Petersma, F. T., Thomas, L., Thode, A. M., Harris, D., Marques, T. A., Cheoo, G. V., & Kim, K. H. (2023). Accommodating False Positives Within Acoustic Spatial Capture–Recapture, with Variable Source Levels, Noisy Bearings and an Inhomogeneous Spatial Density. Journal of Agricultural, Biological and Environmental Statistics. https://doi.org/10.1007/s13253-023-00563-0

Tenorio-Halle, L., Thode, A. M., Lammers, M. O., Conrad, A. S., & Kim, K. H. (2022). Multi-target 2D tracking method for singing humpback whales using vector sensors. Journal of the Acoustical Society of America, 151(1), 126–137. https://doi.org/10.1121/10.0009165

Thode, A. M., Norman, R. G., Conrad, A. S., Tenorio-Halle, L., Blackwell, S. B., & Kim, K. H. (2021). Measurements of open-water arctic ocean noise directionality and transport velocity. Journal of the Acoustical Society of America, 150(3), 1954–1966. https://doi.org/10.1121/10.0006206

Tenorio-Halle, L., Thode, A. M., Swartz, S. L., & Urban, R. J. (2021). Using anisotropic and narrowband ambient noise for continuous measurements of relative clock drift between independent acoustic recorders. Journal of the Acoustical Society of America, 149(6), 4094–4105. https://doi.org/10.1121/10.0004996

Oedekoven, C. S., Marques, T. A., Harris, D., Thomas, L., Thode, A. M., Blackwell, S. B., Conrad, A. S., & Kim, K. H. (2021). A comparison of three methods for estimating call densities of migrating bowhead whales using passive acoustic monitoring. Environmental and Ecological Statistics, 25. https://doi.org/10.1007/s10651-021-00506-3

Blackwell, S. B., Thode, A. M., Conrad, A. S., Ferguson, M. C., Berchok, C. L., Stafford, K. M., Marques, T. A., & Kim, K. H. (2021). Estimating acoustic cue rates in bowhead whales, Balaena mysticetus, during their fall migration through the Alaskan Beaufort Sea. Journal of the Acoustical Society of America, 149(5), 3611–3625. https://doi.org/10.1121/10.0005043

Ozanich, E., Thode, A., Gerstoft, P., Freeman, L. A., & Freeman, S. (2021). Deep embedded clustering of coral reef bioacoustics. Journal of the Acoustical Society of America, 149(4), 2587–2601. https://doi.org/10.1121/10.0004221

Thode, A. M., Conrad, A. S., Ozanich, E., King, R., Freeman, S. E., Freeman, L. A., Zgliczynski, B., Gerstoft, P., & Kim, K. H. (2021). Automated two-dimensional localization of underwater acoustic transient impulses using vector sensor image processing (vector sensor localization). Journal of the Acoustical Society of America, 149(2), 770–787. https://doi.org/10.1121/10.0003382

Frouin-Mouy, H., Tenorio-Halle, L., Thode, A., Swartz, S., & Urban, J. (2020). Using two drones to simultaneously monitor visual and acoustic behaviour of gray whales (Eschrichtius robustus) in Baja California, Mexico. Journal of Experimental Marine Biology and Ecology, 525. https://doi.org/10.1016/j.jembe.2020.151321

Thode, A. M., Blackwell, S. B., Conrad, A. S., Kim, K. H., Marques, T., Thomas, L., Oedekoven, C. S., Harris, D., & Broker, K. (2020). Roaring and repetition: How bowhead whales adjust their call density and source level (Lombard effect) in the presence of natural and seismic airgun survey noisea). Journal of the Acoustical Society of America, 147(3), 2061–2080. https://doi.org/10.1121/10.0000935

Bonnel, J., Thode, A., Wright, D., & Chapman, R. (2020). Nonlinear time-warping made simple: A step-by-step tutorial on underwater acoustic modal separation with a single hydrophone. Journal of the Acoustical Society of America, 147(3), 1897–1926. https://doi.org/10.1121/10.0000937

Lopez-Urban, A., Thode, A., Duran, C. B., Urban, J., & Swartz, S. (2018). Two new grey whale call types detected on bioacoustic tags. Journal of the Marine Biological Association of the United Kingdom, 98(5), 1169–1175. https://doi.org/10.1017/s0025315416001697

