Cowles, T.J. 2003. Planktonic layers: physical and biological interactions on the small scale. In: Handbook of Scaling Methods in Aquatic Ecology: Measurements, Analysis, Simulation. CRC Press, Boca Raton, FL.

Eisner, L., M. Twardowski, T. Cowles, and M.J. Perry. 2003. Resolving phytoplankton photoprotective:photosynthetic carotenoid ratios on fine scales using in situ spectral absorbtion measurements. Limnol. Oceanogr. 48: 632-646

Barth, J.A., T.J. Cowles, P.M. Kosro, R.K. Shearman, A. Huyer, and R.L. Smith. 2002. Injection of carbon from the shelf to offshore beneath the euphotic zone in the California Current. J. Geophys. Res. 107:

Alldredge, A.L., T.J. Cowles, S. MacIntyre, J.E.B. Rines, P.L. Donaghay, C.F. Greenlaw, D.V. Holliday, M.M. Dekshenieks, J.M. Sullivan, J.R.V. Zaneveld. 2002. Occurrence and mechanisms of formation of a dramatic thin layer of marine snow in a shallow Pacific fjord. Mar. Ecol. Prog. Ser. 233: 1-12.

Sherr, E.B., B.F. Sherr, and T.J. Cowles. 2001. Mesoscale variability in bacterial activity in the Northeast Pacific Ocean off Oregon, USA. Aquat. Microb. Ecol. 25: 21-30

Barth, J.A., T.J. Cowles, and S.D. Pierce. 2001. Mesoscale physical and bio-optical structure of the Antarctic Polar Front near 170o W during spring. J. Geophys. Res. 106: 13,879-13,902

Potter, N. D. and T. J. Cowles. 2000. A high-speed, wireless network for ship-to-ship and ship-to-shore data exchange. J. Atmos. Oceanic Technol. 17: 963-970

Cowles, T.J., R.A. Desiderio, and M-E. Carr. 1998. Small-scale planktonic structure: persistence and trophic consequences. Oceanography 11: 4-9

Murphy, A.M. and T.J. Cowles. 1997. Effects of darkness on multi-excitatioin in vivo fluoresence and survival in a marine diatom. Limnol. Oceanogr. 42: 1444-1453

Desiderio, R.A., C. Moore, C. Lantz, and T.J. Cowles. 1997. Multiple excitation fluorometer for in situ oceanographic applications. Applied Optics 36: 1289-1296

Neuer, S. and T.J. Cowles. 1995. Comparative cell-specific grazing rates in field populations of ciliates and dinoflagellates. Mar. Ecol. Prog. Ser. 125: 259-267

Cowles, T.J. and L. Fessenden. 1995. Copepod grazing and finescale vertical distribution patterns during the Marine Light-Mixed Layers experiment. J. Geophys. Res. 100: 6677-6686

Neuer, S. and T.J. Cowles. 1994. Protist herbivory in the Oregon upwelling system. Mar. Ecol. Prog. Ser. 113: 147-162

Fessenden, L. and T.J. Cowles. 1994. Copepod predation on phagotrophic ciliates in Oregon coastal waters. Mar. Ecol. Prog. Ser. 107: 103-111

Cowles, T.J. and R.A. Desiderio. 1993. Resolution of biological microstructure through in situ fluorescence emission spectra: an oceanographic application using optical fibers. Oceanography 6: 105-111

Cowles, T.J., R.A. Desiderio, and S. Neuer. 1993. In situ characterization of phytoplankton from vertical profiles of fluorescence emission spectra. Mar. Biol. 115: 217-222

Desiderio, R.A., T.J. Cowles, J.N. Moum, and M. Myrick. 1993. Microstructure profiles of laser induced chlorophyll fluorescence spectra: Evaluation of backscatter and forward scatter fiber optic sensors. J. Atmos. Oceanic Technol. 10: 209-224

Hood, R.R., S. Neuer, and T.J. Cowles. Autotrophic production, biomass, and species composition at two stations across an upwelling front. Mar. Ecol. Prog. Ser. 83: 221-232

Miller, C. B., T. J. Cowles, P. H. Wiebe, N. J. Copley, and H. Grigg. 1991. Mechanisms of the resting phase in Calanus finmarchicus (Gunnerus). Mar. Ecol. Prog. Ser. 72: 79-91

Cowles, T.J., R.A. Desiderio, J.N. Moum, M. Myrick, D. Garvis, and S. Angel. 1990. Fluorescence microstructure using a laser/fiber optic profiler. Proc. Soc. Photo-Opt. Instrum. Eng., Ocean Optics X., 336-345