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Eamonn Kennedy

Eamonn Kennedy, PhD

Languages spoken: English

Academic Information

Departments Primary - Internal Medicine

Divisions: Epidemiology

Academic Office Information

Dr. Kennedy's research interests include epidemiological investigations and evidence-based interventions, particularly those targeting Veteran health and chronic complex comorbidity following traumatic brain injury. His work centers on the intersection of machine learning methods and clinically impactful research.

Education History

Postdoctoral Fellowship Harper Cancer Research Institute, University of Notre Dame
Postdoctoral Fellow
University College Dublin
Graduate Training University College Dublin
University College Dublin

Selected Publications

Journal Article

  1. Gugger JJ, Kennedy E, Panahi S, Tate DF, Roghani A, Van Cott AC, Lopez MR, Altalib H, Diaz-Arrastia R, Pugh MJ (2022). Multimodal Quality of Life Assessment in Post-9/11 Veterans With Epilepsy: Impact of Drug Resistance, Traumatic Brain Injury, and Comorbidity. Neurology, 98(17), e1761-e1770.
  2. Kennedy E, Panahi S, Stewart IJ, Tate DF, Wilde EA, Kenney K, Werner JK, Gill J, Diaz-Arrastia R, Amuan M, Van Cott AC, Pugh MJ (2022). Traumatic Brain Injury and Early Onset Dementia in Post 9-11 Veterans. Brain Inj, 36(5), 1-8.
  3. Pugh MJ, Kennedy E, Gugger JJ, Mayo J, Tate D, Swan A, Kean J, Altalib H, Gowda S, Towne A, Hinds S, Van Cott A, Lopez MR, Jaramillo CA, Eapen BC, McCafferty RR, Salinsky M, Cramer J, McMillan KK, Kalvesmaki A, Diaz-Arrastia R, MINUTE Study Group (2022). The Military Injuries: Understanding Post-Traumatic Epilepsy Study: Understanding Relationships among Lifetime Traumatic Brain Injury History, Epilepsy, and Quality of Life. J Neurotrauma, 38(20), 2841-2850.
  4. Kennedy E, Geiser J, Arcadia CE, Weber PM, Rose C, Rubenstein BM, Rosenstein JK (2021). Secret messaging with endogenous chemistry. Sci Rep, 11(1), 13960.
  5. Shakya P, Kennedy E, Rose C, Rosenstein JK (2021). High-Dimensional Time Series Feature Extraction for Low-Cost Machine Olfaction. IEEE Sens J, 21(3), 2495-2504.
  6. Rosenstein JK, Rose C, Reda S, Weber PM, Kim E, Sello J, Geiser J, Kennedy E, Arcadia C, Dombroski A, Oakley K, Chen SL, Tann H, Rubenstein BM (2020). Principles of Information Storage in Small-Molecule Mixtures. IEEE Trans Nanobioscience, 19(3), 378-384.
  7. Arcadia CE, Kennedy E, Geiser J, Dombroski A, Oakley K, Chen SL, Sprague L, Ozmen M, Sello J, Weber PM, Reda S, Rose C, Kim E, Rubenstein BM, Rosenstein JK (2020). Multicomponent molecular memory. Nat Commun, 11(1), 691.
  8. Hu K, Kennedy E, Rosenstein JK (2020). Radio-Frequency Electrochemical Sensor Arrays for Biological Imaging. Biophys J, 118(3), 622a.
  9. Kennedy EM, Dowall SD, Salguero FJ, Yeates P, Aram M, Hewson R (2019). A vaccine based on recombinant modified Vaccinia Ankara containing the nucleoprotein from Lassa virus protects against disease progression in a guinea pig model. Vaccine, 37(36), 5404-5413.
  10. Kennedy E, Arcadia CE, Geiser J, Weber PM, Rose C, Rubenstein BM, Rosenstein JK (2019). Encoding information in synthetic metabolomes. PLoS One, 14(7), e0217364.
  11. Rigo E, Dong Z, Park JH, Kennedy E, Hokmabadi M, Almonte-Garcia L, Ding L, Aluru N, Timp G (2019). Measurements of the size and correlations between ions using an electrolytic point contact. Nat Commun, 10(1), 2382.
  12. Shakya P, Kennedy E, Rose C, Rosenstein JK (2019). Time series feature extraction for machine olfaction. IEEE Sens J, 1(4), 1.
  13. Kennedy E, Arcadia C, Wilkinson CK (2019). A 'molecular thumb drive' stores big files in small droplets. Nature, 571(7764).
  14. Hu K, Kennedy E, Rosenstein JK (2019). High frequency dielectric spectroscopy array with code division multiplexing for biological imaging. IEEE Biomed Circuits Syst Conf, 1-4.
  15. Ozmen M, Kennedy E, Rose J, Shakya P, Rosenstein JK, Rose C (2018). High speed chemical vapor communication using photoionization detectors in turbulent flow. IEEE Trans Mol Biol Multiscale Commun, 4(3), 160-170.
  16. Ozmen M, Kennedy E, Rose J, Shakya P, Rosenstein JK, Rose C (2018). High Speed Chemical Vapor Communication Using Photoionization Detectors in Turbulent Flow. IEEE Trans Mol Biol Multiscale Commun, 4(4), 160-170.
  17. Shakya P, Kennedy E, Rose C, Rosenstein JK (2018). Correlated transmission and detection of concentration-modulated chemical vapor plumes. IEEE Sens J, 18(16), 6504-6509.
  18. Kennedy E, Hokmabadi M, Dong Z, McKelvey K, Nelson EM, Timp G (2018). Method for Dynamically Detecting Secretions from Single Cells Using a Nanopore. Nano Lett, 18(7), 4263-4272.
