About

William (Brad) Barbazuk is a professor in the Department of Biology at the University of Florida. He earned his Ph.D. from Simon Fraser University in 1997. His research uses computational, comparative, and functional genomics to study genome architecture, function, and evolution. His lab works with crop genomes, particularly maize and tomato, as well as model (Arabidopsis) and non-model genomes, applying comparative analysis and computational methods to investigate gene structure, gene content, gene/genome organization, and regulation. His research projects include the analysis of next-generation sequencing data from multiple platforms to examine and characterize genomes and transcriptomes, as well as gene annotation and structure, which are foundational for plant molecular genetics and crop improvement. He collaborates on improving gene prediction in maize and tomato using tools like TWINSCAN. Additionally, his lab studies alternative splicing in plants, exploring its role in gene regulation, stress response, domestication, and trait selection, utilizing the increasing availability of plant genome sequence data to identify functionally important splicing events and their evolutionary conservation.

Research topics

• Biology
• Machine Learning
• Artificial Intelligence
• Genetics
• Computer Science
• Biochemistry
• Botany
• Zoology
• Neuroscience
• Cell biology

Selected publications

• simCRISPR: Modeling Experimental Complexity in Pooled CRISPR Screens

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-05-15

  article

  Abstract Pooled CRISPR screens are widely used to investigate gene function and uncover genetic interactions. However, benchmarking computational methods for detecting gene-by-environment (GxE) interactions remains difficult because ground truth is rarely available and existing simulation tools are not designed for GxE screening contexts. To address this, we developed simCRISPR , a flexible simulation framework for generating pooled CRISPR screen data under complex experimental designs. Using simulated datasets informed by empirical CRISPR screen designs, we evaluated commonly used analysis methods, comparing normalization strategies based on safe-harbor versus non-targeting sgRNAs and assessing empirical log 2 FC thresholds as an additional effect-size criterion. We found that safe-harbor-based normalization improved interaction detection when DNA damage-related effects were present, particularly when combined with empirical log 2 FC thresholding for DESeq2. Application of this workflow to a doxorubicin GxE screen further showed that safe-harbor-based normalization reduced bias in log 2 FC distributions and identified additional biologically relevant candidates. simCRISPR is available at https://github.com/bachergroup/simCRISPR .

  PublisherDOI

• Population genomics of the gametophyte‐only fern <i>Vittaria appalachiana</i> provides insights into clonal plant evolution

  New Phytologist · 2025-02-04 · 1 citations

  article

  How asexually reproducing organisms maintain genetic diversity and adaptive potential is a long-standing question in evolutionary biology. Asexual lineages have historically been thought of as evolutionary dead ends, yet some exhibit remarkable persistence through time. The gametophyte-only fern Vittaria appalachiana is a clonal eukaryote, the focus of extensive study due to its peculiar habit and life history, and is an excellent system to explore the consequences of asexuality. Using reduced representation sequencing and life cycle simulations, we assess theoretical expectations for genomic consequences of long-term asexual reproduction and test hypotheses about its origin and demographic history. We show that V. appalachiana colonies are not patches of single genotypes but are mosaics of genetic diversity, and the accumulation of mutations in the absence of recombination plays an important role in driving this diversity. We identify increased genomic variation, excess heterozygosity, decreased population differentiation, and increased effective population size, all of which are consistent with the expectations for prolonged clonality. Our analyses support the hypothesis that the loss of sexual reproduction in V. appalachiana occurred during the Last Glacial Maximum. Our results from empirical and simulation-based analyses illuminate how an asexual eukaryote generates, retains, and partitions genomic diversity.

  PublisherDOI

• The genome of the vining fern <i>Lygodium microphyllum</i> highlights genomic and functional differences between life phases of an invasive plant

