Christopher D. Faulk

Diet-dependent effects of kombucha on the gut microbiome and its neuroactive potential: Associations with reduced anxiety and depressive-like behaviors in mice

This study shows kombucha alters gut microbiome and neuroactive metabolism in mice, with behavioral benefits dependent on diet.

A Telomere-to-telomere genome of the hibernating fat-tailed dwarf lemur (Cheirogaleus medius)

The paper presents a telomere-to-telomere genome assembly of the fat-tailed dwarf lemur, providing a high-quality genomic resource for studying hibernation and conservation.

Hierarchical Transcriptomic and Epigenetic Recovery and Remodeling in the Developing Hippocampus Following Early-life Environmental Insults: An Iron Deficiency Rat Model

This study examines transcriptomic and epigenetic changes in rat hippocampi after developmental iron deficiency and postnatal iron treatment, showing partial epigenetic recovery and new modifications.

Genomics and reproductive biology of Leptopilina n. sp. Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae): An asexual parasitoid of Caribbean Drosophila

This paper describes a new parasitoid wasp species, Leptopilina n. sp., and presents its genome, Wolbachia endosymbiont, and reproductive biology.

Epigenetic plasticity is a driver of heritable pollution tolerance in Atlantic killifish

The paper shows that PAH-tolerant Atlantic killifish embryos have reduced DNA methylation plasticity compared to sensitive embryos, with implications for heritable epigenetic adaptation.

The Genome of the American Dog Tick (Dermacentor variabilis)

This paper presents the first high-quality genome assembly of the American dog tick, along with methylation analysis and endosymbiont detection, providing new insights into tick genomics and epigenetics.

Epigenomic insights into extreme longevity in the world's oldest terrestrial animal, Jonathan

The paper analyzes the DNA sequence and methylome of Jonathan, a 192-year-old giant tortoise, to identify epigenomic features associated with extreme longevity.

The genome of Przewalski's horse (Equus ferus przewalskii)

The paper presents an improved reference genome for Przewalski's horse using Oxford Nanopore sequencing, revealing methylation patterns and imprinted genes relevant to conservation.

Rapid molecular species identification of mammalian scat samples using nanopore adaptive sampling

This paper develops a method using nanopore adaptive sampling to rapidly identify mammalian species from scat samples, achieving accurate identifications for most samples and detecting a misidentification in one case.

Genome Skimming with Nanopore Sequencing Precisely Determines Global and Transposon DNA Methylation in Vertebrates

This paper demonstrates that nanopore sequencing at low coverage can accurately determine global and transposon DNA methylation in vertebrates.

Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul

The paper assembles a chromosome-level genome and allele-specific DNA methylation map for Pallas's cat using nanopore sequencing.

The Genome of the Soybean Gall Midge (Resseliella maxima)

This paper assembles and annotates the genome of the soybean gall midge, Resseliella maxima, using long-read nanopore sequencing, providing a high-quality reference for studying its biology and plant-insect interactions.

Nanopore adaptive sampling for mitogenome sequencing and bloodmeal identification in hematophagous insects

This paper uses the Oxford Nanopore Adaptive Sampling pipeline to sequence mitogenomes of hematophagous insects and identify their bloodmeal hosts, aiding in disease transmission studies.

De novo sequencing, diploid assembly, and annotation of the black carpenter ant, Camponotus pennsylvanicus, and its symbionts by one person for $1000, using nanopore sequencing.

The paper assembles and annotates the genome of the black carpenter ant and its symbionts using nanopore sequencing from a single individual at a low cost.

The Mitochondrial Genome and Epigenome of the Golden Lion Tamarin from Fecal DNA using Nanopore Adaptive Sequencing

The paper reports a new mitogenome assembly for the golden lion tamarin using nanopore adaptive sequencing and detects DNA hydroxymethylation in mitochondria.