Kolloquium WiSe 2019/20
Prof. Dr. Stefan Bonn
Universitätsklinikum Hamburg-Eppendorf (UKE)
When: Mo, 02.12.2019, at 17:00 c.t.
Where: Room B-201
Technological development and application of Deep Learning in Biomedicine
This presentation will give an overview of recent technological advancements and their application of AI to biomedical use cases.
It will cover generative models such as GANs and Autoencoders for data generation, cohort simulation, latent space modeling, and conditional de-biasing, In addition, we will talk about semi blind source separation in cell deconvolution and image segmentation and classification in disease scenarios. Finally, an outlook on expert systems in clinical diagnosis, prognosis, and treatment are given while the Center for Biomedical AI at the UKE will be introduced.
Prof. Dr. Stefan Bonn is Director of the Institute of Medical Systems Biology and Full Professor at the University Hospital Hamburg-Eppendorf (UKE), Germany.
He is also Senior researcher at the German Center for Neurodegenerative Diseases
Our institute is specialized in the analysis of biomedical data using computational methods. We have over a decade of experience in developing, applying, and teaching algorithms in the fields of machine learning, statistics, and graph theory. We have published seminal articles in the fields of gene regulation (Nat. Gen. 2012, Nat. Neurosci. 2016), genomics (Mol. Sys. Biol. 2017), and deep learning in single cell sequencing (Bioarchives 2018, Nat. Comm. in revision). We already collaborate strongly with the Huber group, integrating cytokine, scRNA-seq, and clinical data into holistic models of disease, and we personally know the applicant.
2008 – 2011 Post-Doctoral Fellow, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
2012 – 2017 Principal Investigator, NGS Core of the German Center for Neurodegenerative Diseases, Göttingen, Germany
2012 – 2017 Independent Research Group Leader, Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany
Since 2017 Director of the Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Clinic Hamburg-Eppendorf, Germany
Since 2017 Senior Researcher, German Center for Neurodegenerative Diseases, Tübingen, Germany
Awards and Honors
2008 – 2011 EMBL Interdisciplinary Postdoctoral Fellowship (EIPOD)
2011 Postdoctoral Fellowship (DFG)
Since 2014 Founder of Nanotag Biosciences GmbH, Göttingen, Germany
Since 2017 Founder and shareholder of Genevention GmbH, Göttingen, Germany
Some thematic publications (last two years)
Realistic in silico generation and augmentation of single cell RNA-seq data using Generative Adversarial Neural Networks. Machart P, Marouf M, Magruder DS, Bansal V, Kilian C, Krebs CF, Bonn S, bioRxiv, 390153
Genome-wide association study results for educational attainment aid in identifying genetic heterogeneity of schizophrenia. Bansal V, Mitjans M, Burik CAP, Linner RK, Okbay A, Rietveld CA, Begemann M, Bonn S, Ripke S, de Vlaming R, Nivard MG, Ehrenreich H, Koellinger PD. Nat Comm. Accepted
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 Dec 14;13(12):959.
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 Jan;19(1):102-10.
List of active research funding
- KFO 296/P8 (German Research Foundation):
Diet during pregnancy and maternal obesity (2018 – 2022) ca. 150.000 €
- SFB 1286/Z2 (German Research Foundation):
The synaptic integrative data strategy (2017 – 2021) ca. 700.000 €
- BMBF IDSN (German Ministry for Education and Science):
The integrative data strategy in neurodegeneration (2016 – 2019) ca. 500.000 €
- iMed (Helmholtz Association):
Analysis of infectious diseases (2016 – 2019) ca. 120.000 €
- BO4221 (German Research Foundation):
Cell type-specific gene-regulatory network of learning (2014 – 2018) ca. 500.000 €
Prof. Dr. Frank Steinicke