Recent Publications:

Koda, S.A., McCauley, M., Farrell, J.A., Duffy, I. Duffy, F. Loesgen, S., Whilde, J., Duffy. D.J. 2023. A novel eDNA approach for rare species monitoring: application of longread shotgun sequencing to Lynx rufus soil pawprints. Biological Conservation, 287, 110315.

Whitmore, L., McCauley, M., Farrell, J.A., Stammnitz, M.R., Koda, S.A., Mashkour, N., Summers, V., Osborne, T.Z., Whilde, J., Duffy, D.J., 2023. Inadvertent human genomic bycatch and intentional capture raise beneficial application and ethical concerns with environmental DNA. Nature Ecology and Evolution 7: 873-888

Bentley, B.P., Carrasco-Valenzuela, T., Ramos, E.K.S., Pawar, H., Arantes, L.S., Alexander, A., Banerjee, S.M., Masterson, P., Kuhlwilm, M., Pippel, M., Mountcastle, J., Haase, B., Silva, M.U., Formenti, G., Howe, K., Chow, W., Tracey A., Sims, Y., Pelan, S., Wood, J., Yetsko, K., Perrault, J.R., Stewart, K., Benson, S.R., Levy, Y., Todd, E.V., Shaffer, H.B., Scott, P., Henen, B.T., Murphy, R.W., Mohr, D.W., Scott, A.F, Duffy, D.J., Gemmell, N.J., Suh, A., Winkler, S., Thibaud-Nissen, F., Nery, M.F., Marques-Bonet, T., Antunes, A, Tikochinski, Y., Dutton, P.H., Fedrigo, O., Myers, E.W., Jarvis, E.D., Mazzoni, C.J., and Komoroske, L.M. 2023. Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories. Proceedings of the National Academy of Sciences of the United States of America (PNAS). 7 (120), e2201076120. doi:10.1073/pnas.2201076120. IF 12.779

Manes, C., Herren, R.M., Page, A., Dunlap, F.D., Skibicki, C.A., Rollinson Ramia, D.R., Farrell, J.A., Capua, I., Carthy, R. R. and Duffy, D.J. 2023. Green turtle fibropapillomatosis: Tumor morphology and growth rate in a rehabilitation setting. Veterinary Sciences. 10 (7), 421. IF 2.4.

Farrell, J.A., Whitmore, L., Mashkour, N., Rollinson Ramia, D., Thomas, R.S., Eastman, C.B., Burkhalter, B., Yetsko, K., Mott, C., Wood, L., Zirkelbach, B., Meers, L., Kleinsasser, P., Stock, S., Libert, E., Herren, R., Eastman, S., Crowder, W., Bovery, C., Anderson, D., Godfrey, D., Condron, N., and Duffy, D.J. 2022. Detection and population genomics of sea turtle species via non-invasive environmental DNA analysis of nesting beach sand tracks and oceanic water. Molecular Ecology Resources, 22 (7), 2471-2493. https:// IF 7.090. Altmetric score 98. Includes the involvement of citizen scientists.

Romano, D., García-Gutiérrez, L., Aboud, N., Duffy, D.J., Flaherty, K.T., Frederick, D.T., Kolch, W., and Matallanas, D. 2022. Proteasomal Down-Regulation of the Proapoptotic Mst2 Pathway Contributes to Braf Inhibitor Resistance in Melanoma. Life Science Alliance 5, no. 10: e202201445.

Beigzadeh, K., Rieland, J., Eastman, C., Duffy, D.J. and Love, B.J. 2022. Characterization of Ingested Plastic Microparticles Extracted from Sea Turtle Post-Hatchlings at Necropsy. Microplastics 1(2), 254-262.

Romano, D., Garcia-Gutierrez, L., Duffy, D. J., Flaherty, K., Frederick, D. T., Kolch W. and Matallanas D. (2022). Proteasomal downregulation of the pro-apoptotic MST2 pathway contributes to BRAF inhibitor resistance in melanoma. bioRxiv: 2022.2002.2021.481296.

