Kurzprofil Prof. Dr. Ralf Zimmer

Das Portraitfoto zeigt den Kopf von Dr. Ralf Zimmer. Er hat hellbraune Haare und trägt eine Brille mit dunklem Rand.
Foto: privat

Leiter der Sektion III & Leiter der Arbeitsgruppe Network Regulation and Modeling / Machine Learning

Lise-Meitner-Str. 34
85354 Freising
Germany

Tel.: +49 152 0152 3334

E-Mail  ORCID 

Forschungsthema

Die Arbeitsgruppe „Network Regulation & Modeling / Machine Learning“ erforscht und verwendet Methoden der Bioinformatik, der Systembiologie, des maschinellen Lernens und der künstlichen Intelligenz, um auf molekularer Ebene zu verstehen, wie bestimmte Lebensmittelinhaltsstoffe auf Konsumentinnen und Konsumenten wirken.

Wir modellieren biologische Netzwerke und ihre Regulationsmechanismen mittels kausaler Systemmodelle und validieren diese durch In-silico-Simulationen und *omics-Perturbationsexperimente mithilfe von Hochdurchsatz-Sequenzierung und Proteomik. Unser Ziel ist es, Datenbanken aufzubauen, die Lebensmittel über deren molekulare Komponenten mit biochemischen Netzwerken und zellulären Phänotypen verbinden.

Die algorithmische Methodenentwicklung führen wir in Kooperation mit den Münchner Universitäten, die Hochdurchsatzexperimente mit den Kliniken sowie Service Providern der Transkriptomik und Proteomik durch. Die Methoden und die Datenbanken sollen es künftig ermöglichen, in Zusammenarbeit mit Partnern aus der Lebensmittel- und Biotech-Branche innovative Anwendungen zu entwickeln.

 

Berufliche Laufbahn

2001-today Full professor (C4) for Practical Informatics and Bioinformatics at LMU München, Department of Informatics, Faculty of Mathematica, Informatics and Statistics, Ludwig-Maximilians-Universität München
1997 Visiting faculty Biochemistry (Prof. Doug Brutlag)+Statistics (Prof. Sam Karlin), Stanford University, Palo Alto, CA, USA
1995 Visiting scientist (Lab for Mathematical Biology, Prof. Ruth Nussinov), NIH, National Cancer Institute Institute(NCI), Washington, DC, USA
1990-2004 Staff scientist, Project leader, and Group Leader, Institute for Algorithms and Scientific Computing (SCAI), Director: Prof. Thomas Lengauer), Algorithm design and analysis, Bioinformatics algorithms, Systems modeling, Petri nets, Systems Biology, GMD German National Research Center for Information Technology (now: Fraunhofer Society), Schloss Birlinghoven, St. Augustin, Germany
1990-2000 Lecturing positions at CAU Kiel, U. Halle, U. Hildesheim, U. Bonn
1990 Doctorate in Computer Science and Applied Mathematics (summa cum laude, CAU Dissertation Award)
1987-1990 PhD student and research assistant, CAU Kiel and Research Center for Information Technology (GMD), Department of Prof. Petri
1986 Diploma with distinction
1981-1986 Degree in Computer Science, Applied Mathematics and Operations Research at the Friedrich-Wilhelms-University of Bonn
   

Preise und Ehrungen

2013 Representative member of LMU professors in the board of the LMU München
2011 Elected member of the academic senate of the LMU München
2010-2012 Director of the department Informatics of the LMU München
2008-2016 Elected member of the DFG review board ‘foundations of medicine and biology, bioinformatics‘
2001-2008 Director of the DFG center Bioinformatics Munich (BIM)
2000/2001 Offers for full professorships (C4) at several universities (Saarbrücken, Frankfurt, Düsseldorf/FZ Jülich LMU München)
1990 Best dissertation award, CAU Kiel, Germany

Lehrerfahrungen

25 years of teaching bioinformatics/systems biology at LMU and TUM. Responsible for the joint B.Sc. and M.Sc. degree programs in bioinformatics at LMU and TUM Munich since 2001. Founding director of the degree programs within the framework of the 2001-2008 DFG-funded Center for Bioinformatics Munich (BIM) and its subsequent continuation. Graduate education in the Faculty of Mathematics, Informatics and Statistics, in the context of international research training groups (spokesperson of IRTG RECESS) and SFBs (SFB1123 Atherosclerosis), BioSysNet, QBM (Quantitative Biology Munich), Elite Graduate Program Data Science and Munich Center for Machine Learning (MCML).

Regular teaching in the B.Sc. and M.Sc. programs in bioinformatics (LMU/TUM) and computer science (LMU):

  • Winter Term: Bioinformatics Programming [Tutorial],Algorithmic Bioinformatics II [9 ECTS], (Proseminar,) Problem-based Learning II [5 ECTS], Programming course: Practical course Genome oriented Bioinformatics [10 ECTS], (Seminar,) Algorithmic Bioinformatics: Graphs, Networks, and Systems [9 ECTS], Bioinformatics Pearls: ENCODE and the Regulatory Genome [9 ECTS], Bioinformatics Pearls: Reproducibility [9 ECTS], (Individual) Research Bioinformatics practical (Expression analysis, Regulatory networks, Systems Biology) [12 ECTS]
  • Summer Term: Algorithmic Bioinformatics I [9 ECTS], (Proseminar,) Problem-based Learning I [4 ECTS], Practical course Expression and Network Analysis [12 ECTS], (Seminar), Algorithmic Bioinformatics: Computational Systems Biology [9 ECTS], Bioinformatics Pearls: Combinatorial Algorithms [9 ECTS], Practical course (Complex human diseases, Text and Data Mining, Reproducibility) [12 ECTS]

