Refereed

* Denotes authorship by an advised student.

Manjur, S.M., V. Senyurek, A. Skarke, and A. Gurbuz (In Review). Deep Learning Based Sequential Processing of Multibeam Echosounder Images for Automated Detection of Seafloor Gas Seeps. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing.

Bashit, M.S., N.G. Pricope, D. McCraine, A. Skarke, and Q. Meng (In Review). Optimizing Interpolation Methods and Assessing Accuracy of UAS-Echo Sounder Data for Enhanced Bathymetric Mapping in Inland Waters. International Journal of Applied Earth Observation and Geoinformation.

Manjur, S.M., V. Senyurek, R. Kalski*, S. Gupta*, A. Skarke, and A. Gurbuz (2025). Automated Detection of Seafloor Gas Seeps in Multibeam Echosounder Data with anAttention-Guided Convolutional Neural Network. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 18, 5633–5645. doi:10.1109/JSTARS.2025.3535234

Ruppel, C. D., A.D. Skarke, N.C. Miller, M.W. Kidiwela*, J. Kluesner, and W. Baldwin (2024). Methane seeps on the U.S. Atlantic margin: An updated inventory and interpretative framework. Marine Geology 471, 107287. doi:10.1016/j.margeo.2024.107287

Osorio, R. J., A. Linhoss, A. Skarke, M.G. Brasher, and M. McFarland, M. (2023). Assessment of marsh terrace designs for wave attenuation utilizing a wave model. Dynamics of Atmospheres and Oceans 105, 101429. doi:10.1016/j.dynatmoce.2023.101429.

Rodolfich, A., E. Sparks, B. Posadas, J. Rodgers, A. Skarke, R. Bradley, and C. Wessel (2023), The distribution and direct impacts of marine debris on the commercial shrimping industry, Mar. Pollut. Bull., 186, 114417, doi:10.1016/j.marpolbul.2022.114417.

Lee*, T. R., B. J. Phrampus, A. Skarke, and W. T. Wood (2022), Global Estimates of Biogenic Methane Production in Marine Sediments Using Machine Learning and Deterministic Modeling. Global Biogeochemical Cycles,1–18, doi:10.1029/2021GB007248.

Rodolfich, A., E. Sparks, B. Posadas, J. Rodgers, A. Skarke, R. Bradley, and C. Wessel (In Review), The distribution and direct impacts of marine debris on the commercial shrimping industry, Nat. Portf., doi:10.21203/rs.3.rs-737430/v1.

Mullins, L. L., J. M. Drymon, M. Moore, A. Skarke, A. Moore, and J. C. Rodgers (2021), Defining distribution and habitat use of west-central Florida’s coastal sharks through a research and education program, Ecol. Evol., 11(22), 16055–16069, doi:10.1002/ece3.8277.

Lee*, T. R., Phrampus, B. J., Obelcz, J., Wood, W. T., & Skarke, A. (2020). Global marine isochore estimates using machine learning. Geophysical Research Letters, 47, e2020GL088726. doi: 10.1029/2020GL088726

Gabitov, R., C. Borrelli, J. Buettner, B. Kirkland, A. Skarke, D. Trail, B. Garner, M. Testa, M. Wahidi, C. Hoff, S. Khasanov, G. Panieri, R. Thirumalai, J. Thomas, J. Weremeichik, and I. Zverkova (2019), Characterization of Carbonate Crust from a Recently Discovered Methane Seep on the North Atlantic Continental Margin of the USA, Minerals, 9(138), 1–15, doi:10.3390/min9030138.

McVeigh, D., A. Skarke, A.E. Dekas, C. Borelli, W. Hong, J. Marlow, A. Pasulka, S. Jungbluth, R. Barco, and A. Djurhuus (2018), Characterization of Benthic Biogeochemistry and Ecology at Three Methane Seep Sites on the Northern US Atlantic Margin. Deep Sea Research Part II. doi: 10.1016/j.dsr2.2018.03.001

Marlow, J., C. Borrelli, S. P. Jungbluth, C. Hoffman, J. Marlow, P. R. Girguis, A. Dekas, A. Skarke, M. D. Blackman, D. Fornari, A. Soule, C. Van Dover, L. Bagge, R. Barco, B. Boulahanais, K. Bowman, M. Brugler, S. Bush, A. Djurhuus, J. Fernandez, R. Fulweiler, J. Kinsey, K. Kocot, D. McVeigh, M. Navarro, A. Netburn, A. Pasulka, K. Twing, A. Wagner, and J. Zambon (2017), Telepresence is a potentially transformative tool for field science, Proceedings of the National Academy of Sciences of the United States of America, 114(19), 4841–4844, doi:10.1073/pnas.1703514114.

