＜學術期刊論文＞
- Tsai, C.-T.、Lin, C.-H.、Chang, C.-Y.，"Analysis of Codon Usage Bias and Base Compositional Constraints in Iridovirus"，Virus Research，2007 (SCI).
- Chen, W.-Y、John, J. A. C.、Lin, C.-H.、Chang, C.-Y.，"Expression Pattern of Metallothionein, MTF-1 Nuclear Translocation and Its DNA-Binding Activity in Zebrafish (Danio rerio) Induced by Zinc and Cadmium."，Environmental Toxicology and Chemistry，Vol. 26，2007，pp.110-117 (SCI).
- Lin, C.-H.、John, J. A. C.、Lin, C.-H.、Chang, C.-Y.，"Inhibition of Nervous Necrosis Virus Propagation by Fish Mx Proteins."，Biochemical and Biophysical Research Communications，Vol. 351，2006，pp.534-539 (SCI).
- Cheng, C.-A.、John, J. A. C.、Wu, M.-S.、Lee, C.-Y.、Lin, C.-H.，"Characterization of Serum Immunoglobulin M of Grouper and CDNA Cloning of Its Heavy Chain."，Veterinary Immunology and Immunopathology，Vol. 109，2006，pp.255-265 (SCI).
- Nie, Z.、Tzeng, Y.-K.、Chang, H.-C.、Chiu, C.-C.、Chang, C.-Y.，"Microscopy-Based Mass Measurement of A Single Whole Virus in A Cylindrical Ion Trap."， Angewandte Chemie International Edition，Vol. 45，2006，pp.8131-8134(SCI).
- Tsai, C.-T.、Ting, J.-W.、Wu, M.-H.、Wu, M.-F.、Guo, I.-C.，"Complete Genome Sequence of the Grouper Iridovirus and Comparison of Genomic Organization with Other Iridoviruses."，Journal of Virology，Vol. 79，No. 4，2005，pp.2010-2023 (SCI).
- Lin, C.-H.、 John, J. A. C.、Ou, L.-W.、Chen, J.-C.、Lin, C.-H.，"Cloning and Characterization of Metallothionein Gene in Ayu Plecoglossus altivelis."，Aquatic toxicology，Vol. 66，2004，pp.111-124 (SCI).
- Chen, W.-Y.、John, J. A. C.、Lin, C.-H.、Lin, H.-F.、Wu, S.-C.，"Expression of Metallothionein Gene during Embryonic and Early Larval Development in Zebrafish."，Aquatic toxicology，Vol. 69，2004，pp.215-227 (SCI).
- Ting, J.-W.、Wu, M.-F.、Tsai, C.-T.、Lin, C.-C.、Guo, I.-C.，"Identification and Characterization of a Novel Gene of Grouper Iridovirus (GIV) Encoding a Purine Nucleoside Phosphorylase."，Vol. 85，2004，pp.2883-2892 (SCI).
- Lai, Y.-S.、John, J. A. C.、Lin, C.-H.、Guo, I.-C.、Chen, S.-C.，"Establishment of Cell Lines from a Tropical Grouper, Epinephelus awoara (Temminck & Schlegel), and Their Susceptibility to Grouper Irido- and Nodaviruses."，Journal of Fish Diseases，Vol. 26，2003，pp.31-42 (SCI).
- Herzog, W.、Zeng, X.、Lele, Z.、Sonntag, C.、Ting, J.-W.，"Adenohypophysis Formation in the Zebrafish and Its Dependence on Sonic Hedgehog."，Developmental Biology ，Vol. 254，2003，pp.36-49.
- Murali, S.、Wu, M.-F.、Guo, I.-C.、Chen, S.-C.、Yang, H.-W.，"Molecular Characterization and Pathogenicity of A Grouper Iridovirus (GIV) Isolated from Yellow Grouper Epinephelus awoara (Temminck & Schlegel)."，Journal of Fish Diseases，Vol. 25，2002，pp.91-100 (SCI).
- Chiu, C.-C.、John, J. A. C.、Hseu, T.-H.、Chang, C.-Y.，"Expression of Ayu Pit-1 in Escherichia coli: Its Purification and Immunohistochemical Detection Using Monoclonal Antibody."，Protein Expression and Purification，Vol. 24，2002，pp.292-301 (SCI).
- Chen, W.-Y.、John, J. A. C.、Lin, C.-H.、Chang, C.-Y.，"Molecular Cloning and Developmental Expression of Zinc Finger Transcription Factor MTF-1 Gene in Zebrafish, Danio rerio."，Biochemical and Biophysical Research Communications ，Vol. 291，2002，pp.798-805 (SCI).
- Cheng, C.-A.、 Lu, K.-L.、Liu, E.-L.、Yang, T.-Y.、Lee, C.-Y.，"Growth Promotion of Ayu (Plecoglossus altivelis) by Gene Transfer with Rainbow Trout Growth Hormone Gene."，Zoological Studies ，Vol. 41，No. 3，2002，pp.303-310(SCI).
- Chang, C.-C.、Tsai, C.-T.、Chang, C.-Y.，"Structural Restoration of Inactive Recombinant Fish Growth Hormones by Chemical Chaperonin and Solvent Restraint Approaches. "，Vol. 15，2002，pp.437-441 (SCI).
- Lai, Y.-S.、John, J. A. C.、Guo, I.-C.、Chen, S.-C.、Fang, K.，"In Vitro Efficiency of Intra- and Extracellular Immunization with Mouse Anti-YGNNV Antibody against Yellow Grouper Nervous Necrosis Virus."，Vaccine，Vol. 20，2002，pp.3221-3229 (SCI).
