Dr. med., Dr. rer. nat. Steve Hoffmann

Dr. med., Dr. rer. nat. Steve Hoffmann
Tel: 0341 - 97 16711
E-Mail: steve@bioinf.uni-leipzig.de
Web: http://hoffmann.bioinf.uni-leipzig.de/LIFE/Home.html
Room: 320.5
Position: Project Leader
Group: Transcriptome Bioinformatics

Academic Career

Scientific Interests

Publications

2016 (4)

  • 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 (5)

  • 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.
  • S. Hoffmann, P. F. Stadler, K. Strimmer. A simple data-adaptive probabilistic variant calling model. Algorithms Mol Biol. 2015. 10: 10.
  • 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.

2014 (5)

  • 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.
  • 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.
  • M. Löffler, M. Kreuz, A. Haake, D. Hasenclever, H. Trautmann, C. Arnold, K. Winter, K. Koch, W. Klapper, R. Scholtysik, M. Rosolowski, S. Hoffmann, O. Ammerpohl, M. Szczepanowski, D. Herrmann, R. Kuppers, C. Pott, R. Siebert. Genomic and epigenomic co-evolution in follicular lymphomas. Leukemia. 2014.
  • 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.

2013 (3)

  • 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.
  • 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.
  • 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.

2012 (4)

  • 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.
  • 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. Otto, P. F. Stadler, S. Hoffmann. Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics. 2012. 28: 1698-704.
  • 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.

2011 (8)

  • 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.
  • 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.
  • 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.
  • S. Hoffmann. Computational analysis of high throughput sequencing data. Methods Mol Biol. 2011. 719: 199-217.
  • M. Hoffmann, J. P. Kuska, M. Zscharnack, M. Löffler, J. Galle. Spatial organization of mesenchymal stem cells in vitro--results from a new individual cell-based model with podia. PLoS One. 2011. 6: e21960.
  • 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.
  • 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.
  • D. Buck, S. Cepok, S. Hoffmann, V. Grummel, A. Jochim, A. Berthele, H. P. Hartung, R. Wassmuth, B. Hemmer. Influence of the HLA-DRB1 genotype on antibody development to interferon beta in multiple sclerosis. Arch Neurol. 2011. 68: 480-7.

2010 (4)

  • 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.
  • 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 2010. 80-7.
  • A. Krinner, M. Hoffmann, M. Löffler, D. Drasdo, J. Galle. Individual fates of mesenchymal stem cells in vitro. BMC Syst Biol. 2010. 4: 73.
  • 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:

2009 (8)

  • 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.
  • H. Schmidt, H. Taubert, H. Lange, K. Kriese, W. D. Schmitt, S. Hoffmann, F. Bartel, S. Hauptmann. Small polydispersed circular DNA contains strains of mobile genetic elements and occurs more frequently in permanent cell lines of malignant tumors than in normal lymphocytes. Oncol Rep. 2009. 22: 393-400.
  • 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.
  • 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.
  • 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.
  • J. Erlecke, I. Hartmann, M. Hoffmann, T. Kroll, H. Starke, A. Heller, A. Gloria, H. G. Sayer, T. Johannes, U. Claussen, T. Liehr, I. F. Loncarevic. Automated detection of residual cells after sex-mismatched stem-cell transplantation - evidence for presence of disease-marker negative residual cells. Mol Cytogenet. 2009. 2: 12.
  • J. Galle, M. Hoffmann, G. Aust. From single cells to tissue architecture-a bottom-up approach to modelling the spatio-temporal organisation of complex multi-cellular systems. J Math Biol. 2009. 58: 261-283.
  • S. Cepok, H. Schreiber, S. Hoffmann, D. Zhou, O. Neuhaus, G. von Geldern, S. Hochgesand, S. Nessler, V. Rothhammer, M. Lang, H. P. Hartung, B. Hemmer. Enhancement of Chemokine Expression by Interferon Beta Therapy in Patients With Multiple Sclerosis. Arch Neurol. 2009.

2008 (2)

  • 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.
  • M. Hoffmann, H. H. Chang, S. Huang, D. E. Ingber, M. Löffler, J. Galle. Noise-driven stem cell and progenitor population dynamics. PLoS One. 2008. 3: e2922.

Miscellaneous