Assistant Research Professor
Dr. Brian Barnes
Brian Barnes


2009-2013 — Ph.D. (Marine Science), College of Marine Science, University of South Florida

2006-2009 — M.S. (Marine Science), Virginia Institute of Marine Science, College of William and Mary

2004 — B.S. (Zoology & Psychology), University of Florida


Aug 2022-present Assistant Research Professor, College of Marine Science, University of South Florida

Dec 2015-present — Research Associate, College of Marine Science, University of South Florida

Nov 2013-Dec 2015 — Post Doctoral Associate, College of Marine Science, University of South Florida

Research Interests:

My overarching interest is in research and monitoring of reef systems & ecology with an emphasis on preservation and restoration. Current work is to improve understanding of coral health and ecology in the Florida Keys reef tract through combination of multiple remote sensing techniques. Past projects include larval-adult interactions on oyster reefs, comparative ecology of native and non-native oyster reefs, physical and biological changes associated with barrier-island inlet morphology, spiny lobster disease dynamics, coral reef ecology and monitoring, and installation and maintenance of NDBC & SeaKeys stations.


BB Barnes, SW Bailey, C Hu, BA Franz (2022) Vicarious Calibration of the Long Near Infrared Band: Cross-Sensor Differences in Sensitivity. IEEE Trans. Geosci. Remote Sens. 60:4208109

M Xu, C Hu, RG Najjar, M Hermann, H Briceno, BB Barnes, JOR Johansson, D English (2022) Estimating estuarine primary production using satellite data and machine learning. Int J Appl Earth Obs Geoinf. 110:102821

HM Dierssen, R Vandermeulen, BB Barnes, A Castagna, E Knaeps, Q Vanhellemont (2022) QWIP: A quantitative metric for quality control of aquatic reflectance spectral shape using the apparent visible wavelength. Front. Mar. Sci. 3:869611

R Elahi, PJ Edmunds, RD Gates, IB Kuffner, BB Barnes, I Chollet, TA Courtney, JR Guest, EA Lenz, LT Toth, TS Viehman, ID Williams (2022) Scale dependence of coral reef oases and their environmental correlates. Ecological Applications :e2651

Y Zhang, C Hu, VH Kourafalou, Y Liu, DJ McGillicuddy, BB Barnes, JM Hummon (2022) Physical characteristics and evolution of a long-lasting mesoscale cyclonic eddy in the Straits of Florida. Front. Mar. Sci. 9:779450

S Zhang, C Hu, BB Barnes, TN Harrison (2022) Monitoring Sargassum inundation on beaches and nearshore waters using PlanetScope/Dove observations. IEEE Geosci. Remote Sens. Lett. 19:1503605

C Hu, L Qi, Y Xie, S Zhang, BB Barnes (2022) Spectral characteristics of sea snot reflectance observed from satellites: Implications for remote sensing of marine debris. Remote Sens Environ 269:112842

BB Barnes, C Hu, SW Bailey, N Pahlevan, BA Franz (2021) Cross-calibration of MODIS and VIIRS long near infrared bands. Remote Sens Environ 260:112439

RA Garcia, Z Lee, BB Barnes, C Hu, HM Dierssen, EJ Hochberg (2020) Benthic classification and IOP retrievals in shallow water environments using MERIS imagery. Remote Sens Environ 249:112015

CC Lee, BB Barnes, SC Sheridan, ET Smith, C Hu, DE Pirhalla, V Ransibrahmanakul, RE Adams (2020) Using Machine Learning to Model Water Clarity in the Great Lakes. J Great Lakes Res

TA Courtney, BB Barnes, I Cholett, R Elahi, K Gross, JR Guest, IB Kuffner, EA Lenz, CS Rogers, LT Toth, AJ Anderson (2020) Disturbances drive changes in coral community assemblages and coral calcification capacity. Ecosphere 11:e03066

ET Smith, CC Lee, BB Barnes, RE Adams, DE Pirhalla, V Ransibrahmanakul, C Hu, SC Sheridan (2020) A synoptic climatological analysis of the atmospheric drivers of water clarity variability in the Great Lakes. J Appl Meteorol Climatol 59:915-935

BB Barnes, C Hu, SW Bailey, BA Franz (2020) Sensitivity of Satellite Ocean Color Data to System Vicarious Calibration of the Long Near Infrared Band. IEEE Trans. Geosci. Remote Sens.

L Qi, C Hu, K Mikelsons, M Wang, V Lance, S Sun, BB Barnes, J Zhao, and D Van der Zande (2020). In search of floating algae and other organisms in global oceans and lakes. Remote Sens. Environ., 239: 111659

C Hu, BB Barnes, L Feng, M Wang, L Jiang (2019) On the interplay between ocean color data quality and data quantity: Impacts of quality control flags. IEEE Geosci. Remote Sens. Lett. 17:745-749

M Wang, C Hu, BB Barnes, G Mitchum, B Lapointe (2019) The Great Atlantic Sargassum Belt. Science 365: 83-87.