Fitzpatrick, P. J., Y. Lau, R. Moorhead, A. Skarke, D. Merritt, K. Kreider, J. Masters, R. Carlon, G. Hine, T. Lampoudi, and A. Leonardi (2016), Further analysis of the 2014 Gulf of Mexico Wave Glider® field program. Marine Technology Society Journal, 50(3), 72-75. doi:10.4031/MTSJ.50.3.3

DuVal, C., A. Trembanis, and A. Skarke (2016), Characterizing and hindcasting ripple bedform dynamics: Field test of non-equilibrium models utilizing a fingerprint algorithm. Continental Shelf Research, 116, 103-115. doi:10.1016/j.csr.2015.12.015 [PDF]

Quattrini, A.M., M.S Nizinski, J.D Chaytor, A.W.J. Demopoulos, E.B. Roark, S.C. France, J.A. Moore, T. Heyl, P.J. Auster, B. Kinlan, C. Ruppel, K.P. Elliott, B.R.C. Kennedy, E. Lobecker, A. Skarke, and T.M. Shank (2015),  Exploration of the Canyon-Incised Continental Margin of the Northeastern United States Reveals Dynamic Habitats and Diverse Communities. PLoS ONE, 10(10), e0139904. doi:10.1371/journal.pone.0139904 [PDF]

Fitzpatrick, P. J., Y. Lau, D. Merritt, R. Moorhead, A. Skarke, K. Kreider, C. Brown, R. Carlon, G. Hine, T. Lampoudi, and A. Leonardi (2015), A review of the 2014 Gulf of Mexico Wave Glider® field program. Marine Technology Society Journal, 49(3), 64-71. doi:10.4031/MTSJ.49.3.14

Skarke, A., C. Ruppel, M. Kodis*, D. Brothers, and E. Lobecker (2014), Widespread methane leakage from the sea floor on the northern US Atlantic margin, Nature Geoscience, 7(9), 657-661. doi:10.1038/ngeo2232 [PDF]

Brothers, L., C. Van Dover, C. German, C. Kaiser, D. Yoerger, C. Ruppel, E. Lobecker, A. Skarke, and J. Wagner (2013), Evidence for extensive methane venting on the southeastern US Atlantic margin, Geology, 41(7), 807-810. doi: 10.1130/G34217.1[PDF]

Skarke, A., and A. C. Trembanis (2011), Parameterization of bedform morphology and defect density with fingerprint analysis techniques, Continental Shelf Research, 31(16), 1688-1700. doi: 10.1016/j.csr.2011.07.009 [PDF]

Trembanis, A., S. Nebel, A. Skarke, D. Coleman, R. Ballard, A. Yankovsky, I. Buynevich, and S. Voronov (2011), Bedforms, coastal-trapped waves, and scour process observations from the continental shelf of the northern Black Sea, Geological Society of America Special Papers, 473, 165-178. doi:10.1130/2011.2473(10)

Proceedings and Non-Refereed Publications

Manjur, S.M., A. Skarke, and A. Gurbuz (Accepted). Detection and Classification of Gas Seeps in MBES Imagery Using CFAR and Feature-Based Learning, Proceedings of MTS/IEEE Oceans 2025, Chicago, Illinois, USA, Sept 29-Oct 02.

Manjur, S.M., A. Skarke, and A. Gurbuz (Accepted). Evaluating Depth-Dependent Variability in Machine Learning-Based Seafloor Gas Seep Detection Using a Multibeam Echosounder. Proceedings of MTS/IEEE Oceans 2025, Chicago, Illinois, USA, Sept 29-Oct 02.

Manjur, S.M., V. Senyurek, R. Kalski*, A. Skarke, and A. Gurbuz (2025). Machine learning-based seafloor gas seep detection in sonar water column images, Proc. SPIE 13482, Ocean Sensing and Monitoring XVII, 134820F doi:10.1117/12.3054109

Hicks, B., C.O. Ayna, A.C. Gurbuz, V. Senyurek, A. Skarke, and S. Gupta* (2023), Machine learning based automated detection of seafloor gas seeps. Proceedings of MTS/IEEE Oceans 2023, Biloxi, Mississippi, USA, Sept 25-28.

France, S.C., D. Amon, C. Messing, A. Skarke, D. Wagner, M.P. White, B.R.C. Kennedy, and N. Pawlenko (2019), Deep-Sea Exploration of the US Gulf of Mexico with NOAA Ship Okeanos Explorer , in : Raineault, N.A, and J. Flanders (Eds.) New frontiers in ocean exploration: The E/V Nautilus, NOAA Ship Okeanos Explorer, and R/V Falkor 2018 field season. Oceanography, 32(1): doi:10.5670/oceanog.2019.supplement.01.

