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。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 Plants、Molecular Biology and Evolution（2篇）、Plant Journal、Plant Physiology和Molecular Phylogenetics and Evolution等刊物上发表论文30余篇，以合作者在Science、PNAS、Nature Communications、Molecular Biology and Evolution、Plant Journal、Plant Physiology和Genetics等刊物上发表论文20余篇。曾主持国家自然科学基金之青年基金、主任基金、面上项目（2项）、“国家杰出青年科学基金”、重点项目（2项）和重大研究计划集成项目，是中国科学院“知识创新工程重要方向项目”和“科技创新交叉与合作团队”项目的主持人和国家重大科学研究计划项目的课题负责人。被Molecular Biology and Evolution、New Phytologist、Frontiers in Plant Evolution and Development、Journal of Genetics and Genomics、Journal of Systematics and Evolution、《植物学报》、《生物多样性》和《科技导报》等刊物聘为Editor、Associate Editor、副主编或编委。2011年获“国家杰出青年科学基金”资助，2012年获“中国科学院青年科学家奖”，2013年获“中国青年科技奖”，2014年入选科技部“中青年科技创新领军人才”并获“全国优秀科技工作者”荣誉称号，2016年入选国家“万人计划”领军人才。

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、分子遗传学和基因组学研究手段，揭示花部结构起源和多样化的分子机制。近年来关注的科学问题包括：1）花器官身份决定程序起源和多样化的原因和机制；2）花瓣形态和结构多样化的动因和机制；3）新性状起源的分子机制和叠加效应。

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）。

主持的科研项目

主持国家自然科学基金“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）

主持国家自然科学基金重点项目“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）

主持中国科学院“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）

主持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）

主持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）

主持了国家自然科学基金面上项目“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）

主持了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）

主持了国家自然科学基金重点项目“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）

主持了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）

主持了国家自然科学基金委面上基金项目“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）

主持了国家自然科学基金委创新研究群体基金项目“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）

主持了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）

主持了国家自然科学基金委青年基金项目“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）

2017

Shan HY, Kong HZ*. 2017. How did the flower originate? Chinese Science Bulletin 62(21): 2323-2334.

2016

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

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 (4): 416-472

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 FLOWERING LOCUS C MADS-box gene subfamilies provide new insights into their evolution. Frontiers in Plant Science 7: 598 [PDF]

Ye L., Wang B., Zhang W., Shan H.*, Kong H.*, 2016. Gains and losses of cis-regulatory elements led to divergence of the Arabidopsis APETALA1 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 (recommended by F1000Prime) [PDF]

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 [PDF]

2015

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

Li L., Yu X.-X., Guo C.-C, Duan X.-S, Shan H.-Y., Zhang R., Xu G.-X., Kong H.-Z.*, 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 Evolution53: 285-296[PDF]

2014

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 [PDF]

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 [PDF]

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 [PDF]

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

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

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

孔宏智, 2014. 从基因组到多样性. 生物多样性22: 1-2

2013

Amborella Genome Project, 2013. The Amborella genome and the evolution of flowering plants. Science 342: 1241089 [PDF]

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 [PDF]

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 [PDF]

2012

孔宏智, 2012. 生物多样性是如何产生的？生物多样性20: 117-118

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 [PDF]

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 [PDF]

2011

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 [PDF]

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: 870-83 [PDF]

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 [PDF]

Li A., Xu G. Kong H.*, 2011. Mechanisms underlying copy number variation in F-box genes: evidence from comparison of 12 Drosophila species. Biodiversity Science 19: 3-16 (in Chinese, with English abstract) [PDF]

2010及以前

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 [PDF]

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 [PDF]

Xue H., Xu G., Guo C., Shan H., Kong H.*, 2010. Comparative evolutionary analysis of MADS-box genes in Arabidopsis thaliana and A. lyrata. Biodiversity Science 18: 109-119 [PDF]

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

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 [PDF]

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 [PDF]

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 (4): 379-409

Wang X., Kong H., Ma H.*, 2009. F-box proteins regulate ethylene signaling and more. Genes & Development 23: 391-396 [PDF]

