1995年毕业于西北大学生物学系，2000年在中国科学院植物研究所获博士学位并留所工作，历任助理研究员、副研究员、研究员，2002至2004年在美国宾夕法尼亚州立大学进行合作研究。现任系统与进化植物学国家重点实验室主任、标本馆馆长，兼任中国科学院大学岗位教授、中国植物学会副秘书长、常务理事、系统与进化植物学专业委员会主任和青年工作委员会主任。主要从事植物系统学、进化发育生物学和调控基因组学研究，在“重复基因的结构和表达分化”、“花发育调控网络的进化”、“花基本结构起源和多样化的分子机制”及“花瓣发育、进化和缺失的分子机制”等研究中取得了重要进展，以第一或通讯作者在PNAS（3篇）、Nature子刊（3篇）、Science Advances、The Plant Cell（3篇）和Molecular Biology and Evolution（2篇）等刊物上发表论文近50篇，以合作者在Science、Nature和PNAS等刊物上发表论文40余篇。曾主持国家自然科学基金之青年科学基金项目、主任基金项目、面上项目（2项）、重点项目（3项）、重大研究计划集成项目和创新研究群体项目，以及中国科学院知识创新工程重要方向项目、科技创新交叉与合作团队项目、基础前沿科学研究计划从0到1原始创新项目和王宽诚率先人才计划卢嘉锡国际团队项目。被Molecular Biology and Evolution（2015-2019）、New Phytologist（2010至今）、Journal of Integrative Plant Biology（2020至今）、Frontiers in Plant Science（2016至今）、Journal of Genetics and Genomics（2013-2019）、Journal of Systematics and Evolution（2008至今）、《植物学报》（2009-2018）、《生物多样性》（2009至今）和《科技导报》（2014至今）等刊物聘为Editor、Associate Editor、副主编或编委。曾获“国家杰出青年科学基金”资助，入选科技部“中青年科技创新领军人才”和“国家百千万人才工程”，获“中国科学院青年科学家奖”、“中国青年科技奖”和首届“吴征镒植物学奖”之“青年创新奖”。
主要研究领域：
1．植物进化发育生物学
采用进化生物学、发育生物学、分子遗传学、基因组学、计算机模拟和生态学研究手段，揭示植物新性状（特别是花部性状）起源和多样化的分子机制。近年来关注的科学问题包括：1）花和花器官起源和多样化的原因和机制；2）叶性器官形态和结构复杂化和多样化的动因和机制；3）植物器官复杂着色模式形成的分子机制；4）花瓣蜜距起源和多样化的分子机制。
2．基因、基因家族和调控网络的进化
利用分子进化和生物信息学研究手段，在基因组层面上研究重要核基因家族起源和演变的过程和规律，揭示相关调控网络起源、维持和多样化的机制。近年来关注的科学问题包括：1）花发育调控网络进化的过程和规律；2）重复基因结构和表达分化的模式、规律和机制。
3．植物系统学和分子生物地理学
在形态学（广义）、解剖学、细胞学和分子系统学研究的基础上，重建重要植物类群的进化历史，并结合植物地理学和古生物、古地理和古气候的资料，探讨其起源、演化和分布过程。曾对金粟兰科植物进行了较为深入的研究，近年来主要关注毛茛目（特别是毛茛科）植物。
主持的科研项目
国家自然科学基金委创新研究群体项目“植物新性状起源和适应性进化”（32221001; 直接经费1000万; 2023.01-2027.12）。
中国科学院王宽诚率先人才计划卢嘉锡国际团队项目“植物发育、分化与适应性进化国际团队”（GJTD-2020-05; 300万; 2021.01-2023.12）。
国家自然科学基金委重点项目“毛茛科植物花瓣蜜距起源和多样化的分子机制研究”（31930008; 直接经费307万; 2020.01-2024.12）。
中国科学院基础前沿科学研究计划从0到1原始创新项目“叶性器官形状和结构的复杂化和多样化：从数学模拟到分子机制的解析”（ZDBS-LY-SM002; 300万; 2019.09-2024.09）。
中国科学院战略性先导科技专项（B类）之子课题“花瓣形态和结构多样化的遗传基础”（XDB27010304; 直接经费225万; 2018.06-2023.05）。
国家自然科学基金委“微进化过程的多基因作用机制”重大研究计划之集成项目“新性状起源的分子机制和叠加效应研究——以黑种草属植物花瓣的表型复杂化为例”（91631308; 直接经费275万; 2017.01-2019.12）。
国家自然科学基金委重点项目“毛茛科植物花瓣形态和结构的适应性进化及其分子机制研究”（31330007; 320万; 2014.01-2018.12）。
