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Sebastian Martin Waszak

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Related publications (29)

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Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping

Sebastian Martin Waszak

Background: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatri ...

2023

Clinical efficacy of ONC201 in H3K27M-mutant diffuse midline gliomas is driven by disruption of integrated metabolic and epigenetic pathways

Sebastian Martin Waszak

H3K27M-mutant diffuse midline glioma (DMG) patients have no proven effective therapies. ONC201 has recently demonstrated efficacy in these patients, but the mechanism behind this remains unknown. We assessed clinical outcomes, tumor sequencing, and tissue/ ...

2023

Isocitrate dehydrogenase 1 primes group-3 medulloblastomas for cuproptosis

Sebastian Martin Waszak

MYC-driven group-3 medulloblastomas (MBs) are malignant pediatric brain cancers without cures. To define actionable metabolic dependencies, we identify upregulation of dihydrolipoyl transacetylase (DLAT), the E2-subunit of pyruvate dehydrogenase complex (P ...

Elsevier BV2025

Pan-cancer atlas of somatic core and linker histone mutations

Sebastian Martin Waszak

Recent genomic data points to a growing role for somatic mutations altering core histone and linker histone-encoding genes in cancer. However, the prevalence and the clinical and biological implications of histone gene mutations in malignant tumors remain ...

2023

Genetic modeling of ELP1-associated Sonic hedgehog medulloblastoma identifies MDM2 as a selective therapeutic target

Sebastian Martin Waszak

Germline loss-of-function (LOF) variants in Elongator acetyltransferase complex subunit 1 (ELP1) are the most prevalent predisposing genetic events in childhood medulloblastoma (MB), accounting for ∼30% of the Sonic hedgehog (SHH) 3 subtype. The mechanism( ...

Elsevier BV2025

The Germline and Somatic Origins of Prostate Cancer Heterogeneity

Sebastian Martin Waszak

Newly diagnosed prostate cancers differ dramatically in mutational composition and lethality. The most accurate clinical predictor of lethality is tumor tissue architecture, quantified as tumor grade. To interrogate the evolutionary origins of prostate can ...

AMER ASSOC CANCER RESEARCH2025

Somatic CpG hypermutation is associated with mismatch repair deficiency in cancer

Sebastian Martin Waszak

Somatic hypermutation in cancer has gained momentum with the increased use of tumour mutation burden as a biomarker for immune checkpoint inhibitors. Spontaneous deamination of 5-methylcytosine to thymine at CpG dinucleotides is one of the most ubiquitous ...

2024

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

Bart Deplancke, Jeffrey David Jensen, Sebastian Martin Waszak, Andreas Massouras

Understanding the relationship between genetic and phenotypic variation is one of the great outstanding challenges in biology. To meet this challenge, comprehensive genomic variation maps of human as well as of model organism populations are required. Here ...

Public Library of Science2012

Personal receptor repertoires: olfaction as a model

Sebastian Martin Waszak

Background: Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor proteins in different human individual ...

BioMed Central2012

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data

Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Alisa Yurovsky

Motivation: High-throughput sequencing technologies enable the genome-wide analysis of the impact of genetic variation on molecular phenotypes at unprecedented resolution. However, although powerful, these technologies can also introduce unexpected artifac ...

Oxford University Press2014

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

Bart Deplancke, David Hacker, Sebastian Martin Waszak, Sunil Kumar Raghav, Alisa Yurovsky, Gilles Udin

Chromatin state variation at gene regulatory elements is abundant across individuals, yet we understand little about the genetic basis of this variability. Here, we profiled several histone modifications, the transcription factor (TF) PU.1, RNA polymerase ...

Elsevier2015

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Alina Isakova, Carine Delattre-Gubelmann, Jovan Simicevic, Antonina Iagovitina

The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression b ...

Nature / European Molecular Biology Organization2013

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

Bart Deplancke, David Hacker, Sebastian Martin Waszak, Sunil Kumar Raghav, Alisa Yurovsky, Gilles Udin

DNA sequence variation has been associated with quantitative changes in molecular phenotypes such as gene expression, but its impact on chromatin states is poorly characterized. To understand the interplay between chromatin and genetic control of gene regu ...

American Association for the Advancement of Science2013

A systems approach to elucidate the genetic architecture of molecular phenotypes

Sebastian Martin Waszak

A growing body of evidence suggests that changes in gene regulatory DNA are the major genetic determinants of variation in complex phenotypes; however, the underlying genes as well as cascades of intermediate molecular events remain in most cases elusive. ...

EPFL2014

Genome-wide Screens Implicate Loss of Cullin Ring Ligase 3 in Persistent Proliferation and Genome Instability in TP53-Deficient Cells

Sebastian Martin Waszak, Ruxandra-Andreea Lambuta

TP53 deficiency is the most common alteration in cancer; however, this alone is typically insufficient to drive tumorigenesis. To identify genes promoting tumorigenesis in combination with TP53 deficiency, we perform genome-wide CRISPR-Cas9 knockout screen ...

2020

Germline analysis of an international cohort of pediatric diffuse midline glioma patients

Sebastian Martin Waszak

Factors that drive the development of diffuse midline gliomas (DMG) are unknown. Our study aimed to determine the prevalence of pathogenic/likely pathogenic (P/LP) germline variants in pediatric patients with DMG. We assembled an international cohort of 25 ...

Oxford University Press (OUP)2025

A Dual Program for Translation Regulation in Cellular Proliferation and Differentiation

Sebastian Martin Waszak

A dichotomous choice for metazoan cells is between proliferation and differentiation. Measuring tRNA pools in various cell types, we found two distinct subsets, one that is induced in proliferating cells, and repressed otherwise, and another with the oppos ...

Cell Press2014

Germline loss-of-function variant in the E3 ubiquitin ligase TRAF2 in a young adult patient with medulloblastoma: a case report

Sebastian Martin Waszak

We identified a rare heterozygous germline loss-of-function variant in the tumor necrosis factor receptor-associated factor 2 (TRAF2) in a young adult patient diagnosed with medulloblastoma. This variant is located within the TRAF-C domain of the E3 ubiqui ...

BioMed Central2024

The gut microbiome in pediatric diffuse midline gliomas: Correlative study results from the PNOC022 trial

Sebastian Martin Waszak

10015 Background: The gut microbiome exerts a multifaceted influence on treatment outcomes across various cancers, yet its potential role in diffuse midline gliomas (DMGs) remains under-explored. In this report, we present the gut microbiome findings from ...

American Society of Clinical Oncology (ASCO)2025

Identification of the transcription factor ZEB1 as a central component of the adipogenic gene regulatory network

Didier Trono, Bart Deplancke, Sebastian Martin Waszak, Sunil Kumar Raghav, Petra Catalina Schwalie, Gilles Udin, Andrea Corsinotti

Adipose tissue is a key determinant of whole body metabolism and energy homeostasis. Unraveling the regulatory mechanisms underlying adipogenesis is therefore highly relevant from a biomedical perspective. Our current understanding of fat cell differentiat ...

Elife Sciences Publications Ltd2014