Eamonn Kennedy

Eamonn Kennedy, PhD

Languages spoken: English

Academic Information

Departments Primary - Internal Medicine

Divisions: Epidemiology

Lab

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

Education History

Undergraduate University College Dublin
 BSc
Graduate Training University College Dublin
 MS
Graduate Training University College Dublin
 PhD
Postdoctoral Fellowship University of Notre Dame
 Postdoctoral Fellow

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. (2021). 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. 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.
  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. 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.
  8. 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.
  9. 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.
  10. Hu K, Kennedy E, Rosenstein JK (2020). Radio-Frequency Electrochemical Sensor Arrays for Biological Imaging. Biophys J, 118(3), 622a.
  11. Shakya P, Kennedy E, Rose C, Rosenstein JK (2019). Time series feature extraction for machine olfaction. IEEE Sens J, 1(4), 1.
  12. Kennedy E, Arcadia C, Wilkinson CK (2019). A 'molecular thumb drive' stores big files in small droplets. Nature, 571(7764).
  13. 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.
  14. 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.
  15. 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.
  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(3), 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 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. Kennedy E, Al-Majmaie R, Al-Rubeai M, Zerulla D, Rice JH (2015). Quantifying nanoscale biochemical heterogeneity in human epithelial cancer cells using combined AFM and PTIR absorption nanoimaging. J Biophotonics, 8(1-2), 133-41.
  25. 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.
  26. 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.
  27. Yarrow F, Kennedy E, Salaun F, Rice JH (2010). Sub-wavelength infrared imaging of lipids. Biomed Opt Express, 2(1), 37-43.
  28. Kennedy E, Shakya P, Ozmen M, Rose C, Rosenstein JK (2018). Spatiotemporal information preservation in turbulent vapor plumes. Appl Phys Lett, 112(26), 264103.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. Yarrow F, Kennedy E, Rice JH (2011). IR absorption nanoscopy and nanoimaging of hemoglobin. Eur Biophys J, 1-5.
  42. Kennedy E, Yarrow F, Rice JH (2011). Mid-infrared nanoimaging and nanoscopy of hemoglobin. J Biophotonics, 1-5.
  43. Roghani A,Wang CP,Henion A,Amuan M,Altalib H,LaFrance WC,Baca C,Van Cott A,Towne A,Kean J,Hinds SR,Kennedy E,Panahi S,Pugh MJ (2024). Mortality among veterans with epilepsy: Temporal significance of traumatic brain injury exposure. Epilepsia, 65(8), 2255-2269.
  44. Kennedy E,Ozmen M,Bouldin ED,Panahi S,Mobasher H,Troyanskaya M,Martindale SL,Merritt VC,O'Neil M,Sponheim SR,Remigio-Baker RA,Presson A,Swan AA,Werner JK,Greene TH,Wilde EA,Tate DF,Walker WC,Pugh M (2024). Phenotyping Depression After Mild Traumatic Brain Injury: Evaluating the Impact of Multiple Injury, Gender, and Injury Context. Journal of neurotrauma, 41(7-8), 924-933.
  45. Panahi S,Mayo J,Kennedy E,Christensen L,Kamineni S,Sagiraju HKR,Cooper T,Tate DF,Rupper R,Pugh M (2024). Identifying clinical phenotypes of frontotemporal dementia in post-9/11 era veterans using natural language processing. Frontiers in neurology, 15,
  46. Wade BSC,Tate DF,Kennedy E,Bigler ED,York GE,Taylor BA,Troyanskaya M,Hovenden ES,Goodrich-Hunsaker N,Newsome MR,Dennis EL,Abildskov T,Pugh MJ,Walker WC,Kenney K,Betts A,Shih R,Welsh RC,Wilde E (2024). Microstructural Organization of Distributed White Matter Associated With Fine Motor Control in US Service Members With Mild Traumatic Brain Injury. Journal of neurotrauma, 41(1-2), 32-40.
  47. Panahi S,Kennedy E,Roghani A,VegaYon G,VanCott A,Gugger JJ,Raquel Lopez M,Jo Pugh (2023). Veteran perspectives of epilepsy care: Impact of Veteran satisfaction, knowledge, and proactivity. Epilepsy & behavior, 144,
  48. Henion AK,Wang CP,Amuan M,Altalib HH,Towne AR,Hinds SR,Baca C,Lafrance WC,Van Cott AC,Kean J,Roghani A,Kennedy E,Panahi S,Pugh MJ (2023). Role of Deployment History on the Association Between Epilepsy and Traumatic Brain Injury in Post-9/11 Era US Veterans. Neurology, 101(24), E2571-E2584.
  49. Esmaeili A,Dismuke-Greer C,Pogoda TK,Amuan ME,Garcia C,Del Negro A,Myers M,Kennedy E,Cifu D,Pugh M (2024). Cannabis use disorder contributes to cognitive dysfunction in Veterans with traumatic brain injury. Frontiers in neurology, 15,
  50. Kennedy E,Manhapra A,Miles SR,Martindale S,Rowland J,Mobasher H,Myers M,Panahi S,Walker WC,Pugh M (2024). The Impact of Non-Pain Factors on Pain Interference Among U.S. Service Members and Veterans with Symptoms of Mild Traumatic Brain Injury. Journal of neurotrauma,
  51. Swan AA,Kennedy E,Cooper DB,Amuan ME,Mayo J,Tate DF,Song K,Eapen BC,Van Cott AC,Lopez MR,Pugh M (2023). Comorbidity and polypharmacy impact neurobehavioral symptoms and symptom validity failure among post-9/11 veterans with mild traumatic brain injury. Frontiers in neurology, 14,
  52. Stewart IJ,Amuan ME,Wang CP,Kennedy E,Kenney K,Werner JK,Carlson KF,Tate DF,Pogoda TK,Dismuke-Greer CE,Wright WS,Wilde EA,Pugh M (2022). Association between Traumatic Brain Injury and Subsequent Cardiovascular Disease among Post-9/11-Era Veterans. Frontiers in neurology, 79(11), 1122-1129.
  53. Kennedy E,Dennis EL,Lindsey HM,deRoon-Cassini T,Du Plessis S,Fani N,Kaufman ML,Koen N,Larson CL,Laskowitz S,Lebois LAM,Morey RA,Newsome MR,Palermo C,Pastorek NJ,Powers A,Scheibel R,Seedat S,Seligowski A,Stein DJ,Stevens J,Sun D,Thompson P,Troyanskaya M,van Rooij SJH,Watts AA,Tomas CW,Williams W,Hillary FG,Jo Pugh M,Wilde EA,Tate D (2022). Harmonizing PTSD Severity Scales Across Instruments and Sites. Neuropsychology, 37(4), 398-408.
  54. Elbogen EB,Amuan M,Kennedy E,Blakey SM,Graziano RC,Hooshyar D,Tsai J,Nelson RE,Vanneman ME,Jones AL,Pugh M (2022). Criminal Legal Involvement Among Recently Separated Veterans: Findings From the LIMBIC Study. Neuropsychology, 46(5), 385-394.
  55. Shakya P,Kennedy E,Rose C,Rosenstein J (2021). High-Dimensional Time Series Feature Extraction for Low-Cost Machine Olfaction. Neuropsychology, 21(3), 2495-2504.
  56. Ozmen M,Kennedy E,Rose J,Shakya P,Rosenstein JK,Rose (2018). High Speed Chemical Vapor Communication Using Photoionization Detectors in Turbulent Flow. Neuropsychology, 4(3), 160-170.
  57. Kennedy E,Shakya P,Ozmen M,Rose C,Rosenstein J (2018). Spatiotemporal information preservation in turbulent vapor plumes. Neuropsychology, 112(26),
  58. Al-Majmaie R,Kennedy E,Al-Rubeai M,Rice J,Zerulla (2015). AFM-based bivariate morphological discrimination of apoptosis induced by photodynamic therapy using photosensitizer-functionalized gold nanoparticles. Neuropsychology, 5(101), 82983-82991.
  59. Mousavi Z,Kennedy E,Fanning S,Rice J,Butler (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. Neuropsychology, 42, 277-283.
  60. Harsha Vardhan Reddy M,Al-Shammari R,Al-Attar N,Kennedy E,Rogers L,Lopez S,Senge M,Keyes T,Rice (2014). Micro- or nanorod and nanosphere structures derived from a series of phenyl-porphyrins. Neuropsychology, 16(9), 4386-4393.
  61. Lordan F,Damm S,Kennedy E,Mallon C,Forster R,Keyes T,Rice (2013). The Effect of Ag Nanoparticles on Surface-Enhanced Luminescence from Au Nanovoid Arrays. Neuropsychology, 8(4), 1567-1575.
  62. Al-Alttar N,Kopf I,Flavin K,Kennedy E,Giordani S,Rice (2013). Surface-enhanced Raman scattering spectra of radial breathing and G band modes in functionalised nanotubes. Neuropsychology, 568-569, 95-100.
  63. Al-Attar N,Kopf I,Kennedy E,Flavin K,Giordani S,Rice (2012). Surface-enhanced Raman scattering from small numbers of purified and oxidised single-walled carbon nanotubes. Neuropsychology, 535, 146-151.
  64. Yarrow F,Kennedy E,Salaun F,Rice (2011). Sub-wavelength infrared imaging of lipids. Neuropsychology, 2(1), 37-43.