中国科学院科技创新交叉与合作团队项目“Eco-Evo-Devo与Genomics创新团队”（100万; 2013.01-2015.12）。
国家杰出青年科学基金项目“植物进化与发育”（31125005; 240万; 2012.01-2015.12）。
科技部重大科学研究计划项目“植物减数分裂过程中染色体相互作用的分子机理”之课题“减数分裂共性和特性的分子基础”（2011CB944604; 428万; 2011.01-2015.08）。
国家自然科学基金委面上项目“重复基因在编码区分化的机制及其进化意义的研究”（30970210; 35万; 2010.01-2012.12）。
中国科学院知识创新工程重要方向项目“花部性状发育和演化的遗传调控及其分子机制”（KSCX2-YW-R-135; 100万; 2007.01-2010.12）。
国家自然科学基金委重点项目“基部真双子叶植物中A、B、C和E类MADS-box基因的进化”（30530090; 160万; 2006.01-2009.12）。
中国科学院植物研究所领域前沿项目“植物进化过程中关键性状的进化发育遗传学研究”（100万; 2005.12-2008.11）。
国家自然科学基金委面上项目“金粟兰中5个MADS-box基因的功能与进化研究”（30470116; 21万; 2005.01-2007.12）。
国家自然科学基金委创新研究群体项目“植物进化机制的进化发育生物学研究”之子课题“AP3类MADS-box基因的功能及其进化研究”（30121003; 35万; 2005.01-2006.12）。
国家自然科学基金委主任基金项目“被子植物中最简单的花的发育与进化”（30240002; 15万; 2002.05-2003.05）。
国家自然科学基金委青年科学基金项目“金粟兰科的系统发育和分子生物地理学研究”（30100011; 19万; 2002.01-2004.12）。
研究论文（注*为通讯作者）
2024
94. Ren X., Zhang X., Qi X., Zhang T., Wang H., Twell D., Gong Y., Fu Y., Wang B., Kong H.*, Xu B.*, 2024. The BNB-GLID module regulates germline fate determination in Marchantia polymorpha. The Plant Cell koae206.
93. Li S., Fan J., Xue C., Shan H., Kong H.*, 2024. Spur development and evolution: An update. Current Opinion in Plant Biology 81: 102573.
2023
92. Cheng J., Yao X., Li X., Yue L., Duan X., Li B., Fu X., Li S., Shan H., Yin X., Whitewoods C., Coen E., Kong H.*, 2023. Diversification of ranunculaceous petals in shape supports a generalized model for plant lateral organ morphogenesis and evolution. Science Advances 9: eadf8049.
91. Zhao H., Liao H., Li S., Zhang R., Dai J., Ma P., Wang T., Wang M., Yuan Y., Fu X., Cheng J., Duan X., Xie Y., Zhang P., Kong H.*, Shan H.*, 2023. Delphinieae flowers originated from the rewiring of interactions between duplicated and diversified floral organ identity and symmetry genes. The Plant Cell 35: 994-1012. (Cover Story)
90. Yuan Y., Li X., Yao X., Fu X., Cheng J., Shan H., Yin X.*, Kong H.*, 2023. Mechanisms underlying the formation of complex color patterns on Nigella orientalis (Ranunculaceae) petals. New Phytologist 237: 2450-2466.
2022
89. 薛成, 李波卡, 雷天宇, 山红艳, 孔宏智*, 2022. 生物多样性起源与进化研究进展. 生物多样性30: 22460.
