1. Bolton, E. W., K. A. Maasch and J. M. Lilly (1995). A wavelet analysis of Plio-Pleistocene climate indicators: A new view of periodicity evolution. Geophysical Research Letters, 22: 2753–2756. doi 10.1029/95GL02799 pdf
  2. Lilly, J. M., and J. Park (1995). Multiwavelet spectral and polarization analysis. Geophysical Journal International, 122: 1001–1021. doi 10.1111/j.1365-246X.1995.tb06852.x pdf
  3. Lilly, J. M., P. B. Rhines, M. Visbeck, R. E. Davis, J. R. N. Lazier, F. Schott and D. Farmer (1999). Observing deep convection in the Labrador Sea during winter 1994–95. Journal of Physical Oceanography, 29: 2065–2098. doi 10.1175/1520-0485(1999)029 <2065:ODCITL>2.0.CO;2 pdf
  4. Lilly, J. M., and P. B. Rhines (2002). Coherent eddies in the Labrador Sea observed from a mooring. Journal of Physical Oceanography, 32: 585–598. doi 10.1175/1520-0485(2002)032 <0585:CEITLS> 2.0.CO;2 pdf
  5. Lilly, J. M., P. B. Rhines, F. Schott, K. Lavender, J. Lazier, U. Send, and E. D’Asaro (2003). Observations of the Labrador Sea eddy field. Progress in Oceanography, 59: 75–176. doi 10.1016/ j.pocean.2003.08.013 pdf
  6. Lilly, J. M., and E. E. Lettvin (2004). The “switch-on” problem for linear time-invariant operators. Signal Processing, 84: 763–784. doi 10.1016/j.sigpro.2003.12.011 pdf
  7. Bunge, L., C. Provost, J. M. Lilly, M. D’Orgeville, A. Kartavtseff, and J.-L. Mélice (2006). Variability of the horizontal velocity structure in the Upper 1600 m of the water column on the Equator at 10°W. Journal of Physical Oceanography, 36: 1287–1304. doi 10.1175/JPO2908.1 pdf
  8. Lilly, J. M., and J.-C. Gascard (2006). Wavelet ridge diagnosis of time-varying elliptical signals with application to an oceanic eddy. Nonlinear Processes in Geophysics, 13: 467–483. doi 10.5194/npg-13-467-2006 pdf
  9. Rilling, G., P. Flandrin, P. Gonçalves, and J. M. Lilly (2007). Bivariate empirical mode decomposition. IEEE Signal Processing Letters, 14 (12): 936–939. doi 10.1109/LSP.2007.904710 pdf
  10. Lagerloef, G., F. R. Colomb, D. Le Vine, F. Wentz, S. Yueh, C. Ruf, J. Lilly, J. Gunn, Y. Chao, A. deCharon, G. Feldman, and C. Swift, (2008). The Aquarius/SAC-D mission: Designed to meet the salinity remote-sensing challenge Oceanography, 21 (1): 69–81. doi 10.5670/oceanog.2008.68 pdf
  11. Lilly, J. M., and S. C. Olhede, (2009). Higher-order properties of analytic wavelets. IEEE Transactions on Signal Processing, 57 (1): 146–160. doi 10.1109/TSP.2008.2007607 pdf
  12. Rykova, T., F. Straneo, J. M. Lilly, and I. Yashayaev (2009). Irminger Current anticyclones in the Labrador Sea observed in the hydrographic record, 1990–2004. Journal of Marine Research, 67 (3): 361–384. doi 10.1109/10.1357/002224009789954739 pdf
  13. Lilly, J. M., and S. C. Olhede (2009). Wavelet ridge estimation of jointly modulated multivariate oscillations. 43rd Asilomar Conference on Signals, Systems, and Computers, 452–456. Refereed conference proceedings paper. doi 10.1109/ACSSC.2009.5469858 pdf
  14. Lilly, J. M., and S. C. Olhede (2010). Bivariate instantaneous frequency and bandwidth. IEEE Transactions on Signal Processing, 58 (2): 591–603. doi 10.1109/TSP.2009.2031729 pdf
