Institute for Medical Systems Biology (IMSB)

Stefan Bonn

Mission Statement

“Infer differential cell-cell communication patterns, underlying transcriptional and gene regulatory changes to elucidate pathogenic transformations”

— Stefan Bonn, PhD

Team Members

Post Doc

Maksims Fiosins, PhD

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Junior Group Leader

Sonja Hänzelmann, PhD

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PhD Student

Fabian Hausmann

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PhD Student

Robin Khatri

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Post Doc

Yu Zhao, PhD

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Assistant Professor

Marina Zimmermann, PhD

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Focal segmental glomerulosclerosis (FSGS) is a major glomerular cause of end stage renal disease. FSGS represents a pattern of response to injury, subsequent damage and loss of podocytes regardless of the underlying etiology. It is hypothesized that the primary form of FSGS is caused by an unknown circulating factor that leads to disturbed cell-cell-interaction and often to early and devastating recurrence after kidney transplantation. Modeling global communications among cells requires accurate representations of cell-cell signaling links and effective systems-level analyses. With the advent of single cell sequencing (scRNA-seq), it is possible to estimate cell heterogeneity at a high resolution allowing detailed cataloguing of cell types and prediction of cellular differentiation trajectories and communication. The goal of this project is to elucidate the pathologic transformations occurring in (recurrent) FSGS.

Stefan Bonn, PhD

Director of the Institute of Medical Systems Biology
Senior researcher
Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf (UKE)
Falkenried 94
20251 Hamburg, Germany


Current Position
since 2017 Professor and Director of the Institute of Medical Systems Biology at the Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, Germany
Academic qualifications
2008 - 2012- 2020

Postdoctoral Fellow, European Molecular Biology Laboratory (EMBL). Advisors: Eileen Furlong, PhD & Ann-Claude Gavin, PhD

2004 - 2007

PhD Thesis, University of Heidelberg, Max-Planck-Institute for Medical Research (MPI-MR), Heidelberg, Germany. Advisor: Prof. Dr. Peter Seeburg


Master thesis, Universität Bayreuth, Deutsches Krebsforschungszentrum, Heidelberg, Deutschland

Previous professional career

Scientific postgraduate education:

2017 - 2021 Senior researcher, German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
2012 - 2017

Head of the genomic core, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany

2012 - 2017

Independent Research Group Leader, German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany

Selected awards and honors
2018 - 2020

Member of the advisory board of the Center for Biostructural Imaging in Neurodegeneration, Göttingen, Germany


Member of the advisory board of Genevention GmbH


Invitation to the symposium “Sino-German Frontiers of Science” of the Alexander von Humboldt-Society and the Chinese Academy of Sciences

2011 - 2012

DFG Scholarship for postdocs

2008 - 2011

EMBL interdisciplinary postdoctoral fellowship (eIPOD)

2004 - 2012

EMBO and Marie-Curie travel grants for advanced training in bioinformatics

Selected publications


Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Bonn S, Zinzen RP, Girardot C, Gustafson EH, Perez-Gonzalez A, Delhomme N, Ghavi-Helm Y, Wilczyński B, Riddell A, Furlong EE. Nat Genet. 2012;44:148-156.


Oasis: online analysis of small RNA deep sequencing data.
Capece V, Garcia Vizcaino JC, Vidal R, Rahman RU, Pena Centeno T, Shomroni O, Suberviola I, Fischer A, Bonn S. Bioinformatics. 2015;31(13):2205-2207.


DNA methylation changes in plasticity genes accompany the formation and maintenance of memory. .
Halder R, Hennion M, Vidal RO, Shomroni O, Rahman RU, Rajput A, Centeno TP, van Bebber F, Capece V, Garcia Vizcaino JC, Schuetz AL, Burkhardt S, Benito E, Navarro Sala M, Javan SB, Haass C, Schmid B, Fischer A, Bonn S. Nat Neurosci. 2016;19(1):102-110.


TAp73 is a central transcriptional regulator of airway multiciliogenesis.
Nemajerova A, Kramer D, Siller SS, Herr C, Shomroni O, Pena T, Gallinas Suazo C, Glaser K, Wildung M, Steffen H, Sriraman A, Oberle F, Wienken M, Hennion M, Vidal R, Royen B, Alevra M, Schild D, Bals R, Dönitz J, Riedel D, Bonn S, Takemaru K, Moll UM, Lizé M. Genes Dev. 2016;30:1300:1312.


The landscape of human mutually exclusive splicing.
Hatje K, Rahman RU, Vidal RO, Simm D, Hammesfahr B, Bansal V, Rajput A, Mickael ME, Sun T, Kollmar M*, Bonn S*. Mol Syst Biol. 2017;13:959.


OTTO: a new strategy to extract mental disease-relevant combinations of GWAS hits from individuals.
Ehrenreich H, Mitjans M, Van der Auwera S, Centeno TP, Begemann M, Grabe HJ, Bonn S, Nave KA. Mol Psychiatry. 2018;23(2):476-486.


Epigenetic alterations in longevity regulators, reduced life span, and exacerbated aging-related pathology in old father offspring mice.
Xie K, Ryan DP, Pearson BL, Henzel KS, Neff F, Vidal RO, Hennion M, Lehmann I, Schleif M, Schröder S, Adler T, Rathkolb B, Rozman J, Schütz AL, Prehn C, Mickael ME, Weiergräber M, Adamski J, Busch DH, Ehninger G, Matynia A, Jackson WS, Wolf E, Fuchs H, Gailus-Durner V, Bonn S, Hrabě de Angelis M, Ehninger D. Proc Natl Acad Sci U S A. 2018;115(10):E2348-E2357.


Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia.
Bansal V, Mitjans M, Burik CAP, Linnér RK, Okbay A, Rietveld CA, Begemann M, Bonn S, Ripke S, de Vlaming R, Nivard MG, Ehrenreich H, Koellinger PD. Nat Commun. 2018;9(1):3078.


Precisely measured protein lifetimes in the mouse brain reveal differences across tissues and subcellular fractions.
Fornasiero EF, Mandad S, Wildhagen H, Alevra M, Rammner B, Keihani S, Opazo F, Urban I, Ischebeck T, Sakib MS, Fard MK, Kirli K, Centeno TP, Vidal RO, Rahman RU, Benito E, Fischer A, Dennerlein S, Rehling P, Feussner I, Bonn S, Simons M, Urlaub H, Rizzoli SO. Nat Commun. 2018;9:4230.


Targeting myelin lipid metabolism as a potential therapeutic strategy in a model of CMT1A neuropathy.
Fledrich R, Abdelaal T, Rasch L, Bansal V, Schütza V, Brügger B, Lüchtenborg C, Prukop T, Stenzel J, Rahman RU, Hermes D, Ewers D, Möbius W, Ruhwedel T, Katona I, Weis J, Klein D, Martini R, Brück W, Müller WC, Bonn S, Bechmann I, Nave KA, Stassart RM, Sereda MW. Nat Commun. 2018;9(1):3025.



Open Positions

We are looking for highly motivated and ambitious postdocs, PhD students, master students, and student research assistants.

July 9, 2024 | Seminar
Open Positions

We are constantly looking for highly motivated, talented and team-oriented researchers to join our team ...

Martinistraße 52
Campus Research N27
20246 Hamburg Germany
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University Medical Center Hamburg - Eppendorf