Leif S. Ludwig

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics

The paper introduces circVDJ-seq for efficient T cell receptor profiling from single-cell and spatial multi-omics data, revealing distinct immune microenvironments and T cell clonality patterns in various clinical contexts.

Clonal lineage tracing of innate immune cells in human cancer

The paper uses mtDNA mutations to trace clonal relationships of innate immune cells in cancer, showing myeloid clones are linked to monocytes and have distinct epigenetic profiles.

Coordinated IFN-γ/TNF Axis Drives Selective Loss of Activated Enteric Glia in Inflammatory Bowel Diseases

This study identifies IBD type-associated EGC activation signatures and reveals TNF/IFN-γ-driven necroptosis of activated enteric glia in inflammatory bowel diseases.

Cryo-mtscATAC-seq for single-cell mitochondrial DNA genotyping and clonal tracing in archived human tissues

The paper introduces Cryo-mtscATAC-seq to genotype mitochondrial DNA and trace clones in frozen human tissues, revealing clonal patterns in various diseases.

Population-scale sequencing resolves correlates and determinants of latent Epstein-Barr Virus infection

The paper uses population-scale whole genome sequencing to identify EBV DNA as a biomarker for respiratory, autoimmune, and cardiovascular diseases and identifies genetic determinants of EBV persistence.

Somatic epimutations enable single-cell lineage tracing in native hematopoiesis across the murine and human lifespan

This paper introduces EPI-clone, a method using DNA methylation to trace clonal lineages in hematopoiesis without genetic engineering, showing clonal complexity declines with age in mice and expands in humans.

IBDome: An integrated molecular, histopathological, and clinical atlas of inflammatory bowel diseases

This study integrates multi-omic and multimodal data from IBD patients to identify molecular, histopathological, and clinical features associated with inflammatory bowel diseases.

Tissue-specific apparent mtDNA heteroplasmy and its relationship with ageing and mtDNA gene expression

The paper maps tissue-specific mtDNA heteroplasmy and its associations with age and mtDNA gene expression using bulk RNAseq data from GTEx.

Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference

The paper identifies artifacts in single-cell mtDNA variant calling that mislead phylogenetic inference and warns against using low-evidence variant workflows.

Transcript-specific enrichment enables profiling rare cell states via scRNA-seq

This paper introduces PERFF-seq, a method to profile rare cell states via scRNA-seq by enriching for specific RNA transcripts, demonstrating its application in immune and brain tissues.

Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness

The paper identifies a synonymous mtDNA variant that affects codon-anticodon affinity and shows its impact on cellular fitness in immune cells.

Single-cell multi-omics reveals dynamics of purifying selection of pathogenic mitochondrial DNA across human immune cells

The paper uses single-cell multi-omics to study how pathogenic mtDNA mutations are subject to purifying selection in immune cells from Pearson syndrome patients.

Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations

The paper develops a method to detect mitochondrial mutations from single-cell RNA-seq to identify clonal expansions in human hematopoiesis.

cDNA-detector: Detection and removal of cDNA contamination in DNA sequencing libraries

cDNA-detector identifies and removes exogenous cDNA contamination in DNA sequencing data, improving accuracy in downstream analysis.

Single-cell multimodal profiling of proteins and chromatin accessibility using PHAGE-ATAC

The paper introduces PHAGE-ATAC, a method for simultaneous single-cell measurement of surface proteins, chromatin accessibility, and mtDNA-based clonal tracing, and demonstrates its application in human immune cells.

Scalable, multimodal profiling of chromatin accessibility and protein levels in single cells

This paper introduces ASAP-seq, a method to simultaneously profile chromatin accessibility, protein levels, and mtDNA in single cells, demonstrating its application in hematopoietic differentiation and T cell perturbations.

Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

Across 1,176,683 airway and lung cells from 22 datasets, ACE2 rises with age, in males and in smokers' multiciliated cells, and is lowest in young children.

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

The paper performs a pooled loss-of-function screen in hematopoietic cells to identify genes underlying GWAS loci associated with red blood cell traits, finding 77 genes at 38 loci with biological relevance.

Interrogation of human hematopoiesis at single-cell and single-variant resolution

This study fine-maps genetic variants associated with blood cell traits and identifies cell types and causal mechanisms using single-cell chromatin accessibility data from the UK Biobank.

The Genetic Landscape of Diamond-Blackfan Anemia

This study identifies genetic mutations in 78% of Diamond-Blackfan anemia patients using whole exome sequencing, finds new RP genes, and reports genotype-phenotype associations.