Institut für Klinische Pathologie

• Spatially resolved metabolomics, lipidomics, proteomics
• Tumor microenvironment and heterogeneity
• Method establishment for mass spectrometry imaging (Quality control, standardization and reproducibility)
• Mass spectrometry data science, open science and open data

• MALDI mass spectrometry imaging (M3+ Sprayer, timsTOF fleX mass spectrometer)
• Organotypic tissue slice cultures
• Computational mass spectrometry tools and workflows (mainly in the Galaxy platform: https://github.com/foellmelanie)

Open positions: Our group welcomes motivated scientists and clinicians to apply for internships, fellowships, as well as for Bachelor's, Master's, and Medical doctoral theses. We have an open position for a laboratory technical assistant and a PhD student: https://www.uniklinik-freiburg.de/karriere/stellenangebote.html.

Alumni:
Thanks to our former group members for their great work.
Nadine Meier, CTA
Ziba Sabet, visiting scientist, Charles University, Prague (CZ)
Jannik Witte, Master thesis
Johanna Thiery, Master thesis
Larissa Meyer, Master thesis

Internal collaborations

• Peter Bronsert (Institute for Surgical Pathology)
• Christoph Schell (Institute for Surgical Pathology)
• Oliver Schilling (Institute for Surgical Pathology)
• Robert Zeiser (Department of Medicine I)
• Bertram Bengsch (Department of Medicine II)
• Maike Hofmann (Department of Medicine II)
• Luciana Hannibal (Department of Pediatrics)
• Stefan Fichtner-Feigl (Department of General and Visceral Surgery)
• Philipp Holzner (Department of General and Visceral Surgery)
• Freiburg Galaxy Team (Department of Computer Science)
• Sebastian Baasch (Institute for Immunodeficiency)
• Henrik Heiland (Department of Neurosurgery)

External collaborations

• Ulrich Wellner, Rüdiger Braun (University of Lübeck)
• Carsten Hopf (Mannheim University of Applied Sciences)
• Jörg Bartsch (Philipps University of Marburg)
• Cläre von Neubeck (University of Duisburg-Essen)
• Pia Hönscheid (Dresden University of Technology)
• Axel Walch (Helmholtz Center Munich)
• Magnus Palmblad (Leiden University, Netherlands)
• Olga Vitek (Northeastern University, Boston, USA)
• Galaxy-P Team (University of Minnesota, USA)

2024:

• Lakkimsetty SS, Weber A, Bemis KA, Stehl V, Bronsert P, Föll MC, Vitek O. MSIreg : an R package for unsupervised coregistration of mass spectrometry and H&E images. Peng H, editor. Bioinformatics. 2024 Nov 1;40(11):btae624. doi: 10.1093/bioinformatics/btae624
• Kurowski K, Timme S, Föll MC, Backhaus C, Holzner PA, Bengsch B, Schilling O, Werner M, Bronsert P. AI-Assisted High-Throughput Tissue Microarray Workflow. Methods Protoc. 2024 Nov 25;7(6):96. doi: 10.3390/mps7060096
• Bretaudeau A, Bromhead C, Burke ML, Capon PK, Čech M, Chavero-Díez M, Chilton JM, Collins TJ, Coppens F, Coraor N, Cuccuru G, Cumbo F, Davis J, De Geest PF, de Koning W, Demko M, DeSanto A, Begines JMD, Doyle MA, DroesbekeB, Erxleben-Eggenhofer A, Föll MC, Formenti G, Fouilloux A, Gangazhe R, Genthon T, Goecks J, Beltran ANG, Goonasekera NA, Goué N, Griffin TJ, Grüning BA, Guerler A, Gundersen S, Gustafsson OJR, Hall C, Harrop TW, Hecht H, Heidari A,Heisner T, Heyl F, Hiltemann S, Hotz H, Hyde CJ, Jagtap PD, Jakiela J, Johnson JE, Joshi J, Jossé M, Jum’ah K, Kalaš M, Kamieniecka K, Kayikcioglu T, Konkol M,Kostrykin L, Kucher N, Kumar A, Kuntz M, Lariviere D, Lazarus R, Le Bras Y, Le Corguillé G, Lee J, Leo S, Liborio L, Libouban R, Tabernero DL, Lopez-Delisle L, Los LS, Mahmoud A, Makunin I, Marin P, Mehta S, Mok W, Moreno PA, Morier-Genoud F, Mosher S, Müller T, Nasr E, Nekrutenko A, Nelson TM, Oba AJ, Ostrovsky A, Polunina PV, Poterlowicz K, Price EJ, Price GR, Rasche H, Raubenolt B, Royaux C, Sargent L, Savage MT, Savchenko V, Savchenko D, Schatz MC, Seguineau P, Serrano-Solano B, Soranzo N, Srikakulam SK, Suderman K, Syme AE, Tangaro MA, Tedds JA, Tekman M, Thang WCM, Thanki AS, Uhl M, van den Beek M, Varshney D, Vessio J, Videm P, Von Kuster G, Watson GR, Whitaker-Allen N, Winter U, Wolstencroft M, Zambelli F, Zierep P, Zoabi R. The Galaxy platform for accessible,reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Res. 2024 Jul 5;52(W1):W83–94. doi: 10.1093/nar/gkae410
• Stillger MN, Li MJ, Hönscheid P, Von Neubeck C, Föll MC. Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma. PROTEOMICS. 2024 Jun;24(12–13):2300001. doi: 10.1002/pmic.202300001