88. Fu X., Shan H., Yao X., Cheng J., Jiang Y., Yin X., Kong H.*, 2022. Petal development and elaboration. Journal of Experimental Botany 73: 3308-3318.
87. Geng F., Xie J., Xue C., Sun L., Li J., Niu C., Huang L., Zhang X., Kang J., Kong H.*, Ren Y.*, Zhang J.*, 2022. Loss of innovative traits underlies multiple origins of Aquilegia ecalcarata. Journal of Systematics and Evolution 60: 1291-1302.
2021
86. Richardson A. E.*, Cheng J., Johnston R., Kennaway R., Conlon B. R., Rebocho A. B., Kong H., Scanlon M. J.*, Hake S., Coen E.*, 2021. Evolution of the grass leaf by primordium extension and petiole-lamina remodeling. Science 374: 1377-1381.
85. Qin L., Hu Y., Wang J., Wang X., Zhao R., Shan H., Li K., Xu P., Wu H., Yan X., Liu L., Yi X., Wanke S., Bowers J. E., Leebens-Mack J. H., dePamphilis C. W., Soltis P. S., Soltis D. E., Kong H., Jiao Y.*, 2021. Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome. Nature Plants 7: 1239-1253.
84. Shan H., Kong H.*, 2021. The genome of Ginkgo biloba refined. Nature Plants 7: 714-715. (News & Views)
2020
83. Liu P., Zhang X., Mao J., Hong Y., Zhang R., E Y., Nie S., Jia K., Jiang C., He J., Shen W., He Q., Zheng W., Abbas S., Jewaria P. K., Tian X., Liu C., Jiang X., Yin Y., Liu B., Wang L., Jin B., Ma Y., Qiu Z., Baluska F., Samaj J., He X., Niu S., Xie J., Xie L., Xu H., Kong H., Ge S., Dixon R. A., Jiao Y.*; Lin J.*, 2020. The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements. Genome Biology 21: 291.
82. Duan X., Zhao C., Jiang Y., Zhang R., Shan H.*, Kong H.*, 2020. Parallel evolution of apetalous lineages within the buttercup family (Ranunculaceae): outward expansion of AGAMOUS1, rather than disruption of APETALA3-3. The Plant Journal 104: 1169-1181.
81. Zhang R., Fu X., Zhao C., Cheng J., Liao H., Wang P., Yao X., Duan X., Yuan Y., Xu G., Kramer E. M., Shan H., Kong H.*, 2020. Identification of the key regulatory genes involved in elaborate petal development and specialized character formation in Nigella damascena (Ranunculaceae). The Plant Cell 32: 3095-3112. (Commented by Chris Whitewoods, 2020. A Damascene moment: the genetic basis of complex petals in Nigella. The Plant Cell 32: 3041-3042; recommended by PHYS.ORG: https://phys.org/news/2020-08-uncovering-developmental-mechanisms-elaborate-petals.html)
80. Zhang R., Min Y., Holappa L. D., Walcher-Chevillet C. L., Duan X., Donaldson E., Kong H., Kramer E. M.*, 2020. A role for the Auxin Response Factors ARF6 and ARF8 homologs in petal spur elongation and nectary maturation in Aquilegia. New Phytologist 227: 1392-1405.
79. Jiang Y., Wang M., Zhang R., Xie J., Duan X., Shan H., Xu G.*, Kong H.*, 2020. Identification of the target genes of AqAPETALA3-3 (AqAP3-3) in Aquilegia coerulea (Ranunculaceae) helps understand the molecular bases of the conserved and nonconserved features of petals. New Phytologist 227: 1235-1248.
78. Xie J., Zhao H., Li K., Zhang R., Jiang Y., Wang M., Guo X., Yu B., Kong H.*, Jiao Y.*, Xu G.*, 2020. A chromosome-scale reference genome of Aquilegia oxysepala var. kansuensis. Horticulture Research 7: 113.
