• 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
  

2020

• Pan-cancer analysis of whole genomes.
  Campbell PJ, Getz G, Korbel Jea, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium
  Nature 2020, 578(7793), 82-93
  
• Mice Are Not Humans: The Case of p53.
  Fischer M
  Trends Cancer 2020 (epub ahead of print)
  
• Dichotomous Impact of Myc on rRNA Gene Activation and Silencing in B Cell Lymphomagenesis.
  Joshi* G, Eberhardt* AO, Lange L, Winkler R, Hoffmann S, Kosan C, Bierhoff H
  Cancers (Basel) 2020, 12(10), E3009. doi: 10.3390/cancers12103 * equal contribution
  
• Bashing irreproducibility with shournal
  Kirchner T, Riege K, Hoffmann S
  bioRxiv 2020, https://doi.org/10.1101/2020.08.
  
• Dissecting the DNA binding landscape and gene regulatory network of p63 and p53
  Riege K, Kretzmer H, McDade SS, Hoffmann S, Fischer M
  bioRxiv 2020, doi.org/10.1101/2020.06.11.14554
  
• The HPA stress axis shapes aging rates in long-lived, social mole-rats
  Sahm A, Hoffmann S, Koch P, Henning Y, Bens M, Groth M, Burda H, Begall S, Ting S, Goetz M, Van Daele P, Staniszewska M, Klose J, Fragoso Costa P, Platzer M, Szafranski** K, Dammann** P
  bioRxiv 2020, https://doi.org/10.1101/2020.02. ** co-senior authors
  
• Tumor suppressor p53: from engaging DNA to target gene regulation.
  Sammons*/** MA, Nguyen*/** TAT, McDade*/** SS, Fischer*/** M
  Nucleic Acids Res 2020, 48(16), 8848-69 * equal contribution, ** 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 2020 (epub ahead of print)
  

2019

• Conservation and divergence of the p53 gene regulatory network between mice and humans.
  Fischer M
  Oncogene 2019, 38(21), 4095-109
  
• 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