  15. Lilly, J. M., and S. C. Olhede (2010). On the analytic wavelet transform. IEEE Transactions on Information Theory, 56 (8): 4135–4156. doi 10.1109/TIT.2010.2050935 pdf
  16. Lilly, J. M. (2011). Modulated oscillations in three dimensions. IEEE Transactions on Signal Processing, 59 (12): 5930–5943. doi 10.1109/TSP.2011.2164914 pdf
  17. Lilly, J. M., R. K. Scott, and S. C. Olhede (2011). Extracting waves and vortices from Lagrangian trajectories. Geophysical Research Letters, 38 L23605: 1–5. doi 10.1029/2011GL049727 pdf vortexmovie.mp4
  18. Lilly, J. M., and S. C. Olhede (2012). Analysis of modulated multivariate oscillations. IEEE Transactions on Signal Processing, 60 (2): 600–612. doi 10.1109/TSP.2011.2173681 pdf
  19. Hattermann, T., O. A. Nøst, J. M. Lilly, and L. H. Smedsrud (2012). Two years of oceanic observations below the Fimbul Ice Shelf, Antarctica. Geophysical Research Letters, 39 L12605: 1–6. doi 10.1029/2012GL051012 pdf
  20. Lilly, J. M., and S. C. Olhede (2012). Generalized Morse wavelets as a superfamily of analytic wavelets. IEEE Transactions on Signal Processing, 60 (11): 6036–6041. doi 10.1109/TSP.2012.2210890 pdf
  21. Bower, A. S., R. M. Hendry, D. E. Amrhein, and J. M. Lilly (2013). Direct observations of formation and propagation of subpolar eddies into the subtropical North Atlantic. Deep-Sea Research, 39: 15–41. doi 10.1016/j.dsr2.2012.07.029 pdf
  22. Hattermann, T., L. H. Smedsrud, O. A. Nøst, J. M. Lilly, and B. K. Galton-Fenzi (2014). Eddy-resolving simulations of the Fimbul ice shelf cavity circulation: basal melting and exchange with open ocean. Ocean Modelling, 82: 28–44. doi 10.1016/j.ocemod.2014.07.004 pdf
  23. Waterman, S. N., and J. M. Lilly (2015). Geometric decomposition of eddy feedbacks in barotropic systems. Journal of Physical Oceanography, 45 (4): 1009–1024. doi 110.1175/JPO-D-14-0177.1 pdf
  24. Wain, D. J., J. M. Lilly, A. H. Callaghan, I. Yashayaev, and B. Ward (2015). A breaking internal wave in the surface ocean boundary layer. Journal of Geophysical Research, 120 (6): 4151–4161. doi 10.1002/2014JC010416 pdf
  25. Stewart, K. D., P. Spence, S. Waterman, J. Le Sommer, J.-M. Molines, J. M. Lilly, and M. H. England (2015). Anisotropy of eddy variability in the global ocean. Ocean Modelling, 95 (4): 53–65. doi 10.1016/j.ocemod.2015.09.005 pdf
  26. Bartlett, T. E., A. M. Sykulski, S. C. Olhede, J. M. Lilly, and J. J. Early (2015). A power variance test for nonstationarity in complex-valued signals. IEEE 14th International Conference on Machine Learning and Applications (ICMLA), 911–916. Refereed conference proceedings paper. doi 10.1109/ICMLA.2015.122 pdf
  27. Sykulski, A. M., S. C. Olhede, J. M. Lilly, and E. Danioux (2016). Lagrangian time series models for ocean surface drifter trajectories. Journal of the Royal Statistical Society: Series C, 65 (1): 29–50. doi 10.1111/rssc.12112 pdf
  28. Elipot, S., R. Lumpkin, R. C. Perez, J. M. Lilly, J. J. Early, and A. M. Sykulski (2016). A global surface drifter data set at hourly resolution. Journal of Geophysical Research: Oceans, 121 (5): 2937–2966. doi 10.1002/ 2016JC011716 pdf Download Data