Ausgewählte Publikationen

  1. Pekayvaz K, Losert C, Knottenberg V, Gold C, van Blokland IV, Oelen R, Groot HE, Benjamins JW, Brambs S, Kaiser R, Gottschlich A, Hoffmann GV, Eivers L, Martinez-Navarro A, Bruns N, Stiller S, Akgöl S, Yue K, Polewka V, Escaig R, Joppich M, Janjic A, Popp O, Kobold S, Petzold T, Zimmer R, Enard W, Saar K, Mertins P, Huebner N, van der Harst P, Franke LH, van der Wijst MGP, Massberg S, Heinig M, Nicolai L, Stark K. Multiomic analyses uncover immunological signatures in acute and chronic coronary syndromes. Nat Med. 2024 Jun;30(6):1696-1710. doi: 10.1038/s41591-024-02953-4. Epub 2024 May 21. PMID: 38773340; PMCID: PMC11186793.
  2. Kaiser R, Gold C, Joppich M, …,  Zimmer R, Massberg S, Stark K, Nicolai L, Pekayvaz K. Peripheral priming induces plastic transcriptomic and proteomic responses in circulating neutrophils required for pathogen containment. Sci Adv. 2024 Mar 22;10(12):eadl1710. doi: 10.1126/sciadv.adl1710. Epub 2024 Mar 22. PMID: 38517968.
  3. Weinberger T, Denise M, Joppich M, Fischer M, Garcia Rodriguez C, Kumaraswami K, Wimmler V, Ablinger S, Räuber S, Fang J, Liu L, Liu WH, Winterhalter J, Lichti J, Thomas L, Esfandyari D, Percin G, Matin S, Hidalgo A, Waskow C, Engelhardt S, Todica A, Zimmer R, Pridans C, Gomez Perdiguero E, Schulz C. Resident and recruited macrophages differentially contribute to cardiac healing after myocardial ischemia. Elife. 2024 May 22;12:RP89377. doi: 10.7554/eLife.89377. PMID: 38775664; PMCID: PMC11111219.
  4. Pekayvaz K, Gold C, Hoseinpour P, Engel A, Martinez-Navarro A, Eivers L, Coletti R, Joppich M, Dionísio F, Kaiser R, Tomas L, Janjic A, Knott M, Mehari F, Polewka V, Kirschner M, Boda A, Nicolai L, Schulz H, Titova A, Kilani B, Lorenz M, Fingerle-Rowson G, Bucala R, Enard W, Zimmer R, Weber C, Libby P, Schulz C, Massberg S, Stark K. Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation. Immunity. 2023 Oct 10;56(10):2325-2341.e15. doi: 10.1016/j.immuni.2023.08.002. Epub 2023 Aug 30. PMID: 37652021; PMCID: PMC10588993.
  5. Pekayvaz K, Leunig A, Kaiser R, Joppich M, …, Zimmer R, Mertins P, Hubner N, Hoelscher M, Massberg S, Stark K, Nicolai L. Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection. Nat Commun. 2022 Feb 23;13(1):1018.
  6. Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, Göbel M, Döring K, Menegatti J, Antrobus R, Matheson NJ, Künzig FWH, Mastrobuoni G, Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R, Landthaler M, Grässer F, Lehner PJ, Friedel CC, Erhard F, Dölken L.Integrative functional genomics decodes herpes simplex virus. Nat Commun.2020;11(1):2038.
  7. Ammar C, Gruber M, Csaba G, Zimmer R. MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins. Mol Cell Proteom. 2019;18(9):1880-1892.
  8. Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach  NC, Sieber SA, Haslbeck M, Zimmer R, Buchner  J. The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins. Cell Reports. 2019;29(13):4593-4607.e8.
  9. Erhard F, Halenius A, … Zimmer R, Dölken L. Improved Ribo-seq enables identification of cryptic translation events. Nat Methods. 2018;15(5):363-366. doi:10.1038/nmeth.4631
  10. Berchtold E, Csaba G, Zimmer R. RelExplain-integrating data and networks to explain biological processes. Bioinformatics. 2017 Feb 6. doi: 10.1093/bioinformatics/btx060.
  11. Florian Erhard, Ralf Zimmer, Count ratio model reveals bias affecting NGS fold changes, Nucleic Acids Research 2015 Jul 8. pii: gkv696.
  12. Andrzej J. Rutkowski, Florian Erhard, Anne L'Hernault, Thomas Bonfert, Markus Schilhabel, Colin Crump, Philip Rosenstiel, Stacey Efstathiou, Ralf Zimmer, Caroline C. Friedel, Lars Dölken. Wide-spread disruption of host transcription termination in HSV-1 infection. Nat Commun., vol 6, no. 7126, 2015.
  13. Florian Erhard, Jürgen Haas, …, Mihaela Zavolan, Lars Dölken, Ralf Zimmer. Widespread context-dependency of microRNA-mediated regulation. Genome Research, 2014 Mar 25 2014.
  14. Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel, A context-based approach to identify the most likely mapping for RNA-seq experiments, BMC Bioinformatics, 13(Suppl 6), pp. S9, 2012.