1. 藻類與水質優養化
2. 藻類活性物質及藻毒.
3. 長期生態研究
4. 藻類生態生理.
5. 水污染藻類指標及古環境之藻類指標.

● 藻類相剋物質及活性物質之鑑定和功能研究，特別針對淡水域之優勢藻種。
● 應用藻類於湖積物之研究，以矽藻為指標，探討古環境變遷。
● 自1986年起長期監測翡翠水庫之水質優養化與水中藻類之關係。提供管理之和防除水質優養化之對策。

● 研究藻類之生態生理，特別對有害藻類之成因及防除策略進行研究。
● 長期執行鴛鴦湖生態系研究，特別側重該生態系之酸性環境之原因、影響等。

1. Lan, Y.H., Wang, W.C., Tsai, J.W., Lin, F.P., Chou, H.M., Liu, W.C., Wu, J.T., Chiu, C.Y. ，2011，〈 Influence of stratification and mixing regime on lake metabolism in the Yuan-yang Lake, Chi-lan Shan, Taiwan.〉，《Journal of Forestry Research》，33, 77-90。(Others)
2. Wang, L.C., Wu J.T.*, Chen, S.H. , 2011, “Climate changes inferred from integrated multi-site pollen data in northern Taiwan. ”, Journal of Asian Earth Sciences, 40,1164-1170. (SCI) (IF: 2.215; SCI ranking: 22.8%)
3. Wang, W.C., Lan, Y.H., Tsai, J.W., Lin, F.P., Chou H.M., Liu W.C., Wu, J.T., Chiu, C.Y., 2011, “Effect of metrological conditions on water mixing regime in summer and winter seasons of Yuan-Yang Lake, Chi-Lan Shan, Taiwan. ”, Quarterly Journal of Chinese Forestry, 44, 41-53. (Others)
4. Tsai, J.W., Kratz, T.K., Hanson, P.C., Kimura, N., Liu, W.C., Lin, F.P., Chou, H.M., Wu, J.T., Chiu, C.Y. , 2011, “Metabolic changes and the resistance and resilience of a subtropical heterotrophic lake to typhoon disturbance. ”, Canadian Journal of Fisheries and Aquatic Sciences, 68(5), 768-780. (SCI) (IF: 2.166; SCI ranking: 13%,19.4%)
5. T.N.Yang, T.Q.Lee, P.A.Meyers, C.W. Fan, R.F. Chen, K.Y.Wei, Y.G. Chen, J.T. Wu, 2011, “The effect of typhoon induced rainfall on settling fluxes of particles and organic carbon in Yuanyang Lake, subtropical Taiwan”, JOURNAL OF ASIAN EARTH SCIENCES, 40(6), 1171-1179. (SCI) (IF: 2.215; SCI ranking: 22.8%)
6. Yang, T.N., Lee, T.Q., Meyers, P.A., Fan, C.W., Chen, R.F., Wei, K.Y., Chen, Y.G., Wu, J.T., 2011, “The effect of typhoon induced rainfall on settling fluxes of particles and organic carbon in Yuanyang Lake, subtropical Taiwan.”, Journal of Asian Earth Sciences, 40, 1171-1179. (SCI) (IF: 2.215; SCI ranking: 22.8%)
7. Babu B., Wu J.T., 2010, “Biodegradation of phthalate esters by cyanobacteria”, Journal of Phycology, 46(6), 1106-1113. (SCI) (IF: 2.239; SCI ranking: 26.6%,18.3%)
8. H.L.Hsieh, L.F. Fan, C.P. Chen, J.T. Wu, W.C. Liu, 2010, “Effects of semidiurnal dital circulation on the distribution of holo- and meroplankton in a subtropical estuary.”, JOURNAL OF PLANKTON RESEARCH, 32(6), 829-841. (SCI) (IF: 1.749; SCI ranking: 36.6%,37.3%)
9. J.T. Wu*, L.C. Kow, 2010, “Alteration of phytoplankton assemblages caused by changes in water hardness in Feitsui Reservoir”, BOTANICAL STUDIES, 51(4), 521-529. (SCI) (IF: 0.842; SCI ranking: 60.1%)
10. Y.C.Shin, B.Y.Liu, J.Y.Tsai, J.T.Wu, L.K.Chang, S.C. Chang*, 2010, “Biochemical characterization of the small ubiquitin-like modifiers of Chlamydomonas reinhardtii”, PLANTA, 232, 649-662. (SCI) (IF: 3.098; SCI ranking: 13.3%)
11. B. Babu, J.T. Wu*, 2010, “Biodegradation of phthalate esters by cyanobacteria”, JOURNAL OF PHYCOLOGY, 46(6), 1106-1113. (SCI) (IF: 2.239; SCI ranking: 26.6%,18.3%)