2023:

• Bemis KA*, Föll MC*, Guo D, Lakkimsetty SS, Vitek O. Cardinal v.3: a versatile open-source software for mass spectrometry imaging analysis. Nat Methods. 2023
  Dec;20(12):1883–6. doi: 10.1038/s41592-023-02070-z. *equal contribution
• Mehta S, Bernt M, Chambers M, Fahrner M, Föll MC, Gruening B, Horro C, Johnson JE, Loux V, Rajczewski AT, Schilling O, Vandenbrouck Y, Gustafsson OJR, Thang WCM, Hyde C, Price G, Jagtap PD, Griffin TJ. A Galaxy of informatics resources for MS-based proteomics. Expert Rev Proteomics. 2023 Nov 2;20(11):251–66.
  doi:10.1080/14789450.2023.2265062.
• Cosenza-Contreras M, Schäfer A, Sing J, Cook L, Stillger MN, Chen CY, Hidalgo JV, Pinter N, Meyer L, Werner T, Bug D, Haberl Z, Kübeck O, Zhao K, Stei S, Gafencu AV, Ionita R, Brehar FM, Ferrer-Lozano J, Ribas G, Cerdá-Alberich L, Martí-Bonmatí L, Nimsky C, Van Straaten A, Biniossek ML, Föll M, Cabezas-Wallscheid N, Büscher J, Röst H, Arnoux A, Bartsch JW, Schilling O. Proteometabolomics of initial and recurrent glioblastoma highlights an increased immune cell signature with altered lipid metabolism. Neuro-Oncol. 2023 Oct 26;noad208.
  doi: 10.1093/neuonc/noad208.
• Kocsmár É, Schmid M, Cosenza-Contreras M, Kocsmár I, Föll M, Krey L, Barta BA, Rácz G, Kiss A, Werner M, Schilling O, Lotz G, Bronsert P. Proteome alterations in human autopsy tissues in relation to time after death. Cell Mol Life Sci. 2023 May;80(5):117.
  doi: 10.1007/s00018-023-04754-3.
• Guo D, Föll MC, Bemis KA, Vitek O. A noise-robust deep clustering of biomolecular ions improves interpretability of mass spectrometric images. Bioinformatics. 2023 Feb 3;39(2):btad067.
  doi: 10.1093/bioinformatics/btad067.
• Hiltemann S, Rasche H, Gladman S, Hotz HR, Larivière D, Blankenberg D, Jagtap, PD, Wollmann T, Bretaudeau A, Goué N, Griffin TJ, Royaux C, Le Bras Y, Mehta S, Syme A, Coppens F, Droesbeke B, Soranzo N, Bacon W, Psomopoulos F, Gallardo-Alba C, Davis J, Föll MC, Fahrner M, Doyle MA, Serrano-Solano B, Fouilloux AC, van Heusden P, Maier W, Clements D, Heyl F, Galaxy Training Network, Grüning B, Batut B. Galaxy Training: A powerful framework for teaching!. PLOS Comput Biol. 2023 Jan 9;19(1):e1010752.
  doi: 10.1371/journal.pcbi.1010752.

2022:

