubramanian, Matthias Schlesner, Shashwat Sahay, Marc Weniger, Debora Pehl, Helena Radbruch, Anja Osterloh, Agnieszka Korfel, Martin Misch, Julia Onken, Katharina Faust, Peter Vajkoczy, Dag Moskopp, Yawen Wang, Andreas Jödicke, Lorenz Trümper, Ioannis Anagnostopoulos, Dido Lenze, Ralf Küppers, Michael Hummel, Clemens A. Schmitt, Otmar D. Wiestler, Stephan Wolf, Andreas Unterberg, Roland Eils, Christel Herold-Mende, Benedikt Brors, Reiner Siebert, Susanne Wagner, Andrea Haake, Julia Richter, Gesine Richter, Chris Lawerenz, Jürgen Eils, Jules Kerssemakers, Christina Jaeger-Schmidt, Ingrid Scholz, Anke K. Bergmann, Christoph Borst, Friederike Braulke, Birgit Burkhardt, Alexander Claviez, Martin Dreyling, Sonja Eberth, Hermann Einsele, Norbert Frickhofen, Siegfried Haas, Martin-Leo Hansmann, Dennis Karsch, Nicole Klepl, Michael Kneba, Jasmin Lisfeld, Luisa Mantovani-Löffler, Marius Rohde, German Ott, Christina Stadler, Peter Staib, Stephan Stilgenbauer, Thorsten Zenz, Dieter Kube, Wolfram Klapper, Ulrike Kostezka, Peter Möller, Andreas Rosenwald, Monika Szczepanowski, Ole Ammerpohl, Sietse M. Aukema, Vera Binder, Arndt Borkhardt, Jessica I. Hoell, Ellen Leich, Peter Lichter, Inga Nagel, Jordan Pischimariov, Bernhard Radlwimmer, Philip Rosenstiel, Markus Schilhabel, Stefan Schreiber, Inga Vater, Rabea Wagener, Stephan H. Bernhart, Hans Binder, Gero Doose, Steve Hoffmann, Lydia Hopp, others. The genomic and transcriptional landscape of primary central nervous system lymphoma. Nature communications. 2022. 13: 2558.

2021 (9)

