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1. YANG, Q. and E. A. PESSAGNO, JR., 1989. Upper Tithonian Vallupinae from the Taman Formation, east-central Mexico. Micropaleont., 35(2): 114-134.
2. PESSAGNO, E. A., JR., SIX, W. M., and YANG, Q., 1989. Xiphostylidae Haeckel and Parvivaccidae, n. fam., (Radiolaria) from the Jurassic of North America. Micropaleontology, 35 (3): 193-255.
3. YANG, Q. and WANG, Y. J., 1990. A taxonomic study of Upper Jurassic Radiolaria from Rutog County, Xizang (Tibet). Acta Micropalaeontologica Sinica, 7(3): 195-218. Nanjing.
4. YANG Qun, 1991. Paleobiogeographic analysis of Jurassic Radiolaria. In: Jin, Y.-G., et al. (Eds.), Palaeoecology of China, Volume 1, pp. 233-248.
5. YANG, Q., and MIZUTANI, S., 1991. Radiolaria from the Nadanhada Terrane, NE China. Journal of Earth Sciences, Nagoya University, 38: 49-78.
6. 杨 群、王玉净、刘荣芝，1992. 黑龙江省那丹哈达地体中的 T/J 界线地层. 科学通报, 1992(6): 547-549.
7. WANG, Y.-J. and YANG, Q., 1992. Neogene and Quaternary Radiolaia from ODP Leg 125. Proc. ODP, Sci. Results, 125:95-112.
8. Yang Qun, 1993. Taxonomic studies of Upper Jurassic (Tithonian) Radiolaria from the Taman Formation, east-central Mexico. Palaeoworld No. 3 (专刊). 164 页, 35 插图, 26 图版.
9. Yang Qun, Mizutani, S. and Nagai, H. 1993. Biostratigraphic correlation between the Nadanhada terrane, northeast China, and the Mino terrane, central Japan. Jour. Earth Sci., Nagoya Univ., vol. 40, 27-43.
10. Yang Qun, 1993. Radiolarian assemblages from T/J boundary strata in the Nadanhada Terrane, northeast China. Palaeoworld, 2, 270-294.
11. Wang Yujing, Cheng Yennien and Yang Qun. 1994. Biostratigraphy and systematics of Permian radiolarians in China. In: Jin Y, Utting J and Wardlaw B R, Eds, Permian Stratigraphy, Environments and Resources, Volume 1: Palaeontology & Stratigraphy, pp. 172-202.
12. YANG QUN, 1995. Middle Jurassic (Bajocian) Radiolaria from the Snowshoe Formation, east-central Oregon (USA) and the OFFICERENSE Zone worldwide. Bull. Natl. Mus. Natur. Sci., No. 6: 55-89.
13. 杨 群、尚庆华，1995. 分子古生物学进展: 化石DNA的研究。Palaeowold，6，78-81。
14. 杨 群，1995，古生物学领域的新辟园地 - 分子古生物研究。古生物学报，34卷3期，265-276。
15. 程延年，杨群，王玉净，叶贵玉，1995. 亚洲东部放射虫地层的对比研究 (课题报告). Palaeoworld, 6: 84-86.
16. Yang Qun and Matsuoka, A., 1997. A comparative study on radiolarian biostratigraphy of the Taman Formation, east-central Mexico, and an Upper Jurassic/Lower Cretaceous section at ODP 801, west Pacific. Science Reports of Niigata University, Ser. E, No. 12:29-49.
17. 周祖仁、杨群、盛金章，1997. 假希瓦格蜓属（Pseudoschwagerina）和球希瓦格 蜓属（Sphaeroschwagerina）。微体古生物学报，14(2): 111-128。
18. 杨洪、程安进、杨群，1998. 地质体中的主要生物分子：研究范畴与方法。地质论评, 44（1）：44-51。
19. 刘德明，周建平，杨群，1999. 浙江长兴二叠系-三叠系界线地层中的氨基酸. 古生物学报,38(1):86-93.