  19. Kennedy E, Shakya P, Ozmen M, Rose C, Rosenstein JK (2018). Spatiotemporal information preservation in turbulent vapor plumes. Appl Phys Lett, 112(26), 264103.
  20. Ozmen M, Kennedy E, Rose J, Shakya P, Rosenstein JK, Rose C (2018). High speed chemical vapor communication using photoionization detectors. IEEE Glob Commun Conf, 1-6.
  21. Webster J, Shakya P, Kennedy E, Caplan M, Rose C, Rosenstein JK (2018). TruffleBot: Low-cost multi-parametric machine olfaction. IEEE Biomed Circuits Syst Conf, 1-4.
  22. Dong Z, Kennedy E, Hokmabadi M, Timp G (2017). Discriminating Residue Substitutions in a Single Protein Molecule Using a Sub-nanopore. ACS Nano, 11(6), 5440-5452.
  23. Kolmogorov M, Kennedy E, Dong Z, Timp G, Pevzner PA (2017). Single-molecule protein identification by sub-nanopore sensors. PLoS Comput Biol, 13(5), e1005356.
  24. Kennedy E, Kolmogorov M, Dong Z, Pevzner P, Timp G (2017). Single Molecule Identification Against Proteomes using Sub-Nanometer Pores. Biophys J, 112(3), 486a.
  25. Dong Z, Kennedy E, Timp G (2017). Using a Sub-nanopore to Discriminate Residue Substitutions in a Single Protein Molecule. NanoWorld Journal, 3(Supp 1), 1-5.
  26. Kennedy E, Dong Z, Tennant C, Timp G (2016). Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore. Nat Nanotechnol, 11(11), 968-976.
  27. Kennedy E, Nelson EM, Tanaka T, Damiano J, Timp G (2016). Live Bacterial Physiology Visualized with 5 nm Resolution Using Scanning Transmission Electron Microscopy. ACS Nano, 10(2), 2669-77.
  28. Dong Z, Kennedy E, Tennant C, Timp GL (2016). Detecting the Sequence of Amino Acid Quadromers in Protein Molecules using a Sub-Nanometer-Diameter Pore. Biophys J, 110(3), 509a.
  29. Al-Attar N, Kennedy E, Kelly G, Rice JH (2015). Photoluminescence blinking from single CdSeS/ZnS quantum dots in a conducting polymer matrix. J Phys Chem C Nanomater Interfaces, 119(11), 6278-6287.
  30. Al-Majmaie R, Kennedy E, Al-Rubeai M, Rice JH, Zerulla D (2015). AFM-based bivariate morphological discrimination of apoptosis induced by photodynamic therapy using photosensitizer-functionalized gold nanoparticles. RSC Adv, 5(101), 82983-82991.
  31. Kennedy E, Al-Majmaie R, Al-Rubeai M, Zerulla D, Rice JH (2013). Quantifying nanoscale biochemical heterogeneity in human epithelial cancer cells using combined AFM and PTIR absorption nanoimaging. J Biophotonics, 8(1-2), 133-41.
  32. Kennedy E, Al-Majomaie R, Al-Rubeai M, Zerulla D, Rice JH (2014). Nanoscale precision subcellular chemical identification using quantitative IR nanoimage analysis based on multiple-IR laser illumination. Conf Lasers Electro Optics, 1-2.
  33. Reddy MH, Al-Shammari RM, Al-Attar N, Kennedy E, Rogers L, Lopez S, Senge MO, Keyes TE, Rice JH (2014). Micro- or nanorod and nanosphere structures derived from a series of phenyl-porphyrins. Phys Chem Chem Phys, 16(9), 4386-93.
  34. Mousavi ZE, Kennedy E, Fanning S, Rice JH, Butler F (2014). The effect of Quaternary Ammonium Compounds on the attachment of wild and adapted Pseudomonas putida strains to different contact materials used in the food sector. Food Control, 42, 277-283.
  35. Reeves HE, Lotz SB, Kennedy E, Randall LP, Coldham NG, La Ragione RM (2013). Evaluation of an autogenous vaccine in cattle against Escherichia coli bearing the CTX-M-14 plasmid. Res Vet Sci, 94(3), 419-24.
  36. Lordan F, Damm S, Kennedy E, Mallon C, Forster RJ, Keyes TE, Rice JH (2013). The effect of Ag nanoparticles on surface-enhanced luminescence from Au nanovoid arrays. Plasmonics, 8(4), 1567-1575.
  37. Al-Alttar N, Kopf I, Flavin K, Kennedy E, Giordani S, Rice JH (2013). Surface-enhanced Raman scattering spectra of radial breathing and G band modes in functionalised nanotubes. Chem Phys Lett, 568-569, 95-100.
  38. Kennedy E, Al-Majmaie R, Al-Rubeai M, Zerulla D, Rice JH (2013). Nanoscale infrared absorption imaging permits non-destructive intracellular photosensitizer localization for subcellular uptake analysis. RSC Adv, 3(33), 13789-13795.
  39. Al-Attar N, Kopf I, Kennedy E, Flavin K, Giordani S, Rice JH (2012). Surface-enhanced Raman scattering from small numbers of purified and oxidised single-walled carbon nanotubes. Chem Phys Lett, 535, 146-151.
  40. Yarrow F, Kennedy E, Rice JH (2011). IR absorption nanoscopy and nanoimaging of hemoglobin. Eur Biophys J, 1-5.
  41. Kennedy E, Yarrow F, Rice JH (2011). Mid-infrared nanoimaging and nanoscopy of hemoglobin. J Biophotonics, 1-5.
  42. Yarrow F, Kennedy E, Salaun F, Rice JH (2010). Sub-wavelength infrared imaging of lipids. Biomed Opt Express, 2(1), 37-43.


