• 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
  

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
  
• 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
  
• 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
  bioRxiv 2021
  
• 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
  
• Alternative Animal Models of Aging Research
  Holtze S, Gorshkova E, Braude S, Cellerino A, Dammann P, Hildebrandt TB, Hoeflich A, Hoffmann S, Koch P, Terzibasi Tozzini E, Skulachev M, Skulachev VP, Sahm A
  Front Mol Biosci 2021, 8, doi: 10.3389/fmolb.2021.660959.
  
• Mutational mechanisms shaping the coding and noncoding genome of germinal center derived B-cell lymphomas.
  Hübschmann D, Kleinheinz K, Wagener R, Bernhart SH, López C, Toprak UH, Sungalee S, Ishaque N, Kretzmer H, Kreuz M, Waszak SM, Paramasivam N, Ammerpohl O, Aukema SM, Beekman R, Bergmann AK, Bieg M, Binder H, Borkhardt A, Borst C, Brors B, Bruns P, Carrillo de Santa Pau E, Claviez A, Doose G, Haake A, Karsch D, Haas S, Hansmann ML, Hoell JI, Hovestadt V, Huang B, Hummel M, Jäger-Schmidt C, Kerssemakers JNA, Korbel JO, Kube D, Lawerenz C, Lenze D, Martens JHA, Ott G, Radlwimmer B, Reisinger E, Richter J, Rico D, Rosenstiel P, Rosenwald A, Schillhabel M, Stilgenbauer S, Stadler PF, Martín-Subero JI, Szczepanowski M, Warsow G, Weniger MA, Zapatka M, Valencia A, Stunnenberg HG, Lichter P, Möller P, Loeffler M, Eils R, Klapper W, Hoffmann S, Trümper L, ICGC MMML-Seq consortium, ICGC DE-Mining consortium, BLUEPRINT consortium, Küppers R, Schlesner M, Siebert R
  Leukemia 2021 (epub ahead of print) published during change of institution
  
• Increased longevity due to sexual activity in mole-rats is associated with transcriptional changes in HPA stress axis.
  Sahm* A, Platzer M, Koch P, Henning Y, Bens M, Groth M, Burda H, Begall S, Ting S, Goetz M, Van Daele P, Staniszewska M, Klose J, Costa PF, Hoffmann** S, Szafranski** K, Dammann** P
  Elife 2021, 10, e57843 ** co-senior authors, * corresponding author
  
• The analysis of epigenomic evolution
  Sahm** A, Koch P, Horvath S, Hoffmann** S
  bioRxiv 2021 ** co-corresponding authors
  
• Loss of hepatic Mboat7 leads to liver fibrosis.
  Thangapandi VR, Knittelfelder O, Brosch M, Patsenker E, Vvedenskaya O, Buch S, Hinz S, Hendricks A, Nati M, Herrmann A, Rekhade DR, Berg T, Matz-Soja M, Huse K, Klipp E, Pauling JK, Wodke JA, Miranda Ackerman J, Bonin Mv, Aigner E, Datz C, von Schönfels W, Nehring S, Zeissig S, Röcken C, Dahl A, Chavakis T, Stickel F, Shevchenko A, Schafmayer C, Hampe J, Subramanian P
  Gut 2021, 70(5), 940-50