20. Yang Qun, William R. Gower Jr., Li Chunxiang, Chen Peiji and David L. Vesely. 1999. Atrial Natriuretic Peptide and its Prohormone within Metasequoia. The Proceedings of the Society for Experimental Biology and Medicine, 221: 188-192.
21. Li Chunxiang, Cheng Anjin and Yang Qun, 1999. A preliminary study on DNA survival curves under simulated sedimentary envrionment. Palaeoworld, 12: 1-12.
22. Yang Qun, Ozawa T, Hayashi S and Wang Bo, 1999. Extraction, PCR amplification and cloning of aDNA from human remains of the Warring States (475-221 B.C.). Palaeoworld, 12: 13-24.
23. Liu Demin, Cao Changqun and Yang Qun, 1999. Trace analysis of amino acids in Permian/Triassic boundary sediments by electron captures gas chromatography. Palaeoworld, 12: 35-50.
24. Yang Qun, Matsuoka A, Wang Yujing, Kobayashi K, Nagahashi T and Zeng Qinggao, 2000. A Middle Triassic radiolarian assemblage from Quxia, Lhaze County, southern Tibet. Science Report (Geology), Niigata Univ., Ser E, 15: 1-7.
25. Lü Baozhong, Yang Qun, Jian Wang and Pan I-hung, 2000. Hemerythrin and its significance on nonlinear evolution. Journal of Genetics and Molecular Biology. 11(1): 23-28。
26. Matsuoka A and Yang Qun, 2000. A direct correlation between North American and Japan-Pacific radiolarian zonal scheme for the Upper Jurassic. GeoResearch Forum, 6: 119-128.
27. Yang Qun and Lü Baozhong, 2001. Molecular respiratory mechanisms in the Cambrian metazoans. Journal of Genetics and Molecular Biology, 12(1): 10-11.
28. Matsuoka A, Qun Yang, Kobayashi K, Nagahashi T, Takei M, Qinggao Zeng and Yujing Wang, 2001. Siliceous deposits in the Yarlung-Zangbo Suture Zone, southern Tibet, China: paleoceanographiy in the east Tethys. Topics in Paleontology, 2: 39-44.
29. Leng Qin, Yang Hong, Yang Qun and Zhou Jianping, 2001. Variation of cuticle micromorphology of Metasequoia glyptostroboides (Taxodiaceae). Botanical Journal of the Linnean Society, 136: 207-219.
30. 郝家胜，夏凤生，杨群，2001. 苔藓动物的起源与系统发生。微体古生物学报，18(4): 385-391.
31. Matsuoka A, Yang Qun, Kobayashi K, Takei M., Nagahashi T, Zeng. Qinggao and Wang Yujing 2002. Jurassic-Cretaceous radiolarian biostratigraphy and sedimentary environments of the Ceno-Tethys: records from the Xialu Chert in the Yarlung-Zangbo Zone, southern Tibet. Jour. Asian Ear. Sci., 20: 277-287.
