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Benjamin, C.S., P.L. Cadeliña, A.T. Yñiguez, C.L. Villanoy. 2019. Development and application of a low-cost rapid assessment system for coastal benthic habitats. Environmental monitoring and assessment, 191(10): 633.

Andres, J.K., A.T. Yñiguez, J. Maister, A.D. Turner, D.E. Olano, J. Mendoza, L. Salvador-Reyes, R.V. Azanza. 2019. Saxitoxin uptake, assimilation, depuration and transformation in the Southeast Asian Green-Lipped Mussel (Perna viridis). Toxins 11(8), 468; https://doi.org/10.3390/toxins11080468.

Patrick P.R. and A.T. Yñiguez. 2019. Larval connectivity patterns of the North Indo-West Pacific coral reefs. PLOS One. 14(7): e0219913. https://doi.org/10.1371/journal.pone.0219913

Benico, G.A., K. Takahashi, W.M. Lum, A.T. Yñiguez, R.V. Azanza, S.C.Y. Leong, P. T. Lim, M. Iwataki. 2019. First report of Biecheleriopsis adriatica in Bolinao, Northwestern Philippines and its wide distribution in Southeast Asia and adjacent waters. Philippine Journal of Natural Sciences. [pdf]

Onda, D.F.L., M.A. Santos, D. dela Cruz-Papa, A.T. Yñiguez, R.V. Azanza, M.A. Siringan. 2019. Microbial oceanography studies in the context of climate change in the Philippines. Philippine Science Letters 12(1): 9 – 23 (http://www.philsciletters.org/2019-9.html).

Yñiguez, A.T., J. Maister, C.L. Villanoy, J.D. Deauna, E. Peñaflor, A. Almo, L.T. David, G.A. Benico, E. Hibay, I. Mora, S. Arcamo, J. Relox, and R.V. Azanza. 2018. Insights into the dynamics of harmful algal blooms in a tropical estuary through an integrated hydrodynamic-Pyrodinium­-shellfish model. Harmful Algae 80: 1-14. https://doi.org/10.1016/j.hal.2018.08.010

Gajigan AP, AT Yñiguez, CL Villanoy, ML San Diego-McGlone, GS Jacinto, C Conaco. 2018. Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines. PeerJ 6:e4781  https://doi.org/10.7717/peerj.4781

Camoying, M. and A.T. Yñiguez. 2016. FlowCAM optimization: attaining good quality images for higher taxonomic classification resolution of natural phytoplankton samples. Limnology and Oceanography Methods 14(5): 305-314. doi: 10.1002/lom3.10090. [pdf]

Yñiguez, A.T., J. W. McManus, and L. Collado-Vides. 2015. Consequences of morphological plasticity and fragmentation on space occupation of coral reef macroalgae. Ecological Modelling 309-310: 128-142. doi:10.1016/j.ecolmodel.2015.04.024  [pdf]

Cayetano, A., A. T.Yñiguez, C.L. Villanoy,  J.D. Deauna, E. Peñaflor, J.D. Palermo, L.David, G. A. Benico, R.V. Azanza.  2013. Improving the validity and robustness of a harmful algal bloom model through genetic algorithm-based optimization. Journal of Environmental Science and Management 1:21-28. [pdf]

Yñiguez, A., A. Cayetano, C.L. Villanoy, I. Alabia, I. Fernandez, J.D. Palermo, G. A. Benico, F.P. Siringan, R.V. Azanza. 2012. Investigating the roles of intrinsic and extrinsic factors in the blooms of Pyrodinium bahamense var. compressum using an individual-based model. Procedia Environmental Sciences 13: 1462-1476.  [pdf]

Villanoy, C.L., O. Cabrera, A. Yñiguez, A., M. Camoying, A. de Guzman, L. David and P. Flament. 2011. Monsoon-driven coastal upwelling.  Oceanography 24 (1): 98-107.  [pdf]

Yñiguez, A., J. McManus and L. Collado-Vides. 2010. Capturing the dynamics in benthic structures: environmental effects on morphology in the macroalgal genera Halimeda and Dictyota. Marine Ecology Progress Series 411: 17-32. [pdf] [supplement]

Yñiguez, A., J. McManus and D. DeAngelis. 2008. Allowing macroalgae growth forms to emerge: use of an agent-based model to understand the growth and spread of macroalgae in Florida coral reefs. Ecological Modelling 216: 60-74.  [pdf]

Azanza, R.V., F. Siringan, M.L. San-Diego-McGlone, A. Yñiguez, N.  Macalalad and P.B. Zamora. 2004. Horizontal dinoflagellate cyst distribution, sediment characteristics and benthic flux in Manila Bay, Philippines. Phycological Research 52: 376-386.  [pdf]

Yñiguez, A. 2006. Allowing macroalgae growth forms to emerge: use of an agent-based model to understand the growth and spread of macroalgae in Florida coral reefs. Reef Encounter 34.

Minett, J.W., M. Hongbin, A.M. Perez, J. Qi, A.B. Smith, Y. Wang, H. Yang, A. Yñiguez. (alphabetical order). 2004. Processes of Extinction. In Proceedings of the Complex Systems Summer School, Santa Fe Institute and Qingdao University, Qingdao, China, July 5-30, 2004.

Lindeman, K., R. Fortuna, A. Yñiguez, and M. Brandt. 2001. Research and Management Recommendations for Caribbean Coral Reefs from Past Workshops. In: Proceedings of the Priorities for Caribbean Coral Reef Research Workshop, Doubletree Hotel, Miami, 3-5 October 2001.

Villanoy, C., R.V.Azanza, G. Jacinto, A. Casil, A. Yñiguez, I. Velasquez and K. Cordero. 2001. Research status and needs on physical and chemical oceanography in relation to harmful algal blooms. In: Proceedings of the 1st National Harmful Algal Bloom Conference/ Workshop, Marine Science Institute, C.S., U.P. Diliman, Quezon City, Philippines, 24 August 2000.

Siringan, F., R.V. Azanza, J. Duyanen, M. McGlone, M. Agustin, R. Dizon, N. Macalalad, Y. Yacat, A. Yñiguez, and P. Zamora. 2001. Sediment control on “Toxic Algal Blooms” and records of bloom occurrences in the bay. In: Proceedings of the 1st National Harmful Algal Bloom Conference/ Workshop, Marine Science Institute, C.S., U.P. Diliman, Quezon City, Philippines, 24 August 2000.