Dr. rer. nat. Stephan Bernhart

Dr. rer. nat. Stephan Bernhart

PROJECT LEADER

Transcriptome Bioinformatics

berni@bioinf.uni-leipzig.de

+49 (0) 341 - 97 16661

Room: 320.5

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

SCIENTIFIC INTERESTS

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

PUBLICATIONS

2020 (2)

  • 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.
  • 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.

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.

MISCELLANEOUS