32. Yang Qun, Matsuoka A. and Wang Yujing, 2002. Advance in radiolarian micropaleontololgical studies in southern Tibet. Acta Micropalaeontological Sinica, 19(2): 105-111. (西藏南部放射虫微体古生物研究进展)
33. Wang Yujing, Yang Qun, Matsuoka A, Kobayashi K, Nagahashi T and Zeng Qinggao, 2002. Triassic radiolarians from the Yarlung-Zangbo Suture Zone in Jinlu area, Zetang County, southern Tibet. Acta Micropalaeontological Sinica, 19（3）：215-227。(西藏南部泽当县雅鲁藏布缝合带中的三叠纪放射虫)
34. Li Chunxiang and Yang Qun, 2002. Divergence time estimates for major lineages of Cupressaceae (s.l.). Acta Phytotaxonomica Sinica, 40(4): 323-333. (广义柏科主要分类群起源时间得推测。植物分类学报)
35. 郝家胜，杨群，李春香，张克云，孙晓燕，2002。苔藓动物18S rRNA基因的分子系统发育初探。微体古生物学报，19（2）：199-205。
36. Yang Qun, Sun Xiaoyan, Zhang Keyun, Wu Ping, 2003. Arthropod phylogenetic chronology. Journal of Genetics and Molecular Biology, 14(3):145～158
37. Hao Jiasheng, Yang Qun, et al., 2003. Molecular phylogeny of lophotrochozoa based on 18S rRNA gene sequences – with comment on the phylogenetic position of Bryozoa. Journal of Genetics and Molecular Biology, 14(2): 64-72
38. Zhang Keyun, Sun Xiaoyan, Yang Qun*, 2003. Molecular Phylogeny of Ostracoda Based on 18S and 28S rDNA Sequence data. Journal of Genetics and Molecular Biology, 14(4): 224-232
39. Li Gang and Yang Qun, 2003. Discovery of Early Cretaceous radiolarians from the Longzhaogou Group in eastern Heilongjiang Province. Cretaceous Research, 24(6): 691~696
40. 王玉净、杨群，2003. 广东韶关仁化地区中二叠世孤峰组的放射虫动物群。微体古生物学报，20（4）：333～341
41. 王玥、杨群，2003. 化石记录的再评估。古生物学报，42(2)：297～302
42. 张克云、孙晓艳、杨 群*, 2003. 介形纲丽足目和速足目及相关类群18S rDNA分子系统发育的研究. 古生物学报, 42 (3): 452～459
43. Li Chunxiang, Lu Shugang, Yang Qun*, 2004. Asian origin for Polystichum (Dryopteridaceae) based on rbcL sequences. Chinese Science Bulletin 49(11): 1-5
44. Yang Qun, Wang Yujing, Yin Leiming, Shu Liangshu, Lou Fasheng, Wang Bo. 2005. On the age of the ophiolitic complexes in northeastern Jiangxi: a micropaleontological analysis. Acta Geologica Sinica, 79(3): 801–805
45. Hao Jiasheng, Li Chunxiang, Sun Xiaoyan, Yang Qun*. 2005. Phylogeny and divergence time estimation of cheilostome bryozoans based on mitochodrial 16S rRNA sequences. Chinese Science Bulletin, 50(12): 1205-1211
46. 王玉净、杨群、郭通珍，2005. 青海可可西里地区中三叠世晚期放射虫Spongoserrula rauana动物群。微体古生物学报，22(1): 1-9
47. Lü Baozhong and Yang Qun, 2005. Upgrading functional replacement: evolutionary evidence from molecular respiratory proteins. Journal of Genetics and Molecular Biology, 16(3): 128-137.
48. MATSUOKA A, YANG Q, TAKEI M, 2005. Latest Jurassic–earliest Cretaceous radiolarian fauna from the Xialu chert in the Yarlung Zangbo suture zone, southern Tibet: Comparison with coeval western Pacific radiolarian faunas and paleoceanographic implications. The Island Arc, 14(4): 338–345
49. Sun Xiaoyan, Yang Qun*, Shen Yanbin. 2006. Jurassic radiation of large Branchiopoda (Arthropoda: Crustacea) using secondary structure-based phylogeny and relaxed molecular clocks. Progress in Natural Science, 16 (special issue): 292-302.
50. Wang Yujing, Yang Qun, Cheng Y.-N., Li Jiaxiang. 2006. Lopingian (Upper Permian) radiolarian biostratigraphy of South China. Palaeoworld, 15(1): 31-53.
51. Yeh K.-Y., Yang Qun*, 2006. Radiolarian assemblages from T/J boundary strata, Nadanhada Terrane, NE China. Acta Micropalaeontologica Sinica, 23(4): 317-360.
52. Yang Qun, Ma Junye, Sun Xiaoyan, Cong Peiyun, 2007. Phylochronology of early metazoans: combined evidence from molecular and fossil data. Geological Magazine, 42(3/4): 281-295.
