Marleen M. Nieboer
YOU?
Author Swipe
View article: Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning
Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning Open
Over the past years, large consortia have been established to fuel the sequencing of whole genomes of many cancer patients. Despite the increased abundance in tools to study the impact of SNVs, non-coding SVs have been largely ignored in t…
View article: svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning
svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning Open
Motivation Despite the fact that structural variants (SVs) play an important role in cancer, methods to predict their effect, especially for SVs in non-coding regions, are lacking, leaving them often overlooked in the clinic. Non-coding SV…
View article: Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development
Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development Open
Our data strongly support the hypothesis that NS is initiated by whole-genome duplication, followed by chromosome copy number alterations in the cancer stem cell population, and accumulation of low numbers of somatic mutations, even in the…
View article: TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors
TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors Open
Most tumors are composed of a heterogeneous population of subclones. A more detailed insight into the subclonal evolution of these tumors can be helpful to study progression and treatment response. Problematically, tumor samples are typica…
View article: Molecular Heterogeneity and Early Metastatic Clone Selection in Testicular Germ Cell Cancer Development
Molecular Heterogeneity and Early Metastatic Clone Selection in Testicular Germ Cell Cancer Development Open
Background Testicular germ cell cancer (TGCC), being the most frequent malignancy in young Caucasian males, is initiated from an embryonic germ cell. This study determines intratumor heterogeneity to unravel tumor progression from initiati…
View article: Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Mapping and phasing of structural variation in patient genomes using nanopore sequencing Open
View article: Mapping and phasing of structural variation in patient genomes using nanopore sequencing
Mapping and phasing of structural variation in patient genomes using nanopore sequencing Open
Structural genomic variants form a common type of genetic alteration underlying human genetic disease and phenotypic variation. Despite major improvements in genome sequencing technology and data analysis, the detection of structural varia…