About

Dr. Ryan Duffy is a Professor in the Department of Psychology within the College of Liberal Arts and Sciences at the University of Florida. His contact information includes an email address (rduf@ufl.edu), a phone number ((352) 273-2199), and an office located in 218 Psychology Building. He is associated with the Counseling Psychology Program. The webpage provides a link to his personal website at http://www.drryanduffy.com/ which is hosted on resources not maintained by the University of Florida. The page does not include additional details about his research focus, background, or key contributions.

Research topics

• Biology
• Ecology
• Environmental planning
• Environmental health
• Geography
• Cancer research
• Medicine
• Oceanography
• Pathology
• Computational biology
• Virology
• Geology
• Zoology
• Genetics
• Fishery

Selected publications

• Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring

  NAR Genomics and Bioinformatics · 2026-03-27

  articleOpen accessSenior author

  Abstract As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.

  PublisherDOI

• PERSPECTIVES ON THE APPLICATION OF ENVIRONMENTAL DNA/RNA APPROACHES TO MOSQUITO SURVEILLANCE AND CONTROL IN FLORIDA

  Journal of the Florida Mosquito Control Association · 2025-05-21

  articleOpen accessSenior author

  Mosquito-borne diseases threaten four billion people globally, impacting public health and economies. Health, tourism, and agriculture in the United States are all affected by mosquitoes and the diseases they carry. Florida, in particular, faces increasing risks due to urban expansion, longer breeding seasons, and invasive mosquito species. The resurgence of locally contracted malaria in 2023, alongside threats like dengue, Zika, and chikungunya, highlights the urgent need for advanced monitoring. Beyond human health, mosquitoes also endanger Florida’s livestock, pets, and wildlife, adding to economic and ecological concerns.Environmental DNA/RNA (eDNA/eRNA), which captures genetic material from environmental samples, presents a groundbreaking solution. Already proven effective for tracking arthropod pests and disease vectors, eDNA can enhance mosquito surveillance by detecting species presence and assessing control effectiveness through DNA shed in the environment. Given Florida’s advanced mosquito control network, the state offers an ideal testing ground for implementing eDNA approaches.Integrating eDNA analysis into mosquito control strategies could revolutionize surveillance, providing a more efficient and cost-effective method for early detection. Additionally, eDNA/eRNA analysis of wastewater could enable real-time pathogen monitoring, while genomic tools could track insecticide resistance. eDNA and eRNA can be used together to obtain a comprehensive picture of biological communities. While eDNA captures both recent past and present evidence of an organism’s presence, eRNA primarily reflects current biological activity. This complementary approach allows researchers to detect species and assess their biological functions. This paper reviews the latest advancements in eDNA technologies and explores their potential to improve Florida’s mosquito surveillance, offering a powerful tool to enhance disease prevention, reduce economic losses, and strengthen public health efforts.

  PublisherOA PDFDOI

• Shotgun sequencing of airborne eDNA achieves rapid assessment of whole biomes, population genetics and genomic variation

  Nature Ecology & Evolution · 2025-06-03 · 16 citations

  articleOpen accessSenior author

  Biodiversity and its associated genetic diversity are being lost at an unprecedented rate. Simultaneously, the distributions of flora, fauna, fungi, microbes and pathogens are rapidly changing. Novel technology can help to capture and record genetic diversity before it is lost and to measure population shifts and pathogen distributions. Here we report the rapid application of shotgun long-read environmental DNA (eDNA) analysis for non-invasive biodiversity, genetic diversity and pathogen assessments from air. We also compared air eDNA with water and soil eDNA. Coupling long-read sequencing with established cloud-based biodiversity pipelines enabled a 2-day turnaround from airborne sample collection to completed analysis by a single investigator. To determine the full utility of airborne eDNA, we also conducted a local bioinformatic analysis and deep short-read shotgun sequencing. From outdoor air eDNA alone, comprehensive genetic analysis was performed, including population genetics (phylogenetic placement) of a charismatic mammal (bobcat, Lynx rufus) and a venomous spider (golden silk orb weaver, Trichonephila clavipes), and haplotyping humans (Homo sapiens) from natural complex community settings, such as subtropical forests and temperate locations. The rich datasets also enabled deeper analysis of specific species and genomic regions of interest, including viral variant calling, human variant analysis and antimicrobial resistance gene surveillance from airborne DNA. Our results highlight the speed, versatility and specificity of pan-biodiversity monitoring via non-invasive eDNA sampling using current benchtop/portable and cloud-based approaches. Furthermore, they reveal the future feasibility of scaling down (equipment and temporally) these approaches for near real-time analysis. Together these approaches can enable rapid simultaneous detection of all life and its genetic diversity from air, water and sediment samples for unbiased non-targeted information-rich genomics-empowered (1) biodiversity monitoring, (2) population genetics, (3) pathogen and disease-vector genomic surveillance, (4) allergen and narcotic surveillance, (5) antimicrobial resistance surveillance and (6) bioprospecting.

