Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts

KE Dougan, RA González-Pech, TG Stephens… - Trends in …, 2022 - cell.com
Modern microbial taxonomy generally relies on the use of single marker genes or sets of
concatenated genes to generate a framework for the delineation and classification of …

A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data

J Van Etten, TG Stephens, D Bhattacharya - Systematic biology, 2023 - academic.oup.com
In the age of genome sequencing, whole-genome data is readily and frequently generated,
leading to a wealth of new information that can be used to advance various fields of …

Alignment-free analysis of whole-genome sequences from Symbiodiniaceae reveals different phylogenetic signals in distinct regions

R Lo, KE Dougan, Y Chen, S Shah… - Frontiers in Plant …, 2022 - frontiersin.org
Dinoflagellates of the family Symbiodiniaceae are predominantly essential symbionts of
corals and other marine organisms. Recent research reveals extensive genome sequence …

Comparative study of encoded and alignment-based methods for virus taxonomy classification

MA Shaukat, TT Nguyen, EB Hsu, S Yang, A Bhatti - Scientific reports, 2023 - nature.com
The emergence of viruses and their variants has made virus taxonomy more important than
ever before in controlling the spread of diseases. The creation of efficient treatments and …

The genome of a giant clam zooxanthella (Cladocopium infistulum) offers few clues to adaptation as an extracellular symbiont with high thermotolerance

RA González-Pech, J Shepherd, ZL Fuller… - BMC genomics, 2024 - Springer
Abstract Background Cladocopium infistulum (Symbiodiniaceae) is a dinoflagellate
specialized to live in symbiosis with western Pacific giant clams (Tridacnidae). Unlike coral …

Estimating Genome-wide Phylogenies Using Probabilistic Topic Modeling

M Khodaei, SV Edwards, P Beerli - bioRxiv, 2023 - biorxiv.org
Inferring the evolutionary history of species or populations with genome-wide data is gaining
ground, but computational constraints still limit our abilities in this area. We developed an …