1. Chen, Cheng-Wei, Van Truong Do, Quang Cuong Truong, Viet Dai Dang, Hong Truong Luu, Yi-Shan Chao, Yao-Moan Huang, and Kuo-Fang Chung. 2025. Studies of Vietnamese Pteridophyte Flora 3. PhytoKeys 255: 143–169.
  2. Hsu, Hao-Chun, Chia-Lun Hsieh, Cheng-Wei Chen, Yi-Shan Chao, Yao-Moan Huang, Truong Van Do, and Kuo-Fang Chung. 2025. Hidden in Silver Cloud Peak—a Lithophilous Species Primulina cucphuongensis (Gesneriaceae) from Cuc Phuong National Park, Northern Vietnam. Systematic Botany. Accepted.
  3. Chen, Cheng-Wei, Daniele Cicuzza, Stuart Lindsay, Rahayu Sukmaria Sukri, Yi-Shan Chao*, Yao-Moan Huang*, and Kuo-Fang Chung*. 2024. Haplopteris palustris, A new terrestrial vittarioid fern (Pteridaceae; Polypodiales) from Western Malesia. Systematic Botany 49 (1): 227–235
  4. Chao, Yi-Shan*, Li-Chieh Wang, Chia-Tung Chen, Chih-Chiang Wang*. 2024. New distribution of Utricularia warburgii (Lentibulariaceae) from Taiwan. Taiwania 69(4): 560–568.
  5. Chao, Yi-Shan and Young-Fa Chen. 2024. 林下養蜂之粉源植物分子鑑定分析 A DNA barcode-based survey of forest beekeeping pollen plants. Taiwan Journal of Forest Science 39(1): 53–68. https://doi.org/10.7075/TJFS.202403_39(1).0004
  6. Chao, Yi-Shan, Yao-Wei Yang, Chiou-Rong Sheue, and I-Ling Lai. 2024. Niche and phenotypic differentiation in fern hybrid speciation, a case study of Pteris fauriei (Pteridaceae). Annals of Botany 134: 71–84
  7. Chang, Yi-Han, Pi-Fong Lu, and Yi-Shan Chao*. 2024. Nomenclature changes for two ferns. Fern Gazette: 22(4): 186–192.
  8. Kuo, Li-Yaung, Sheng-Kai Tang, Yu-Hsuan Huang, Pei‐Jun Xie, Cheng-Wei Chen, Zhi-Xiang Chang, Tian-Chuan Hsu, Yi-Han Chang, Yi-Shan Chao, Chien-Wen Chen, Susan Fawcett, Joel H. Nitta, Michael Sundue, Tzu-Tong Kao, Hong Truong Luu, Andi Maryani A Mustapeng, Fulgent P. Coritico, Victor B. Amoroso, and Yong Kien Thai. A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples. Scientific Data 11: 1314.
  9. Chen, Cheng-Wei, Maryani A. Mustapeng Andi, Kuo-Fang Chung, and Yi-Shan Chao*. 2023. Phylogenetic placement of Antrophyum kinabaluense, a newly described and rare fern species from Kinabalu Park, Sabah. Sandakania 24: 43–47.
  10. Chao, Yi-Shan, Cheng-Wei Chen, Wen-Liang Chiou, Fulgent P. Coritico, Yi-Han Chang, and Tsung-Yu Aleck Yang*. 2023. Pteris faba and Pteris rubella, two new species in section Hypsopodium (Pteridaceae). New Zealand Journal of Botany 61 (2-3): 118–130
  11. Chen, Cheng-Wei, Leon Perrie, David Glenny, Wen-Liang Chiou, Susan Fawcett, Alan R. Smith, Barbara S. Parris, Atsushi Ebihara, Joel H. Nitta, Daniel Ohlsen, Samuli Lehtonen, Shi-Yong Dong, Marcus Lehnert, Ashley R. Field, Yi-Shan Chao, Andrew G. Murdock, and Michael Sundue. 2022. An annotated checklist of lycophytes and ferns of the Solomon Islands. Fern Gazette 21 (7): 292–419.
