About

John Davis is an associate dean for research and associate director of the Florida Agricultural Experiment Station at the University of Florida's School of Forest, Fisheries, and Geomatics Sciences. He specializes in forest ecosystem health, tree-pathogen coevolution, and forest genomics. Davis earned his Ph.D. in plant breeding and genetics-forestry from Michigan State University in 1989 and has been a faculty member at UF/IFAS since 1992. His research has focused on identifying the function of genes involved in ecologically important traits of Populus and Pinus, and he has served as Co-Director of the Forest Biology Research Cooperative since 2002, supporting research aimed at sustaining healthy forests through outdoor laboratory studies. Davis has successfully contributed to proposals to USDA, NSF, and DOE, resulting in $13 million in extramural and in-kind support for gene discovery and functional studies. He has served on scientific advisory boards for Genome Canada and the Forest Health Initiative, and has been involved in graduate coordination for intercollegiate degree programs in Genetics & Genomics and Plant Molecular and Cellular Biology. Davis has authored 70 peer-reviewed journal articles and 45 technical reports, given numerous international presentations, and received multiple awards for his research and service.

Research topics

• Biology
• Genetics
• Computer Science
• Medicine
• Computational biology
• Bioinformatics
• Immunology
• Psychiatry
• Psychology
• Clinical psychology
• Internal medicine

Selected publications

• Genome Sequence and Population Genomic Analysis of <i>Cronartium quercuum</i> f.sp. <i>fusiforme</i>

  Forest Pathology · 2026-01-08

  article

  ABSTRACT Fusiform rust, caused by Cronartium quercuum f. sp. fusiforme ( Cqf ), is the most severe disease of planted southern pines in the south‐eastern United States. Despite the critical role pathogen genomics play in disease outcomes, the population structure and genetic variability of Cqf remain poorly characterised. To address this gap, we generated a high‐quality chromosome‐scale genome assembly of Cqf and leveraged this resource to perform the population genomic analyses of 274 haploid pycniospore samples derived from controlled inoculations with geographically diverse aeciospore collections. The assembled Cqf genome (87.03 Mbp across 19 contigs) displayed high completeness (BUSCO: 91.1%) and structural continuity (Scaffold N50: 5.4 Mbp), establishing a robust reference for population‐genetic analysis. PCA, DAPC and ADMIXTURE revealed a pronounced east–west structure indicating five genetically distinct metapopulations (Western Gulf, Upper Central Gulf, Lower Central Gulf, Lower Atlantic Coast/Eastern Piedmont, Mid‐Atlantic Coast). AMOVA revealed that high levels of variation exist in Cqf , with the greatest proportion of genetic variation occurring in local populations (85.5%) with moderate differentiation among regional metapopulations ( Φ = 0.117). Sliding‐window F ST analyses highlighted the genomic regions of elevated differentiation, including loci encoding candidate secreted effector proteins. Genetic diversity metrics revealed evidence of non‐random mating in some regions. These results refine the understanding of Cqf population structure, confirm the relevance of USDA Resistance Screening Center geographic zones and provide novel genomic resources to support breeding for durable fusiform rust resistance in southern pines.

  PublisherDOI

• Constitutive and inducible oleoresin defenses share genetic architectures and mechanisms in <i>Pinus taeda</i>

  New Phytologist · 2026-04-16

  articleOpen access

  The oleoresin defense system of loblolly pine (Pinus taeda) protects trees from insects and pathogens and is an important source of renewable biofuels and chemicals, but the genetic basis of oleoresin production is poorly understood. We characterized the genetic architecture of oleoresin flow, resin canal number, stem wood terpene content, and monoterpene composition in two clonal populations of P. taeda. We used quantitative genetic analyses, genome-wide association studies (GWASs), multiplex network learning, and gene expression profiling to elucidate shared gene networks underlying defense traits and to identify high-quality candidates for breeding and engineering loblolly pine. Genetic analyses revealed polygenic inheritance and trait-to-trait correlations provide strong evidence for shared genes regulating constitutive and induced oleoresin flow. We identified 236 single nucleotide polymorphisms associated with oleoresin flow, resin canal number, and terpene composition and highlight candidate genes likely involved in terpene biosynthesis, cambial meristem reprogramming, and pathogen perception and immune signaling. Fourteen GWAS candidates were methyl jasmonate-responsive in tissues where resin canals initiate and terpene production occurs. Integrating quantitative genetics, GWAS, gene expression, and multiplex network analyses enabled the prioritization of high-quality candidate genes. This work advances the development of more resilient loblolly pine optimized for ecological performance, renewable chemical, and biofuel production.