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 [PDF]

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 (1): 2-26

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 Phytologist178: 544-558 [PDF]

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 Arabidopsis ATK5 and ATK1 genes: critical roles in meiosis and gametophyte development.The Plant Journal53: 1013-1026 [PDF]

Zhu X.-Y., Chase M. W., Qiu Y.-L., Kong H.-Z., Dilcher D. L., Li J.-H., Chen Z.-D., 2007. Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids. BMC Evolutionary Biology 7: 217 [PDF]

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 [PDF]

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 [PDF]

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 (3): 253-271

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 (6): 927-939 [PDF]

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 (12): 785-795 [PDF]

Lin Z., Kong H., Nei M.*, Ma H.*, 2006. Origins and evolution of the recA/RAD51 gene family: Evidence for ancient gene duplication and symbiotic gene transfer. Proceedings of the National Academy of Sciences USA103: 10328-10333 [PDF]

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. Genetics169: 2209-2223 [PDF]

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 [PDF]

Li G.-S., Meng Z.*, Kong H.-Z., Chen Z.-D., Theissen G., Lu A.-M.*, 2005. Characterization of candidate class A, B, and E floral homeotic gene from the perianthless basal angiosperm Chloranthus spicatus (Chloranthaceae). Development Genes and Evolution 215 (9): 437-449 [PDF]

Soltis D. E.*, Albert V. A., Kim S., Yoo M.-J. , Soltis P. S., Frohlich M. W., Leebens-Mack J., Kong H., Wall K., Ma H., dePamphilis C.W. 2005. Evolution of the Flower. In Diversity and Evolution of Plants, Ed. R. Henry. CABI Publishers pp. 165-200

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 [PDF]

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 [PDF]

Li G., Meng Z.*, Kong H., Chen Z., Lu A., 2003. ABC model and floral evolution. Chinese Science Bulletin 48 (23): 2415-2421 (in Chinese); 48 (24): 2651-2657

Zhang F.-M., Kong H.-Z., Ge S.*, 2003. Allozyme variation and population differentiation of the Aconitum delavayi complex in the Hengduan Mountains of China. Biochemical Genetics 41: 47-55 [PDF]

Kong H.-Z.*, Chen Z.-D., Lu A.-M., 2002. Phylogenetic relationships within Chloranthus Sw. (Chloranthaceae) based on nuclear ITS and plastid trnL-F sequence data. American Journal of Botany89 (6): 940-946 [PDF]

Kong H.-Z.*, Lu A.-M., Endress P. K., 2002. Floral organogenesis of Chloranthus sessilifolius K. F. Wu (Chloranthaceae) with special emphasis on the morphological nature of the androecium of Chloranthus Sw. Plant Systematics and Evolution232: 181-188 [PDF]

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 (1): 33-36

Kong H.-Z., 2001. Comparative morphology of leaf epidermis in the Chloranthaceae. Botanical Journal of the Linnean Society 136: 279-294

Kong H.-Z., 2000. Karyotypes of Sarcandra Gardn. and Chloranthus Sw. (Chloranthaceae) from China. Botanical Journal of the Linnean Society133: 327-342

Kong H.-Z., Chen Z.-D., 2000. Phylogeny in Chloranthus Swartz (Chloranthaceae) inferred from sequence analysis of nrDNA ITS region. Acta Botanica Sinica 42 (7): 762-764 [PDF]

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 (8): 885-889

Kong H.-Z., 2000. Taxonomic notes on Chloranthus henryi Hemsl. and its allies. Acta Phytotaxonomica Sinica 38 (4): 355-365 [PDF]

Kong H.-Z.*, Liu J.-Q., 1999. Karyomorphology of the genus Pomatosace Maxim. (Primulaceae). Acta Phytotaxonomica Sinica 37 (5): 445-450 [PDF]

Kong H.-Z., Yang Q.-E.*, 1997. Karyomorphology and relationships of the genus Circaeaster Maxim. Acta Phytotaxonomica Sinica 35 (6): 494-499 [PDF]