• Yamel Cardona Gloria, Stephan H. Bernhart, Sven Fillinger, Olaf-Oliver Wolz, Sabine Dickhöfer, Jakob Admard, Stephan Ossowski, Sven Nahnsen, Reiner Siebert, Alexander N. R. Weber. Absence of Non-Canonical, Inhibitory MYD88 Splice Variants in B Cell Lymphomas Correlates With Sustained NF-κB Signaling. Frontiers in Immunology. 2021. 12:
• Luis Coronel, Konstantin Riege, Katjana Schwab, Silke Förste, David Häckes, Lena Semerau, Stephan H Bernhart, Reiner Siebert, Steve Hoffmann, Martin Fischer. Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress. Nucleic acids research. 2021. 49: 7437-7456.
• E. de Guillebon, M. Jimenez, L. Mazzarella, F. Betsou, P. Stadler, I. Peták, E. Jeannot, L. Chanas, N. Servant, G. Marret, B. A. Duso, F. Legrand, K. N. Kornerup, S. H. Bernhart, G. Balogh, R. Dóczi, P. Filotás, G. Curigliano, I. Bièche, J. Guérin, A. Dirner, C. Neuzillet, N. Girard, E. Borcoman, L. Larbi Chérif, P. Tresca, D. B. Roufai, C. Dupain, S. Scholl, F. André, X. Fernandez, T. Filleron, M. Kamal, C. Le Tourneau. Combining immunotherapy with an epidrug in squamous cell carcinomas of different locations: rationale and design of the PEVO basket trial. ESMO Open. 2021. 6: 100106.
• 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.
• Laura Krieg, Konrad Didt, Isabel Karkossa, Stephan H Bernhart, Stephanie Kehr, Narmadha Subramanian, Andreas Lindhorst, Alexander Schaudinn, Shirin Tabei, Maria Keller, Michael Stumvoll, Arne Dietrich, Martin von Bergen, Peter F Stadler, Jurga Laurencikiene, Martin Krüger, Matthias Blüher, Martin Gericke, Kristin Schubert, Peter Kovacs, Rima Chakaroun, Lucas Massier. Multiomics reveal unique signatures of human epiploic adipose tissue related to systemic insulin resistance. Gut. 2021. gutjnl-2021-324603.
• Chiara Pighi, Taek-Chin Cheong, Mara Compagno, Enrico Patrucco, Maddalena Arigoni, Martina Olivero, Qi Wang, Cristina Lopez, Stephan H Bernhart, Bruno M. Grande, Teresa Poggio, Fernanda Langellotto, Lisa Bonello, Riccardo Dall'Olio, Sandra Martínez-Martín, Luca Molinaro, Paola Francia di Celle, Jonathan R Whitfield, Laura Soucek, Claudia Voena, Raffaele A Calogero, Ryan D Morin, Louis Michael Staudt, Reiner Siebert, Alberto Zamò, Roberto Chiarle. Frequent mutations of FBXO11 highlight BCL6 as a therapeutic target in Burkitt lymphoma. Blood Advances. 2021.
• Maria Schmidt, Mamoona Arshad, Stephan H. Bernhart, Siras Hakobyan, Arsen Arakelyan, Henry Loeffler-Wirth, Hans Binder. The Evolving Faces of the SARS-CoV-2 Genome. Viruses. 2021. 13: 1764.
• 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.
• 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.
• Paurnima Patil, Agata Cieslak, Stephan H Bernhart, Umut H Toprak, Rabea Wagener, Cristina López, Laura Wiehle, Susanne Bens, Janine Altmüller, Marek Franitza. Reconstruction of rearranged T‐cell receptor loci by whole genome and transcriptome sequencing gives insights into the initial steps of T‐cell prolymphocytic leukemia. Genes, Chromosomes and Cancer. 2020. 59: 261-267.
• 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 (5)

• Gero Doose, Stephan H Bernhart, Rabea Wagener, Steve Hoffmann. DIEGO: detection of differential alternative splicing using Aitchison’s geometry. Bioinformatics. 2018. 34: 1066-1068.
• Hilmar Quentmeier, Claudia Pommerenke, Stephan H Bernhart, Wilhelm G Dirks, Vivien Hauer, Steve Hoffmann, Stefan Nagel, Reiner Siebert, Cord C Uphoff, Margarete Zaborski. RBFOX2 and alternative splicing in B-cell lymphoma. Blood cancer journal. 2018. 8: 1-4.
• 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:
• A Ustaszewski, J Paczkowska, J Janiszewska, S Hartmann, J Bein, S Bernhart, R Siebert, ML Hansmann, M Giefing. PO-379 Novel tumour specific miRNA expressed in classical hodgkin lymphoma cell lines. 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 (1)

• Christina FS Mages, Axel Wintsche, Stephan H Bernhart, Gerd A Mueller. The DREAM complex through its subunit Lin37 cooperates with Rb to initiate quiescence. Elife. 2017. 6: e26876.

2016 (12)

• 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.
• Kebria Hezaveh, Andreas Kloetgen, Stephan H Bernhart, Kunal Das Mahapatra, Dido Lenze, Julia Richter, Andrea Haake, Anke K Bergmann, Benedikt Brors, Birgit Burkhardt. 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.
• 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.
• Martin Hölzer, Verena Krähling, Fabian Amman, Emanuel Barth, Stephan H Bernhart, Victor AO Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald. Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Scientific reports. 2016. 6: 34589.
• 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.
• Jessica Okosun, Rachel L Wolfson, Jun Wang, Shamzah Araf, Lucy Wilkins, Brian M Castellano, Leire Escudero-Ibarz, Ahad Fahad Al Seraihi, Julia Richter, Stephan H Bernhart. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nature genetics. 2016. 48: 183.
• J. Okosun, R. L. Wolfson, J. Wang, S. Araf, L. Wilkins, B. M. Castellano, L. Escudero-Ibarz, A. F. Al Seraihi, J. Richter, S. H. Bernhart, A. Efeyan, S. Iqbal, J. Matthews, A. Clear, J. A. Guerra-Assuncao, C. Bodor, H. Quentmeier, C. Mansbridge, P. Johnson, A. Davies, J. C. Strefford, G. Packham, S. Barrans, A. Jack, M. Q. Du, M. Calaminici, T. A. Lister, R. Auer, S. Montoto, J. G. Gribben, R. Siebert, C. Chelala, R. Zoncu, D. M. Sabatini, J. Fitzgibbon. Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma. Nat Genet. 2016. 48: 183-8.
• 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 (5)