77. Liao H., Fu X., Zhao H., Cheng J., Zhang R., Yao X., Duan X., Shan H., Kong H.*, 2020. The morphology, molecular development and ecological function of pseudonectaries on Nigella damascena (Ranunculaceae) petals. Nature Communications 11: 1777. (Recommended by Faculty Opinions: https://facultyopinions.com/prime/737746780 and Plant Science Research Weekly of Plantae; featured article of Nature Communications: https://www.nature.com/collections/jgjcebchgg)
76. Zhang J., Fu X., Li R., Zhao X., Liu Y., Li M., Zwaenepoel A., Ma H., Goffinet B., Guan Y., Xue J., Liao Y., Wang Q., Wang Q., Wang J., Zhang G., Wang Z., Jia Y., Wang M., Dong S., Yang J., Jiao Y., Guo Y., Kong H., Lu A., Yang H., Zhang S.*, Van de Peer Y.*, Liu Z.*, Chen Z.*, 2020. The hornwort genome and early land plant evolution. Nature Plants 6: 107-118.
75. Zhang L.*, Chen F., Zhang X., Li Z., Zhao Y., Lohaus R., Chang X., Dong W., Ho S. Y. W., Liu X., Song A., Chen J., Guo W., Wang Z., Zhuang Y., Wang H., Chen X., Hu J., Liu Y., Qin Y., Wang K., Dong S., Liu Y., Zhang S., Yu X., Wu Q., Wang L., Yan X., Jiao Y., Kong H., Zhou X., Yu C., Chen Y., Li F., Wang J., Chen W., Chen X., Jia Q., Zhang C., Jiang Y., Zhang W., Liu G., Fu J., Chen F., Ma H., Van de Peer Y., Tang H., 2020. The water lily genome and the early evolution of flowering plants. Nature 577: 79-84.
2019
74. Shan H., Cheng J., Zhang R., Yao X., Kong H.*, 2019. Developmental mechanisms involved in the diversification of flowers. Nature Plants 5: 917-923.
73. Yao X., Zhang W., Duan X., Yuan Y., Zhang R., Shan H., Kong H.*, 2019. The making of elaborate petals in Nigella through developmental repatterning. New Phytologist 223: 385-396.
72. Zhai W., Duan X., Zhang R., Guo C., Li L., Xu G., Shan H., Kong H.*, Ren Y.*, 2019. Chloroplast genomic data provide new and robust insights into the phylogeny and evolution of the Ranunculaceae. Molecular Phylogenetics and Evolution 135: 12-21.
71. 王宏哲, 张睿, 程劼, 段晓姗, 赵慧琪, 山红艳, 孔宏智*, 2019. 花基本结构的多样性及其分子机制. 中国科学：生命科学49: 292-300.
2018
70. 陈凡, 钱前, 王台, 董爱武, 漆小泉, 左建儒, 杨淑华, 林荣呈, 萧浪涛, 顾红雅, 陈之端, 姜里文, 白永飞, 孔宏智, 种康, 2018. 2017年中国植物科学若干领域重要研究进展. 植物学报53: 391-440.
69. Zhang L., Kong H., Ma H., Yang J.*, 2018. Phylogenomic detection and functional prediction of genes potentially important for plant meiosis. Gene 643: 83-97.
2017
68. Harkess A., Zhou J., Xu C., Bowers J. E., Van der Hulst R., Ayyampalayam S., Mercati F., Riccardi P., McKain M. R., Kakrana A., Tang H., Ray J., Groenendijk J., Arikit S., Mathioni S. M., Nakano M., Shan H., Telgmann-Rauber A., Kanno A., Yue Z., Chen H., Li W., Chen Y., Xu X., Zhang Y., Luo S., Chen H., Gao J., Mao Z., Pires J. C., Luo M., Kudrna D., Wing R. A., Meyers B. C., Yi K., Kong H., Lavrijsen P., Sunseri F., Falavigna A., Ye Y.*, Leebens-Mack J. H.*, Chen G.*, 2017. The asparagus genome sheds light on the origin and evolution of a young Y chromosome. Nature Communications 8:1279.
67. Kramer E. M.*, Kong H., Rausher M. D., 2017. Plant evolutionary developmental biology. Introduction to a special issue. New Phytologist 216: 335-336.
