Herring CA, Simmons RK, Freytag S, Poppe D, Moffet JJD, Pflueger J, Buckberry S, Vargas-Landin DB, Clément O, Echeverría EG, Sutton GJ, Alvarez-Franco A, Hou R, Pflueger C, McDonald K, Polo JM, Forrest ARR, Nowak AK, Voineagu I, Martelotto L, Lister R. Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution. Cell. 2022;185(23):10.1016/j.cell.2022.09.039
Freytag S, Lister R. schex avoids overplotting for large single-cell RNA-sequencing datasets. Bioinformatics. 2020;36(7):10.1093/bioinformatics/btz907
Freytag S, Tian L, Lönnstedt I, Ng M, Bahlo M. Comparison of clustering tools in R for medium-sized 10x Genomics single-cell RNA-sequencing data. F1000Research. 2018;7:10.12688/f1000research.15809.1
Freytag S, Burgess R, Oliver KL, Bahlo M. brain-coX: investigating and visualising gene co-expression in seven human brain transcriptomic datasets. Genome Medicine. 2017;9(1):10.1186/s13073-017-0444-y
Causer A, Lu T, Kriel J, Moffet JJD, Fitzgerald CCJ, Newman A, Vu H, Tan X, Vo T, Cui C, Narayana VK, Whittle JR, Best SA, Freytag S, Nguyen Q. SpaMTP: integrative statistical analysis and visualization of spatial metabolomics and transcriptomics data. Nature Methods. 2026;23(8):10.1038/s41592-026-03140-8
Pandya T, Zagorulya M, Leung MM, Augustine M, Liu LY, Leppä A-M, Baruchel U, Ng SW, Klockner T, Mugabo M, Griffen AJ, Blyuss O, Iliakis CS, Grenov A, Haase K, Muller DC, Chan KH, Wu J, Burk VA, Wright N, Le Marois A, Pazukhina E, Ward S, Slawinski H, Pelletier M, Murphy C, Park MD, Snoeks T, Suarez-Bonnet A, Priestnall SL, Hardas A, Grieco C, Archer A, Celik A, Jimenez-Sanchez A, Scott R, Zahed H, Montégut L, Meza R, Durney CH, Lam S, Karasaki T, Vermeulen RCH, Xu H, Serrano-Fernandez P, Crnogorac-Jurcevic T, Menon U, Apostolidou S, Zaikin A, Gunu R, Whitwell HJ, Huang Z, Li Z, Hu X, Zhu B, Li L, Chirlaque M-D, Guevara M, Kolijn PM, Guenoun A, Mookherjee N, Johansson M, Wang Z, Chatterjee N, Chiu C-H, Chen Z, Pe’er D, Sahai E, Freytag S, Wack A, Gunter MJ, Merad M, Zhang J, Carlsten C, Yang P-C, Chen H-Y, Platz EA, LaFave LM, Smith-Byrne K, Jamal-Hanjani M, Litchfield K, Nene NR, McGranahan N, Grönroos E, Hill W, Weeden CE, Swanton C. Plasma signals of lung tumor promotion for molecular cancer prevention. Cell. 2026;189(13):10.1016/j.cell.2026.05.005
Vo T, Savary C, Jackson ER, Douglas AM, Murdoch HJ, Jayaraman R, Bessler N, Persson ML, McEwen H, McLachlan T, Duchatel RJ, Petraello B, Agnihotri S, Anastas J, Baker SJ, Becher OJ, Castel D, Chavez L, Koldobskiy MA, Deogharkar A, Mota M, Dirks PB, Doherty R, de la Nava D, Duncan B, du Chatinier A, Galban S, Marques JG, Hanson CM, Hara T, Herrington C, Ji S, Jones C, Kleinman CL, Krug B, Lin FY, Lu QR, Messinger D, Mody RJ, Mukherji D, Parthasarathy A, Peterson E, Phoenix TN, Pichumani K, Prensner JR, Ramakrishna S, Ramsoomair CK, Sajjakulnukit P, Sarmashghi S, Syed S, Tamplin OJ, Trout M, Freytag S, Valvo VM, Wahl DR, Al-Holou WN, Wechsler-Reya RJ, Koschmann C, Venneti S, Filbin MG, Dun MD. Cutting through complexity: Spatial multi-omics in the fight against diffuse intrinsic pontine glioma/diffuse midline glioma. Neuro-Oncology Pediatrics. 2026;2(3):10.1093/neuped/wuag036
Kriel J, Moffet JJD, Lu T, Fatunla OE, Narayana VK, Valkovic A, Maluenda A, McConville MJ, Tsui E, Whittle JR, Best SA, Freytag S. An integrative spatial multi-omic workflow for unified analysis of tumor tissue. Cell Reports Methods. 2026;6(2):10.1016/j.crmeth.2026.101306
Moore Z, Storey C, Brown DV, Valkovic A, Spiteri M, Pignatelli JF, Oliver SJ, Fakhri A, Drummond KJ, Hart J, Harris L, Malinowski S, Ligon KL, Sieber OM, Whittle JR, Freytag S, Best SA. Patient-derived organoids and neurospheres recapitulate salient features of primary tumor heterogeneity. Neuro-Oncology Advances. 2026;8(1):10.1093/noajnl/vdaf247
Oppel E, Weber FV, Kendziora B, Weiss BG, Wiggenhauser PS, Ihler F, Bertlich M, Aszodi-Pump N, Spiegel JL, French LE, Freytag S, Bertlich M. Species-specific outcomes in wasp sting challenges during venom immunotherapy and their respective follow-up. Allergologie select. 2026;10(01):10.5414/alx02653e
