Publications at FLI

2023

• Crafting figures to describe cellular processes.
  Kmiecik** SW, Shi** Q, Chen** YG, Moormann** J, Hildebrandt** TM, Schade** A, Fischer** M, Kim** KQ
  Trends Biochem Sci 2023, 48(6), 491-4 ** co-corresponding authors
  
• Focal structural variants revealed by whole genome sequencing disrupt the histone demethylase KDM4C in B cell lymphomas.
  Lopez C, Schleussner N, Bernhart SH, Kleinheinz K, Sungalee S, Sczakiel HL, Kretzmer H, Toprak UH, Glaser S, Wagener R, Ammerpohl O, Bens S, Giefing M, Sanchez JCG, Apic G, Hubschmann D, Janz M, Kreuz M, Mottok A, Muller JM, Seufert J, Hoffmann S, Korbel JO, Russell RB, Schule R, Trumper L, Klapper W, Radlwimmer B, Lichter P, Kuppers R, Schlesner M, Mathas S, Siebert R
  Haematologica 2023, 108(2), 543-54
  
• Age-Associated Changes in Endothelial Transcriptome and Epigenetic Landscapes Correlate With Elevated Risk of Cerebral Microbleeds.
  Mohan K, Gasparoni G, Salhab A, Orlich MM, Geffers R, Hoffmann S, Adams RH, Walter J, Nordheim A
  J Am Heart Assoc 2023, 12(17), e031044
  
• The Tgf-β family member Gdf6Y determines the male sex in Nothobranchius furzeri by suppressing oogenesis-inducing genes
  Richter A, Mörl H, Thielemann M, Kleemann M, Geißen R, Schwarz R, Albertz C, Koch P, Petzold A, Groth M, Hartmann N, Herpin A, Englert C
  bioRxiv 2023, 10.1101/2023.05.26.542338
  
• Multi-omics analysis identifies RFX7 targets involved in tumor suppression and neuronal processes.
  Schwab K, Coronel L, Riege K, Sacramento EK, Rahnis N, Häckes D, Cirri E, Groth M, Hoffmann S, Fischer M
  CELL DEATH DISCOV 2023, 9(1), 80
  
• 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 2023, 20(8), 1159-69
  
• Leveraging quantum computing for dynamic analyses of logical networks in systems biology.
  Weidner FM, Schwab JD, Wölk S, Rupprecht F, Ikonomi N, Werle SD, Hoffmann S, Kühl M, Kestler HA
  PATTERNS 2023, 4(3), 100705
  

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, 41(7), 1063-9 * equal contribution, ** co-corresponding authors
  
• Synthesizing genome regulation data with vote-counting.
  Fischer M, Hoffmann S
  Trends Genet 2022, 38(12), 1208-16
  
• Coordinating gene expression during the cell cycle.
  Fischer M, Schade AE, Branigan TB, Müller GA, DeCaprio JA
  Trends Biochem Sci 2022, 47(12), 1009-22