66. 王小菁, 萧浪涛, 董爱武, 王台, 钱前, 漆小泉, 陈凡, 左建儒, 杨淑华, 顾红雅, 陈之端, 姜里文, 白永飞, 孔宏智, 种康, 2017. 2016年中国植物科学若干领域重要研究进展. 植物学报52: 394-452.
65. 山红艳, 孔宏智*, 2017. 花是如何起源的？科学通报62: 2323-2334.
64. Huang J., Li Z., Biener G., Xiong E., Malik S., Eaton N., Zhao C. Z., Raicu V., Kong H., Zhao D.*, 2017. Carbonic anhydrases function in anther cell differentiation downstream of the receptor-like kinase EMS1. The Plant Cell 29: 1335-1356.
2016
63. 杨淑华, 王台, 钱前, 王小菁, 左建儒, 顾红雅, 姜里文, 陈之端, 白永飞, 孔宏智, 陈凡, 萧浪涛, 董爱武, 种康, 2016. 2015年中国植物科学若干领域重要研究进展. 植物学报51: 416-472.
62. Ye L., Wang B., Zhang W., Shan H.*, Kong H.*, 2016. Gains and losses of cis-regulatory elements led to divergence of the ArabidopsisAPETALA1 and CAULIFLOWER duplicate genes in the time, space, and level of expression and regulation of one paralog by the other. Plant Physiology 171: 1055-1069. (Commented by Gunter Theissen and Francois Parcy at Flowering Highlights; recommended by F1000Prime: https://facultyopinions.com/prime/726292577; Top Topics from 2016ofPlant Physiology)
61. Yu X., Duan X., Zhang R., Fu X., Ye L., Kong H., Xu G.*, Shan H.*, 2016. Prevalent exon-intron structural changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERINGLOCUSCMADS-box gene subfamilies provide new insights into their evolution. Frontiers in Plant Science 7: 598.
60. Wang P., Liao H., Zhang W., Yu X., Zhang R., Shan H., Duan X., Yao X., Kong H.*, 2016. Flexibility in the structure of spiral flowers and its underlying mechanisms. Nature Plants 2: 15188. (Commented by Douglas E. Soltis, 2016. Diversification of the flower. Nature Plants 2: 15211.)
59. 孔宏智*, 2016. 生物多样性事业呼唤对物种概念和物种划分标准的深度讨论. 生物多样性24: 977-978.
2015及以前
58. 种康, 王台, 钱前, 王小菁, 左建儒, 顾红雅, 姜里文, 陈之端, 白永飞, 杨淑华, 孔宏智, 陈凡, 萧浪涛, 2015. 2014年中国植物科学若干领域重要研究进展. 植物学报50: 412-459.
57. Li L., Yu X., Guo C., Duan X., Shan H., Zhang R., Xu G., Kong H.*, 2015. Interactions among proteins of floral MADS-box genes in Nuphar pumila (Nymphaeaceae) and the most recent common ancestor of extant angiosperms help understand the underlying mechanisms of the origin of the flower. Journal of Systematics and Evolution 53: 285-296. (Cover Story)
56. Li H., Meng F., Guo C., Wang Y., Xie X., Zhu T., Zhou S., Ma H., Shan H.*, Kong H.*, 2014. MeioBase: a comprehensive database for meiosis. Frontiers in Plant Science 5: 728.
55. Zeng L., Zhang Q., Sun R., Kong H., Zhang N.*, Ma H.*, 2014. Resolution of deep angiosperm phylogeny using conserved nuclear genes and estimates of early divergence times. Nature Communications 5: 4956.
54. Jia R., Guo C., Xu G., Shan H., Kong H.*, 2014. Evolution of the cyclin gene family in plants. Journal of Systematics and Evolution 52: 651-659.
53. 袁明, 瞿礼嘉, 王小菁, 钱前, 杨维才, 王台, 孔宏智, 蒋高明, 种康, 2014. 2013年中国植物科学若干领域重要研究进展. 植物学报49: 347-406.
52. 孔宏智*, 2014. 从基因组到多样性. 生物多样性22: 1-2.
