Applications from highly motivated undergraduates (medicine, natural sciences, bioinformatics...) that like to do a bachelor/master/ medical doctoral thesis work or be student helpers are always welcome.
Concerning PhD or post-doc positions, please ask to discuss the current possibilities in the lab.
Please note that we currently cannot accept student apprentices.
Contact of the Research Group of Prof. Dr. Julia Neumann
Congratulations to Yannis who published his recent work in Brain Pathology! How might artificial intelligence help in diagnostic neuropathology? Using explainable AI, we asked whether deep neural networks can predict the molecular subtype of spinal cord ependymomas based on hematoxylin and eosin stained whole‐slide images. We further aimed to prospectively improve the consistency of histology-based diagnoses with molecular classification (DNA methylation profiling) by identifying and quantifying distinct morphological patterns of these molecular ependymoma types. Our approach may serve as a supplementary resource for integrated diagnostics and may even help to establish a standardized, high-quality level of histology-based diagnostics across institutions. Read the full article in our open access publication: http://doi.org/10.1111/bpa.13239
Congratulations to Matthias who published his recent work in Neuro-Oncology! We used a multi-omics approach (integrating DNA methylation, RNA expression and proteome data) with the aim to further understand the pathophysiology of so called embryonal tumors with multilayered rosettes (ETMR). These brain tumors are rare but deadly and affect small children. Therefore, novel therapeutic approaches are desperately needed. We show that these tumors display a unique proteome profile that associates with histomorphology. Moreover, we could reveal that ETMR harbor proteasome regulatory proteins in abundancy, implicating their strong dependency on the proteasome machinery to safeguard proteostasis. Of note, ETMR tumor cells were highly vulnerable towards treatment with the proteasome inhibitor Marizomib. Hence, proteasome inhibition might be a new promising therapeutic option in ETMR. Read the full article in our open access publication: https://academic.oup.com/neuro-oncology/advance-article/doi/10.1093/neuonc/noad265/7503967<https://academic.oup.com/neuro-oncology/advance-article/doi/10.1093/neuonc/noad265/7503967#google_vignette>
Very honored for being awarded with the Werner Otto Award for Basic Research related to our work on proteomics in brain tumors (with focus on medulloblastoma, https://www.nature.com/articles/s41467-022-31007-x , https://www.biorxiv.org/content/10.1101/2023.01.09.523234v1 ). ). It was a real honor and a pleasure to meet and discuss with Prof. Otto and the colleagues from the advisory board of the Werner Otto Foundation ( https://www.werner-otto-stiftung.de/ ). Thanks to my great team , without yo our achievements would not be possible! And many thanks to the Werner Otto Foundation for supporting research! https://www.werner-otto-stiftung.de/foerderung-von-forschung/preis-der-werner-otto-stiftung/#preistraeger
Congratulations to Nigar Mammadova for being awarded with a Werner Otto stipend for her planned MD thesis work. Nigar will analyse the role of LIN28A in malignant brain tumors. Thank you to the Werner Otto Foundation ( https://www.werner-otto-stiftung.de ) for supporting the next generation of clinician scientists!
Congratulations to Piotr Sumislawski for being awarded with the Hans Sautter-Promotionspreis for his doctoral thesis in the field of ophthalmology! He was one of my first MD students (proud doctoral supervisor speaking :)). The award ceremony took place today at the Erika-Haus. Thanks so much to the Förderkreis des UKE for this great event and for honoring the work of young scientists ( https://www.uke.de/allgemein/ueber-uns/freundes-und-foerderkreis/index.html )!
Ever wondered about the sleeping beauty problem, if life is a simulation or what cyborg cockroaches might be useful for? We learned about these things and more at today's science slam at our christmas get together. Thanks to my fantastic team for this great year we could spend and work together! I am looking forward to 2024!
Congratulations to Jelena for publishing as first author in Analytical Chemistry! Her work focused on spatial proteomics in the developing mouse brain using nanosecond infrared laser ablation (NIRL).
Big thanks to Jan Hahn and Manuela Moritz for the great collaborative work! Check it out at https://pubs.acs.org/doi/10.1021/acs.analchem.3c02637
We attended the international congress of neuropathology in Berlin (ICN2023, https://icn2023.de/ ) and enjoyed connecting to neuropathologists all over the world. Congratulations also to Jelena Navolic from our goup who was awarded with a poster prize for her work studying disordered brain migration in vivo! Well done, dear Jelena!
Summer get together enjoying the beauty of Hamburg. It was great to canoe in Hamburg's canals with the best team!