Dekas, A. E., and A. Skarke (2017), Early-career scientists explore newly discovered methane seeps, Eos, 98, doi: c10.1029/2017EO068011. Published on 10 March 2017.

Crawford, A., and A. Skarke (2014), Automatic detection of sand ripple features in sidescan sonar imagery. Proceedings of MTS/IEEE Oceans 2014, Saint Johns, Newfoundland, Canada, Sept 14-19. doi:10.1109/oceans.2014.7003117 [PDF]

Kraatz, L.M., A. Skarke, A.C. Trembanis, and C.T. Friedrichs (2011), Approaches for quantifying seabed morphology – techniques for utilizing rotary sonar systems. Proceedings of the International Conference on Coastal Sediments 2011.

Skarke, A., B.L. Lipphardt Jr., P. Muscarella, K.C. Wong, A. Trembanis, and M. Badiey (2008), Comparison of HF radar and ADCP surface currents at the Delaware Bay mouth. Proceedings of the IEEE/OES/CMTC Ninth Working Conference on Current Measurement Technology. doi:10.1109/CCM.2008.4480866 [PDF]

Conference (Last 5 Years)

Manjur, S.M., V. Senyurek, R. Kalski*, A. Skarke, and A. Gurbuz (Accepted). Detection and Classification of Gas Seeps in MBES Imagery Using CFAR and Feature-Based Learning, OCEANS 2025 Great Lakes, Sept. 29- Oct. 2, 2025.

Manjur, S.M., V. Senyurek, R. Kalski*, A. Skarke, and A. Gurbuz (Accepted). Evaluating Depth-Dependent Variability in Machine Learning-Based Seafloor Gas Seep Detection Using Multibeam Echosounder, OCEANS 2025 Great Lakes, Sept. 29- Oct. 2, 2025.

Manjur, S.M., V. Senyurek, R. Kalski*, A. Skarke, and A. Gurbuz (2025). Machine learning-based seafloor gas seep detection in sonar water column images, SPIE 13482, Ocean Sensing and Monitoring XVII. May.

Skarke, A., A.C. Gurbuz, V. Senyurek, S. Manjur, R. Kalski*, and S. Gupta* (2024) Automated Detection of Seafloor Gas Seeps with an Attention-Guided Convolutional Neural Network. Abstract OS43A-0573 presented at 2024 Fall Meeting, American Geophysical Union, 09-13 Dec.

Kalski*, R., and A. Skarke (2024) Detection of Seafloor Seeps Using Range-Amplitude Classification Model. Abstract OS43A-0575 presented at 2024 Fall Meeting, American Geophysical Union, 09-13 Dec.

Movahedi, N., L. Zheng, X. Cai, R. Tian, L. Linker, A. Skarke, and J. Heiss (2024) A nested hydrodynamic modeling approach for simulating realistic pressures along estuarine bedforms. Abstract H43F-0927 presented at 2024 Fall Meeting, American Geophysical Union, 09-13 Dec.

Griesel, M., N. Movahedi, L. Zheng, X. Cai, R. Tian, L. Linker, A. Skarke, and J. Heiss (2024) Benthic Exchange in Large Estuaries: The Role of Alternating Tidal Currents and Surface Water Salinity Oscillations. Abstract H43I-0994 presented at 2024 Fall Meeting, American Geophysical Union, 09-13 Dec.

Virden, M., M. Drymon, A. Skarke, K. Smith, N. Temple, and E. Sparks (2024) Accuracy of Structure-from-Motion Derived Digital Elevation Models and Species-Specific Correction Methods. Presented at 2024 Bays and Bayous Symposium, 19-20 Nov.

Gupta*, S. and A. Skarke (2024) Computational Ecology for Seafloor Habitat Mapping: Insights from Backscatter and Bathymetric Data Analysis. Presented at the 2024 Benthic Ecology Meeting. April 10 - 14, 2024.

Skarke, A., A.C. Gurbuz, V. Senyurek, B. Hicks, C.O. Anya, G.E. Hernandez*, and S. Gupta* (2023) Machine Learning Based Automated Detection of Seafloor Gas Seeps. Abstract OS21C-1429 presented at 2023 Fall Meeting, American Geophysical Union, 11-15 Dec.

Hicks, B., C. Ayna, A, Gurbuz, V. Senyurek, A. Skarke, S. Gupta* (2023) Machine Learning Based Automated Detection of Seafloor Gas Seeps. Presented at OCEANS 2023 Gulf Coast, September 26, 2023.

Skarke, A., A. Shiller, N. Dimova, A. Moody, Z. Peoples*(2023), Impact of Submarine Groundwater Discharge on Water Quality in Mississippi Sound. Presented at the 2023 State of The Coast Conference, May 31, 2023.

