代表性论文与专著
1. Dong, S. C., Shi, Y. K. *, Ran, Y. Z., Wu, H. J., Deng, Y. Y., Fan, J. X., Dai, X. Y. 2024. Biological Classification System Knowledge Graph and Semi-automatic Construction of Its Invertebrate Fossil Branches. Journal of Earth Science. 35（6）：2119-2128.
2. 赖牧晨，史宇坤*，鲁铮博，施玉洁，黄浩. 2024. 构建生物地层复合序列的两种定量方法: 以华南石炭纪生物地层为例。地层学杂志48（2）：172-182.
3. Huang, H. H., Shi, Y. K.*, Chen, Q., Xu, H. Q., Song, S. C., Shi, Y. J., Shen, F. R., Fan, J. X. 2024. An image dataset of fusulinid foraminifera generated with the aid of deep learning. Geoscience Data Journal, 11, 46–56. https://doi.org/10.1002/gdj3.215
4. Hou, C.B., Lin, X.Y., Huang, H.H.（共同第一作者）, Xu, S., Fan, J.X., Shi, Y.K. *, & Lv, H.R*. 2023. Fossil image identification using deep learning ensembles of data augmented multiviews. Methods in Ecology and Evolution, 14：3020-3034. https://doi.org/10.1111/2041-210X.14229
5. 宋思存，张子航，史宇坤*. 2022. 定量古生物学常用Q型多变量线性回归方法例析. 微体古生物学报，39(2)：190-199.
6. 史宇坤，许姝艺，董少春. 2022. 基于知识图谱的增强型混合式教学法的教学实践与思考，高校地质学报，28(6): 387-393.
7. 宋思存，张书涵，张子航，史宇坤*. 2021. 定量古生物学常用R型多变量线性回归方法例析. 微体古生物学报，38(3)：292-300.
8. 文蝶, 黄浩, 史宇坤*, 杨孙容, 杨娇, 王媛，侯旭东，樊隽轩. 2021. 地球科学大数据的管理与共享:以英国地质调查局为例. 高校地质学报, 27(1)：045-057.
9. Deng, Y. Y., Fan, J. X.*, Zhang, S.H., Fang, X., Chen, Z.Y., Shi, Y.K. *, Wang, H. W., Wang, X. B., Yang, J., Hou, X.D., Wang, Y., Zhang, Y.D., Chen, Q., Yang, A. H., Fan, R., Dong, S.C., Xu, H.Q., Shen, S.Z., 2021. Timing and patterns of the Great Ordovician Biodiversification Event and Late Ordovician mass extinction. Earth-Science Reviews, 220, 103743. https://doi.org/10.1016/j.earscirev.2021.103743
10. Shi, Y. K., Wang, X. D., Fan, J. X., Huang, H., Xu, H. Q., Zhao, Y. Y., Shen, S. Z. 2021. Carboniferous-earliest Permian marine evolutionary biodiversification event (CPBE) during the Late Paleozoic Ice Age. Earth-Science Reviews, 220，p. 103699. https://doi.org/10.1016/j.earscirev.2021.103699
11. Wang, X.D.*, Hu, K.Y.*, Shi, Y.K.*, Chen, J.T., Yang, S.R., Ye, X.Y., Li, X.M., Song, Y.F., Chen, B., Chang, X.L.，Yao, L., Zhang, Y.C., Fan, J.X., Shen, S.Z. 2021. The missing upper Carboniferous in the Cimmerian continent: A critical review. Earth-Science Reviews, 217, p.103627.
12. Chen, Y. N., Shi, Y.K.*, Huang, S.L., 2021. Species-Specific Settling Behaviors of Benthic Foraminifera: Size, Density and Structure. Journal of Foraminiferal Research 51 (2): 69–80. https://doi.org/10.2113/gsjfr.51.2.69
13. Shi, Y.K. 2021. Heterochronic origin of spherical fusulinid foraminifera in the late Paleozoic. Paleobiology 47(1): 115-133.https://doi.org/10.1017/pab.2020.53
14. 鲁铮博, 史宇坤*, 华洪, 拓守廷, 叶训焱，邓怡颖，樊隽轩，2020. 国际大洋科学钻探的数据资源与共享现状，高校地质学报，26(4)：472-480.
15. 黄明立，田坤烜，史宇坤*，2020. 滇黔桂盆地早二叠世亚丁斯克期的沉积环境分异与䗴有孔虫响应，地学前缘，27（6）：1-16.
16. Fan, J., Shen, S., Erwin, D. H., Sadler, P. M., MacLeod, N., Cheng, Q., Hou, X., Yang, J., Wang, X., Wang, Y., Zhang, H., Chen, X., Li, G., Zhang, Y., Shi, Y., Yuan, D., Chen, Q., Zhang, L., Li, C. and Zhao, Y. 2020. A high-resolution summary of Cambrian to Early Triassic marine invertebrate biodiversity. Science 67(6475):272-277. https://science.sciencemag.org/content/367/6475/272
17. 王向东，胡科毅，黄兴，乔丽，王秋来，沈阳，盛青怡，李小铭，林巍，史宇坤，2020. 中国石炭纪地层及标志化石图集. 浙江大学出版社.
