@neumann-lab.bsky.social
Emmy Noether Research Group Leader,
Professor for Molecular Pathology in Neuro-Oncology, Neuropathologist at University Hospital Hamburg-Eppendorf
Research Interests: Proteomics, DNA-methylomics, Bioinformatics, Preclinical Models,
Digital Pathology
Professor for Molecular Pathology in Neuro-Oncology, Neuropathologist at University Hospital Hamburg-Eppendorf
Research Interests: Proteomics, DNA-methylomics, Bioinformatics, Preclinical Models,
Digital Pathology
Fast execution - 5 mins runtime for 200 samples using combined segmentation (versus 40 mins runtime for established algorithms conumee and conumee 2)
#DNAmethylation #EPICv2 #bioinformatics #braintumor #neurooncology #neuropathology #ukeHamburg #zmnh #diagnostics
#DNAmethylation #EPICv2 #bioinformatics #braintumor #neurooncology #neuropathology #ukeHamburg #zmnh #diagnostics
September 24, 2025 at 7:05 PM
Fast execution - 5 mins runtime for 200 samples using combined segmentation (versus 40 mins runtime for established algorithms conumee and conumee 2)
#DNAmethylation #EPICv2 #bioinformatics #braintumor #neurooncology #neuropathology #ukeHamburg #zmnh #diagnostics
#DNAmethylation #EPICv2 #bioinformatics #braintumor #neurooncology #neuropathology #ukeHamburg #zmnh #diagnostics
Broad applicability - single sample or combined sample analyses, all array types (450K, EPIC, EPICv2, mouse), integration of conumee and conumee 2
Flexible visualisation - Intensity Plot and Frequency Plot
High sensitivity. - Up to 96% for all array types for focal chromosomal aberrations
Flexible visualisation - Intensity Plot and Frequency Plot
High sensitivity. - Up to 96% for all array types for focal chromosomal aberrations
September 24, 2025 at 7:05 PM
Broad applicability - single sample or combined sample analyses, all array types (450K, EPIC, EPICv2, mouse), integration of conumee and conumee 2
Flexible visualisation - Intensity Plot and Frequency Plot
High sensitivity. - Up to 96% for all array types for focal chromosomal aberrations
Flexible visualisation - Intensity Plot and Frequency Plot
High sensitivity. - Up to 96% for all array types for focal chromosomal aberrations
The Cumulative CNV (CCNV) R package combines established segmentation methods and a newly implemented algorithm for thorough and fast CNV analysis at unprecedented accessibility enabling the analyses of large case series.
Advantages:
Easy to use - Only one package and line of code
Advantages:
Easy to use - Only one package and line of code
September 24, 2025 at 7:05 PM
The Cumulative CNV (CCNV) R package combines established segmentation methods and a newly implemented algorithm for thorough and fast CNV analysis at unprecedented accessibility enabling the analyses of large case series.
Advantages:
Easy to use - Only one package and line of code
Advantages:
Easy to use - Only one package and line of code
Copy number variation (CNV) patterns can be inferred from global DNA methylation data, which are commonly analyzed in routine brain tumor diagnostics.
CNV analyses depict alterations of DNA quantities across chromosomes that are crucial for tumor diagnostics and classification.
CNV analyses depict alterations of DNA quantities across chromosomes that are crucial for tumor diagnostics and classification.
September 24, 2025 at 7:05 PM
Copy number variation (CNV) patterns can be inferred from global DNA methylation data, which are commonly analyzed in routine brain tumor diagnostics.
CNV analyses depict alterations of DNA quantities across chromosomes that are crucial for tumor diagnostics and classification.
CNV analyses depict alterations of DNA quantities across chromosomes that are crucial for tumor diagnostics and classification.
