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Alex Harkess

HudsonAlpha Institute for Biotechnology · US
Area of research
Plant Science · Molecular Biology
Research interest
Research interests include Chromosomal and Genetic Variations, Plant Reproductive Biology, Genomics and Phylogenetic Studies, and Plant Molecular Biology Research.
h-index
27
citations
4,409
works
126
NIH funding
primary concept
email

Recent publications

Trait Mapping Utilizing a Newly Constructed Genome for Allohexaploid Invasive Eurasian Watermilfoil ( <scp> <i>Myriophyllum spicatum</i> </scp> ) Reveals a Non‐Target Site <scp>QTL</scp> Associated With Fluridone Resistance
Evolutionary Applications 2026cited by 0position: middledoi
Leveraging whole-genome re-sequencing for diversity, population structure, and a public mid-density genotyping enrichment panel in crimson clover ( <i>Trifolium incarnatum L</i> .) for breeding purposes
bioRxiv (Cold Spring Harbor Laboratory) 2026cited by 0position: middledoi
Haplotype-phased genomes elucidate genetic architecture of environmental adaptation and domestication traits in Silphium
Research Square 2026cited by 0position: lastdoi
Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome
Nature 2025cited by 31position: middledoi
Mesopolyploidy as a taxonomic clade marker for <i>Brassica</i> and relatives (tribe Brassiceae)
Annals of Botany 2025cited by 2position: middledoi
Long-Read Low-Pass Sequencing for High-Resolution Trait Mapping
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 1position: middledoi
A haplotype-resolved, chromosome-scale genome assembly for the southern live oak, <i>Quercus virginiana</i>
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 1position: lastdoi
Characterization of the complete plastid genome sequence of <i>Magnolia buenaventurensis</i> Á.J. Pérez &amp; E. Rea (Magnoliaceae), a newly described species endemic to the Ecuadorian Andes
Mitochondrial DNA Part B 2025cited by 0position: middledoi
Gene duplication dynamics and regulatory evolution shape the diversification of Asteraceae
bioRxiv (Cold Spring Harbor Laboratory) 2025cited by 0position: middledoi
ZW sex chromosome structure in Amborella trichopoda
Nature Plants 2024cited by 26position: lastdoi
A chromosome-scale assembly for ‘d’Anjou’ pear
G3 Genes Genomes Genetics 2024cited by 15position: lastdoi
An X-linked sex determination mechanism in cannabis and hop
bioRxiv (Cold Spring Harbor Laboratory) 2024cited by 14position: lastdoi
Elucidation of the pathway for biosynthesis of saponin adjuvants from the soapbark tree
Science 2023cited by 157position: middledoi
Complex scaffold remodeling in plant triterpene biosynthesis
Science 2023cited by 127position: middledoi
Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset
Current Biology 2023cited by 124position: middledoi
Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics
Nature Plants 2023cited by 88position: middledoi
Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance
New Phytologist 2023cited by 20position: middledoi
Complementing model species with model clades
The Plant Cell 2023cited by 15position: lastdoi
A chromosome-scale assembly for ‘d’Anjou’ pear
bioRxiv (Cold Spring Harbor Laboratory) 2023cited by 1position: lastdoi
GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
eLife 2022cited by 396position: middledoi
Dynamic genome evolution in a model fern
Nature Plants 2022cited by 194position: middledoi
Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes
Frontiers in Plant Science 2022cited by 49position: middledoi
Representing sex chromosomes in genome assemblies
Cell Genomics 2022cited by 41position: lastdoi
A phased, chromosome-scale genome of ‘Honeycrisp’ apple (Malus domestica)
Gigabyte 2022cited by 33position: middledoi
Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes
Frontiers in Plant Science 2022cited by 26position: middledoi
Automated imaging of duckweed growth and development
Plant Direct 2022cited by 19position: lastdoi
GENESPACE: syntenic pan-genome annotations for eukaryotes
bioRxiv (Cold Spring Harbor Laboratory) 2022cited by 15position: middledoi
The contributions of Nettie Stevens to the field of sex chromosome biology
Philosophical Transactions of the Royal Society B Biological Sciences 2022cited by 8position: lastdoi
A phased, chromosome-scale genome of ‘Honeycrisp’ apple ( <i>Malus domestica</i> )
bioRxiv (Cold Spring Harbor Laboratory) 2022cited by 3position: middledoi
Author response: GENESPACE tracks regions of interest and gene copy number variation across multiple genomes
2022cited by 2position: middledoi

Grants

Collaborative Research: EDGE FGT: Development of Sphagnum (peat) moss as a lab model system for physiological, molecular and functional genomics studies
NSF2421469$674,0852024–2028PIRePORTER
CAREER: Characterizing the repeated evolution of dioecy in plants to engineer artificial chromosomes
NSF2239530$1,283,7532023–2028PIRePORTER
Collaborative Research: EDGE FGT: Transformation and Genomic Resources to Advance Diverse, Emerging Model Angiosperms
NSF2335775$159,7162023–2025PIRePORTER
Collaborative Research: EDGE FGT: Transformation and Genomic Resources to Advance Diverse, Emerging Model Angiosperms
NSF2128196$236,9082021–2023PIRePORTER
NSF Postdoctoral Fellowship in Biology FY 2016
NSF1611853$216,0002016–2019PIRePORTER

Frequent collaborators

Sarah B. Carey · HudsonAlpha Institute for Biotechnology10 papers (2021–2026)Jim Leebens‐Mack · University of California, Berkeley6 papers (2014–2024)Jeremy Schmutz · The University of Texas at Austin6 papers (2022–2025)Claude W. dePamphilis · Pennsylvania State University5 papers (2020–2022) · 5 papers (2020–2022)Laramie Aközbek · HudsonAlpha Institute for Biotechnology5 papers (2022–2026)Haley Hale · HudsonAlpha Institute for Biotechnology5 papers (2022–2026)Huiting Zhang · Pennsylvania State University4 papers (2021–2022)Blake C. Meyers · University of California, Davis4 papers (2020–2022)Paula E. Ralph · University of Arizona4 papers (2020–2022)J. Chris Pires · University of California, Berkeley4 papers (2020–2025)Melissa A. Wilson · National Human Genome Research Institute4 papers (2022–2022)Josh Clevenger · The Ohio State University4 papers (2024–2026)Loren Honaas · Pennsylvania State University4 papers (2021–2022) · 3 papers (2020–2022)Walid Korani · University of Georgia3 papers (2024–2026)Joseph W. Carlson · Lawrence Berkeley National Laboratory3 papers (2022–2022)Zachary Meharg · HudsonAlpha Institute for Biotechnology3 papers (2025–2026)Patrick P. Edger · University of Arizona3 papers (2020–2025)Eric Wafula · Pennsylvania State University3 papers (2021–2022)