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Profiling Numerical and Structural Chromosomal Instability in Different Cancer Types
Many cancers display whole chromosome instability (W-CIN) and structural chromosomal instability (S-CIN), referring to increased rates of acquiring numerically and structurally abnormal chromosome changes. Thi...
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Article
Open AccessGeneration of realistic synthetic data using Multimodal Neural Ordinary Differential Equations
Individual organizations, such as hospitals, pharmaceutical companies, and health insurance providers, are currently limited in their ability to collect data that are fully representative of a disease populati...
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Article
Open AccessLoss of USP28 and SPINT2 expression promotes cancer cell survival after whole genome doubling
Whole genome doubling is a frequent event during cancer evolution and shapes the cancer genome due to the occurrence of chromosomal instability. Yet, erroneously arising human tetraploid cells usually do not p...
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Article
Open AccessSystems approaches identify the consequences of monosomy in somatic human cells
Chromosome loss that results in monosomy is detrimental to viability, yet it is frequently observed in cancers. How cancers survive with monosomy is unknown. Using p53-deficient monosomic cell lines, we find t...
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Open AccessThe p53/p73 - p21CIP1 tumor suppressor axis guards against chromosomal instability by restraining CDK1 in human cancer cells
Whole chromosome instability (W-CIN) is a hallmark of human cancer and contributes to the evolvement of aneuploidy. W-CIN can be induced by abnormally increased microtubule plus end assembly rates during mitos...
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Article
Open AccessDNA replication stress mediates APOBEC3 family mutagenesis in breast cancer
The APOBEC3 family of cytidine deaminases mutate the cancer genome in a range of cancer types. Although many studies have documented the downstream effects of APOBEC3 activity through next-generation sequencin...
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Open AccessLearning (from) the errors of a systems biology model
Mathematical modelling is a labour intensive process involving several iterations of testing on real data and manual model modifications. In biology, the domain knowledge guiding model development is in many c...
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Book
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Membrane Transport in Yeast, An Introduction
Research on membrane transport has made continuous progress in the last decades and remains an active field of scientific investigation. In the case of yeast, most of the research has been conducted for the mo...
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Mathematical Modelling of Cation Transport and Regulation in Yeast
Mathematical modelling of ion transport is a strategy to understand the complex interplay between various ionic species and their transporters. Such models should provide new insights and suggest new interesti...
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Article
Expression of regulators of mitotic fidelity are associated with intercellular heterogeneity and chromosomal instability in primary breast cancer
Regulators of transition through mitosis such as SURVIVIN and Aurora kinase A (AURKA) have been previously implicated in the initiation of chromosomal instability (CIN), a driver of intratumour heterogeneity. ...
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Correction: Corrigendum: Replication stress links structural and numerical cancer chromosomal instability
Nature 494, 492–496 (2013); doi:10.1038/nature11935 In this Letter we inadvertently omitted full details of The Cancer Genome Atlas data sets. The Acknowledgements should have included these sentences: “The re...
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Article
Replication stress links structural and numerical cancer chromosomal instability
A mechanism to explain chromosomal instability (CIN) in colorectal cancer is demonstrated; three new CIN-suppressor genes (PIGN, MEX3C and ZNF516) encoded on chromosome 18q are identified, the loss of which leads...
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Article
How dynamical models can learn from the data—an example with a simplified ENSO model
Most dynamical models of the natural system contain a number of empirical parameters which reflect our limited understanding of the simulated system or describe unresolved subgrid-scale processes. While the pa...
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Article
Ring test assessment of the mKir2.1 growth based assay in Saccharomyces cerevisiae using parametric models and model-free fits
Inward rectifying K+ (Kir) channels are a subfamily of the potassium channel superfamily. They mediate potassium influx into the cells, a process responding to the polarization state, a variety of intracellular m...
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Article
Automatic Scoring and Quality Assessment Using Accuracy Bounds for FP-TDI SNP Genoty** Data
Background: Human diversity, namely single nucleotide polymorphisms (SNPs), is becoming a focus of biomedical research. Despite the binary nature of SNP determination, the majority of genoty** ...
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Article
Toward an accurate statistics of gapped alignments
Sequence alignment has been an invaluable tool for finding homologous sequences. The significance of the homology found is often quantified statistically by p-values. Theory for computing p-values exists for gapl...