51. 张睿*, 国春策, 山红艳, 孔宏智, 2014. 发育重塑与生物多样性. 生物多样性22: 66-71.
50. 国春策*, 张睿, 山红艳, 孔宏智, 2014. 调控进化与形态多样性. 生物多样性22: 72-79.
49. 钱前, 瞿礼嘉, 袁明, 王小菁, 杨维才, 王台, 孔宏智, 蒋高明, 种康, 2013. 2012年中国植物科学若干领域重要研究进展. 植物学报48: 231-287.
48. Amborella Genome Project, 2013. The Amborella genome and the evolution of flowering plants. Science 342: 1241089.
47. Zhang R., Guo C., Zhang W., Wang P., Li L., Duan X., Du Q., Zhao L., Shan H., Hodges S. A., Kramer E. M., Ren Y.*, Kong H.*, 2013. Disruption of the petal identity gene APETALA3-3 is highly correlated with loss of petals within the buttercup family (Ranunculaceae). Proceedings of the National Academy of Sciences USA 110: 5074-5079.
46. Kahloul S., El Beji I. H. S., Boulaflous A., Ferchichi A., Kong H., Mouzeyar S.*, Bouzidi M. F., 2013. Structural, expression and interaction analysis of rice SKP1-like genes. DNA Research 20: 67-78.
45. 瞿礼嘉, 钱前, 袁明, 王小菁, 杨维才, 王台, 孔宏智, 蒋高明, 种康, 2012. 2011年中国植物科学若干领域重要研究进展. 植物学报47: 309-356.
44. Wang B., Zhang N., Guo C., Xu G., Kong H., Shan H.*, 2012. Evolutionary divergence of the APETALA1 and CAULIFLOWER proteins. Journal of Systematics and Evolution 50: 502-511.
43. 孔宏智*, 2012. 生物多样性是如何产生的？生物多样性20: 117-118.
42. Xu G., Guo C., Shan H., Kong H.*, 2012. Divergence of duplicate genes in exon–intron structure. Proceedings of the National Academy of Sciences USA 109: 1187-1192.
41. 袁明, 王小菁, 钱前, 杨维才, 瞿礼嘉, 王台, 孔宏智, 许亦农, 蒋高明, 种康, 2011. 2010年中国植物科学若干领域重要研究进展. 植物学报46: 233-275
40. Liu Y., Guo C., Xu G., Shan H., Kong H.*, 2011. Evolutionary pattern of the regulatory network for flower development: insights gained from a comparison of two Arabidopsis species. Journal of Systematics and Evolution 49: 528-538.
39. Zhang Q., Antonelli A., Feild T.S., Kong H.*, 2011. Revisiting taxonomy, morphological evolution, and fossil calibration strategies in Chloranthaceae. Journal of Systematics and Evolution 49: 315-329. (Cover Story)
38. Sharma B., Guo C., Kong H., Kramer E. M.*, 2011. Petal-specific subfunctionalization of an APETALA3 paralog in the Ranunculales and its implications for petal evolution. New Phytologist 191: 870-883.
37. 李安, 徐桂霞, 孔宏智*, 2011. F-box基因拷贝数目变异的机制研究：以12种果蝇为例. 生物多样性19: 3-16.
36. Liu C., Zhang J., Zhang N., Shan H., Su K., Zhang J., Meng Z., Kong H.*, Chen Z.*, 2010. Interactions among proteins of floral MADS-box genes in basal eudicots: implications for evolution of the regulatory network for flower development. Molecular Biology and Evolution 27: 1598-1611.
35. Gao X., Liang W., Yin C., Ji. S., Wang H., Su X., Guo C., Kong H., Xue H., Zhang D.*, 2010. The SEPALLATA-Like gene OsMADS34 is required for rice inflorescence and spikelet development. Plant Physiology 153: 728-740.
34. 薛皓月, 徐桂霞, 国春策, 山红艳, 孔宏智*, 2010. 拟南芥和琴叶拟南芥中MADS-box基因的比较进化分析. 生物多样性18: 109-119.