Yetsko, K., Farrell, J., Blackburn, N. B., Whitmore, L., Stammnitz, M. R., Whilde, J., Eastman, C., Rollinson Ramia, D., Thomas, R., Krstic, A., Linser, P., Creer, S., Carvalho, G., Devlin, M., Nahvi, N., Leandro, A. C., deMaar, T. W., Burkhalter, B., Murchison, E.P., Schnitzler, C. and Duffy, D. J. (2021). Molecular characterization of a marine turtle tumor epizootic, profiling external, internal and postsurgical regrowth tumors. Communications Biology. 2021;4(1):152.

Eastman, C., Farrell, J., Whitmore, L., Rollinson Ramia, D., Thomas, R., Prine, J., Eastman, S., Osborne, T. Z., Martindale, M. Q., and Duffy, D. J. (2020). Plastic Ingestion in Post-hatchling Sea Turtles: Assessing a Major Threat in Florida Near Shore Waters. Frontiers in Marine Science.

Yetsko, K., Farrell, J., Stammnitz, M. R., Whitmore, L., Whilde, J., Eastman, C., Rollinson Ramia, D., Thomas, R., Krstic, A., Linser, P., Creer, S., Carvalho, G., Burkhalter, B., Murchison, E.P., Schnitzler, C. and Duffy, D. J. (2020). Mutational, transcriptional and viral shedding dynamics of the marine turtle fibropapillomatosis tumor epizootic. bioRxiv (Preprint). DOI: 10.1101/2020.02.04.932632.

Duffy, D. J. and Burkhalter, B. (2020). When is a lab animal not a lab animal? - Rehabilitation of tumor-afflicted sea turtles, and their utilization as a natural model for human and wildlife cancers. Lab Animal, Nature, 49, 95–98

Duffy, D. J. and Martindale, M. Q. (2019). Perspectives on the expansion of human precision oncology and genomic approaches to sea turtle fibropapillomatosis. Communications Biology, 2 (1): 54. Invited comment paper.

Whilde, J., Whitmore, L., Yang, C., Eastman, C., Thomas, R., Burkhalter, B., Martindale, M. Q. and Duffy, D. J. (2019). Behaviour of juvenile green turtles (Chelonia mydas) before and after fibropapillomatosis tumour removal. Testudo, 9 (1): 22-35.

Duffy, D. J., Schnitzler, C., Karpinski, L., Thomas, R., Whilde, J., Eastman, C., Yang, C., Krstic, A., Rollinson, D., Zirkelbach, B., Yetsko, K., Burkhalter, B. and Martindale, M. Q. (2018). Sea turtle fibropapilloma tumors share genomic drivers and therapeutic vulnerabilities with human cancers. Communications Biology, 1  (1): 63. Cover feature.

Farrell, J., Thomas, R., Martindale, M. Q. and Duffy, D. J. (2018). Characterisation of fibropapillomatosis tumour growth profiles in green sea turtles (Chelonia mydas). Testudo, 8 (5): 12-29. Invited submission, and cover feature.

Duffy, D. J., Konietzny, A., Krstic, A., Mehta, J. P., Halasz, M. and Kolch, W. (2018). Identification of a MYCN and Wnt related VANGL2-ITLN1 fusion gene in neuroblastoma, by RNA sequencing. Gene Reports, 1 (C): 187-200.

Whilde, J., Martindale, M. Q. and Duffy, D. J. (2017) Precision wildlife medicine: Applications of the human-centred precision medicine revolution to species conservation. Global Change Biology, 23 (5): 1792–1805. Cover feature.

Duffy, D. J., Krstic, A., Schwarzl, T., Halasz, M., Konietzny, A., Iljin, K., Higgins, D. G. and Kolch, W. (2017). Retinoic Acid and TGFβ signalling cooperate to overcome MYCN-induced retinoid resistance. Genome Medicine, 9 (15).

Daly, C., Shine, L., Heffernan, T., Deeti, S., Reynolds, A., O’Connor, J. J., Dillon, E. T., Duffy D. J., Kolch, W., Cagney, G. and Kennedy, B. N. (2017). A brain-derived neurotrophic factor mimetic is sufficient to restore cone photoreceptor visual function in an inherited blindness model. Scientific Reports. 7, 11320.

