Khanh Ngoc Dinh

Serval: A modular framework for decoding imaging based spatial transcriptomics data

Serval is a modular framework for decoding spatial transcriptomics data that introduces Cosine, a method improving transcript recovery and correlation with expression references.

Wavelet Based Whole Genome Doubling Aware Single Cell Copy Number Calling

Songbird is a single cell whole genome sequencing copy number caller that detects whole genome duplication and outperforms existing tools in breakpoints identification and true copy number detection.

Correction of the cytosine deamination artifacts in FFPE-based sequencing experiments

This study evaluates methods to correct cytosine deamination artifacts in FFPE sequencing, finding enzymatic repair is most effective and FFPErase is the best computational method.

COATS Identifies Copy-Number-Dependent Drivers and Enablers of Aneuploidy in Cancer

COATS identifies copy-number-dependent oncogenes and tumor suppressors associated with aneuploidy across 33 cancer types, revealing genes that drive or enable chromosomal instability.

Accurate detection of tumor clonality and ongoing expansion mode from genomic data

DECODE improves tumor clonality and expansion mode detection by accounting for sequencing biases and neutral tail in SFS, showing better performance on synthetic data and clinical relevance in glioma.

BESTish: A Diffusion-Approximation Framework for Inferring Selection and Mutation in Clonal Hematopoiesis

BESTish infers mutation fitness, mutation rate, and environmental strength in clonal hematopoiesis using a diffusion-approximation framework applied to VAF datasets.

Statistical and Evolutionary Analysis of Sequenced DNA from Breast Cancer FFPE Specimens

The paper analyzes FFPE breast cancer specimens to assess recoverable molecular evolution features using computational methods despite sequencing artifacts.

Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer

This study shows that ongoing whole-genome doubling in ovarian cancer promotes cell diversity and immune dysregulation through chromosomal instability and quiescent states.

CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution

CINner models chromosomal instability in cancer, showing how selection parameters and WGD influence tumor progression and heterogeneity.

The Origin of Bladder Cancer from Mucosal Field Effects

This study identifies molecular changes in bladder mucosa that initiate cancer, revealing inflammation's role and mutation patterns linked to early carcinogenesis.