• Pinter N, Glätzer D, Fahrner M, Fröhlich K, Johnson J, Grüning BA, Warscheid B, Drepper F, Schilling O, Föll MC. MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone. J Proteome Res. 2022 Jun 3;21(6):1558–65.
  doi: 10.1021/acs.jproteome.2c00051.
• Galaxy community: Ostrovsky AE, Mahmoud A, Lonie AJ, Syme A, Fouilloux A, Bretaudeau A, Nekrutenko A, Kumar A, Eschenlauer AC, DeSanto AD, Guerler A, Serrano-Solano B, Batut B, Grüning BA, Langhorst BW, Carr B, Raubenolt BA, Hyde CJ,  Bromhead CJ, Barnett CB, Royaux C, Gallardo C, Blankenberg D, Fornika DJ, Baker D,  Bouvier D, Clements D, de Lima Morais DA, Lopez Tabernero D, Lariviere D,  Nasr E, Afgan E, Zambelli F, Heyl F, Psomopoulos F, Coppens F, Price GR, Cuccuru G, Le Corguillé G, Von Kuster G, Akbulut GG, Rasche H, Hotz HR, Eguinoa I, Makunin I, Ranawaka IJ, Taylor JP, Joshi J, Hillman-Jackson J, Goecks J, Chilton JM,  Kamali K, Suderman K, Poterlowicz K, Le Bras Y, Lopez-Delisle L, Sargent L, Bassetti ME, Tangaro MA, van den Beek M, Čech M, Bernt M, Fahrner M, Tekman M, Föll MC, Schatz MC, Crusoe MR, Roncoroni M, Kucher N, Coraor N, Stoler N, Rhodes N, Soranzo N, Pinter N, Goonasekera NA, Moreno PA, Videm P, Petera M, Mandreoli P, Jagtap PD, Gu Q, Weber RJM, Lazarus R, Vorderman RHP, Hiltemann S, Golitsynskiy S, Garg S, Bray SA, Gladman SL, Leo S, Mehta SP, Griffin TJ, Jalili V, Vandenbrouck Y, Wen V, Nagampalli VK, Bacon WA, de Koning W, Maier W,  Briggs PJ. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 2022 Apr 21; gkac247.
  doi: 10.1093/nar/gkac247.
• Föll MC, Volkmann V, Enderle-Ammour K, Timme S, Wilhelm K, Guo D, Vitek O, Bronsert P, Schilling O. Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the Galaxy framework. Clin Proteomics. 2022 Dec;19(1):8.
  doi: 10.1186/s12014-022-09347-z.
• Fahrner M, Föll MC, Grüning BA, Bernt M, Röst H, Schilling O. Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework. GigaScience. 2022 Feb 15;11:giac005.
  doi: 10.1093/gigascience/giac005.

2021:

• Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T,  Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaino JA, Bai M, Sachsenberg T, Levitsky L, Perez-Riverol Y. A proteomics sample metadata representation for multiomics integration and big data analysis. Nat Commun. 2021 Dec;12(1):5854.
  doi: 10.1038/s41467-021-26111-3.
• Serrano-Solano B*, Föll MC*, Gallardo-Alba C, Erxleben A, Rasche H, Hiltemann S, Fahrner M, Dunning MJ, Schulz M, Scholtz B, Clements D, Nekrutenko A, Batut B, Grüning B. Fostering accessible online education using Galaxy as an e-learning platform. Palagi PM, editor. PLOS Comput Biol. 2021 May 13;17(5):e1008923.
  doi: 10.1371/journal.pcbi.1008923.
  *equal contribution.

2020:

• Guo D, Föll MC, Volkmann V, Enderle-Ammour K, Bronsert P, Schilling O, Vitek O. Deep multiple instance learning classifies subtissue locations in mass spectrometry images from tissue-level annotations. Bioinformatics. 2020 Jul;36(Supplement_1):i300-8.
  doi: 10.1093/bioinformatics/btaa436.

2019:

• Föll MC, Moritz L, Wollmann T, Stillger MN, Vockert N, Werner M, Bronsert P, Rohr K, Grüning BA, Schilling O. Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. GigaScience. 2019 Dec 1;8(12).
  doi: 10.1093/gigascience/giz143.

2018:

• Oria VO, Bronsert P, Thomsen AR, Föll MC, Zamboglou C, Hannibal L, Behringer S, Biniossek ML, Schreiber C, Grosu AL, Bolm L, Rades D, Keck T, Werner M, Wellner UF, Schilling O. Proteome Profiling of Primary Pancreatic Ductal Adenocarcinomas Undergoing Additive Chemoradiation Link ALDH1A1 to Early Local Recurrence and Chemoradiation Resistance. Transl Oncol. 208 Dec; 11(6):1307-22.
  doi: 10.1016/j.tranon.2018.08.001.
• Föll MC, Fahrner M, Oria VO, Kühs M, Biniossek ML, Werner M, Bronsert P, Schilling O. Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization. Clin Proteomics. 2018 Dec; 15(1):11.
  doi: 10.1186/s12014-018-9188-y.
• Föll MC, Fahrner M, Gretzmeier C, Thoma K, Biniossek ML, Kiritsi D, Meiss F, Schilling O, Nyström A, Kern JS. Identification of tissue damage, extracellular matrix remodeling and bacterial challenge as common mechanisms associated with high-risk cutaneous squamous cell carcinomas. Matrix Biol. 2018 Mar; 66:1-21.
  doi: 10.1016/j.matbio.2017.11.004.
• Müller AK, Föll M, Heckelmann B, Kiefer S, Werner M, Schilling O, Biniossek ML, Jilg CA, Drendel V. Proteomic Characterization of Prostate Cancer to Distinguish Nonmetastasizing and Metastasizing Primary Tumors and Lymph Node Metastases. Neoplasia. 2018;20(2):140-51.
  doi: 10.1016/j.neo.2017.10.009.