53. 丛培允, 杨群*, 2007. 多足动物亚门主要类群的系统关系与谱系年代分析---基于形态、化石和分子综合数据, 微体古生物学报, 24(4): 407-421
54. 马俊业, 杨群*, 2007. 网角海绵目（Dictyoceratida）谱系发育与形态发生分析. 古生物学报, 46(4): 473-480 [Phylogeny and morphogenesis of Dictoceratida (Porifera: Demospongiae)]
55. 张克云, 徐明旭, 杨寿运, 孙捷, 杨群*, 2007. 速足目主要类群系统发育的分子证据. 古生物学报，46(4): 464-472 [Molecular phylogeny of major groups of Podocopida]
56. 王玉净, 杨群*, 2007. 中国石炭－二叠纪放射虫化石带及古生物地理学意义. 微体古生物学报, 24(4): 338-346 [Carboniferous-Permian radiolarian biozones of China and the palaeobiogeographic implication]
57. Gai Yonghua, Song Daxiang, Sun Hongying, Yang Qun, Zhou Kaiya, 2008. The complete mitochondrial genome of Symphylella sp. (Myriapoda: Symphyla): Extensive gene order rearrangement and evidence in favor of Progoneata. Molecular Phylogenetics and Evolution, 49:574-585.
58. Cong Peiyun, Xia Xuhua, Yang Qun*, 2009. Monophyly of the ring-forming group in Diplopoda (Myriapoda, Arthropoda) based on SSU and LSU ribosomal RNA sequences. Progress in Natural Sciences, 19: 1297-1303.
59. 杨群，丛培云，孙晓燕，马俊业，盖永华，李春香，郝家胜，夏旭华，2009. 谱系年代研究进展. 古生物学报，48(3): 364-374.
60. Hao Jiasheng, Sun Xiaoyan, Shi Qinghui, Yang Qun. 2010. Phylogenetic position of Bryozoa among metazoan groups: evidence from near-complete LSU and SSU rRNA sequences. Acta Micropalaeontologica Sinica, 27(1): 1-12.
61. Xiao Shuhai, Yang Qun, Luo Zhexi, 2010. A Golden Age of Paleontology in China? A SWOT Analysis. Palaeontologia Electronica, Vol. 13, Issue 1; 3E:4p.
62. 李春香, 陆树刚, 马俊业, 杨群. 2010. 里白科植物的系统发育和分歧时间估计——基于叶绿体三个基因序列的证据. 古生物学报, 49 (1) : 64 – 72
63. Yang Qun, Luo Hui, Wang Yujing, Aitchison, J., 2011. Radiolarians through time: Systematics, biostratigraphy and paleoceanographic significance. Palaeoworld, 20(2/3): 99-101
64. Wang Yujing, Yang Qun*, 2011. Biostratigraphy, phylogeny and paleobiogeography of Carboniferous–Permian radiolarians in South China. Palaeoworld, 20(2/3): 134-145.
65. Xia Xuhua, Yang Qun. 2011. A Distance-based Least-square Method for Dating Speciation Events. Molecular Phylogenetics and Evolution. 59(2): 342-353.
66. 孙晓燕，夏旭华，杨群*, 2011. 基于28S rDNA D1-D2基因片段与16S rDNA部分序列联合分析的叶肢介系统发育研究. 微体古生物学报. 28(4):370-380.
67. Xia Xuhua, Yang Qun. 2012. Non-AUG initiation codon and downstream inframe AUG in Pyrococcus horikoshii: evaluating two hypotheses. Proceedings of 5th International Conference on Bioinformatics and Biomedical Engineering (iCBBE 2011). 4 printed pages. （EI）
68. Li Chunxiang, Lu Shugang, Sun Xiaoyan, Yang Qun, 2011. Phylogenetic positions of the enigmatic Asiatic fern genera Diplaziopsis and Rhachidosorus from analyses of four plastid genes. American Fern Journal, 101 (3): 142-155.
69. 孙晓燕，杨群*，2012。叶肢介颈器的超微形态特征及其演化意义。古生物学报 51（3）： 281－289。
70. Li Chunxiang, Lu Shugang, Ma Junye, Gai Yonghua, Barrington, DS, Yang Qun. 2012. From the Himalayan region or the Malay Archipelago: Molecular dating to trace the origin of a fern genus Phymatopteris (Polypodiaceae). Chinese Science Bulletin, 57 (35): 4569-4577.