  PublisherOA PDFDOI

• Rapid pan-biodiversity lifeform and genomic diversity detection from shotgun sequencing of air eDNA

  Research Square · 2025-02-05

  preprintOpen access1st authorCorresponding
  PublisherOA PDFDOI

• International overview of sea turtle fibropapillomatosis: a survey of expert opinions and trends

  Frontiers in Cell and Developmental Biology · 2024-08-22 · 3 citations

  articleOpen accessSenior authorCorresponding

  Introduction Marine environments offer a wealth of opportunities to improve understanding and treatment options for cancers, through insights into a range of fields from drug discovery to mechanistic insights. By applying One Health principles the knowledge obtained can benefit both human and animal populations, including marine species suffering from cancer. One such species is green sea turtles ( Chelonia mydas ), which are under threat from fibropapillomatosis (FP), an epizootic tumor disease (animal epidemic) that continues to spread and increase in prevalence globally. In order to effectively address this epizootic, a more thorough understanding is required of the prevalence of the disease and the approaches to treating afflicted turtles. Methods To identify knowledge gaps and assess future needs, we conducted a survey of sea turtle FP experts. The survey consisted of 47 questions designed to assess general perceptions of FP, the areas where more information is needed, local FP trends, the disease status, and mitigation needs, and was voluntarily completed by 44 experts across a broad geographic range. Results Over 70% of respondents both recognized FP as a cancerous panzootic disease, and reported that FP is increasing in prevalence. They report several factors contributing to this increase. Nearly all of the respondents reported that FP research, patient treatment and rehabilitation required more funding in their area, and reported inadequate facilities and capacity for dealing with FP patients. Treatment approaches varied: just over 70% of the medical experts that responded surgically remove FP tumors, either using laser or scalpel. Just under half of respondents use anti-cancer drugs in their treatment of FP. Internal tumors were reported as justification for euthanasia by 61.5% of respondents, and 30.8% reported severe external tumors to be sufficient grounds for euthanasia. Most medical respondents (93.3%) routinely perform necropsy on deceased or euthanized FP-afflicted turtles. Over 80% of respondents considered large-scale multidisciplinary collaboration ‘extremely important’ for advancing the field of FP research. Discussion The survey responses provide a valuable insight into the current status of FP in sea turtles, FP treatment, rehabilitation and research, and help to identify critical FP-related areas most in need of attention.

  PublisherOA PDFDOI

• Global overview of sea turtle fibropapillomatosis tumors: a survey of expert opinions and trends

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-06-07

  preprintOpen accessSenior authorCorresponding

  Abstract Marine environments offer a wealth of opportunities to improve understanding and treatment options for cancers, through insights into a range of fields from drug discovery to mechanistic insights. By applying One Health principles the knowledge obtained can benefit both human and animal populations, including marine species suffering from cancer. One such species is green sea turtles ( Chelonia mydas ), which are under threat from fibropapillomatosis (FP), an epizootic tumor disease (animal epidemic) that continues to spread and increase in prevalence globally. In order to effectively address this epizootic, a more thorough understanding is required of the prevalence of the disease and the approaches to treating afflicted turtles. To identify knowledge gaps and assess future needs, we conducted a survey of sea turtle FP experts. The survey consisted of 47 questions designed to assess general perceptions of FP, the areas where more information is needed, local FP trends, the disease status, and mitigation needs, and was voluntarily completed by 44 experts across a broad geographic range. The survey responses provided a valuable overview of the current FP status in sea turtles, FP research, and insight into the approaches currently taken by turtle rehabilitation facilities around the world. Over 70% of respondents both recognized FP as a cancerous panzootic disease, and reported that FP is increasing in prevalence. They report several factors contributing to this increase. Nearly all of the respondents reported that FP research, patient treatment and rehabilitation required more funding in their area, and reported inadequate facilities and capacity for dealing with FP patients. Treatment approaches varied: just over 70% of the medical experts that responded surgically remove FP tumors, either using laser or scalpel. Just under half of respondents use anti-cancer drugs in their treatment of FP. Internal tumors were reported as justification for euthanasia by 61.5% of respondents, and 30.8% reported severe external tumors to be sufficient grounds for euthanasia. Most medical respondents (93.3%) routinely perform necropsy on deceased or euthanized FP-afflicted turtles. Over 80% of respondents considered large-scale multidisciplinary collaboration ‘extremely important’ for advancing the field of FP research. The survey responses provide a valuable insight into the current state of FP treatment, rehabilitation and research, and help to identify critical FP-related research and rehabilitation areas most in need of attention.

  PublisherOA PDFDOI

• Environmental DNA without borders

  EMBO Reports · 2024-09-25 · 10 citations

  articleOpen accessSenior author

  Towards the 10th anniversary of the Nagoya Protocol, it is time to embrace key technology developments and adapt existing red tape for genomic monitoring.