  12. Andi, Maryani A. Mustapeng, Cheng-Wei Chen, Yi-Shan Chao, Shi-Yong Dong, Joan T. Pereira, Geofarry Gunsalam, Markus Gumbilil & Monica Suleiman 2022. A revised ferns and lycophytes checklist for Sabah, Malaysian Borneo. Sandakania 23: 27–79.
  13. Chao, Yi-Shan*, Atsushi Ebihara, Wen-Liang Chiou, Jer-Min Tsai, Yu-Wen Huang, and Tom A. Ranker. 2022. Reticulate evolution in the Pteris fauriei group (Pteridaceae). Scientific Reports 12: 9145.
  14. Chen, Cheng-Wei, Yi-Shan Chao*, Maryani A. Mustapeng Andi, Stuart Lindsay, Yao-Moan Huang*, Michael Kessler, Hong Truong Luu, and Ching-Ming Hsieh. 2022. Insights into the systematics of Old World taenitidoid ferns (Pteridoideae; Pteridaceae): evidence from phylogeny and micromorphology. Botanical Journal of the Linnean Society: In press.
  15. Ebihara, Atsushi, Yi-Shan Chao, and Hironobu Kanemitsu. 2022. The distribution of Pteris wulaiensis (Pteridaceae) in Japan. Bulletin of the National Science Museum. Series B 48: 53–59.
  16. Chao, Yi-Shan*, Wen-Liang Chiou, Atsushi Ebihara, Tian-Chuan Hsu, Yi-Han Chang, and Chien-Yu Lin. 2021. Taxonomic and nomenclatural novelties in the Pteris fauriei group (Pteridaceae). Taiwania 66: 307–316.
  17. Chen, Cheng-Wei, Yi-Shan Chao*, Andi Maryani A. Mustapeng, Noorhana Mohd Sapawi, Yao-Moan Huang, and Alan R. Smith. 2021. Two new fern species from Gunung Mulu National Park, Sarawak, Malaysia. Systematic Botany 46 (3): 739–749.
  18. Fujiwara, Tao, Junki Ogiso, Sousuke Ishii, Kei Togo, Narumi Nakato, Shunsuke Serizawa, Yi-Shan Chao, Hyoung-Takim, Atsushi Ebihara, Yasuyuki Watano. 2021. Species delimitation in the Phegopteris decursivepinnata polyploid species complex (Thelypteridaceae). Acta Phytotaxonomica et Geobotanica 72(3): 205–226.
  19. Chen, Cheng-Wei, Tian-Chuan Hsu, Yi-Shan Chao, Ping-Fong Lu, Chia-Wei Li, Nguyen Khanh Trinh Tram, Ich Le Phuoc Thanh Nguyen, Minh Tri Dang, Hong Truong Luu, and Barbara Parris. 2020. A newly recorded genus and twelve newly recorded species of ferns for Vietnam from Lang Biang Plateau. Phytotaxa 443: 121–143.
  20. Chao, Yi-Shan*. 2019. New record of Pteris esquirolii in Taiwan, with two similar new species, Pteris rugosifolia and Pteris subesquirolii. Systematic Botany 44 (2): 274–281.
  21. Hsu, Tian-Chuan, Yu-Fang Huang, Yi-Shan Chao*. 2019. Systematics of Hymenophyllum subg. Mecodium (Hymenophyllaceae) in Taiwan. Systematic Botany 44(4): 753–767.
  22. Chao, Yi-Shan*, Yu-Fang Huang, Shi-Yong Dong, Yao-Moan Huang, Ho-Yih Liu*. 2019. Bolbitis lianhuachihensis (Dryopteridaceae), a new species from Taiwan. PhytoKeys 131: 6981.