71. Gai Yonghua, Ma Huiqin, Sun Xiaoyan, Ma Junye, Yang Qun*, 2013. The complete mitochondrial genome of Cermatobius longicornis (Chilopoda: Lithobiomorpha: Henicopidae). Mitochondrial DNA, 24(4): 331–332.
72. Sun XY, Yang Qun, Xia XH, 2013. An Improved Implementation of Effective Number of Codons (Nc). Molecular Biology and Evolution, 30(1):191-6.（Epub August 21, 2012）
73. Li Chunxiang and Yang Qun. 2013. Notes on the divergence time of the fern genus Asplenium from fossil and molecular evidence. Cretaceous Research, 45:352-355. [pdf]
74. Yang Qun, Yeh Kuei-yu. 2015. Radiolarian faunal transition in the Triassic-Jurassic boundary strata, Nadanhada Terrane, NE China. Radiolaria, 35，Proceedings of 14th INTERRAD, 161-162.
75. Shi Qing-Hui, Sun Xiao-Yan, Wang Yun-Liang, Hao Jia-Sheng*, Yang Qun*, 2015. Morphological characters are compatible with mitogenomic data in resolving the phylogeny of nymphalid butterflies (Lepidoptera:Papilionoidea:Nymphalidae). PLoSONE 10(4): e0124349. doi:10.1371/journal.pone.012434
76. Li Chunxiang, Lu Shugang, Ma Junye, Gai Yonghua,Yang Qun, 2016. Phylogeographic history of the woodwardioid ferns, including species from Himalaya, Palaeoworld, 25: 318-324.
77. Wörheide G*., Dohrmann M., Yang Qun*, 2016. Molecular paleobiology – progress and perspectives. Palaeoworld, 25: 138-148.
78. Ma Junye, Yang Qun*. 2016. Early Divergence Dates of Demosponges Based on Mitogenomics and Evaluated Fossil Calibrations. Palaeoworld, 25:.209-302.
79. Sun Xiaoyan, Xia Xuhua, Yang Qun*, 2016. Dating the origin of the major lineages of Branchiopoda. Palaeoworld, 25: 303-317
80. Yang Qun, Wang Yongdong, Reich M., Reitner J., 2016. Systematics and biodiversity of fossil Lagerstätten. Palaeoworld, 25:135-137.
81. 杨群，2017. 2016年古生物学热点回眸。科技导报，35（1）：86-95（A sample of hot research topics in paleontology in 2016. Science & Technology Review）
82. 吴浩若，许波，杨群*，2017. 西藏南部早白垩世贝里阿斯期放射虫化石组合。微体古生物学报，34（4）: 343-359
83. Su Chengyong, Shi Qinghui, Sun Xiaoyan, Ma Junye, Li Chuxiang, Hao Jiasheng*, Yang Qun*, 2017. Dated phylogeny and dispersal history of the butterfly subfamily Nymphalinae (Lepidoptera: Nymphalidae). Scientific Reports, 7: 8799 | DOI:10.1038/s41598-017-08993-w.
84. 蔡华伟，杨群*，2017年古生物学热点回眸。科技导报，36（1）：163-175
85. Li Chunxiang, Robbin C. Moran, Junye Ma, Bo Wang, Jiasheng Hao, Qun Yang, 2018 (in press). A mid-Cretaceous tree fern of Thyrsopteridaceae (Cyatheales) trapped in Myanmar amber. Cretaceous Research, in press.
86. Chunxiang Li, Li-Bing Zhang, Junye Ma, Jiasheng Hao, Qun Yang. 2018 (in press). On the systematic position of the early Cretaceous Athyrium on the basis of molecular and morphological analyses. Cretaceous Research, in press.
87. Su, Yunliang Wang, Xiaoyan Sun, Ruisong Tao, Hongchun Pan, Jiasheng Hao*，Qun Yang*, in prep. Diversification pattern and molecular high-altitude adaptation of the Parnassius butterflies (Lepidoptera: Papilionidae) revealed by comparative transcriptomics analysis.
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