Tenorio-Halle, L., Thode, A. M., Sarkar, J., Verlinden, C., Tippmann, J., Hodgkiss, W. S., & Kuperman, W. A. (2017). A double-difference method for high-resolution acoustic tracking using a deep-water vertical array. Journal of the Acoustical Society of America, 142(6), 3474–3485. https://doi.org/10.1121/1.5014050

Wild, L., Thode, A., Straley, J., Rhoads, S., Falvey, D., & Liddle, J. (2017). Field trials of an acoustic decoy to attract sperm whales away from commercial longline fishing vessels in western Gulf of Alaska. Fisheries Research, 196, 141–150. https://doi.org/10.1016/j.fishres.2017.08.017

Blackwell, S. B., Nations, C. S., Thode, A. M., Kauffman, M. E., Conrad, A. S., Norman, R. G., & Kim, K. H. (2017). Effects of tones associated with drilling activities on bowhead whale calling rates. PLOS ONE, 12(11). https://doi.org/10.1371/journal.pone.0188459

Ozanich, E., Gerstoft, P., Worcester, P. F., Dzieciuch, M. A., & Thode, A. (2017). Eastern Arctic ambient noise on a drifting vertical array. Journal of the Acoustical Society of America, 142(4), 1997–2006. https://doi.org/10.1121/1.5006053

Thode, A. M., Blackwell, S. B., Conrad, A. S., Kim, K. H., & Macrander, A. M. (2017). Decadal-scale frequency shift of migrating bowhead whale calls in the shallow Beaufort Sea. Journal of the Acoustical Society of America, 142(3), 1482–1502. https://doi.org/10.1121/1.5001064

Thode, A., Bonnel, J., Thieury, M., Fagan, A., Verlinden, C., Wright, D., Berchok, C., & Crance, J. (2017). Using nonlinear time warping to estimate North Pacific right whale calling depths in the Bering Sea. Journal of the Acoustical Society of America, 141(5), 3059–3069. https://doi.org/10.1121/1.4982200

Bonnel, J., Caporale, S., & Thode, A. (2017). Waveguide mode amplitude estimation using warping and phase compensation. Journal of the Acoustical Society of America, 141(3), 2243–2255. https://doi.org/10.1121/1.4979057

Thode, A. M., Blackwell, S. B., Seger, K. D., Conrad, A. S., Kim, K. H., & Macrander, A. M. (2016). Source level and calling depth distributions of migrating bowhead whale calls in the shallow Beaufort Sea. Journal of the Acoustical Society of America, 140(6), 4288–4297. https://doi.org/10.1121/1.4968853

Thode, A., Wild, L., Straley, J., Barnes, D., Bayless, A., O’Connell, V., Oleson, E., Sarkar, J., Falvey, D., Behnken, L., & Martin, S. (2016). Using line acceleration to measure false killer whale (Pseudorca crassidens) click and whistle source levels during pelagic longline depredation. Journal of the Acoustical Society of America, 140(5), 3941–3951. https://doi.org/10.1121/1.4966625

Seger, K. D., Thode, A. M., Urban, J., Martinez-Loustalot, P., Jimenez-Lopez, M. E., & Lopez-Arzate, D. (2016). Humpback whale-generated ambient noise levels provide insight into singers’ spatial densities. Journal of the Acoustical Society of America, 140(3), 1581–1597. https://doi.org/10.1121/1.4962217

Thode, A. M., Kim, K. H., Norman, R. G., Blackwell, S. B., & Greene, C. R. (2016). Acoustic vector sensor beamforming reduces masking from underwater industrial noise during passive monitoring. Journal of the Acoustical Society of America, 139(4), EL105–EL111. https://doi.org/10.1121/1.4946011

Seger, K. D., Thode, A. M., Swartz, S. L., & Urban, J. (2015). The ambient acoustic environment in Laguna San Ignacio, Baja California Sur, Mexico. Journal of the Acoustical Society of America, 138(5), 3397–3410. https://doi.org/10.1121/1.4935397