Review

  1. Pugh MJ, Kennedy E, Prager EM, Humpherys J, Dams-O'Connor 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.
  2. Kennedy E,Yoxall E,Rice (2013). Nanoscale spectroscopy in the infrared with applications to biology. Neuropsychology, 305-344.

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.
  4. Hu K,Kennedy E,Rosenstein J (2019). High Frequency Dielectric Spectroscopy Array with Code Division Multiplexing for Biological Imaging. Neuropsychology,
  5. Webster J,Shakya P,Kennedy E,Caplan M,Rose C,Rosenstein J (2018). TruffleBot: Low-Cost Multi-Parametric Machine Olfaction. Neuropsychology,
  6. Ozmen M,Kennedy E,Rose J,Shakya P,Rosenstein JK,Rose (2018). High Speed Chemical Vapor Communication Using Photoionization Detectors. Neuropsychology,
  7. Kennedy E,Al-Majomaie R,Al-Rubeai M,Zerulla D,Rice J (2014). Nanoscale precision subcellular chemical identification using quantitative IR nanoimage analysis based on multiple-IR laser illumination. Neuropsychology,
  8. Kennedy E,Al-Majomaie R,Zerulla D,Al-Rubeai M,Rice J (2014). Human epithelial cancer cells studied using combined AFM-IR absorption nanoimaging. Neuropsychology, 9129,
  9. Al-Majmaie R,Alattar N,Kennedy E,Al-Rubeai M,Rice J,Zerulla (2013). Raman spectroscopy for intracellular localisation of meso- tetraphenylporphyrin-gold nanoparticles conjugates. Neuropsychology, 8815,

Letter

  1. Kennedy E, Yarrow F, Rice JH (2011). Nanoscale spectroscopy and imaging of hemoglobin. [Letter to the editor]. J Biophotonics, 4(9), 588-91.
  2. 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.

Other

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