• G. Doose, A. Haake, S. H. Bernhart, C. Lopez, S. Duggimpudi, F. Wojciech, A. K. Bergmann, A. Borkhardt, B. Burkhardt, A. Claviez, L. Dimitrova, S. Haas, J. I. Hoell, M. Hummel, D. Karsch, W. Klapper, K. Kleo, H. Kretzmer, M. Kreuz, R. Kuppers, C. Lawerenz, D. Lenze, M. Loeffler, L. Mantovani-Loffler, P. Moller, G. Ott, J. Richter, M. Rohde, P. Rosenstiel, A. Rosenwald, M. Schilhabel, M. Schneider, I. Scholz, S. Stilgenbauer, H. G. Stunnenberg, M. Szczepanowski, L. Trumper, M. A. Weniger, S. Hoffmann, R. Siebert, I. Iaccarino. MINCR is a MYC-induced lncRNA able to modulate MYC's transcriptional network in Burkitt lymphoma cells. Proc Natl Acad Sci U S A. 2015. 112: E5261-70.
• 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.
• Helene Kretzmer, Stephan H Bernhart, Wei Wang, Andrea Haake, Marc A Weniger, Anke K Bergmann, Matthew J Betts, Enrique Carrillo-de-Santa-Pau, Gero Doose, Jana Gutwein. DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control. Nature genetics. 2015. 47: 1316.
• 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.
• R. Wagener, S. M. Aukema, M. Schlesner, A. Haake, B. Burkhardt, A. Claviez, H. G. Drexler, M. Hummel, M. Kreuz, M. Loeffler, M. Rosolowski, C. Lopez, P. Moller, J. Richter, M. Rohde, M. J. Betts, R. B. Russell, S. H. Bernhart, S. Hoffmann, P. Rosenstiel, M. Schilhabel, M. Szczepanowski, L. Trumper, W. Klapper, R. Siebert. The PCBP1 gene encoding poly(rC) binding protein I is recurrently mutated in Burkitt lymphoma. Genes Chromosomes Cancer. 2015. 54: 555-64.

2013 (4)

• 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.
• 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.

2012 (6)

• Conrad Helm, Stephan H Bernhart, Christian Höner zu Siederdissen, Birgit Nickel, Christoph Bleidorn. Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Molecular phylogenetics and evolution. 2012. 64: 198-203.
• 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.
• R. Lorenz, I. L. Hofacker, S. H. Bernhart. Folding RNA/DNA hybrid duplexes. Bioinformatics. 2012. 28: 2530-1.
• Ronny Lorenz, Ivo L Hofacker, Stephan H Bernhart. Folding RNA/DNA hybrid duplexes. Bioinformatics. 2012. 28: 2530-2531.
• Julia Richter, Matthias Schlesner, Steve Hoffmann, Markus Kreuz, Ellen Leich, Birgit Burkhardt, Maciej Rosolowski, Ole Ammerpohl, Rabea Wagener, Stephan H Bernhart. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nature genetics. 2012. 44: 1316.
• 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.

2011 (6)

• Stephan H Bernhart, Ullrike Mückstein, Ivo L Hofacker. RNA Accessibility in cubic time. Algorithms for Molecular Biology. 2011. 6: 3.
• 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.
• 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.
• 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.
• 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.
• 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.

2008 (3)

• 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.
• 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.
• 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.

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