Crance, J., Berchok, C., Bonnel, J., & Thode, A. (2015). Northeasternmost record of a North Pacific fin whale (Balaenoptera physalus) in the Alaskan Chukchi Sea. Polar Biology, 38(10), 1767–1773. https://doi.org/10.1007/s00300-015-1719-7

Blackwell, S. B., Nations, C. S., McDonald, T. L., Thode, A. M., Mathias, D., Kim, K. H., Greene, C. R., & Macrander, A. M. (2015). Effects of airgun sounds on bowhead whale calling rates: Evidence for two behavioral thresholds. PLOS ONE, 10(6). https://doi.org/10.1371/journal.pone.0125720

Straley, J., O’Connell, V., Liddle, J., Thode, A., Wild, L., Behnken, L., Falvey, D., & Lunsford, C. (2015). Southeast Alaska Sperm Whale Avoidance Project (SEASWAP): a successful collaboration among scientists and industry to study depredation in Alaskan waters. Ices Journal of Marine Science, 72(5), 1598–1609. https://doi.org/10.1093/icesjms/fsv090

O’Connell, V., Straley, J., Liddle, J., Wild, L., Behnken, L., Falvey, D., & Thode, A. (2015). Testing a passive deterrent on longlines to reduce sperm whale depredation in the Gulf of Alaska. Ices Journal of Marine Science, 72(5), 1667–1672. https://doi.org/10.1093/icesjms/fsv014

Thode, A., Mathias, D., Straley, J., O’Connell, V., Behnken, L., Falvey, D., Wild, L., Calambokidis, J., Schorr, G., Andrews, R., Liddle, J., & Lestenkof, P. (2015). Cues, creaks, and decoys: using passive acoustic monitoring as a tool for studying sperm whale depredation. Ices Journal of Marine Science, 72(5), 1621–1636. https://doi.org/10.1093/icesjms/fsv024

Abadi, S. H., Thode, A. M., Blackwell, S. B., & Dowling, D. R. (2014). Ranging bowhead whale calls in a shallow-water dispersive waveguide. Journal of the Acoustical Society of America, 136(1), 130–144. https://doi.org/10.1121/1.4881924

Bonnel, J., Thode, A. M., Blackwell, S. B., Kim, K., & Macrander, A. M. (2014). Range estimation of bowhead whale (Balaena mysticetus) calls in the Arctic using a single hydrophone. Journal of the Acoustical Society of America, 136(1), 145–155. https://doi.org/10.1121/1.4883358

Straley JM, Schorr GS, Thode AM, Calambokidis J, Lunsford CR, Chenoweth EM, O?Connell VM, & Andrews RD. (2014). Depredating sperm whales in the Gulf of Alaska: local habitat use and long distance movements across putative population boundaries. Endangered Species Research, 24(2), 125–135. https://doi.org/10.3354/esr00595

Thode, A. M., Wild, L., Mathias, D., Straley, J., & Lunsford, C. (2014). A comparison of acoustic and visual metrics of sperm whale longline depredation. Journal of the Acoustical Society of America, 135(5), 3086–3100. https://doi.org/10.1121/1.4869853

Blackwell, S. B., Nations, C. S., McDonald, T. L., Greene, C. R., Thode, A. M., Guerra, M., & Macrander, A. M. (2013). Effects of airgun sounds on bowhead whale calling rates in the Alaskan Beaufort Sea. Marine Mammal Science, 29(4), E342–E365. https://doi.org/10.1111/mms.12001

Mathias, D., Thode, A. M., Straley, J., & Andrews, R. D. (2013). Acoustic tracking of sperm whales in the Gulf of Alaska using a two-element vertical array and tags. Journal of the Acoustical Society of America, 134(3), 2446–2461. https://doi.org/10.1121/1.4816565

Walker, S. C., Yardim, C., Thode, A., & Arias-Castro, E. (2013). Using Fisher information to quantify uncertainty in environmental parameters estimated from correlated ambient noise. Journal of the Acoustical Society of America, 133(4), EL228–EL234. https://doi.org/10.1121/1.4792836

