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Hoffmann Research Group

Selected Publications

  • metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.
    Jühling F, Kretzmer H, Bernhart SH, Otto C, Stadler PF, Hoffmann S
    Genome Res 2016, 26(2), 256-62
  • Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer.
    Bernhart SH, Kretzmer H, Holdt LM, Jühling F, Ammerpohl O, Bergmann AK, Northoff BH, Doose G, Siebert R, Stadler PF, Hoffmann S
    Sci Rep 2016, 6, 37393
  • Fast mapping of short sequences with mismatches, insertions and deletions using index structures.
    Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J
    PLoS Comput Biol 2009, 5(9), e1000502
  • DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.
    Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S
    Nucleic Acids Res 2011, 39(Web Server issue), W112-7
  • The primary transcriptome of the major human pathogen Helicobacter pylori.
    Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J
    Nature 2010, 464(7286), 250-5
  • DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control.
    Kretzmer H, Bernhart SH, Wang W, Haake A, Weniger MA, Bergmann AK, Betts MJ, Carrillo-de-Santa-Pau E, Doose G, Gutwein J, Richter J, Hovestadt V, Huang B, Rico D, Jühling F, Kolarova J, Lu Q, Otto C, Wagener R, Arnolds J, Burkhardt B, Claviez A, Drexler HG, Eberth S, Eils R, Flicek P, Haas S, Humme M, Karsch D, Kerstens HHD, Klapper W, Kreuz M, Lawerenz C, Lenzek D, Loeffler M, López C, MacLeod RAF, Martens JHA, Kulis M, Martín-Subero JI, Möller P, Nage I, Picelli S, Vater I, Rohde M, Rosenstiel P, Rosolowski M, Russell RB, Schilhabel M, Schlesner M, Stadler PF, Szczepanowski M, Trümper L, Stunnenberg HG, Küppers R, Ammerpohl O, Lichter P, Siebert R, Hoffmann S, Radlwimmer B
    Nat Genet 2015, 47(11), 1316-25
  • Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing.
    Richter J, Schlesner M, Hoffmann S, Kreuz M, Leich E, Burkhardt B, Rosolowski M, Ammerpohl O, Wagener R, Bernhart SH, Lenze D, Szczepanowski M, Paulsen M, Lipinski S, Russell RB, Adam-Klages S, Apic G, Claviez A, Hasenclever D, Hovestadt V, Hornig N, Korbel JO, Kube D, Langenberger D, Lawerenz C, Lisfeld J, Meyer K, Picelli S, Pischimarov J, Radlwimmer B, Rausch T, Rohde M, Schilhabel M, Scholtysik R, Spang R, Trautmann H, Zenz T, Borkhardt A, Drexler HG, Möller P, MacLeod RAF, Pott C, Schreiber S, Trümper L, Loeffler M, Stadler PF, Lichter P, Eils R, Küppers R, Hummel M, Klapper W, Rosenstiel P, Rosenwald A, Brors B, Siebert R, ICGC MMML-Seq Project
    Nat Genet 2012, 44(12), 1316-20
  • A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection.
    Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt LM, Teupser D, Hackermüller J, Stadler PF
    Genome Biol 2014, 15(2), R34
  • Fast and sensitive mapping of bisulfite-treated sequencing data.
    Otto C, Stadler PF, Hoffmann S
    Bioinformatics 2012, 28(13), 1698-704

Publications at FLI

2019

  • Conservation and divergence of the p53 gene regulatory network between mice and humans.
    Fischer M
    Oncogene 2019 (epub ahead of print)
  • Genomic and transcriptomic changes complement each other in the pathogenesis of sporadic Burkitt lymphoma.
    López C, Kleinheinz K, Aukema SM, Rohde M, Bernhart SH, Hübschmann D, Wagener R, Toprak UH, Raimondi F, Kreuz M, Waszak SM, Huang Z, Sieverling L, Paramasivam N, Seufert J, Sungalee S, Russell RB, Bausinger J, Kretzmer H, Ammerpohl O, Bergmann AK, Binder H, Borkhardt A, Brors B, Claviez A, Doose G, Feuerbach L, Haake A, Hansmann ML, Hoell J, Hummel M, Korbel JO, Lawerenz C, Lenze D, Radlwimmer B, Richter J, Rosenstiel P, Rosenwald A, Schilhabel MB, Stein H, Stilgenbauer S, Stadler PF, Szczepanowski M, Weniger MA, Zapatka M, Eils R, Lichter P, Loeffler M, Möller P, Trümper L, Klapper W, ICGC MMML-Seq Consortium, Hoffmann S, Küppers R, Burkhardt B, Schlesner M, Siebert R
    Nat Commun 2019, 10(1), 1459

2018

  • DIEGO: Detection of Differential Alternative Splicing using Aitchison's Geometry.
    Doose G, Bernhart SH, Wagener R, Hoffmann S
    Bioinformatics 2018, 34(6), 1066-8
  • RBFOX2 and alternative splicing in B-cell lymphoma.
    Quentmeier H, Pommerenke C, Bernhart SH, Dirks WG, Hauer V, Hoffmann S, Nagel S, Siebert R, Uphoff CC, Zaborski M, Drexler HG, ICGC MMML-Seq Consortium
    Blood Cancer J 2018, 8(8), 77
  • Higher gene expression stability during aging in long-lived giant mole-rats than in short-lived rats.
    Sahm A, Bens M, Henning Y, Vole C, Groth M, Schwab M, Hoffmann S, Platzer* M, Szafranski* K, Dammann* P
    Aging (Albany NY) 2018, 10(12), 3938-56 * equal contribution