Dr. Heather Kates, Ph.D.

Bioinformatics analyst with ten years of experience in programming (R, Python as needed), pipeline development (HPC and cluster computing), genomic data processing, and statistical analysis.

Research Expertise

Genomics

Transcriptomics

Metabolomics

multi-omics integration

About

Bioinformatics analyst with ten years of experience in programming (R, Python as needed), pipeline development (HPC and cluster computing), genomic data processing, and statistical analysis. I have experience analyzing scRNA, RNAseq, spatial transcriptomics, GWAS, ChIP-Seq, ATAC-seq, metabolomics, and proteomics data. I build efficient and innovative workflows to distill significant signals from biological data and communicate them in a way that supports progress and insights.

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Publications

A targeted enrichment strategy for massively parallel sequencing of angiosperm plastid genomes

Applications in Plant Sciences

2013

Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae

Molecular Plant

2018

A database-driven approach identifies additional diterpene synthase activities in the mint family (Lamiaceae)

Journal of Biological Chemistry

2019

Allele phasing has minimal impact on phylogenetic reconstruction from targeted nuclear gene sequences in a case study of Artocarpus

American Journal of Botany

2018

High‐throughput methods for efficiently building massive phylogenies from natural history collections

Applications in Plant Sciences

2021

Distributions, conservation status, and abiotic stress tolerance potential of wild cucurbits (Cucurbita L.)

PLANTS, PEOPLE, PLANET

2019

The Effects of Herbarium Specimen Characteristics on Short-Read NGS Sequencing Success in Nearly 8000 Specimens: Old, Degraded Samples Have Lower DNA Yields but Consistent Sequencing Success

Frontiers in Plant Science

2021

Two shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants

Unknown Venue

2022

Phylogeny and Biogeography of Morus (Moraceae)

Agronomy

2023

Fagalean phylogeny in a nutshell: Chronicling the diversification history of Fagales

Unknown Venue

2023

Pumpkins, Squashes, and Gourds (Cucurbita L.) of North America

North American Crop Wild Relatives, Volume 2

2019

Phylogenomic Analyses Reveal Widespread Gene Flow During the Early Radiation of Oaks and Relatives (Fagaceae: Quercoideae)

Unknown Venue

2023

Testing the evolutionary drivers of nitrogen-fixing symbioses in challenging soil environments

Unknown Venue

2022

Spatial phylogenetics of Fagales: Investigating the history of temperate forests

Unknown Venue

2023

Investigating miR-9 as a mediator in laryngeal cancer health disparities

Frontiers in Oncology

2023

Phylogenetic diversity and regionalization of root nodule symbiosis

Unknown Venue

2023

Spatial phylogenetics of Fagales: Investigating drivers of temperate forest distributions

Journal of Biogeography

2024

Anatomy of a mega-radiation: Biogeography and niche evolution inAstragalus

Unknown Venue

2023

Rapid in situ diversification rates in Rhamnaceae explain the parallel evolution of high diversity in temperate biomes from global to local scales

New Phytologist

2024

Phylogenetic diversity and regionalization in the temperate arid zone

Unknown Venue

2023

Abstract C048: Computational pathway analysis of differentially expressed miRNAs in Black compared with White laryngeal squamous cell carcinoma

Cancer Epidemiology, Biomarkers & Prevention

2023

GeoMX Digital Spatial Profiler Whole Transcriptome Assay for Human Pancreas v1

Unknown Venue

2022

Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade

Unknown Venue

2021

Domesticated mammals and birds: Species accounts

The Process of Animal Domestication

2022

Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications

Frontiers in Ecology and Evolution

2021

Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci

Molecular Phylogenetics and Evolution

2017

Population genetic variation, geographic structure, and multiple origins of autopolyploidy in Galax urceolata

American Journal of Botany

2015

Phylogenomic analysis of the hemp family (Cannabaceae) reveals deep cyto‐nuclear discordance and provides new insights into generic relationships

Journal of Systematics and Evolution

2022

Education

University of Florida

Genomics / December, 2017

Gainesville, Florida, United States of America

Experience

University of Florida Department of Pathology & Immunology

Bioinformatics Analyst III / October, 2023 — Present

University of Florida Department of Pathology & Immunology

Data Management Analyst III / January, 2022 — October, 2023

University of Florida

Postdoctoral Researcher / January, 2018 — December, 2021

PhD Candidate and Research Fellow / August, 2011 — December, 2017

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