  Proceedings of the National Academy of Sciences · 2025-09-25 · 3 citations

  articleOpen accessCorresponding

  Functional and genomic studies on the differences between the gametophyte and sporophyte life phases of plants remain scarce, yet unraveling these dynamics is crucial to understanding the biology of plants and the success of each phase under different conditions. Here, we provide a reference genome for the highly invasive fern Lygodium microphyllum and compare the transcriptomic and epigenomic landscapes of its gametophyte and sporophyte life phases. Under ambient conditions, we found differential regulation and splicing of developmental genes (homeobox and MADS-box clades) may play a role in the genomic determination of the haploid and diploid life stages. We generated a base pair-resolution methylome of a fern gametophyte, and determined that methylation patterns are remarkably similar between vegetative tissues despite their morphological and functional differences. We further explored the physiological and transcriptomic responses of gametophytes and sporophytes to freezing stress, the most likely abiotic factor limiting further range expansion of this invasive species. While controlled by the same genome, we show that life phases and tissues use alternative molecular pathways in response to freezing and greater physiological resilience in the gametophyte life stage to this stressor. Our results underscore the need to incorporate both life phases when developing effective mitigation strategies, as differential responses to environmental stressors between phases reveal opportunities for management approaches (e.g., targeting gametophytes in addition to sporophytes). These genomic resources fill a gap in our understanding of fundamental plant biology and inform invasive species research.

  PublisherOA PDFDOI

• Development of a homeolog-specific gene editing system in an evolutionary model for the study of polyploidy in nature

  Frontiers in Genome Editing · 2025-08-29 · 1 citations

  articleOpen access

  Polyploidy, or whole-genome duplication (WGD), is a significant evolutionary force. Following allopolyploidy, duplicate gene copies (homeologs) have divergent evolutionary trajectories: some genes are preferentially retained in duplicate, while others tend to revert to single-copy status. Examining the effect of homeolog loss (i.e., changes in gene dosage) on associated phenotypes is essential for unraveling the genetic mechanisms underlying polyploid genome evolution. However, homeolog-specific editing has been demonstrated in only a few crop species and remains unexplored beyond agricultural applications. Tragopogon (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy in nature. In this study, we developed a CRISPR-mediated homeolog-specific editing platform in allotetraploid T. mirus . Using the MYB10 and DFR genes as examples, we successfully knocked out the targeted homeolog in T. mirus (4 x ) without editing the other homeolog (i.e., no off-target events). The editing efficiencies, defined as the percentage of plants with at least one allele of the targeted homeolog modified, were 35.7% and 45.5% for MYB10 and DFR , respectively. Biallelic modification of the targeted homeolog occurred in the T 0 generation. These results demonstrate the robustness of homeolog-specific editing in polyploid Tragopogon , laying the foundation for future studies of genome evolution following WGD in nature.

  PublisherOA PDFDOI

• The genome of the vining fern <i>Lygodium microphyllum</i> highlights genomic and functional differences between life phases of an invasive plant

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-07 · 1 citations

  preprintOpen access

  Functional and genomic studies on the differences between gametophyte and sporophyte life phases remain scarce, yet unraveling these dynamics is crucial to understanding the biology of plants and the success of each phase under different environments. Here, we provide a novel reference genome for the highly invasive fern Lygodium microphyllum and compare the transcriptomic and epigenomic landscapes of the gametophyte and sporophyte life phases. We found differential regulation of developmental genes (homeobox and MADS-box clades) and usage of alternative isoforms that may play a role in the genomic determination of the haploid and diploid life stages. We further generated the first base pair-resolution methylome of a fern gametophyte, and determined that methylation patterns are remarkably similar between vegetative tissues despite their morphological and functional differences. By examining the physiological and transcriptomic responses of gametophytes and sporophytes to freezing stress, the most likely abiotic factor preventing further expansion of this invasive species, we show that life phases and tissues use alternative molecular pathways to respond to this stressor, underscoring the need to incorporate both life phases when developing effective mitigation strategies. These new genomic resources fill a gap in our understanding of fundamental plant biology and inform invasive species research.

  PublisherOA PDFDOI

• Characterizing common loss-of-function genes and their potential utility in assessing population variability and chemical susceptibility