J Cannizzaro, BB Barnes, C Hu, AA Corcoran, KA Hubbard, E Muhlbach, WC Sharp, LE Brand, CR Kelble (2019) Remote detection of cyanobacterial harmful algal blooms of Synechococcus in Florida Bay using MODIS data. Remote Sens. Environ. 231: 111227

S Chen, C Hu, BB Barnes, R Wanninkhof, W-J Cai, L Barbero, D Pierrot (2019) A machine learning approach to estimate surface ocean pCO2 from satellite measurements. Remote Sens. Environ. 228: 203-226

M Zhang, C Hu, BB Barnes (2019) Performance of POLYMER atmospheric correction of ocean color imagery in the presence of absorbing aerosols. IEEE Trans. Geosci. Remote Sens. 57: 6666-6674.

S Chen, C Hu, BB Barnes, Y Xie, G Lin, and Z Qiu (2019) Improving ocean color data coverage through machining learning. Remote Sens. Environ. 222: 286-302.

R Cunning, RN Silverstein, BB Barnes, AC Baker (2019) Extensive coral mortality and critical habitat loss following dredging associated with remotely-sensed sediment plumes. Mar. Pollut. Bull. 145: 185-199

BB Barnes, JP Cannizzaro, D English, C Hu (2019) Validation of VIIRS and MODIS reflectance data in coastal and oceanic waters: An assessment of methods. Remote Sensing of Environment 220:110-123.

M Zhang, C Hu, J Cannizzaro, D English, BB Barnes, P Carlson, L Yarbro (2018) Comparison of two atmospheric correction approaches applied to MODIS measurements over North American Waters. Remote Sensing of Environment 216: 442-455

JR Guest, PJ Edmunds, RD Gates, IB Kuffner, AJ Andersson, BB Barnes, I Chollett, TA Courtney, R Elahi, K Gross, EA Lenz, S Mitarai, PJ Mumby, HR Nelson, BA Parker, HM Putnam, CS Rogers, LT Toth (2018) A framework for identifying and characterising coral reef “oases” against a backdrop of degradation. Journal of Applied Ecology 55: 2865-2875

BB Barnes, R Garcia, C Hu, Z Lee (2018) Multi-band spectral matching inversion algorithm to derive water column properties in optically shallow waters: An optimization of parameterization. Remote Sens Environ 204: 424-438

J Li, C Hu, Q Shen, BB Barnes, B Murch, L Feng, M Zhang (2017) Recovering low quality MODIS-Terra data over highly turbid waters through noise reduction and vicarious calibration: A case study in Taihu Lake. Remote Sens Environ 197: 72-84

CC Lee, SC Sheridan, BB Barnes, C Hu, DE Pirhalla, V Ransibrahmanakul, K Shein (2017) The development of a non-linear auto-regressive model with exogenous input (NARX) to model climate-water clarity relationships: reconstructing an historical water clarity index for the coastal waters of the southeastern US. Theor. Appl. Climatol., 130: 557-569

L Qi, C Hu, BB Barnes, Z Lee (2017) VIIRS captures phytoplankton vertical migration in the NE Gulf of Mexico. Harmful Algae 66: 40-46

DE Pirhalla, SC Sheridan, CC Lee, BB Barnes, V Ransibrahmanakul, C Hu (2017) Water clarity patterns in South Florida coastal waters and their linkages to synoptic-scale wind forcing. Sat. Oceanog. Meterolog. 1: 1-15.

L Feng, C Hu, BB Barnes, A Mannino, AK Heidinger, K Strabala, LT Iraci (2017) Cloud and sun glint statistics derived from GOES and MODIS observations over the Intra-Americas Seas for GEO-CAPE mission planning. J Geopyhs. Res. Atmospheres. 122: 1725-1745.

C Hu, B Murch, BB Barnes, M Wang, J-P Maréchal, J Franks, D Johnson, B Lapointe, DS Goodwin, JM Schell, ANS Suida (2016) Sargassum watch warns of incoming seaweed. EOS. 97:10-15

BB Barnes and C Hu (2016) Island building in the South China Sea: detection of turbidity plumes and artificial islands using Landsat and MODIS data. Sci. Rep. 6:33194

C Hu, BB Barnes, L Qi, C Lembke, D English (2016) Vertical migration of Karenia brevis in the northeastern Gulf of Mexico observed from glider measurements. Harmful Algae. 58:59-65

BB Barnes and C Hu (2016) Dependence of satellite ocean color data products on viewing angles: A comparison between SeaWiFS, MODIS, and VIIRS. Remote Sens. Environ. 175:120-129

BB Barnes, C Hu, C Kovach, R Silverstein (2015) Sediment plumes induced by the Port of Miami dredging: Analysis and interpretation using Landsat and MODIS data. Remote Sens. Environ. 170:328-339

