Forschungsgruppe Hoffmann

Ausgewählte Publikationen

  • 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

Publikationen am FLI

2022

  • p53-mediated AKT and mTOR inhibition requires RFX7 and DDIT4 and depends on nutrient abundance.
    Coronel* L, Häckes* D, Schwab* K, Riege K, Hoffmann** S, Fischer** M
    Oncogene 2022 (epub ahead of print) * equal contribution, ** co-corresponding authors
  • Locus-specific expression analysis of transposable elements.
    Schwarz R, Koch P, Wilbrandt* J, Hoffmann* S
    Brief Bioinform 2022 (epub ahead of print)

2021

  • Life expectancy, family constellation and stress in giant mole-rats ( Fukomys mechowii).
    Begall S, Nappe R, Hohrenk L, Schmidt TC, Burda H, Sahm A, Szafranski K, Dammann P, Henning Y
    Philos Trans R Soc Lond B Biol Sci 2021, 376(1823), 20200207
  • Favorable outcome of NUTM1-rearranged infant and pediatric B cell precursor acute lymphoblastic leukemia in a collaborative international study.
    Boer JM, Valsecchi MG, Hormann FM, Antić Ž, Zaliova M, Schwab C, Cazzaniga G, Arfeuille C, Cavé H, Attarbaschi A, Strehl S, Escherich G, Imamura T, Ohki K, Grüber TA, Sutton R, Pastorczak A, Lammens T, Lambert F, Li CK, Carrillo de Santa Pau E, Hoffmann S, Möricke A, Harrison CJ, Den Boer ML, De Lorenzo P, Stam RW, Bergmann AK, Pieters R
    Leukemia 2021, 35(10), 2978-82
  • Surprisingly long survival of premature conclusions about naked mole-rat biology.
    Braude S, Holtze S, Begall S, Brenmoehl J, Burda H, Dammann P, Del Marmol D, Gorshkova E, Henning Y, Hoeflich A, Höhn A, Jung T, Hamo D, Sahm A, Shebzukhov Y, Šumbera R, Miwa S, Vyssokikh MY, von Zglinicki T, Averina O, Hildebrandt TB
    Biol Rev Camb Philos Soc 2021, 96(2), 376-93
  • Epigenetic Modifications Associated with Maternal Anxiety during Pregnancy and Children's Behavioral Measures.
    Cao-Lei L, van den Heuvel MI, Huse K, Platzer M, Elgbeili G, Braeken MAKA, Otte RA, Witte OW, Schwab M, Van den Bergh BRH
    Cells 2021, 10(9)
  • Transcription factor RFX7 governs a tumor suppressor network in response to p53 and stress.
    Coronel L, Riege K, Schwab K, Förste S, Häckes D, Semerau L, Bernhart SH, Siebert R, Hoffmann** S, Fischer** M
    Nucleic Acids Res 2021, 49(13), 7437-56 ** co-corresponding authors
  • Abundance and size of hyaluronan in naked mole-rat tissues and plasma.
    Del Marmol D, Holtze S, Kichler N, Sahm A, Bihin B, Bourguignon V, Dogné S, Szafranski K, Hildebrandt TB, Flamion B
    Sci Rep 2021, 11(1), 7951
  • Mice Are Not Humans: The Case of p53.
    Fischer M
    Trends Cancer 2021, 7(1), 12-4
  • TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation
    Fischer M, Riege K, Schwarz R, DeCaprio JA, Hoffman S
    bioRxiv 2021, https://doi.org/10.1101/2021.12.