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-19 · 1 citations

  articleOpen access

  Inter-individual and population variability in susceptibility to chemical exposures confounds determination of threshold exposure levels to protect the most vulnerable. Current risk assessment frameworks, in the absence of empiric chemical-specific data, generally recommend default or probabilistic adjustment factors to account for such variability. We present an experimental approach to incorporate common genetic variants potentially impacting population-level differences in toxicant susceptibility into human cell-based models for any cellular apical endpoint of interest. We focus on the genes with the most common aggregate loss-of-function (LoF) alleles in the gnomAD v3.0 data which we designated as the PopVarLoF set. Unexpectedly, enrichment analysis of these genes found significant overrepresentation of gene products playing important functional roles in toxicology. Interrogation of GWAS and PheWAS databases found that these genes are associated with diverse metabolic phenotypes consistent with the relevance of the PopVarLoF set in studying variability of toxicant response in human populations. We further characterized the PopVarLoF set by developing custom lentiviral CRISPR knockout libraries targeting the PopVarLoF genes to assess their functional essentiality in the HepG2/C3A cell line. Functional disruption of 14 of the PopVarLoF genes (~1 %) without toxicant exposure resulted in significant growth defects in this cell line, consistent with the majority of PopVarLoF gene products having non-essential roles. The development of human cell-based toxicity assays or other NAMs which include the empiric assessment of common genetic sources of population variability in susceptibility to chemical exposure could contribute to more robust risk assessment which protects vulnerable populations while reducing uncertainty.

  PublisherDOI

• Identification of Functional Genetic Components Modulating Toxicity Response to PFOS using Genome-wide CRISPR Screens in HepG2/C3A cells

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-19

  preprintOpen access

  Abstract Perfluorooctane sulfonate (PFOS) poses significant health and environmental risks due to its persistence and widespread use and has been linked to various adverse outcomes, such as liver toxicity. Although the molecular responses and toxicity effects of PFOS exposure have been extensively studied, considerable uncertainty remains regarding the causal mechanisms leading to PFOS-associated adverse effects. To help bridge this gap, we conducted CRISPR screens in HepG2/C3A human liver cells exposed to IC 25 (170 µM) of PFOS to identify genes and pathways influencing PFOS-induced cytotoxicity. Using a genome-wide CRISPR knockout library targeting 18,819 genes, we identified 340 candidate genes that modulate PFOS-induced cytotoxicity when genetically disrupted (189 gene disruptions increased sensitivity and 151 gene disruptions increased resistance). From these candidate genes, we individually disrupted two candidate genes, SLC6A9 which encodes the glycine transporter GlyT1, and CPSF2 , and confirmed increased resistance to PFOS exposure. Further, molecular docking analysis predicts that PFOS directly binds to GlyT1 and functional inhibition of GlyT1 also increases resistance to PFOS exposure. Gene-Disease outcome association analysis using the Comparative Toxicogenomics Database (CTD) indicated an enrichment of candidate genes associated with cancer-related and liver disease phenotypes. KEGG and STRING enrichment analyses found over representation of several biological pathways including DNA damage response and cell cycle. Lastly, cross-species conservation analysis using the top two validated gene targets found that their pathways were highly conserved in several environmentally relevant species. These findings provide new mechanistic and functional insights into PFOS-induced cytotoxicity, highlight potential molecular targets for toxicity mitigation, and establish a foundation for cross-species toxicogenomic modeling of PFOS health effects.

  PublisherOA PDFDOI

• Physiologically Relevant 3D CRISPR Screening Enhances Mechanistic Insight into Chemical Toxicity Compared to 2D Screening

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-19

  articleOpen access

  Abstract Many omics-based approaches in toxicology research primarily rely on correlative data, often lacking functional relationships or causal links between genotypes and phenotypes. CRISPR-based approaches can overcome this limitation by establishing direct causal connections between genes and toxicological phenotypes. Moreover, CRISPR screens enable scalable and systematic interrogation of gene function and associated mechanisms following chemical exposure, predominantly using in vitro models. In line with the paradigm of new approach methodologies (NAMs) in toxicology research, CRISPR screens hold promise to provide an in vitro cell-based functional toxicogenomics approach. One of the main limitations of conventional in vitro assays is their compromised physiological relevance to humans due to their inability to fully recapitulate in vivo physiology. To improve the functional and physiological relevance of the toxicogenomics approach, we developed a 3D CRISPR screening system using HepG2/C3A spheroids generated and cultivated in a continuously rotating bioreactor (ClinoStar). We first performed time-course 3D CRISPR screens to identify genes that confer growth disadvantage or advantage, influencing spheroid development compared to 2D cultures. We then applied this approach to a chemical toxicity study using doxorubicin, comparing the performance of the 3D and 2D systems in identifying chemical-specific mechanisms. The results showed that the 3D system captured more candidate genetic determinants and biological pathways related to DNA damage processes—a known toxicity mechanism of doxorubicin—demonstrating improved performance in identifying chemical-specific pathways over the 2D counterpart. In our screens, we employed custom CRISPR sgRNA libraries representing common human loss-of-function genetic variants (mean allele frequency &gt; 0.1% in all individuals catalogued in the genome aggregation database), which potentially affect toxicity responses. By comparing our CRISPR screen results with previously reported genetic associations for doxorubicin response, we found that the 3D system identified more known associated genes than the 2D system. Together, the 3D CRISPR screening system demonstrated its feasibility and utility for physiologically relevant functional toxicogenomics. This platform enables in vitro NAMs, by providing a scalable and effective approach to identify causal genetic determinants and biological pathways that modulate chemical-induced toxicity.