33. Li H., Liang W., Jia R., Yin C., Zong J., Kong H., Zhang D.*, 2009. The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice. Cell Research 20: 299-313.
32. 王台, 钱前, 袁明, 王小菁, 杨维才, 瞿礼嘉, 孔宏智, 许亦农, 蒋高明, 种康, 2010. 2009年中国植物科学若干领域重要研究进展. 植物学报45: 265-306.
31. Shan H., Zahn L., Guindon S., Wall P. K., Kong H., Ma H., dePamphilis C. W., Leebens-Mack J.*, 2009. Evolution of plant MADS-box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications. Molecular Biology and Evolution 26: 2229-2244.
30. 杨维才, 瞿礼嘉, 袁明, 王小菁, 王台, 孔宏智, 许亦农, 蒋高明, 种康, 2009. 2008年中国植物科学若干领域重要研究进展. 植物学报44: 379-409.
29. Wang X., Kong H., Ma H.*, 2009. F-box proteins regulate ethylene signaling and more. Genes & Development 23: 391-396.
28. Xu G., Ma H., Nei M.*, Kong H.*, 2009. Evolution of F-box genes in plants: different modes of sequence divergence and their relationships with functional diversification. Proceedings of the National Academy of Sciences USA 106: 835-840.
27. 瞿礼嘉, 王小菁, 王台, 杨维才, 许亦农, 袁明, 蒋高明, 孔宏智, 种康, 2009. 2007年中国植物科学若干领域重要研究进展. 植物学报44: 2-26.
26. Su K., Zhao S., Shan H., Kong H., Lu W., Theissen G., Chen Z.*, Meng Z.*, 2008. The MIK region rather than the C-terminal domain of AP3-like class B floral homeotic proteins determines functional specificity in the development and evolution of petals. New Phytologist 178: 544-558.
25. Quan L., Xiao R., Li W., Oh S. A., Kong H., Ambrose J. C., Malcos J. L., Cyr R., Twell D., Ma H.*, 2008. Functional divergence of the duplicated AtKIN14a and AtKIN14b genes: critical roles in Arabidopsis meiosis and gametophyte development. The Plant Journal 53: 1013-1026.
24. Zhu X., Chase M. W., Qiu Y., Kong H., Dilcher D. L., Li J., Chen Z.*, 2007. Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids. BMC Evolutionary Biology 7: 217.
23. Shan H., Zhang N., Liu C., Xu G., Zhang J., Chen Z.*, Kong H.*, 2007. Patterns of gene duplication and functional diversification during the evolution of the AP1/SQUA subfamily of plant MADS-box genes. Molecular Phylogenetics and Evolution 44: 26-41.
22. Xu G., Kong H.*, 2007. Duplication and divergence of floral MADS-box genes in grasses: evidence for the generation and modification of novel regulators. Journal of Integrative Plant Biology 49: 927-939.
21. 种康, 瞿礼嘉, 袁明, 王小菁, 杨维才, 王台, 许亦农, 蒋高明, 孔宏智, 2007. 2006年中国植物科学若干领域重要研究进展. 植物学通报24: 253-271.
20. Kong H.*, Landherr L. L., Frohlich M. W., Leebens-Mack J., Ma H., dePamphilis C. W.*, 2007. Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth. The Plant Journal 50: 873-885.
19. Shan H., Su K., Lu W., Kong H., Chen Z.*, Meng Z.*, 2006. Conservation and divergence of candidate class B genes in Akebia trifoliata (Lardizabalaceae). Development Genes and Evolution 216: 785-795.
18. Lin Z., Kong H., Nei M.*, Ma H.*, 2006. Origins and evolution of the recA/RAD51 gene family: evidence for ancient gene duplication and endosymbiotic gene transfer. Proceedings of the National Academy of Sciences USA 103: 10328-10333.
17. Kim S.*, Koh J., Yoo M. J., Kong H., Hu Y., Ma H., Soltis P. S., Soltis D. E.*, 2005. Expression of floral MADS-box genes in basal angiosperms: Implication for the evolution of floral regulators. The Plant Journal 43: 724-744.