  PublisherOA PDFDOI

• Efficacy and Safety of Sulforaphane Added to Antipsychotics for the Treatment of Negative Symptoms of Schizophrenia

  The Journal of Clinical Psychiatry · 2025-01-20 · 13 citations

  articleOpen access

  Objective: There are few established treatments for negative symptoms in schizophrenia, which persist in many patients after positive symptoms are reduced.Oxidative stress, inflammation, and epigenetic modifications involving histone deacetylase (HDAC) have been implicated in the pathophysiology of schizophrenia.Sulforaphane has antioxidant properties and is an HDAC inhibitor.We conducted a 24-week, double-blind, placebo-controlled study, in Hunan, China, to assess the effect of high-dose sulforaphane (Nutramax extra strength sulforaphane tablets glucoraphanin content 30 mg/ tablet) on reducing negative symptoms in antipsychotic-treated patients with schizophrenia.Methods: Participants were recruited from August 2020 to August 2022 and met DSM-5 criteria for schizophrenia.Participants were randomly assigned (2:1 ) to receive antipsychotics plus sulforaphane (1,700 mg Avmacol Extra Strength sulforaphane daily) or antipsychotics plus placebo for 24 weeks.Fifty-three patients treated with sulforaphane and 24 patients treated with placebo who had at least 1 postintervention clinical scale evaluation were analyzed.The primary outcome measure was change in the Positive and Negative Syndrome Scale (PANSS) negative symptoms.Results: Sulforaphane-treated patients showed a significantly greater decrease in PANSS negative symptom total score (P = .01)and PANSS negative factor score (P = .02)than placebo-treated patients, with the most prominent difference occurring at 24 weeks (P .001)with a large effect size at this time point (d = 0.8).Sulforaphane's effect on decreasing negative symptoms was not mediated by changes in scores of depression or cognitive factors on the PANSS. Conclusions:The results of this study suggest that add-on high-dose sulforaphane may reduce negative symptoms in patients with schizophrenia.The clinical significance of this reduction in negative symptoms needs further evaluation.

  PublisherOA PDFDOI

• Effects of transcranial alternating current stimulation on measures of cognition and symptom scores in Chinese patients with schizophrenia

  Journal of Psychiatric Research · 2025-01-30 · 5 citations

  articleOpen access

  Transcranial alternating current stimulation (tACS) may have effects on cognition and symptoms in psychiatric illness but there have been few randomized controlled studies in people with schizophrenia. We conducted a randomized sham-controlled double-blind study of 40 Hz tACS on measures of cognition and symptoms scores in 50 patients diagnosed with DSM-5 schizophrenia. tACS was delivered in 10 sessions (20 min each) over a 2-week period. Evaluations were conducted with multiple cognitive and symptom batteries after 10 sessions and at 2 weeks and 4 weeks post-treatment, and also on-line during the tACS stimulation session 1. The primary outcome measured changes in the MATRICS overall composite score. The results showed no statistically significant (P < 0.05) effects of active vs. sham on improvement in any of the cognitive measures or PANSS rated positive or negative symptoms. There was a trend (P < 0.06) for the MATRICS Domain score of verbal learning to show greater improvement of active tACS compared to sham within 1-2 days after the 10 tACS sessions. Additional trials are needed to determine the effective tACS parameters targeting cognition and symptoms of schizophrenia.

  PublisherDOI

• Integrative multi-omic profiling in blood reveals distinct immune and metabolic signatures between ACPA-negative and ACPA-positive rheumatoid arthritis