12. L.C. Wang, J.T. Wu*, S.H. Chen, 2010, “Climate changes inferred from integrated multi-site pollen data in northern Taiwan”, JOURNAL OF ASIAN EARTH SCIENCES, 40(6), 1164-1170. (SCI) (IF: 2.215; SCI ranking: 22.8%)
13. L.C. Wang, S.H. Chen, J.T. Wu*, 2010, “Diatoms in Liyu Lake, eastern Taiwan. Taiwania”, TAIWANIA, 55, 228-242. (Others)
14. W.D. Huang, J.S. Yang, J.C. Chen, M.H. Hsu, J.T.Wu*, C.M. Yang*, 2010, “Grey relational analysis of physico-chemical variables and water body reflectance of a Chi-Chi earthquake landslide-dammed lake monitored by SPOT satellite”, THE JOURNAL OF GREY SYSTEM, 22(4), 297-308. (SCI) (IF: 0.37; SCI ranking: 93.5%)
15. J.S. Wang, R. Kumar, C.W. Hsieh, A.Y. Kuo, S. Souissi, M.H. Hsu, J.T. Wu, W.C. Liu, C.F. Wang, Q.C.Chen, 2010, “Patterns of zooplankton distribution along the marine, estuarine and riverine portions of the Danshuei ecosystem in northern Taiwan”, ZOOLOGICAL STUDIES, 49, 335-352.. (SCI) (IF: 1.046; SCI ranking: 44.8%)
16. B. Babu, J.T. Wu*, 2010, “Production of phthalate esters by nuisance freshwater algae and cyanobacteria”, SCIENCE OF THE TOTAL ENVIRONMENT, 408, 4969-4975. (SCI) (IF: 3.19; SCI ranking: 13.5%)
17. Babu, B., Wu, J.T.*, 2010, “Production of phthalate esters by nuisance freshwater algae and cyanobacteria. ”, Science of the Total Environment, 408, 4969-4975. (SCI) (IF: 3.19; SCI ranking: 13.5%)
18. Tseng, Y.F., Hsu, T.C., Chen, Y.L., Kao, S.J., Wu, J.T., Lu, J.C., Lai, J.C., Kuo, H.Y., Lin, C.H., Yamamoto, Y., Xiao, T., Shiah, F.K., 2010, “Typhoon effects on the variation of DOC inventory in a phosphate-limited reservoir”, AQUATIC MICROBIAL ECOLOGY, 60, 247-260. (SCI) (IF: 2.089; SCI ranking: 43.1%,20.4%,57%)
19. Jiunn-Tzong Wu, Yu-Fa Wang, 2009, “Diatoms of the Mysterious Lake, Taiwan”, Taiwania, 54:231-240. (EI)
20. Y.C. Chien, S.C. Wu, J.T. Wu, 2009, “Identification of physical parameters controling the dominance of algal species in a subtropical reservoir”, Water Science and Technology, 60(7), 1779-1786. (SCI) (IF: 1.056; SCI ranking: 68.9%,72.5%,51.3%)
21. S. H. Chen, J. T. Wu*, T. N. Yang, P. P. Chuang, S. Y. Huang and Y. S. Wang, 2009, “Late Holocene paleoenvironmental changes in subtropical Taiwan inferred from pollen and diatoms in lake sediments”, Journal of Paleolimnology, 41, 315-327. (SCI) (IF: 2.676; SCI ranking: 22.8%,14.4%,16.7%)
22. J.W.Tsai, Y. Chou, B.S. Lin, J.T. Wu, C.Y. Chiu*, 2009, “Seasonal dynamics of lake metabolism in Yuan-Yang Lake”, QUARTERLY JOURNAL CHINESE FORESTRY, 42, 335-345. (Others)
23. Jeng-Wei Tsai, Yalan Chou, Bing-Shih Lin, Jiunn-Tzong Wu, Chih-Yu Chiu，2009，〈Seasonal dynamics of lake metabolism in Yuan-Yang Lake〉，《Quaterly Journal of chinese Forestry》，42, 335-345。(EI)
24. B. Babu, J.T. Wu (2008) Production of natural butylated hydroxytoluene as an antioxidant by freshwater phytoplankton. J. Phycol. 44:1447-1454.