16. Li G., Meng Z.*, Kong H., Chen Z., Theissen G., Lu A.*, 2005. Characterization of candidate class A, B and E floral homeotic genes from the perianthless basal angiosperm Chloranthusspicatus (Chloranthaceae). Development Genes and Evolution 215: 437-449.
15. Zahn L. M., Kong H. (equal contribution), Leebens-Mack J. H., Kim S., Soltis P. S., Landherr L. L., Soltis D. E., dePamphilis C. W., Ma H.*, 2005. The evolution of the SEPALLATA subfamily of MADS-box genes: a pre-angiosperm origin with multiple duplications throughout angiosperm history. Genetics 169: 2209-2223.
14. Wang G., Kong H. (equal contribution), Sun Y., Zhang X., Zhang W., Altman N., dePamphilis C. W., Ma H.*, 2004. Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins. Plant Physiology 135: 1084-1099.
13. Kong H., Leebens-Mack J., Ni W., dePamphilis C. W., Ma H.*, 2004. Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications. Molecular Biology and Evolution 21: 117-128.
12. Li G., Meng Z.*, Kong H., Chen Z., Lu A.*, 2003. ABC model and floral evolution. Chinese Science Bulletin 48: 2415-2421 (in Chinese); 48: 2651-2657 (in English).
11. Zhang F., Kong H., Ge S.*, 2003. Allozyme variation and population differentiation of the Aconitumdelavayi complex (Ranunculaceae) in the Hengduan Mountains of China. Biochemical Genetics 41: 47-55.
10. Kong H.*, Lu A., Endress P. K., 2002. Floral organogenesis of Chloranthussessilifolius, with special emphasis on the morphological nature of the androecium of Chloranthus (Chloranthaceae). Plant Systematics and Evolution 232: 181-188.
09. Kong H.*, Chen Z., Lu A., 2002. Phylogeny of Chloranthus (Chloranthaceae) based on nuclear ribosomal ITS and plastid trnL-F sequence data. American Journal of Botany 89: 940-946.
08.刘建全, 何亚平, 孔宏智, 2002. 大吴风草属、假橐吾属花粉表面纹饰及其分类学意义. 西北植物学报22: 33-36.
07. Kong H.*, 2001. Comparative morphology of leaf epidermis in the Chloranthaceae. Botanical Journal of the Linnean Society 136: 279-294.
06. Kong H., 2000. Taxonomic notes on Chloranthus henryi Hemsl. and its allies. Acta Phytotaxonomica Sinica 38: 355-365.
05. 钱韦*, 孔宏智, 刘忠, 杨冬之, 2000. 评统一进化理论——与陈继明先生商榷. 科学通报45: 885-889.
04. Kong H., Chen Z., 2000. Phylogeny in Chloranthus Swartz (Chloranthaceae) inferred from sequence analysis of nrDNA ITS region. Acta Botanica Sinica 42: 762-764.
03. Kong H.*, 2000. Karyotypes of Sarcandra Gardn. and Chloranthus Swartz (Chloranthaceae) from China. Botanical Journal of the Linnean Society 133: 327-342.
02. Kong H.*, Liu J., 1999. Karyomorphology of the genus Pomatosace Maxim. (Primulaceae). Acta Phytotaxonomica Sinica 37: 445-450.
01. Kong H., Yang Q.*, 1997. Karyomorphology and relationships of the genus Circaeaster Maxim. Acta Phytotaxonomica Sinica 35: 494-499.
专著（注*为通讯作者）
02. [美] Futuyama D. J., 生物进化 (第3版), 葛颂, 顾红雅, 饶广远, 张德兴, 杨继, 孔宏智, 王宇飞, 译，2016. 高等教育出版社.
01. Soltis D. E.*, Albert V. A., Kim S., Yoo M. J., Soltis P. S., Frohlich M. W., Leebens-Mack J., Kong H., Wall K., dePamphilis C. W., Ma H., 2005. Evolution of the Flower. In Plant Diversity and Evolution: Genotypic and Phenotypic Variation in Higher Plants, Ed. Henry R. J. CABI Publishers pp. 165-200.
