Johan Hartman

Highly resolved tumor architecture via matched spatial and nucleus transcriptomics from a single tissue section

SIMPlex generates matched spatial and single-nucleus transcriptomic profiles from the same tissue section to resolve cell states with spatial signatures in mouse and human cancer tissues.

Principles of subclonal gene dosage across human cancer

The paper analyzes subclonal gene dosage effects in cancer using DNTR-seq, finding additive and compensatory transcriptional impacts and identifying transient clonality in ovarian and soft tissue sarcomas.

A distal CTCF-binding site drives MYC expression plasticity in a negative feed-forward loop

The paper identifies a CTCF-binding site that regulates MYC expression plasticity through a negative feed-forward loop involving CCAT1 eRNA and MYC protein feedback.

Whole-Brain Three-Dimensional Imaging of RNAs at Single-Cell Resolution

The paper develops TRIC-DISCO, a pipeline for whole-brain 3D RNA imaging in adult mice, enabling single-cell resolution of transcriptional signatures and markers without strict RNase-free conditions.

Prelude to Malignancy: A Gene Expression Signature in Normal Mammary Gland from Breast Cancer Patients Suggests Pre-tumorous Alterations and Is Associated with Adverse Outcomes

Ensembles for improved detection of invasive breast cancer in histological images

This paper compares single and ensemble CNN models for detecting invasive breast cancer in histological images, finding ensembles improve accuracy across internal and external datasets.

Chromatin accessibility profiling in tissue sections by spatial ATAC

This paper introduces spatial ATAC, a method for spatially resolved chromatin accessibility profiling, and demonstrates its application in studying gene regulation in mouse development and human disease.

High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing.

PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data

PhylEx reconstructs clonal structure by integrating bulk DNA-seq and scRNA-seq data, outperforming existing methods in clonal-tree reconstruction and mutation clustering.