Gupta*, S. and A. Skarke (2023), Identification of seafloor gas seeps in sonar data to develop a machine learning detection database. Presented at the 2023 GeoSym Conference, February 9-10, 2023.

Alden*, M., A. Skarke, and J. Freeman*(2022), High-Resolution Mapping of Deep-Sea Benthic Environments Through Orthorectification of Oblique ROV Video Data. Abstract OS22D-0947 presented at 2022 Fall Meeting, American Geophysical Union, 13-17 Dec.

Hernandez*, G., and A. Skarke (2022), Spatial Association Between Methane Seeps and Geomorphology on the Northern US Atlantic Margin. Abstract OS42B-1199 presented at 2022 Fall Meeting, American Geophysical Union, 13-17 Dec.

Skarke, A., G. Hernandez*, and S. Gupta* (2022), Updated Inventory of Methane Seeps on the U.S. Atlantic Margin. Abstract OS42B-1200 presented at 2022 Fall Meeting, American Geophysical Union, 13-17 Dec.

Bassett et al. (2022), NOAA’s southeast deep coral initiative, results and accomplishments 2016-2019. Presented at 2022 Ocean Sciences Meeting, Online., 24 Feb-4 Mar.

Hernandez*, G., and A. Skarke (2022), Evaluating the relationship between methane seeps and surrounding geomorphology on the northern US Atlantic margin. Presented at 2022 Ocean Sciences Meeting, Online., 24 Feb-4 Mar.

Peoples*, Z., and A. Skarke (2022), Characterization of Quaternary stratigraphy in the Mississippi Sound to evaluate the influence of geologic heterogeneity on submarine groundwater transport and discharge. Presented at 2022 Ocean Sciences Meeting, Online., 24 Feb-4 Mar.

Freeman*, J., and A. Skarke (2022), Automated mapping of deep sea ROV video data. Presented at 2022 Ocean Sciences Meeting, Online., 24 Feb-4 Mar.

Lee*, T.R., W. Wood, B. Phrampus, and A. Skarke (2021), Global carbon and methane hydrate inventories in marine sediments using machine learning constraints. Abstract OS22A-02 presented at 2021 Fall Meeting, American Geophysical Union, 13-17 Dec.

Skarke, A., and G. E. Hernandez* (2021), Spatial Association of Methane Seeps and Seafloor Geomorphic Classification on the Northern US Atlantic Margin. OS25B-1016 presented at 2021 Fall Meeting, American Geophysical Union, 13-17 Dec.

French*, J.E., A. Skarke, A. Linhoss, M. Brasher, and R. Osorio (2020), The optimization of marsh terracing as a wetland restoration technique: Mitigating cohesive sediment erosion from wind driven waves. Abstract B052-0013 presented at 2020 Fall Meeting, American Geophysical Union, 1-17 Dec.

Lee*, T.R., B. Phrampus, W. Wood, and A. Skarke (2020), A new estimate of carbon sequestered within the global methane hydrate stability zone using machine-learning predicted inputs. Abstract OS029-0004 presented at 2020 Fall Meeting, American Geophysical Union, 1-17 Dec.

Luciano, A., T.R. Lee*, B. Phrampus, J. Obelcz, W. Wood, A. Skarke (2020), An updated global prediction of marine unit thicknesses for present to middle Miocene sediments using Ocean Drilling Program data. Abstract EP060-0001 presented at 2020 Fall Meeting, American Geophysical Union, 1-17 Dec.

Skarke, A., and G. E. Hernandez* (2020), Spatial Relationship Between Methane Seeps and Geomorphological Properties of the Seafloor on the US Atlantic Margin. OS016-0009 presented at 2020 Fall Meeting, American Geophysical Union, 1-17 Dec.

Osorio, R., A. Linhoss, A. Skarke, M. Brasher, and J. French* (2020), Assessment of wave regimes for optimal implementation of marsh terracing in the northern Gulf of Mexico, a modeling approach. Abstract BBS20414 presented at 2020 Bays and Bayous Symposium, 1-3 Dec.

French*, J. E., A. Skarke, and M. Brasher (2020), Effect of tropical storm and frontal passage on marsh erosion in terraced coastal wetlands. Abstract CP24D-1166 presented at 2020 Ocean Sciences Meeting, San Diego, CA., 16-21 Feb.

Skarke, A. and M. W. Kidiwela* (2020), Discovery and characterization of two methane seep fields with unique fluid discharge features on the US Atlantic continental margin. Abstract IS24C-3317 presented at 2020 Ocean Sciences Meeting, San Diego, CA., 16-21 Feb.