Mathias, D., Thode, A. M., Straley, J., Calambokidis, J., Schorr, G. S., & Folkert, K. (2012). Acoustic and diving behavior of sperm whales (Physeter macrocephalus) during natural and depredation foraging in the Gulf of Alaska. Journal of the Acoustical Society of America, 132(1), 518–532. https://doi.org/10.1121/1.4726005

Thode, A. M., Kim, K. H., Blackwell, S. B., Greene, C. R., Nations, C. S., McDonald, T. L., & Macrander, A. M. (2012). Automated detection and localization of bowhead whale sounds in the presence of seismic airgun surveys. Journal of the Acoustical Society of America, 131(5), 3726–3747. https://doi.org/10.1121/1.3699247

Ponce, D., Thode, A. M., Guerra, M., Urban, R. J., & Swartz, S. (2012). Relationship between visual counts and call detection rates of gray whales (Eschrichtius robustus) in Laguna San Ignacio, Mexico. Journal of the Acoustical Society of America, 131(4), 2700–2713. https://doi.org/10.1121/1.3689851

Guerra, M., Thode, A. M., Blackwell, S. B., & Macrander, A. M. (2011). Quantifying seismic survey reverberation off the Alaskan North Slope. Journal of the Acoustical Society of America, 130(5), 3046–3058. https://doi.org/10.1121/1.3628326

Thode, A., Skinner, J., Scott, P., Roswell, J., Straley, J., & Folkert, K. (2010). Tracking sperm whales with a towed acoustic vector sensor. Journal of the Acoustical Society of America, 128(5), 2681–2694. https://doi.org/10.1121/1.3495945

Thode, A., Kim, K. H., Greene, C. R., & Roth, E. (2010). Long range transmission loss of broadband seismic pulses in the Arctic under ice-free conditions. Journal of the Acoustical Society of America, 128(4), E181–E187. https://doi.org/10.1121/1.3479686

Mathias, D., Thode, A., Straley, J., & Folkert, K. (2009). Relationship between sperm whale (Physeter macrocephalus) click structure and size derived from videocamera images of a depredating whale (sperm whale prey acquisition). Journal of the Acoustical Society of America, 125(5), 3444–3453. https://doi.org/10.1121/1.3097758

Thode, A., Straley, J., Tiemann, C. O., Folkert, K., & O’Connell, V. (2007). Observations of potential acoustic cues that attract sperm whales to longline fishing in the Gulf of Alaska. Journal of the Acoustical Society of America, 122(2), 1265–1277. https://doi.org/10.1121/1.2749450

Tiemann, C. O., Thode, A. M., Straley, J., O’Connell, V., & Folkert, K. (2006). Three-dimensional localization of sperm whales using a single hydrophone. Journal of the Acoustical Society of America, 120(4), 2355–2365. https://doi.org/10.1121/1.2335577

Thode, A. M., Gerstoft, P., Burgess, W. C., Sabra, K. G., Guerra, M., Stokes, M. D., Noad, M., & Cato, D. H. (2006). A portable matched-field processing system using passive acoustic time synchronization. Ieee Journal of Oceanic Engineering, 31(3), 696–710. https://doi.org/10.1109/joe.2006.880431

Thode, A. (2005). Three-dimensional passive acoustic tracking of sperm whales (Physeter macrocephalus) in ray-refracting environments. Journal of the Acoustical Society of America, 118(6), 3575–3584. https://doi.org/10.1121/1.2049068

Sabra, K. G., Roux, P., Thode, A. M., D’Spain, G. L., Hodgkiss, W. S., & Kuperman, W. A. (2005). Using ocean ambient noise for array self-localization and self-synchronization. Ieee Journal of Oceanic Engineering, 30(2), 338–347. https://doi.org/10.1109/joe.2005.850908

Thode, A., & Kim, K. (2004). Multiple-order derivatives of a waveguide acoustic field with respect to sound speed, density, and frequency. Journal of the Acoustical Society of America, 116(6), 3370–3383. https://doi.org/10.1121/1.1760107

Zanolin, M., Ingram, I., Thode, A., & Makris, N. C. (2004). Asymptotic accuracy of geoacoustic inversions. Journal of the Acoustical Society of America, 116(4), 2031–2042. https://doi.org/10.1121/1.1787526