• 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
  

2024

• Gene regulation by the tumor suppressor p53 - The omics era.
  Fischer M
  Bba-Rev Cancer 2024, 1879(4), 189111
  
• Genomregulation durch Tumorsuppressoren und Onkoproteine
  Fischer M
  BIOspektrum 2024, 30, 123
  
• Determinants of p53 DNA binding, gene regulation, and cell fate decisions.
  Fischer** * M, Sammons** * MA
  Cell Death Differ 2024 (epub ahead of print) * equal contribution, ** co-corresponding authors
  
• Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells.
  Gutierrez-Diaz A, Hoffmann S, Gallego-Gómez JC, Bermudez-Santana CI
  Front Bioinform 2024, 4, 1293412
  
• Bashing irreproducibility with shournal.
  Kirchner T, Riege K, Hoffmann S
  Sci Rep 2024, 14(1), 4872
  
• Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold-standard
  Lin YY, Breuer K, Weichenhan D, Lafrenz P, Wilk A, Chepeleva M, Mücke O, Schönung M, Petermann F, Kensche P, Weiser L, Thommen F, Giacomelli G, Nordstroem K, Gonzales-Avalos E, Merkel A, Kretzmer H, Fischer J, Krämer S, Iskar M, Wolf S, Buchhalter I, Esteller M, Lawerenz C, Twardziok S, Zapatka M, Hovestadt V, Schlesner M, Schulz M, Hoffmann S, Gerhauser C, Walter J, Hartmann M, B.Lipka D, Assenov Y, Bock C, Plass C, Toth R, Lutsik P
  bioRxiv 2024, https://doi.org/10.1101/2024.09.
  
• Nonlinear DNA methylation trajectories in aging male mice.
  Olecka* M, van Bömmel* A, Best L, Haase M, Foerste S, Riege K, Dost T, Flor S, Witte OW, Franzenburg S, Groth M, von Eyss B, Kaleta C, Frahm C, Hoffmann S
  Nat Commun 2024, 15(1), 3074 * equal contribution
  
• The Greenland shark (Somniosus microcephalus) genome provides insights into extreme longevity
  Sahm A, Cherkasov* A, Liu* H, Voronov D, Siniuk K, Schwarz R, Ohlenschlaeger O, Foerste S, Bens M, Groth M, Goerlich I, Paturej S, Klages S, Braendl B, Olsen J, Bushnell P, Bech Poulsen A, Ferrando S, Garibaldi F, Lorenzo Drago D, Terzibasi Tozzini E, Mueller FJ, Fischer M, Kretzmer H, Domenici** P, Fleng Steffensen** J, Cellerino** A, Hoffmann** S
  bioRxiv 2024, 10.1101/2024.09.09.611499 * equal contribution, ** co-corresponding authors
  
• Circadian clock disruption engages the DREAM complex in suppressing cellular health
  Santos Valentim I, Javier Romero-Expósito F, Schwab K, Bayar M, Riege K, Fischer M, Olmedo M, Hoffmann S, A.Ermolaeva M
  bioRxiv 2024, https://doi.org/10.1101/2024.06.
  
• p53 target ANKRA2 cooperates with RFX7 to regulate tumor suppressor genes.
  Schwab K, Riege K, Coronel L, Stanko C, Förste S, Hoffmann** S, Fischer** M
  Cell Death Discov 2024, 10(1), 376 ** co-corresponding authors