- Chiu, C.-C.、Ting, J.-W.、Hseu, T.-H.、Chang, C.-Y.，"Characterization of Transactivation Domain and Developmental Expression of Pituitary Specific Transcription Factor, Pit-1 of Ayu (Plecoglossus altivelis)."，General and Comparative Endocrinology，Vol. 127，2002，pp.307-313 (SCI).
＜學術會議論文＞
- Lin, C.H.、John, J.A.C.、Lin, C.H.、Chang, C.Y.，"Molecular Cloning and Tissue-specific Expression of Mx Multi-forms from Grouper."，VNN 2006，Hiroshima，Japan，November 2006，pp.N/A.
- Lin, C.H.、John, J.A.C.、Lin, C.H.、Chang, C.Y.，"Inhibition of NervousNecrosis Virus Propagation by Grouper Mx Proteins."，VNN 2006，Hiroshima，Japan ，November 2006，pp.N/A.
- Chang, C. Y.、Chen, W. Y.、John, J. A. C.，"Excess Heavy Metal Affects Zebrafish Embryo Development Indicated by Metallothionein Express."，AQUA 2006，Florence，Italy，May 2006，pp.N/A.
- Yeh C. H.、Wu, M, H.、Wu, J. C.、Chang, C. Y.，"Study of Mouse Monoclonal Immunoprophylaxis against Fish Nervous Necrosis Virus"，AQUA 2006，Florence，Italy，May 2006，pp.N/A.
- Chang, C.Y.、John, J.A.C.、Wu M.S.、Lee C.Y.、Lin C.H.，"Characterization of serum immunoglobulin M of grouper and cDNA cloning of its heavy chain."，12th International European Association of Fish Pathologists Conference on Fish Diseases，Copenhagen，Denmark，September 2005，pp.N/A.
- Yeh, C.H.、Kung, C.W.、Lin, P.W.、Lee J.C.、Chen, M.J.，"Isolation and Characterization of a Koi Herpesvirus in Common Carp from Taiwan."，12th International European Association of Fish Pathologists Conference on Fish Diseases，Copenhagen，Denmark，September 2005，pp.N/A.
- Tsai, C.-T.、Ting, J.-W.、Wu, M.-H.、Wu, M.-F.、Guo, I.-C.，"Complete Genome Sequence of the Grouper Iridovirus and Comparison of Genomic Organization with Other Iridoviruses."，The 6th International Symposium on Viruses of Lower Vertebrates，Hakodate, Hokkaido，Japan，September 2004，pp.N/A.
- Chang, C.-Y.、Tsai, C.-T.、John, J.A.C.，"Use of iridovirus common genes to construct a consensus iridovirus phylogenetic tree"，The 6th International Symposium on Viruses of Lower Vertebrates，Hakodate, Hokkaido，Japan，September 2004，pp.N/A.
＜專書＞
- ，"Fish Genetics and Aquaculture Biotechnology"，Oxford & IBH Publishing Co. Pvt. Ltd. New Delhi，2005.
＜國科會研究＞
- 張繼堯，「石斑魚虹彩病毒細胞凋亡相關基因之研究」，2006年8月，NSC 95-2311-B-001-069-MY3。
- 張繼堯，「石斑魚健康魚苗之培育」，2006年5月，NSC 95-2622-B-001-001-CC3。
- 張繼堯，「石斑魚無特定病原菌優質種苗之開發」，2005年8月 至 2006年12月，NSC 94-2317-B-001-015-。
- 張繼堯，「斑馬魚第一型金屬應答轉錄因子基因發育期之表現與調控(3/3) 」，2005年8月 至 2006年7月，NSC 94-2311-B-001-018-。
- 張繼堯，「神經壞死病毒與虹彩病毒疫苗枝研發與應用(Ⅲ)」，2005年7月 至 2006年6月，NSC 94-2317-B-001-007-。
- 張繼堯，「斑馬魚第一型金屬應答轉錄因子基因發育期之表現與調控(2/3) 」，2004年8月 至 2005年7月，NSC 93-2311-B-001-032-。
- 張繼堯，「神經壞死病毒及虹彩病毒疫苗之研發與應用(II)」，2004年7月 至 2005年6月，NSC 93-2317-B-001-011-。
＜非國科會研究＞
- 張繼堯，「虹彩病毒分子檢測技術與試劑開發」，，2006年1月 至 2006年12月。
- 張繼堯，「石斑魚虹彩病毒次單位疫苗之研發」，，2005年1月 至 2005年12月。
- 張繼堯，「魚類抗神經壞死病毒之小鼠單株抗體基因預防法」，，2004年1月 至 2004年12月。
- 張繼堯，「石斑魚與病毒交互作用之功能性基因體研究(2/2)」，，2004年1月 至 2004年12月。
＜專利＞
- 張繼堯 ，魚類神經壞死病毒及石斑魚虹彩病毒檢測試劑之開發，編號：中研院技轉合約10T-930506-1N，2005.0820。
- 張繼堯 、丁靜雯、呂昆霖、林志鴻、張家靖,蔡志東，Fish growth hormones，編號：美國 6429305，2001。
＜國際會議補助＞
- 張繼堯，「VNN 2006」，NA，2006.11.28。
- 張繼堯，「AQUA 2006」，NA，2006.05.09。
- 張繼堯，「12th International European Association of Fish Pathologists Conference on Fish Diseases」，NA，2005.09.11。
- 張繼堯，「The 6th International Symposium on Viruses of Lower Vertebrates」，NA，2004.09.19。