Timothy B. Sackton

This study investigates the independent evolution of harmala alkaloids in Syrian rue and ayahuasca plants, revealing convergent genetic and biochemical pathways.

The paper presents chromosome-level genome assemblies and population genetic data for three Phlox species, revealing extensive genetic variation and widespread gene flow during speciation.

The paper identifies convergent and lineage-specific genomic changes in sugar-feeding birds through genome and transcriptome analyses, revealing adaptive mechanisms in metabolic pathways.

The paper identifies convergent genomic adaptations in brood parasitic birds, including genes related to spermatogenesis and nervous system development, across independent origins of parasitism.

The paper analyzes structural variants in three North American jay species using pangenome tools and long-read assemblies, revealing rapid genome evolution and population size effects on SV dynamics.

The paper generates genome assemblies for ten brood parasitic bird species and their outgroups, enabling comparative genomic analyses of obligate brood parasitism evolution.

This paper shows that adrenergic signaling coordinates systemic and local stem cell activation after amputation in axolotls, enhancing regeneration.

This study uses modern and ancient DNA data to show that Madagascar turtle doves colonized Mauritius and Reunion independently from Madagascar before human arrival, challenging historical accounts of human-induced demographic collapse.

The paper introduces clam, a tool that efficiently estimates nucleotide diversity and divergence using variant-only VCFs and callable loci, improving computational performance and storage.

The paper evaluates genome annotation methods across 21 species, finding Stringtie and TOGA as top performers, with RNA-seq data improving annotation quality.

The paper identifies convergent evolutionary changes in noncoding elements associated with short tarsus length in birds and finds these changes are enriched near developmental genes.

BUSTED-E detects positive selection while identifying residual alignment errors in genome-scale datasets, improving accuracy and biological interpretation.

This paper introduces a phylogenetic method to link nucleotide substitution rates to continuous trait evolution, showing associations between conserved sequences and traits like body size and lifespan.

This paper introduces snpArcher, a variant calling workflow for non-model organisms, and applies it to 26 public datasets to enable comparative population genomic analyses.

The paper introduces tools to evaluate single-cell clustering stability using subsampling and the Jaccard similarity index, with an R package and Snakemake workflow for implementation.

HieRFIT improves cell type classification accuracy by using hierarchical random forests with prior cell type relationships, showing effectiveness in cross-dataset and cross-species analyses.

The paper compares short paired-end and long single-end RNA-seq reads, finding that short paired-end reads provide more accurate expression and differential expression results despite fewer total bases.

This study shows that de novo transcriptome assemblies have systematic biases and errors, leading to underestimation of diversity and inaccurate expression estimates, and introduces a method to reduce these issues.

This study provides insights into the biology of the stable fly by combining genome sequencing, microbiome analysis, and RNA-seq to identify genes related to reproduction, host interactions, and pest control.

This paper advocates for integrating natural history-derived phenomic data with comparative genomics to better understand the genetic basis of convergent evolution.

This study shows that H3K9me3 prevents nucleosome deposition at euchromatic promoters, affecting gene expression in C. elegans.