25. J.W. Tsai, T.K. Kratz, , P.C. Hanson, J.T. Wu, W.Y.B. Chang, P.W. Artzberger, B.S. Lin, F. P.H. Lin, M. Chou, C.Y. Chiu (2008) Seasonal dynamics, typhoons and the regulation of lake metabolism in a subtropical humic lake. Freshwater Biol. 53:1929-1941.
26. J.W. Tsai, T.K. Kratz, P.C. Hanson, J.T. Wu, W,Y.B. Chang, P.W. Arzberger, B.S. Lin, F.P. Lin, H.M. Chou, C.Y. Chiu (2008) Seasonal dynamics of lake metabolism in a sub-tropical alpine lake. Verh. Internat. Verein. Limnol. 30:381-385.
27. R.D. Papa, J.T. Wu, S. Baldia, C. Cho, M.A. Cruz, A. Saguiguit, R. Aquino (2008) Blooms of the colonial green algae, Botryococcus braunii Kuetzing, in Paoay Lake, Luzon Island, Philippines. Philippine J. System. Biol. 2(1):21-31.
28. T.K. Yamada, Y. Tsuchikane, J.T. Wu, H. Sekimoto, K. Miyaji, H. Nozaki (2008) Morphology and molecular phylogeny of Eudorina sp. (Volvocaceae, Chlorophyceae) from Taiwan. Hikobia, 15:125-143.
29. S.C. Chang, K.H. Tseng, Y.J. Hsia, C.P. Wang, J.T. Wu (2008) Soil respiration in a subtropical montane cloud forest in Taiwan. Agricul. Forest Meteorol. 148:788-798.
30. Yang, C.P., J.T. Kuo, W.S. Lung, J.S. Lai, and J.T. Wu. (2007) Water quality and ecosystem modeling of tidal wetlands. J. Environ. Eng. (accepted) (SCI, IF: 0.725; Ranking: 75 %)
31. Lai, I.L., W.H. Schroeder, J.T. Wu, L.L. Kuo-Huang, C. Mohl and C.H. Chou. (2007) Tracing the way of fog solutes into yellow cypress foliage and roots. Tree Physiol. (in press) (SCI, IF: 2.297; Ranking: 8.57%)
32. Wang, C. F., M. H. Hsu, W. C. Liu, J. S. Hwang, J. T. Wu and A. Y. Kuo. (2007) Simulation of Water Quality and Plankton Dynamics in Danshuei River Estuary, Taiwan. J. Environ. Sci. Health, 42(7): 933-953. (SCI, IF: 0.669; Ranking: 78.47%)
33. Chang, S.-C., C.-F. Yeh, M.-J. Wu, Y.-J. Hsia, and J.-T. Wu. (2006) Quantifying fog water deposition by in situ exposure experiments in a mountainous coniferous forest in Taiwan. Forest Ecology and Management, 224: 11-18. (SCI, IF: 1.839; Ranking: 11.43%)
34. Lai, I.L., S.C. Chang, P.H. Lin, C.H. Chou and J.T. Wu. (2006) Climatic characteristics of the subtropical mountainous cloud forest at the Yuangyang Lake long-term ecological research site, Taiwan. Taiwania, 51:317-329.
35. Wu, J. T., Y. R. Chiang and W. Y. Huang (2006) Cytotoxic effects of fatty acids on phytoplankton algae and cyanobacteria. Aquat. Toxicol, 80:338-345. (SCI, IF: 2.964; Ranking: 15.79%)