  23. Kuo, Li-Yaung, Tian-Chuan Hsu, Yi-Shan Chao, Wei-Ting Liou, Ho-Ming Chang, Cheng-Wei Chen, Yao-Moan Huang, Fay-Wei Li, Yu-Fang Huang, Wen Shao, Pi-Foung Lu, Chien-Wen Chen, Yi-Han Chang*, Wen-Liang Chiou*. 2019. Updating Taiwanese pteridophyte checklist: a new phylogenetic classification. Taiwania 64: 367–395.
  24. Dong, Shi-Yong, Cheng-Wei Chen, Shi-Shi Tan, Hui-Guo Zhao, Zheng-Yu Zuo, Yi-Shan Chao, and Yi-Han Chang. 2018. New insights on the phylogeny of Tectaria (Tectariaceae), with special reference to Polydictyum as a distinct lineage. Journal of Systematics and Evolution 56 (2): 139–147.
  25. Chao, Yi-Shan*, Yao-Moan Huang. 2018. Spore morphology and its systematic implication in Pteris (Pteridaceae). PLOS ONE 13(11): e0207712.
  26. Chen, Cheng-Wei, Stuart Lindsay, Li-Yaung Kuo, Christopher R. Fraser-Jenkins, Atsushi Ebihara, Hong Truong Luu, Chong Wook Park, Yi-Shan Chao*, Yao-Moan Huang*, and Wen-Liang Chiou. 2017. A systematic study of East Asian vittarioid ferns (Pteridaceae: Vittarioideae). Botanical Journal of the Linnean Society 183: 545–560.
  27. Chao, Yi-Shan, Atsushi Ebihara, Wen-Liang Chiou, Yao-Moan Huang*. 2017. Pteris latipinna sp. nov. (Pteridaceae), a new species segregated from Pteris fauriei. Phytokeys 85: 95–108.
  28. Hsu, Tian-Chuan, Zhi-Hao Chen, Yi-Shan Chao*. 2017. New additions of the bladderworts (Lentibulariaceae) in Taiwan. Taiwania 62 (1): 99‒104.
  29. Chao, Yi-Shan, Andi Maryani A. Mustapeng, Cheng-Wei Chen, Wen-Liang Chiou*. 2017. Pteris borneensis (Pteridaceae), a new species from Borneo, with re-circumscription of Pteris decrescens and Pteris parviloba. Systematic Botany 42(4):1–9.
  30. Fujiwara, Tao, Ayumi Uehara, Tsukasa Iwashina, Sadamu Matsumoto, Yi-Han Chang, Yi-Shan Chao, and Yausyuki Watano*. 2017. Allotetraploid cryptic species in Asplenium normale in the Japanese Archipelago, detected by chemotaxonomic and multilocus genotype approaches. American Journal of Botany 104(9): 1–17.
  31. The Pteridophyte Phylogeny Group (including Yi-Shan Chao). 2016. A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution 54(6): 563–603.
  32. Dong, Shi-Yong, Zheng-Yu Zuo, Yi-Shan Chao, Kipiro Damas, Bernard Sule. 2016. New species of the fern genus Lindsaea (Lindsaeaceae) from New Guinea with notes on the phylogeny of L. sect. Synaphlebium. PLOS ONE 11(10): e0163686.
  33. Chao, Yi-Shan, Ho-Yih Liu, and Wen-Liang Chiou*. 2015. Taxonomic revision of the Pteris cadieri complex (Pteridaceae). Phytotaxa 230: 130–150.
  34. Chao, Yi-Shan, Germinal Rouhan, Victor B. Amoroso, and Wen-Liang Chiou*. 2014. Molecular phylogeny and biogeography of the fern genus Pteris (Pteridaceae). Annals of Botany 114 (1): 109–124.