18. Shi, Y.K., Huang, H., Shen, Z. H., 2019. New insights for ancient foraminifera through 3D visuals of fusulinids. Palaeoworld, 28(4): 478-486.
19. Tian,K.X., Shi, Y.K.*, Yan, Z., 2019. Permian fusulinids from the Deyanqimiao III section of Sonid Right Banner in Inner Mongolia. Acta Micropalaeontologica Sinica, 36(3): 232-250. (in Chinese with English abstract) 田坤烜，史宇坤*，闫振，2019. 内蒙古苏尼特右旗德言其庙剖面二叠纪䗴类动物群，微体古生物学报, 36(3): 232-250.
20. 陈龙，黄明立，史宇坤*，2019. 底栖有孔虫壳体微量元素地球化学指标及其“生命效应”，微体古生物学报，2019，36（2）：103-114
21. 宫巨嵩, 史宇坤*, 2017. 现代大型底栖有孔虫壳体地球化学元素的原位微区分析. 微体古生物学报 34，291-301.
22. 史宇坤, 2017. 形态测量学（Morphometrics）常用方法及其在微体古生物学中的应用. 微体古生物学报, 34(2): 179-191.
23. Shi, Y., Huang, H. and Jin, X., 2017, Depauperate fusulinid faunas of the Tengchong Block in western Yunnan, China, and their paleogeographic and paleoenvironmental indications: Journal of Paleontology 91:12-24.
24. Shi, Y. K. and Macleod, N., 2016, Identification of life-history stages in fusulinid foraminifera: Marine Micropaleontology, v. 122, p. 87-98.
25. 史宇坤，杨湘宁，刘家润。2012。贵州南部宗地地区早石炭世-早二叠世的䗴类。北京：科学出版社。271页。
26. Yukun SHI，Hao Huang , Xiaochi Jin , Xiangning Yang. 2011. Early Permian fusulinids from the Baoshan Block, western Yunnan, China. Journal of Paleontology. 85(3): 489-501.
27. 吴聪，史宇坤，胡修棉，2011. 藏南定日上白垩统平行不整合界线及其浮游有孔虫时代约束. 微体古生物学报 28(4): 381-402.
28. Yukun SHI, Xiangning Yang, Hao Huang, 2009. Differences between subfamilies in diversification process of the Early and Middle Permian fusulinid fauna in South China. Palaeoworld 18: 34-40.
29. 史宇坤，刘家润，杨湘宁，朱李鸣，2009. 贵州省紫云县宗地剖面早石炭世大塘期－早二叠世栖霞期的䗴类动物群. 微体古生物学报26(1): 1-30.
30. Yukun SHI，Xiaochi Jin , Hao Huang , Xiangning Yang, 2008. Permian fusulinids from the Tengchong Block, western Yunnan, China. Journal of Paleontology 82(1): 118-127. (SCI)
31. SHI Yukun, YANG Xiangning, 2005. A statistical test on diversity changes of Early and Middle Permian fusulinacean fauna in South China. Science in China Series D-Earth Sciences 48(7):978-984. (SCI)
32. 史宇坤，杨湘宁，金小赤，2005. 滇西耿马县小新寨中二叠世沙子坡组“Rugososchwagerina”的再研究. 古生物学报44（4）：535-544.
33. 史宇坤，杨湘宁，刘家润，董琳，朱李鸣，林春明，2004. 贵州紫云县宗地乡下二叠统隆林阶生物地层初步研究. 地层学杂志28(4)：326-330.
担任专辑编辑：
Guest associate editor, Abstracts of Deep-time Digital Earth Forum, Acta Geologica Sinica (in English), 2019，93（S1）:1-180. Beijing, China. (ISSN 1000-9515)
特邀主编，深时数字地球专辑：地球科学大数据I、II, 2020-2021, 高校地质学报, Nanjing, China.
科普作品：
1.Yukun Shi, 2020. Supercomputer-assisted algorithm discovers previously unknown high-resolution species diversification. Nature ecology & evolution community. https://natureecoevocommunity.nature.com/users/345905-yukun-shi/posts/58842-supercomputer-assisted-algorithm-discovers-previously-unknown-high-resolution-species-diversification
2.史宇坤，2020. 意大利金钉子科考记（下篇），科学世界4期，p. 94-99.
3.史宇坤，2020. 意大利金钉子科考记（上篇），科学世界3期，p. 92-97.
4.2021 CGTN《多样之境》（参与）
5.2020 北京新京报我们视频、中科院南古所、南京大学《行走两亿年》（参与）
6.2024 南京大学、中科院南古所《穿越两亿年》（参与）
