T. Nicolai Siegel

Super-resolution imaging flow cytometry

This paper introduces super-resolution imaging flow cytometry (SR-IFC) to quantify organelle architecture heterogeneity at population scale, achieving sub-diffraction resolution in microbiology and immunology applications.

First Genome-Wide Centromere Map of Trypanosoma cruzi Reveals Linear and 3D Compartment Boundaries and Spatial Clustering

The paper generates a high-quality genome assembly and centromere map for T. cruzi using Hi-C and ChIP-seq, revealing structural boundaries and 3D clustering of centromeres.

High-resolution scRNA-seq reveals genomic determinants of antigen expression hierarchy in African Trypanosomes

This study uses high-resolution scRNA-seq to uncover how genomic rearrangements during antigen switching in Trypanosoma brucei depend on repair mechanisms and homologous templates.

SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes

The paper uses SLAM-seq and scRNA-seq to show RNA processing and stability independently influence mRNA levels in African trypanosomes.

A phased genome assembly for allele-specific analysis in Trypanosoma brucei

The paper presents an allele-specific genome assembly for Trypanosoma brucei, enabling analysis of allele-specific mechanisms and improving genome assembly benchmarks for highly heterozygous species.

Antigenic variation by switching inter-chromosomal interactions with an RNA splicing locus in trypanosomes

The paper identifies a novel mechanism in trypanosomes where inter-chromosomal interactions between an antigen coding gene and an mRNA splicing locus ensure monogenic antigen expression.

Efficient and specific oligo-based depletion of rRNA

This paper describes an oligo-based method for efficiently depleting rRNA from trypanosomal samples, achieving less than 5% rRNA levels with minimal off-target effects.