Joanna Hård

Phylogenetic tree inference from single-cell RNA sequencing data

This paper introduces a method for inferring phylogenetic trees from single-cell RNA sequencing data by alternating between two tree representations to avoid local optima.

Probabilistic cell lineage inference from mitochondrial mutations

mt-SCITE reconstructs cell lineages from mitochondrial mutations, outperforming existing methods and revealing subclonal relationships in CD8+ T cells post-vaccination.

Scuphr: A probabilistic framework for cell lineage tree reconstruction

Scuphr reconstructs cell lineage trees using bulk and single-cell DNA sequencing data, addressing technical artifacts and improving accuracy over existing methods.

Clonally heritable gene expression imparts a layer of diversity within cell types

The paper identifies heritable transcriptional diversity within cell types by studying clonal human lymphocytes and mouse brain cells, showing clone-specific chromatin accessibility leads to distinct gene expression.

Long-read whole genome analysis of human single cells

This study uses long-read sequencing to analyze the genomic architecture of single human cells, revealing high-resolution genetic variation and structural variants.

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing

Conbase identifies clonal somatic mutations in single cells using read phasing, validated on simulated data and human samples.