  PublisherDOI

• Development of an efficient CRISPR-mediated genome editing platform in the diploid-polyploid model system <i>Tragopogon</i> (Asteraceae)

  Journal of Experimental Botany · 2025-08-25 · 2 citations

  article

  Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force. However, the mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. Tragopogon (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy. In this study, we significantly improved the transformation system and obtained genome-edited T. porrifolius (2x) and T. mirus (4x) primary generation (T0) individuals. Using CRISPR/Cas9, we knocked out the dihydroflavonol 4-reductase (DFR) gene, which controls anthocyanin synthesis, in both species. All transgenic allotetraploid T. mirus individuals had at least one mutant DFR allele, and 71.4% had all four DFR alleles edited. The resulting mutants lacked anthocyanin, and these mutations were inherited in the T1 generation. This study demonstrates a highly efficient CRISPR platform, producing genome-edited Tragopogon individuals that have completed the life cycle. The approaches used and challenges faced in building the CRISPR system in Tragopogon provide a framework for building similar systems in other non-genetic models. Genome editing in Tragopogon paves the way for novel functional biology studies of polyploid genome evolution and the consequences of WGD on complex traits, holding enormous potential for both basic and applied research.

  PublisherDOI

• A Circadian Light Regulator Controls a Core CAM Gene in the Ice Plant's C3-to-CAM Transition

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-06

  preprintOpen access

  Crassulacean acid metabolism (CAM) enhances drought tolerance by shifting carbon fixation to the night, improving water-use efficiency compared to C3 and C4 photosynthesis. However, the molecular regulators of CAM induction remain poorly understood. Here, we generate the first single-nucleus transcriptome atlas of a CAM species, Mesembryanthemum crystallinum, to resolve transcriptional dynamics at the cell-type level during the C3-to-CAM transition. Using snRNA-seq and a 24-hour time-course bulk RNA-seq dataset, we identify PPCK1, a key CAM enzyme regulator, as part of a co-expression network enriched in circadian clock genes and salt-induced pathways. We demonstrate that the ice plant HY5 (McHY5) directly activates PPCK1, a function absent in the C3 model species Arabidopsis thaliana. This discovery reveals a fundamental divergence in transcription factor activity between a CAM and a C3 species, suggesting that CAM evolution in M. crystallinum involved a rewiring of core regulatory elements underlying CAM. Identifying a transcription factor that directly controls a major CAM gene provides a key step toward decoding CAM regulatory architecture and opens new avenues for engineering drought-resilient crops.

  PublisherOA PDFDOI

Recent grants

• Ab Initio Gene Finding in Maize

  NSF · $721k · 2005–2009

• TOOLS-PGR Alternative Splice Isoforms in Plant Genomes: Collection, Characterization and Evolutionary Relationships

  NSF · $458k · 2016–2020

Frequent coauthors

• John D. McPherson

  University of California, Davis

  108 shared

• Stephen L. Johnson

  Transylvania University

  107 shared

• Pamela S. Soltis

  Florida Museum of Natural History

  107 shared

• Patricia Tellis

  McGill University Health Centre

  106 shared

• Marc Ekker

  University of Ottawa

  106 shared

• Mario Chevrette

  McGill University

  106 shared

• Leonard I. Zon

  Boston Children's Museum

  106 shared

• Igor B. Dawid

  Eunice Kennedy Shriver National Institute of Child Health and Human Development

  106 shared

Labs

• William (Brad) BarbazukPI

Education

• PhD, Biology

  Simon Fraser University

  1997

• B.Sc, BioChemistry

  Simon Fraser University

  1990