• 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
  

2025

• Rapid brain tumor classification from sparse epigenomic data.
  Brändl B, Steiger M, Kubelt C, Rohrandt C, Zhu Z, Evers M, Wang G, Schuldt B, Afflerbach AK, Wong D, Lum A, Halldorsson S, Djirackor L, Leske H, Magadeeva S, Smičius R, Quedenau C, Schmidt NO, Schüller U, Vik-Mo EO, Proescholdt M, Riemenschneider MJ, Zadeh G, Ammerpohl O, Yip S, Synowitz M, van Bömmel** A, Kretzmer** H, Müller** FJ
  Nat Med 2025, 31(3), 840-8 ** co-corresponding authors
  
• DNA damage response regulator ATR licenses PINK1-mediated mitophagy.
  Marx* C, Qing* X, Gong* Y, Kirkpatrick J, Siniuk K, Beznoussenko GV, Kidiyoor GR, Kirtay M, Buder K, Koch P, Westermann M, Bruhn C, Brown EJ, Xu X, Foiani M, Wang ZQ
  Nucleic Acids Res 2025, 53(5), gkaf178 * equal contribution
  
• Signatures of Nonlinear Aging: Molecular Stages of Life: Sudden Changes During Aging as Potential Biomarkers for an Age Classification System.
  Olecka** M, Morrison H, Hoffmann** S
  Bioessays 2025 (epub ahead of print) ** co-corresponding authors
  
• Protecting cell cycle integrity: enhanced start-codon stringency in mitosis.
  Omrani O, Siniuk K, Fischer M
  Signal Transduct Target Ther 2025, 10(1), 34
  
• The master male sex determinant Gdf6Y of the turquoise killifish arose through allelic neofunctionalization.
  Richter A, Mörl H, Thielemann M, Kleemann M, Geißen R, Schwarz R, Albertz C, Koch P, Petzold A, Kroll T, Groth M, Hartmann N, Herpin A, Englert C
  Nat Commun 2025, 16(1), 540
  
• Author Correction: Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.
  Vromman M, Anckaert J, Bortoluzzi S, Buratin A, Chen CY, Chu Q, Chuang TJ, Dehghannasiri R, Dieterich C, Dong X, Flicek P, Gaffo E, Gu W, He C, Hoffmann S, Izuogu O, Jackson MS, Jakobi T, Lai EC, Nuytens J, Salzman J, Santibanez-Koref M, Stadler P, Thas O, Vanden Eynde E, Verniers K, Wen G, Westholm J, Yang L, Ye CY, Yigit N, Yuan GH, Zhang J, Zhao F, Vandesompele J, Volders PJ
  Nat Methods 2025 (epub ahead of print)
  
• Gene regulation by convergent promoters.
  Wiechens E, Vigliotti* F, Siniuk* K, Schwarz R, Schwab K, Riege K, van Bömmel A, Görlich I, Bens M, Sahm A, Groth M, Sammons MA, Loewer A, Hoffmann S, Fischer M
  Nat Genet 2025, 57(1), 206-17 * equal contribution
  

2024

• The Aging Synapse: An Integrated Proteomic And Transcriptomic Analysis
  Caterino* C, Ugolini* M, Durso W, Jevdokimenko K, Groth M, Riege K, Görlach M, Fornasiero E, Ori A, Hoffmann S, Cellerino A
  bioRxiv 2024, https://doi.org/10.1101/2024.12. * equal contribution
  
• 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