  PublisherOA PDFDOI

• Future research avenues for the study of fibropapillomatosis in sea turtles

  Frontiers in Ecology and Evolution · 2024-07-10 · 2 citations

  articleOpen access

  Fibropapillomatosis (FP) is a debilitating tumoral disease affecting sea turtles worldwide. While mainly afflicting immature individuals and potentially altering vital functions, the precise impact of this panzootic on turtle health and survival remains unclear. Moreover, the etiological factors implicated in the FP emergence, development and transmission are not yet definitively identified. Among them, an infection by a spreading herpesvirus and the contamination by pollutants (either organic pollutants and trace elements) are suspected. Here, we provide an overview of discoveries, knowledge and propose hypotheses related to FP within five key FP research areas, i.e., virology studies, transmission studies, contamination studies, host genomic studies, and veterinary treatment assays. Moreover, we recommend urgent research avenues to develop at the interface of virology, epidemiology, ecotoxicology, oncology, physiology, immunology, cellular and evolutionary biology, in order to characterize the dynamics of FP and to predict its consequences on sea turtle populations. Importantly, extending the implementation and development of strong collaborations between rehabilitation centers, field biologists and research laboratories at large geographical scale is required to rapidly increase our knowledge on FP and work towards its effective management.

  PublisherOA PDFDOI

• Long-read nanopore shotgun eDNA sequencing for river biodiversity, pollution and environmental health monitoring

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-11-03 · 6 citations

  preprintOpen accessSenior authorCorresponding

  Abstract As global temperatures rise, species populations and biodiversity decline, and infectious diseases emerge all at unprecedented rates, it is more vital than ever to accurately understand the current state of natural habitats. While traditional methods including direct sampling and observation have their merits, newer technologies offer additional sampling capabilities. Here, we assess the feasibility of a single assay: shotgun long-read sequencing, to monitor species eDNA from across the tree of life, from viruses to complex multicellular organisms, across a river system (mountain tributary to sea). We conducted eDNA sampling and shotgun long-read sampling from water taken from the Avoca River watercourse, Co. Wicklow, Ireland, from a mountain tributary through to the sea, and comparative nearby beach sand sampling. We report that shotgun long-read sequencing and metagenomic analysis have utility for the detection and quantification of organismal DNA present in eDNA samples, from across the tree of life, from microbes (including DNA viruses) to mammals. With this single assay we were able to simultaneously quantify differences in eDNA abundance for a broad range of biodiversity and pathogens across sites and sample types. This included human, wildlife, plant and microbial pathogens and parasites with health, agricultural and economic importance. Additionally, the generated eDNA genomic data enabled population genetic applications even from natural complex community settings, as demonstrated here for blue mussels ( Mytilus edulis ). The results demonstrate that Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution and environmental health monitoring. This method is more cost-effective and requires less laboratory preparation time or molecular expertise (barcode/primer design) than alternative biodiversity eDNA approaches (e.g. metabarcoding or qPCR). Shotgun analysis approaches will also benefit from the continual expansion of reference genome databases, for environmental, evolutionary and medical reasons, among others. Computation, cloud and artificial intelligence (AI) tools (such as the cloud-based analyses utilized here) can analyze shotgun sequencing eDNA data in a matter of hours and can be used by conservation practitioners, environmentalists and public health personnel without the need for coding or in-depth bioinformatics skills. The proven citizen/community scientist applicability and ease of eDNA sampling may further revolutionize and democratize biodiversity research, conservation surveillance, and environmental health monitoring. Long-read shotgun sequencing of eDNA offers the means to assess whole ecosystems, and the ecological, trophic, and host-pathogen interactions occurring within them.

  PublisherOA PDFDOI

• Supplementary Figure 3 from GSK3 Inhibitors Regulate <i>MYCN</i> mRNA Levels and Reduce Neuroblastoma Cell Viability through Multiple Mechanisms, Including p53 and Wnt Signaling

  2023-04-03

  preprintOpen access1st authorCorresponding

  <p>PDF - 259K, Figure S3. Additional p53 and neuroblastoma prognostic markers overlap data. A. p53 signalling pathway schematic with LiCl differentially regulated genes overlaid, key as in image and as described in Fig. 5B. B. Overlap between IPA predicted upstream regulators from inhibitor mRNA-seq (top 110) and a 157 neuroblastoma risk stratification gene signature (all 31), image generated using Venny.</p>

  PublisherOA PDFDOI

Frequent coauthors

• Walter Kölch

  77 shared

• Frank Westermann

  Heidelberg University

  77 shared

• Aleksandar Krstić

  University College Dublin

  76 shared

• Daniel Dreidax

  63 shared

• Thomas Schwarzl

  European Molecular Biology Laboratory

  60 shared

• Melinda Halász

  University College Dublin

  55 shared

• Matthias Fischer

  University of Cologne

  45 shared

• Dirk Fey

  43 shared