Duffy, D. J. (2016). Problems, challenges and promises: Perspectives on precision medicine. Briefings in Bioinformatics, 17, 494-504.

Duffy, D. J., Krstic, A., Halasz, M., Schwarzl, T., Fey, D., Iljin, K., Whilde, J., Westermann, F., Higgins, D. G. and Kolch, W. (2016). Wnt signalling is a bi-directional vulnerability of cancer cells. Oncotarget 7 (37), 60310-60331. Selected as an Oncotarget priority research paper.

Henrich, K.-O., Bender, S., Saadati, M., Dreidax, D., Gartlgruber, M., Shao, C., Herrmann, C., Wiesenfarth, M., Parzonka, M., Wehrmann, L., Fischer, M., Duffy, D. J., Bell, E. et al. (2016). Integrative genome-scale analysis identifies epigenetic mechanisms of transcriptional deregulation in unfavorable neuroblastomas. Cancer Research 76 (18), 5523-5537.

Duffy, D. J., Krstic, A., Schwarzl, T., Halasz, M., Iljin, K., Fey, D., Haley, B., Killick, K., Mehta, J. P., Whilde, J., Westermann, F., Higgins, D. G. and Kolch, W. (2015). MYCN  integrative omics enables network-based therapeutic target discovery and patient stratification in neuroblastoma. Oncotarget 6 (41), 43182-43201. Selected as an Oncotarget priority research paper.

Tortolina, L., Duffy, D. J., Maffei, M., Castagnino, N., Carmody, A., Kolch, W., Kholodenko, B., De Ambrosi, C., Barla, A., Nencioni, A. et al. (2015). Advances in dynamic modeling of colorectal cancer signaling network regions, a path toward targeted therapies. Oncotarget 6 (7), 5041-5058.

Schwarzl, T., Krstic, A., Higgins, D. G., Kolch, W. and Duffy, D. J. (2015). Measuring transcription rate changes via time-course 4-thiouridine pulse-labelling improves transcriptional target identification. Journal of Molecular Biology 427, 3368-3374.

Duffy, D. J., Krstic, A., Schwarzl, T., Higgins, D. G. and Kolch, W. (2014). GSK3 inhibitors regulate MYCN mRNA levels and reduce neuroblastoma cell viability through multiple mechanisms, including p53 and Wnt signaling. Molecular Cancer Therapeutics 13, 454-467.

Dreidax, D., Bannert, S., Henrich, K., Schröder, C., Bender, S., Oakes, C., Lindner, S., Schulte, J., Duffy, D. J., Schwarzl, T. et al. (2014). p19-INK4d inhibits neuroblastoma cell growth, induces differentiation and is hypermethylated and downregulated in MYCN-amplified neuroblastomas. Human Molecular Genetics 23, 6826-6837.

Duffy, D. J., Millane, R. C. and Frank, U. (2012). A heat shock protein and Wnt signaling crosstalk during axial patterning and stem cell proliferation. Developmental Biology 362, 271-281. F1000 recommended.

Duffy, D. J. (2012). Instructive reconstruction: A new role for apoptosis in pattern formation. BioEssays 34, 561-564. Editorially highlighted.

Duffy, D. J. and Frank, U. (2011). Modulation of COUP-TF expression in a cnidarian by ectopic Wnt signalling and allorecognition. PLoS ONE 6, e19443.

Millane, R. C., Kanska, J., Duffy, D. J., Seoighe, C., Cunningham, S., Plickert, G. and Frank, U. (2011). Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor. Development 138, 2429-2439.

Duffy, D. J. (2011). Modulation of Wnt signalling: a route to speciation? Communicative & Integrative Biology 4, 59-61. Cover feature.

Duffy, D. J., Plickert, G., Kuenzel, T., Tilmann, W. and Frank, U. (2010). Wnt signaling promotes oral but suppresses aboral structures in Hydractinia metamorphosis and regeneration. Development 137, 3057-3066.