Thomas A. Richards

This paper introduces Concanavalin A as a marker for nuclear envelope imaging in expansion microscopy, revealing diverse mitotic strategies across eukaryotes.

The paper reports a near telomere-to-telomere genome assembly of Micractinium conductrix, enabling genomic studies of endosymbiosis and biotechnological applications.

This paper develops a stable transformation method for Micractinium conductrix SAG 241.80, enabling molecular studies of photosymbiosis in Paramecium bursaria.

The paper develops lrSAGA, a tool to improve genome assembly from long-read MDA sequencing of single cells, achieving higher completeness and fewer misassemblies.

The paper shows that adaptation to free-living conditions in algal endosymbionts leads to loss of host benefits, driven by metabolic trade-offs, with nitrogen availability as a key factor.

This study shows that endosymbiotic algae evolve traits specialized for intracellular niches, reducing their fitness in extracellular environments, thereby stabilizing endosymbiosis through evolutionary entrapment.

The paper uses single-cell sequencing to reveal genetic diversity in Bodo flagellates and their bacterial endosymbionts, showing SSU rDNA is insufficient for species classification.

This study investigates the infection strategies of the marine diatom parasite Pirsonia using genomic and transcriptomic analyses, revealing its reliance on actin-based phagocytosis and surface proteins.

The paper shows hybrid membranes select for D-ribose, deoxyribose, and specific L-amino acids, suggesting membrane permeability influenced life's stereochemistry.

The paper identifies multiple independent reassignments of the UAG stop codon to encode amino acids in Phyllopharyngean ciliates, showing UAG as a sense codon and UAA as the fixed stop codon.

This study identifies an immune-like glycan-sensing/processing network in Paramecium bursaria that regulates its algal endosymbionts through horizontal gene transfers.

The paper presents a de novo genome and transcriptome assembly of Paramecium bursaria 186b, revealing intron characteristics and evolutionary dynamics in ciliates.

The paper investigates the duplication and neofunctionalization of a horizontally-transferred xyloglucanase gene in oomycetes, showing how these variants contribute to plant pathogenesis and host-pathogen co-evolution.

This study identifies viral histone repeats and proposes they represent ancestral intermediates in nucleosome evolution, showing they can self-assemble into eukaryotic-like nucleosomes.

The paper identifies a non-canonical genetic code in a ciliate where UAA and UAG codons specify different amino acids, challenging the universality of the genetic code.

MitoHiFi assembles mitochondrial genomes from PacBio HiFi reads, identifying heteroplasmy variants and excluding nuclear contaminants, and has been used to assemble 374 mitochondrial genomes.

The paper identifies and validates the RNAi pathway in Paramecium bursaria, showing its role in feeding-induced gene knock-down and endosymbiosis genetics.

This paper develops a curated reference database for apicomplexan SSU rRNA sequences and analyzes their distribution across diverse environments, revealing significant molecular diversity, especially in marine settings.