8. BERT was thoroughly tested emphasizing it's broad scope (tested on large-scale data integration tasks with up to 5000 datasets from simulated and experimental data of different quantification techniques and omic types (proteomics, transcriptomics, metabolomics) as well as other datatypes)
August 2, 2025 at 3:56 PM
8. BERT was thoroughly tested emphasizing it's broad scope (tested on large-scale data integration tasks with up to 5000 datasets from simulated and experimental data of different quantification techniques and omic types (proteomics, transcriptomics, metabolomics) as well as other datatypes)
6. BERT is super fast (leverages multi-core and distributed-memory systems for up to 11 × runtime improvement)
7. BERT is available on Bioconductor
7. BERT is available on Bioconductor
August 2, 2025 at 3:56 PM
6. BERT is super fast (leverages multi-core and distributed-memory systems for up to 11 × runtime improvement)
7. BERT is available on Bioconductor
7. BERT is available on Bioconductor
3. BERT retains data in incomplete datasets upon integration
4. BERT can integrate datasets with different compositions and conditions (integration of unbalanced datasets using covariates)
5. BERT can integrate datasets with unknown conditions (using references)
4. BERT can integrate datasets with different compositions and conditions (integration of unbalanced datasets using covariates)
5. BERT can integrate datasets with unknown conditions (using references)
August 2, 2025 at 3:56 PM
3. BERT retains data in incomplete datasets upon integration
4. BERT can integrate datasets with different compositions and conditions (integration of unbalanced datasets using covariates)
5. BERT can integrate datasets with unknown conditions (using references)
4. BERT can integrate datasets with different compositions and conditions (integration of unbalanced datasets using covariates)
5. BERT can integrate datasets with unknown conditions (using references)
BERTs features:
1. BERT can integrate molecular data (Omic data) or other data types (e.g. clinical annotations)
2. BERT tolerates missing data of different types in datasets (e.g. missing at random, missing not at random)
1. BERT can integrate molecular data (Omic data) or other data types (e.g. clinical annotations)
2. BERT tolerates missing data of different types in datasets (e.g. missing at random, missing not at random)
August 2, 2025 at 3:56 PM
BERTs features:
1. BERT can integrate molecular data (Omic data) or other data types (e.g. clinical annotations)
2. BERT tolerates missing data of different types in datasets (e.g. missing at random, missing not at random)
1. BERT can integrate molecular data (Omic data) or other data types (e.g. clinical annotations)
2. BERT tolerates missing data of different types in datasets (e.g. missing at random, missing not at random)
Including TE transcription profiles into the molecular characterization of ATRTs might reveal new tumor vulnerabilities leading to novel therapeutic interventions, such as immunotherapy.
July 23, 2025 at 7:58 PM
Including TE transcription profiles into the molecular characterization of ATRTs might reveal new tumor vulnerabilities leading to novel therapeutic interventions, such as immunotherapy.
--> Differentially transcribed TEs in primary samples are partly reflected in established ATRT-SHH and -MYC cell line models.
July 23, 2025 at 7:58 PM
--> Differentially transcribed TEs in primary samples are partly reflected in established ATRT-SHH and -MYC cell line models.
--> ATRT-MYC showed broadly reduced transcript levels of LINE1 and ERVL-MaLR subfamilies and displayed significantly less LTR and LINE1 loci with bidirectional promoter activity.
July 23, 2025 at 7:58 PM
--> ATRT-MYC showed broadly reduced transcript levels of LINE1 and ERVL-MaLR subfamilies and displayed significantly less LTR and LINE1 loci with bidirectional promoter activity.
--> We investigate the transcriptional profiles of 1.9M LINE1 and LTR elements that differ across ATRT subtypes in primary human samples.
July 23, 2025 at 7:58 PM
--> We investigate the transcriptional profiles of 1.9M LINE1 and LTR elements that differ across ATRT subtypes in primary human samples.
Atypical teratoid rhabdoid tumors (ATRTs) are very aggressive CNS tumors mainly affecting infants.
Transcriptional activity of transposable elements (TEs), like LINE1s and LTRs, is tightly linked with human cancers as a direct consequence of lifting epigenetic repression over TEs.
Transcriptional activity of transposable elements (TEs), like LINE1s and LTRs, is tightly linked with human cancers as a direct consequence of lifting epigenetic repression over TEs.