Great job Shweta! Shweta Godbole presented our work on proteomics in medulloblastoma at the SnoPed2023 conference. Many thanks also to the Kind Philipp Foundation ( https://www.deutsches-stiftungszentrum.de/stiftungen/kind-philipp-stiftung-f%C3%BCr-p%C3%A4diatrisch-onkologische-forschung ) for supporting Shwetas congress participation with a stipend!Classification based on "Omic" data with missing data points
Can we use multidimensional data (e.g. from single cell transcriptomics or proteomics) to classify samples despite missing data? Yannis Schumann worked on a novel algorithm that makes this possible. The article "Robust classification using average correlations as features (ACF)" published in BMC Bioinformatics can be found at: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-023-05224-0 . It was a joint work with the Chair of High Performance Computing at the HSU. Congratulations to Yannis!
Hannah Voß was awarded the first posterprize at the "Neurowoche 2022" in Berlin. She showed our data on proteomics in medulloblastoma. Congratulations!Maximilian Middelkamp
Third in a row - Maximilian Middelkamp successfully defended his medical doctoral thesis today.
He did a great job and had published his results in Acta Neuropathologica Communications
( https://lnkd.in/guv4T3fJ ).
Congratulations from the whole team!Piotr SumislawskiPiotr Sumislawski
Piotr Sumislawski defended his dissertation successfully today. He had studied a rare type of embryonal eye cancer and had published his results together in Oncogenesis
Congratulations from the whole team!
We are on Twitter now! Check it out at
My first doctoral candidate Lisa Ruck successfully defended her doctoral thesis on the role of Lin28A during brain development!
Very happy to announce that our paper on the integration of "omics" data with missing values is now published in Nature communications https://lnkd.in/eT2zcXYm ( https://rdcu.be/cP0ns ). Our algorithm "HarmonizR" is free to use and can be found on GitHub. It allows the integration of independently generated Omic datasets and is of special interest for proteomic datasets that contain lots of missing values. This has been a great interdisciplinary collaboration with the Section Mass Spectrometry and Proteomics; UKE ( Prof. Hartmut Schlüters group ) and the Chair of High Performance Computing, Helmut Schmidt University ( Prof. Philipp Neumanns group ).
Great to be at the ISPNO2022 in Hamburg! We are happy to present our work on pediatric brain tumors and are enjoying great scientific talks.
Thanks to the team and our presenters Jelena Navolic, Matthias Dottermusch, Simon Schlumbohm and Maximilian Middelkamp!
Dr. Matthias Dottermusch
Applying spatial molecular profiling: Matthias' work an a case attributed to a new and rare brain tumor entity - so called central nervous system low-grade diffusely infiltrative tumour with INI1 deficiency (CNS LGDIT-INI1) - is out! It is titled "Spatial molecular profiling of a central nervous system low-grade diffusely infiltrative tumour with INI1 deficiency (CNS LGDIT-INI1) featuring a high-grade AT/RT component" and was published open access in Neuropathology and Applied Neurobiology ( https://onlinelibrary.wiley.com/doi/10.1111/nan.12777 ). Congratulations to Matthias!
LIN28A is expressed in some malignant brain tumors, such as ETMR or AT/RT. In their medical doctoral thesis, Max and Lisa were analyzing the effect of Lin28A overexpression during brain development and could show that Lin28A is not able to induce brain tumors. Their results could now be published open access in Acta Neuropathologica Communications titled: "Overexpression of Lin28A in neural progenitor cells in vivo does not lead to brain tumor formation but results in reduced spine density" ( https://actaneurocomms.biomedcentral.com/articles/10.1186/s40478-021-01289-1 ). Congratulations to both!Hubertus-Wald Poster Award Shweta
Price ceremony: The Hubertus-Wald Poster Award was handed over to Shweta Godbole for her work on integrating Omics data! Thanks to the University Cancer Center Hamburg ( UCCH ) and the Hubertus Wald Foundation for honouring the work of young scientists and congratulations to Shweta!
Matthias' und Piotrs work on the pathogenesis of embryonal eye cancer - so called intraocular medulloepithelioma - was accepted for open access publication in Oncogenesis. The work is titled : "Co-activation of Sonic hedgehog and Wnt signaling in murine retinal precursor cells drives ocular lesions with features of intraocular medulloepithelioma" ( https://rdcu.be/cBsQa ). In their work, Matthias and Piotr show that intraocular medulloepitheliomas are distinct from intracerebral medulloepitheliomas (also referred to as ETMR) and retinoblastomas with respect to gene expression profiles. Moreover, they describe the first preclinical in vivo model for this rare disease. Congratulations to both first authors !
Matthias' exciting case report concerning an uncommon SMARCB1 deficient tumor can be read in the diamond open access journal Free Neuropathology (www.freeneuropathology.org) titled "An atypical teratoid/rhabdoid tumor (AT/RT) with molecular features of pleomorphic xanthoastrocytoma (PXA) in a 62-year-old patient " ( https://www.uni-muenster.de/Ejournals/index.php/fnp/article/view/3640 ).
UCCH Research Retreat 2021:
Shweta Godbole received the UCCH Poster Award 2021 for her work on integrating multimodal omics data in medulloblastoma. Congratulations!