Dr. rer. nat. Stephan Bernhart

Dr. rer. nat. Stephan Bernhart
Tel: 0341 - 97 16661
E-Mail: berni@bioinf.uni-leipzig.de
Web: http://hoffmann.bioinf.uni-leipzig.de/LIFE/Berni.html
Room: 320.4
Position: PostDoc
Group: Transcriptome Bioinformatics

Academic Career

Scientific Interests

Publications

2016 (6)

  • 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.
  • 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.
  • 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.
  • 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.
  • S. H. Bernhart, H. Kretzmer, L. M. Holdt, F. Juhling, 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.

2015 (4)

  • 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.
  • 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.
  • 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.
  • 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.

2013 (2)

  • 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.
  • 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 2013. 1-11.

2012 (2)

  • 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.
  • R. Lorenz, I. L. Hofacker, S. H. Bernhart. Folding RNA/DNA hybrid duplexes. Bioinformatics. 2012. 28: 2530-1.

2011 (4)

  • 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.
  • 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.
  • 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.
  • 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.

2008 (3)

  • 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.
  • 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.
  • 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.

Miscellaneous