  35. Kao, Tzu-Tong, Wen-Liang Chiou, Yuan-Hsu Sheng, Chun-Ming Chen, Yi-Shan Chao, Yao-Moan Huang*. 2014. Hybrid Origins of Nephrolepis ×hippocrepicis Miyam. (Nephrolepidaceae). The International Journal of Plant Reproductive Biology 6: 1–14.
  36. Ding, Hui-Hui (equal contributor), Yi-Shan Chao (equal contributor), John Rey Callado, Shi-Yong Dong*. 2014. Phylogeny and character evolution of the fern genus Tectaria (Tectariaceae) in the Old World inferred from chloroplast DNA sequences. Molecular Phylogenetics and Evolution 80: 66–78.
  37. Ding, Hui-Hui, Yi-Shan Chao, and Shi-Yong Dong*. 2013 Taxonomic novelties in the fern genus Tectaria (Tectariaceae). Phytotaxa 122: 61–64.
  38. Chao, Yi-Shan, Atsushi Ebihara, Yi-Han Chang, Ri-Hong Jiang, Lu Thi Ngan, and Wen-Liang Chiou*. 2013. New distribution of Pteris kawabatae Sa. Kurata and re-circumscription of Pteris arisanensis Tagawa. Taiwania 58: 305–310.
  39. Ebihara, Atsushi *, Narumi Nakato, Sadamu Matsumoto, Yi-Shan Chao, and Li-Yaung Kuo. 2014. Cytotaxonomic studies on thirteen ferns of Taiwan. Bulletin of the National Science Museum. Series B 40: 19–28.
  40. Dong, Shi-Yong*, R. Mujahidin, Ling-Ling Wei, Yi-Shan Chao. 2012. A new species of Asplenium sect. Thamnopteris (Aspleniaceae) from Indonesia. Blumea 57: 190–194.
  41. Chao, Yi-Shan, Ho-Yih Liu, Yu-Chung Chiang, and Wen-Liang Chiou*. 2012 Polyploidy and speciation in the Pteris (Pteridaceae). Journal of Botany vol. 2012, Article ID 817920, 7 pages.
  42. Chao, Yi-Shan, Shi-Yong Dong, Yu-Chung Chiang, Ho-Yih Liu, and Wen-Liang Chiou*. 2012. Extreme multiple reticulate origins of the Pteris cadieri complex. International Journal of Molecular Sciences 13: 4523–4544.
  43. Chao, Yi-Shan, Ya-Nan Wang, Chieh-Ting Wang*. 2012. A DNA barcode for forest. Journal of the Experimental Forest of National Taiwan University 26: 299–304.
  44. Chao, Yi-Shan, Yi-Han Chang, Lu Thi Nga, Do Van Truong, Ho-Yih Liu, and Wen-Liang Chiou*. 2012. Different ploids of Pteris grevilleana Wall. ex Agardh var. ornata Alderw. (Pteridaceae) in Taiwan and Vietnam. Taiwania 57: 278–282.
  45. Ju, Li-Ping (equal contributor), Chia-Chi Kuo, Yi-Shan Chao (equal contributor), Yu-Pin Cheng, Xun Gong, and Yu-Chung Chiang*. 2011. Microsatellite primers in the native perennial cycad, Cycas taitungensis (Cycadaceae). American Journal of Botany e84–e86.
  46. Chao, Yi-Shan, Ho-Yih Liu, Yao-Moan Huang, and Wen-Liang Chiou*. 2010. Reproductive traits of Pteris cadieri and P. grevilleana in Taiwan: Implications for their hybrid origin. Botanical Studies 51: 209–216.
  47. Yang, Yuen-Po, Ho-Yih Liu, and Yi-Shan Chao*. 2009. Trap gland morphology and its systematic implications in Taiwan Utricularia (Lentibulariaceae). Flora 204: 692–699.
  48. 張惠珠、趙怡姍、柯智仁、楊遠波*。2006。墾丁國家公園水生植物物種調查。國家公園學報 16: 19–31。