C Hu, B Murch, AA Corcoran, L Zheng, BB Barnes, RH Weisberg, K Atwood, JM Lenes (2015) Developing a smart semantic web with linked data and models for near real-time monitoring of red tides in the eastern Gulf of Mexico. IEEE Systems J. PP:1-9

JJ Walsh, JM Lenes, BP Darrow, AA Parks, RH Weisberg, L Zheng, C Hu, BB Barnes, KL Daly, GR Brooks, WH Jeffrey, RA Snyder, D Hollander (2015) A simulation analysis of the plankton fate of the Deepwater Horizon oil spills. Cont. Shelf. Res. 107:50-68

BB Barnes, P Hallock, C Hu, F Muller-Karger, DA Palandro, C Walter, R Zepp (2015) Prediction of coral bleaching in the Florida Keys using remotely sensed data. Coral Reefs. 34:491-503.

C Hu, BB Barnes, L Qi, AA Corcoran (2015) A harmful algal bloom of Karenia brevis in the Northeastern Gulf of Mexico as revealed by MODIS and VIIRS: A comparison. Sensors. 15:2873-2887

BB Barnes and C Hu (2015) Cross-sensor continuity of satellite derived water clarity in the Gulf of Mexico: insights into temporal aliasing and implications for long-term water clarity assessment. IEEE Trans. Geosci. Remote Sens. 53:1761-1772

D Sun, C Hu, Z Qiu, JP Cannizzaro, BB Barnes (2014) Influence of a red band-based water classification approach on chlorophyll algorithms for optically complex estuaries. Remote Sens. Environ. 155:289-302

L Qi, C Hu, H Duan, BB Barnes, R Ma (2014) An EOF-based algorithm to estimate chlorophyll a concentrations in Taihu Lake from MODIS land-band measurements: Implications for near real-time applications and forecasting models. Remote Sens. 6:10694-10715

CC Wall, P Simard, M Lindemuth, C Lembke, DF Naar, C Hu, BB Barnes, FE Muller-Karger, DA Mann (2014) Temporal and spatial mapping of red grouper Epinephelus morio sound production. J. Fish Biol. 85:1469-1487

Hu, C., B. B. Barnes, B. Murch, and P. Carlson (2014). Satellite-based virtual buoy system (VBS) to monitor coastal water quality. Optical Engineering. 53(5), 051402. DOI:

Barnes, B. B., C. Hu, J. P. Cannizzaro, S. E. Craig, P. Hallock, D. Jones, J. C. Lehrter, N. Melo, B. A. Schaeffer, and R. Zepp (2014). Estimation of diffuse attenuation of ultraviolet light in optically shallow Florida Keys waters from MODIS measurements. Remote Sens. Environ. 140:519-532.

Barnes, B. B., C. Hu, K. L. Holekamp, S. Blonski, B. A. Spiering, D. Palandro, and B. Lapointe (2014). Use of Landsat data to track historical water quality changes in Florida Keys marine environments. Remote Sens. Environ. 140:485-496.

Zhao, J., B. Barnes, N. Melo, D. English, B. Lapointe, F. Muller-Karger, B. Schaeffer, and C. Hu (2013). Assessment of satellite-derived diffuse attenuation coefficients and euphotic depths in south Florida coastal waters. Remote Sens. Environ., 131:38-50

Barnes, B. B., C. Hu, B. A. Schaeffer, Z. Lee, D. A. Palandro, & J. C. Lehrter (2013) MODIS-derived spatiotemporal water clarity patterns in optically shallow Florida Keys waters: A new approach to remove bottom contamination. Remote Sens. Environ., 134:377-391.

Barnes, B. B., and C. Hu (2013). A hybrid cloud detection algorithm to improve MODIS sea surface temperature data quality and coverage over the eastern Gulf of Mexico. IEEE Trans. Geosci. Remote Sens., 51:3273-3285. doi:10.1109/TGRS.2012.2223217.

Barnes, B., C. Hu, and F. E. Muller-Karger (2011). An Improved High-Resolution SST Climatology to Assess Cold Water Events off Florida. IEEE Geosci. Remote Sens. Lett., 8:769-773.

Lirman, D., S. Schopmeyer, D. Manzello, L.J. Gramer, W. Precht, F. Muller-Karger, K. Banks, B. B. Barnes, E. Bartels, A. Bourque, J. Byrne, S. Donahue, J. Duquesnel, L. Fisher, D. Gilliam, J. Hendee, M. Johnson, K. Maxwell, E. McDevitt, J. Monty, D. Rueda, R. Ruzicka, S. Thanner (2011). Severe 2010 cold-water event caused unprecedented mortality to corals of the Florida Reef Tract and reversed previous survivorship patterns. PloS ONE, 6 (8): e23047. doi:10.1371/journal.pone.0023047.

Barnes, B. B., M. W. Luckenbach, & P. R. Kingsley-Smith. 2010. Oyster reef community interactions: The effect of resident fauna on oyster (Crassostrea spp.) larval recruitment. J Exp Mar Biol Ecol. 391: 169-177.