  29. Sykulski, A. M., S. C. Olhede, and J. M. Lilly (2016). A widely linear complex autoregressive process of order one. IEEE Transactions on Signal Processing, 64 (23): 6200–6210. doi 10.1109/TSP.2016.2599503 pdf
  30. Sykulski, A. M., S. C. Olhede, J. M. Lilly, and J. J. Early (2017). Frequency-domain stochastic modeling of stationary bivariate or complex-valued signals. IEEE Transactions on Signal Processing, 65 (12): 3136–3151. doi 10.1109/TSP.2017.2686334 pdf
  31. Lilly, J. M. (2017). Element analysis: a wavelet-based method for analyzing time-localized events in noisy time series. Proceedings of the Royal Society of London, Series A, 473 (2200): 20160776, 1–28. doi 10.1098/rspa.2016.0776 pdf
  32. Guillaumin, A. P., A. M. Sykulski, S. C. Olhede, J. J. Early, and J. M. Lilly (2017). Analysis of nonstationary modulated time series with applications to oceanographic surface flow measurements. Journal of Time Series Analysis, 38 (5): 668–710. doi 10.1111/jtsa.12244 pdf
  33. Lilly, J. M., A. M. Sykulski, J. J. Early, and S. C. Olhede (2017). Fractional Brownian motion, the Matérn process, and stochastic modeling of turbulent dispersion. Nonlinear Processes in Geophysics, 24: 481–514. doi 10.5194/npg-24-481-2017 pdf turbulencemovie.mp4 dispersionmovie.mp4
  34. Lilly, J. M. (2018). Kinematics of a fluid ellipse in a linear flow. Fluids, 3 (1): 1–29. doi 10.3390/fluids3010016 pdf
  35. Sykulski, A. M., S. C. Olhede, A. P. Guillaumin, J. M. Lilly, and J. J. Early (2019). The de-biased Whittle likelihood. Biometrika, 106 (2): 251–266. doi 10.1093/biomet/asy071 pdf
  36. Bosse, A., I. Fer, J. M. Lilly, and H. Søiland (2019). Dynamical controls on the longevity of a non-linear vortex: The case of the Lofoten Basin Eddy. Scientific Reports, 9 (1): 13448 1–13. doi 10.1038/s41598-019-49599-8 pdf
  37. Trodahl, M., P. E. Isachsen, J. Nilsson, J. M. Lilly, and N. M. Kristensen (2020). The regeneration of the Lofoten Vortex through vertical alignment. Journal of Physical Oceanography, 50 (9): 2689–2711. doi 10.1175/JPO-D-20-0029.1 pdf
  38. Lilly, J. M., and S. Elipot (2021). A unifying perspective on transfer function solutions to the unsteady Ekman problem. Fluids, 6 (2): 85, 1–36 doi 10.3390/fluids6020085 pdf
  39. Lilly, J. M., and P. Pérez-Brunius (2021a). A gridded surface current product for the Gulf of Mexico from consolidated drifter measurements. Earth System Science Data, 13: 645–669. doi 10.5194/essd-13-645-2021 pdf
  40. Lilly, J. M., and P. Pérez-Brunius (2021b). Extracting statistically significant eddy signals from large Lagrangian datasets using wavelet ridge analysis, with application to the Gulf of Mexico. Nonlinear Processes in Geophysics, 28: 181–212. doi 10.5194/npg-28-181-2021 pdf
  41. Klenz, T., Simmons, H. L., Centurioni, L., Lilly, J. M., Early, J. J., & Hormann, V. (2022). Estimates of near-inertial wind power input using novel in situ wind measurements from Minimet surface drifters in the Iceland Basin. Journal of Physical Oceanography, 52(10): 2417–2430. doi 10.1175/JPO-D-21-0283.1 pdf
  42. Lilly, J. M., J. Feske, B. Fox-Kemper, and J. J. Early (2024). Integral theorems for the gradient of a vector field, with a fluid dynamical application. In revision. pdf