  Frontiers in Immunology · 2025-10-29 · 3 citations

  articleOpen access

  Objective: To investigate whether patients with ACPA-negative (ACPA-) and ACPA-positive (ACPA+) rheumatoid arthritis (RA) exhibit distinct immune and metabolic profiles in blood, using integrative proteomic and metabolomic analyses. By uncovering subgroup-specific molecular signatures, we aim to improve the biological understanding of RA heterogeneity and support the development of more precise diagnostic and stratification strategies. Methods: We performed high-throughput proteomic and metabolomic profiling on plasma from a well-characterized cohort comprising 40 patients with ACPA- RA, 40 patients with ACPA+ RA, and 40 healthy controls. To identify key immune and metabolic differences, we applied statistical comparisons, pathway enrichment analyses, and network inference methods. Additionally, an integrative network-based machine learning framework was used to distinguish RA subgroups from controls based on plasma molecular profiles. Results: ACPA- and ACPA+ RA exhibited distinct plasma proteomic and metabolomic biomolecular signatures. Complement proteins (CFB, CFHR5, and F9) and the anti-inflammatory cytokine IL1RN were exclusively elevated in ACPA- RA and remained distinct in a treatment-naïve sub-cohort. Metabolomic analysis revealed subgroup-specific differences in lipid and pyrimidine metabolism, including contrasting patterns in bilirubin-derived metabolites. Correlation analyses identified differential associations between molecular features and clinical inflammatory markers across RA subgroups. An integrative machine learning framework incorporating multi-omic features achieved high classification performance in cross-validation (AUC ≥ 0.90), outperforming models based on single-omic data. Conclusion: This study suggests that ACPA status may not fully capture the biological heterogeneity between ACPA- and ACPA+ RA subgroups, indicating additional immune and metabolic distinctions that warrant further investigation. Our findings highlight the potential of multi-omic profiling to enhance RA diagnostics, refine disease stratification, and inform subgroup-specific disease management strategies.

  PublisherOA PDFDOI

• The scholarship of honorifics

  Crop Science · 2024-03-03

  article1st authorCorresponding

  Abstract Nomination is a scholarly activity, not unlike writing a manuscript or grant proposal. Nomination is elevated by recognizing both recipients and nominators. A nominagraph adds a dimension to the pairwise listing of recipients and nominators on ASA/CSSA/SSSA directories.

  PublisherDOI

• Genomics of Disease Resistance in Loblolly Pine

  Compendium of plant genomes · 2022-01-01

  book-chapterSenior author
  PublisherDOI

• Efficacy of Sulforaphane in Treatment of Children with Autism Spectrum Disorder: A Randomized Double-Blind Placebo-Controlled Multi-center Trial

  Journal of Autism and Developmental Disorders · 2022 · 25 citations

  • Psychology
  • Clinical psychology
  • Psychiatry
  PublisherDOI

• TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes

  mSystems · 2022 · 10 citations

  • Computer Science
  • Computational biology
  • Biology

  Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.

  PublisherDOI

• NLR diversity and candidate fusiform rust resistance genes in loblolly pine

  G3 Genes Genomes Genetics · 2021 · 15 citations

  Senior authorCorresponding
  • Biology
  • Genetics

  Resistance to fusiform rust disease in loblolly pine (Pinus taeda) is a classic gene-for-gene system. Early resistance gene mapping in the P. taeda family 10-5 identified RAPD markers for a major fusiform rust resistance gene, Fr1. More recently, single nucleotide polymorphism (SNP) markers associated with resistance were mapped to a full-length gene model in the loblolly pine genome encoding for a nucleotide-binding site leucine-rich repeat (NLR) protein. NLR genes are one of the most abundant gene families in plant genomes and are involved in effector-triggered immunity. Inter- and intraspecies studies of NLR gene diversity and expression have resulted in improved disease resistance. To characterize NLR gene diversity and discover potential resistance genes, we assembled de novo transcriptomes from 92 loblolly genotypes from across the natural range of the species. In these transcriptomes, we identified novel NLR transcripts that are not present in the loblolly pine reference genome and found significant geographic diversity of NLR genes providing evidence of gene family evolution. We designed capture probes for these NLRs to identify and map SNPs that stably cosegregate with resistance to the SC20-21 isolate of Cronartium quercuum f.sp. fusiforme (Cqf) in half-sib progeny of the 10-5 family. We identified 10 SNPs and 2 quantitative trait loci associated with resistance to SC20-21 Cqf. The geographic diversity of NLR genes provides evidence of NLR gene family evolution in loblolly pine. The SNPs associated with rust resistance provide a resource to enhance breeding and deployment of resistant pine seedlings.

  PublisherDOI

Recent grants

• NIH Grant U01MH026975

  NIH · $56k · 1986

Frequent coauthors

• Harald Hagemann

  University of Hohenheim

  324 shared

• Gary Mongiovi

  University College London

  324 shared

• Rebeca Gómez Betancourt

  324 shared

• Maria Pia Paganelli

  324 shared

• Luca Fiorito

  Belgian Nuclear Research Centre

  324 shared

• Andrew Farrant

  324 shared

• Mary Morgan

  324 shared

• Scott Scheall

  324 shared

Awards & honors

• Served on Scientific Advisory Boards for Genome Canada and f…
• Received numerous awards and honors for his research and ser…