July 23, 2025 at 7:58 PM
Atypical teratoid rhabdoid tumors (ATRTs) are very aggressive CNS tumors mainly affecting infants.
Transcriptional activity of transposable elements (TEs), like LINE1s and LTRs, is tightly linked with human cancers as a direct consequence of lifting epigenetic repression over TEs.
Transcriptional activity of transposable elements (TEs), like LINE1s and LTRs, is tightly linked with human cancers as a direct consequence of lifting epigenetic repression over TEs.
Many thanks to the @dfg.de for funding this research within the #emmynoether programme!
July 22, 2025 at 9:04 PM
Many thanks to the @dfg.de for funding this research within the #emmynoether programme!
We provide molecular insights into these rare and severe brain diseases and reveal novel implications of the oncogenic factor LIN28A in extracellular matrix integrity
July 22, 2025 at 9:04 PM
We provide molecular insights into these rare and severe brain diseases and reveal novel implications of the oncogenic factor LIN28A in extracellular matrix integrity
Alterations of brain layer morphology in these models were mapped to spatial proteome patterns that were acquired with the Nanosecond-infrared laser system
July 22, 2025 at 9:04 PM
Alterations of brain layer morphology in these models were mapped to spatial proteome patterns that were acquired with the Nanosecond-infrared laser system
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In contrast sole stabilisation of CTNNB1 resulted in a distinct developmental brain phenotype similar to Lissencephaly Type 1.
In contrast sole stabilisation of CTNNB1 resulted in a distinct developmental brain phenotype similar to Lissencephaly Type 1.
July 22, 2025 at 9:04 PM
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In contrast sole stabilisation of CTNNB1 resulted in a distinct developmental brain phenotype similar to Lissencephaly Type 1.
In contrast sole stabilisation of CTNNB1 resulted in a distinct developmental brain phenotype similar to Lissencephaly Type 1.
In a nutshell:
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Co-activation of LIN28A and stabilised CTNNB1 in vivo led to pial disruption and neuronal overmigration resembling a servere human developmental disorder of the brain which is called the Cobblestone Lissencephaly Type 2.
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Co-activation of LIN28A and stabilised CTNNB1 in vivo led to pial disruption and neuronal overmigration resembling a servere human developmental disorder of the brain which is called the Cobblestone Lissencephaly Type 2.
July 22, 2025 at 9:04 PM
In a nutshell:
•
Co-activation of LIN28A and stabilised CTNNB1 in vivo led to pial disruption and neuronal overmigration resembling a servere human developmental disorder of the brain which is called the Cobblestone Lissencephaly Type 2.
•
Co-activation of LIN28A and stabilised CTNNB1 in vivo led to pial disruption and neuronal overmigration resembling a servere human developmental disorder of the brain which is called the Cobblestone Lissencephaly Type 2.
Finally, hypomethylation at the FGFR3 locus, together with increased FGFR3 protein expression, was observed in 97% of cases, highlighting FGFR3 as a potential future treatment target.
June 13, 2025 at 9:08 PM
Finally, hypomethylation at the FGFR3 locus, together with increased FGFR3 protein expression, was observed in 97% of cases, highlighting FGFR3 as a potential future treatment target.
DNA methylation profiles were rather homogenous but global DNA hypomethylation was a feature of tumors associated with higher recurrence risk.
June 13, 2025 at 9:08 PM
DNA methylation profiles were rather homogenous but global DNA hypomethylation was a feature of tumors associated with higher recurrence risk.
Of note, classic histopathological criteria such as atypia and the cell proliferation index were not reproducible across neuropathologists.
Instead, patient age and treatment strategy were key factors associated with survival outcomes in the cohort.
Instead, patient age and treatment strategy were key factors associated with survival outcomes in the cohort.
June 13, 2025 at 9:08 PM
Of note, classic histopathological criteria such as atypia and the cell proliferation index were not reproducible across neuropathologists.
Instead, patient age and treatment strategy were key factors associated with survival outcomes in the cohort.
Instead, patient age and treatment strategy were key factors associated with survival outcomes in the cohort.