  1. Pugh MJ, Kennedy E, Prager EM, Humpherys J, Dams-OConnor K, Hack D, McCafferty MK, Wolfe J, Yaffe K, McCrea M, Ferguson AR, Lancashire L, Ghajar J, Lumba-Brown A (2021). Phenotyping the Spectrum of Traumatic Brain Injury: A Review and Pathway to Standardization. [Review]. J Neurotrauma, 38(23), 3222-3234.

Book Chapter

  1. Kennedy E, Yoxall E, Rice J (2018). Nanoscale Spectroscopy in the Infrared with Applications to Biology. In Musa SM (Ed.), Nanoscale Spectroscopy with Applications (1st Edition, pp. 305-344). Boca Raton, FL: CRC Press.

Conference Proceedings

  1. Kennedy E, Al-Majomaie R, Zerulla D, Al-Rubeai M, Rice JH (2014). Human epithelial cancer cells studied using combined AFM-IR absorption nanoimaging. In Popp J, Tuchin VV, Matthews DL, Pavone FS, Garside P (Eds.), Biophotonics: Photonic Solutions for Better Health Care IV, International Society for Optics and Photonics, 9129, 91291M.
  2. Al-Majmaie R, Alattar N, Kennedy E, Al-Rubeai M, Rice JH, Zerulla D (2013). Raman spectroscopy for intracellular localisation of meso-Tetraphenylporphyrin-gold nanoparticles conjugates. In Verma P, Egner A (Eds.), Nanoimaging and Nanospectroscopy, International Society for Optics and Photonics, 8815, 40-44.
  3. Kennedy E, Yarrow F, Rice JH (2011). IR nanoscale spectroscopy and imaging. Instrumentation, Metrology, and Standards for Nanomanufacturing, Optics, and Semiconductors V, International Society for Optics and Photonics, 8105, 51-55.


  1. Kennedy E, Nelson EM, Damiano J, Timp G (2017). Gene Expression in Electron-Beam-Irradiated Bacteria in Reply to "Live Cell Electron Microscopy Is Probably Impossible". [Letter to the editor]. ACS Nano, 11(1), 3-7.
  2. Kennedy E, Yarrow F, Rice JH (2011). Nanoscale spectroscopy and imaging of hemoglobin. [Letter to the editor]. J Biophotonics, 4(9), 588-91.


  1. Kennedy E (2014). Biomedical Applications of Photothermal Induced Resonance Nanoscale Imaging. Dublin, Ireland.
  2. Kennedy E (2011). Infrared Nanoscopy and Chemical Mapping with an Atomic Force Microscope. Dublin, Ireland.