J. Kuipers

Network-based clustering unveils interconnected landscapes of genomic and clinical features across myeloid malignancies

The paper identifies novel subgroups in myeloid malignancies using a network-based clustering approach that integrates genomic and clinical features, improving prognostic accuracy.

Single-cell phylogenies reveal deviations from clock-like, neutral evolution in cancer and healthy tissues

This study uses single-cell DNA sequencing to test for neutral evolution in cancer and healthy tissues, finding deviations from a clock-like model in many datasets.

Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees

This paper introduces TreeMHN, a probabilistic framework for jointly inferring exclusivity patterns and recurrent trajectories from tumor mutation trees, showing improved performance over existing methods.

Mapping single-cell transcriptomes to copy number evolutionary trees

SCATrEx maps single-cell transcriptomes to copy number evolutionary trees, revealing clone-specific gene expression heterogeneity in tumors.

A statistical test for clonal exclusivity in tumour evolution

This paper introduces a statistical test, GeneAccord, to identify clonally exclusive gene pairs in tumours and applies it to AML data, finding 6 exclusive and 2 co-occurring pairs.

Spatial distribution of private gene mutations in clear cell renal cell carcinoma

The paper analyzes intra-tumour heterogeneity and subclonal mutations in clear cell renal cell carcinoma using multi-regional sequencing, finding that most tumours harbor private mutations and clonally exclusive pathway pairs.

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C

This paper compares mutational pathways to lopinavir resistance in HIV-1 subtypes B and C using a probabilistic model, finding distinct initial mutations and diverse evolutionary pathways.

Pancreatic Beta Cell Autophagy is Impaired in Type 1 Diabetes

This study shows impaired autophagy in pancreatic beta cells of type 1 diabetes patients and a mouse model, with reduced autophagosome-lysosome colocalization and telolysosome accumulation.

Single-cell copy number calling and event history reconstruction

This paper develops SCICoNE, a statistical model for single-cell copy number analysis from low-depth sequencing data, showing its accuracy on simulated data and application to breast cancer samples.

Clonal Evolution of Acute Myeloid Leukemia Revealed by High-Throughput Single-Cell Genomics

This study uses single-cell DNA sequencing to analyze clonal diversity in AML, revealing mutation co-occurrence, mutual exclusivity, and evolutionary patterns linked to treatment resistance and poor prognosis.

Mutational interactions define novel cancer subgroups

This study uses a Bayesian network model to analyze mutational interactions across 8,198 cancer samples, identifying 22 novel clusters that improve survival prediction and suggest drug targets.

A statistical test on single-cell data reveals widespread recurrent mutations in tumor evolution

This study tests the infinite sites assumption in tumor evolution using single-cell sequencing data and finds recurrent mutations in multiple datasets.