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 imaging/Mass spectrometry imaging
• Computational mass spectrometry tools and workflows (mainly in the Galaxy platform: https://github.com/foellmelanie)

Open positions: Our group welcomes motivated scientists and clinicians. We currently have projects available for Bachelor, Master and Doctoral Medical Students. 

• Peter Bronsert Lab, Institute for Surgical Pathology, Medical Center, University of Freiburg
• Oliver Schilling Lab, Institute for Surgical Pathology, Medical Center, University of Freiburg
• Luciana Hannibal Lab, Department of Pediatrics, Medical Center, University of Freiburg
• Freiburg Galaxy Team, Department of Computer Science, University of Freiburg
• Karl Rohr Lab, Biomedical Computer Vision Group, BioQuant, Institute of Pharmacy and Molecular Biotechnology, Heidelberg University
• Olga Vitek Lab, Khoury College of Computer Sciences, Northeastern University, Boston, USA
• Galaxy-P Team, Department of Biochemistry, University of Minnesota, Minneapolis, USA

• MALDISTAR project, Center for Mass Spectrometry and Optical Spectroscopy, Mannheim University of Applied Sciences & Center for Industrial Mathematics, University of Bremen

2022:

• 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.