教育经历:

2009 - 2011 , 博士后 , 生物信息学 , 北京大学
2004 - 2009 , 理学博士 , 生物信息学 , 中科院生物物理所
2000 - 2004 , 理学学士 , 应用数学 , 北京大学

工作经历:

2011 - 2020，副研究员，北京大学
2020 - 至今，研究员，北京大学

      1.多组学（Multi-Omics）研究
　　生物信息学是在生命科学的研究中，利用信息技术对大量而复杂的生物数据进行存储、检索和分析，进而揭示生物学奥秘的学科。近年来，随着基因组序列的不断完善和各种大通量采集数据实验方法的开发，对数据的发掘和理解也在生物研究中起到越来越重要的作用。本课题组通过长期基因组序列变异、转录组、表观遗传组及表型组的研究，建立起完善的生物信息分析平台，将不同的组学数据整合，发掘基因在不同组学数据中的关联，形成层级或网络的调控关系，并通过多组学方法发现新的调控因子和调控通路。

2.杂种优势研究
　　杂交优势是自然界普遍存在的一种复杂生物学现象，在农业生产中获得了广泛的应用。但是杂交优势的分子遗传机理迄今尚不清楚。随着分子生物学、基因组学和生物信息学研究的深入和发展，利用系统生物学手段开展杂交优势分子机理的研究，具有重要的科学意义和实际应用价值。基因型异质的亲本其杂交子一代许多性状上不同于双亲，这必然涉及到亲本基因组在杂交遗传背景中相互作用而引起基因表达调控发生变化。目前，我们利用高通量测序技术对具有不同优势的杂交组合的亲本和子一代不同组织在不同环境条件下进行全基因组基因差异表达分析，并进一步分析造成这种差异表达基于顺式作用元件和反式调控因子DNA序列多态性的遗传机制，以及基于DNA甲基化、组蛋白修饰、染色质重塑和非编码RNA的表观遗传机制，全面探索杂交优势的可能分子机制。

3.AI育种
　　 随着AI技术在生命科学和农业生产中的发展，育种从传统育种、分子育种、设计育种逐渐转为AI育种。本课题组通过发掘植物基因型、多组学、表型组、环境组学的复杂关联，建立大模型形成育种知识结构，达到理解植物基因-环境-性状关系，预测性状表现，开展AI育种，创制新品种和新物种。

4.数据库与工具（Databases and Tools）
首个西瓜T2T基因组与突变体库(The first T2T watermelon genome and the mutant library)
http://www.watermelondb.cn

猕猴桃属T2T基因组数据库(T2T Genomic Database for Actinidia Species)
http://8.140.245.74:6688/

拟南芥转光发育单细胞数据库(Single Cell Atlases of Arabidopsis De-Etiolating Seedlings)
http://8.140.245.74:6699/

(#: Co-first author; *: Corresponding author)
2024
1. Sun L#, Zhou J#, Xu X#, Liu Y, Ma N, Liu Y, Nie W, Zou L, Deng XW*, He H*. Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL. Nature Commun. 2024 Jan 2;15(1):35. doi: 10.1038/s41467-023-44347-z.

2. Gao Z#, Su Y#, Chang L, Jiao G, Ou Y, Yang M, Xu C, Liu P, Wang Z, Qi Z, Liu W, Sun L, He G, Deng XW*, He H*. Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids. J Integr Plant Biol. 2024 Feb;66(2):208-227. doi: 10.1111/jipb.13620.

3. Li Z#, Sun L#, Xu X, Liu Y, He H*, Deng XW*. Light control of three-dimensional chromatin organization in soybean. Plant Biotechnol J. 2024 May 19. doi: 10.1111/pbi.14372.

4. Chen W#, Wang X#, Sun J#, Wang X#, Zhu Z#, Ayhan DH, Yi S, Yan M, Zhang L, Meng T, Mu Y, Li J, Meng D, Bian J, Wang K, Wang L, Chen S, Chen R, Jin J, Li B, Zhang X, Deng XW, He H*, Guo L*. Two telomere-to-telomere gapless genomes reveal insights into Capsicum evolution and capsaicinoid biosynthesis. Nature Commun. 2024 May 20;15(1):4295. doi: 10.1038/s41467-024-48643-0.

2023
1. Han X, Zhang Y, Lou Z, Li J, Wang Z, Gao C, Liu Y, Ren Z, Liu W, Li B, Pan W, Zhang H, Sang Q, Wan M, He H*, Deng XW*. Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings. Nature Plants. 2023 Oct 30. doi: 10.1038/s41477-023-01544-4.

2. Gao Z#, Bian J#, Lu F, Jiao Y*, He H*. Triticeae crop genome biology: an endless frontier. Front Plant Sci. 2023 Jul 20;14:1222681.

3. Zhou H, Deng XW*, He H*. Gene expression variations and allele-specific expression of two rice and their hybrid in caryopses at single-nucleus resolution. Front Plant Sci. 2023 May 23;14:1171474.

4. Sun L#, Cao Y#, Li Z#, Liu Y, Yin X, Deng XW*, He H*, Qian W*. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. J Integr Plant Biol. 2023 May 8.

5. Song J#, Sun B#, Chen C, Ning Z, Zhang S, Cai Y, Zheng X, Cao B, Chen G, Jin D, Li B, Bian J, Lei J*, He H*, Zhu Z*. An R-R-type MYB transcription factor promotes non-climacteric pepper fruit carotenoid pigment biosynthesis. Plant Journal. 2023 Aug;115(3):724-741.

6. Han X#, Zhang Y#, Zhang Q#, Ma N, Liu X, Tao W, Lou Z, Zhong C, Deng XW*, Li D*, He H*. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Molecular Plant. 2023 Feb 6;16(2):452-470.

2022
1. Zhang Y#, Fu J#, Wang K#, Han X#, Yan T, Su Y, Li Y, Lin Z, Qin P, Fu C, Deng XW, Zhou D*, Yang Y*, He H*. The telomere-to-telomere gap-free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding. Plant Biotechnol Journal. 2022 Sep;20(9):1642-1644.

2. Deng Y#, Liu S#, Zhang Y#, Tan J, Li X, Chu X, Xu B, Tian Y, Sun Y, Li B, Xu Y, Deng XW, He H*, Zhang X*. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. Molecular Plant. 2022 Jun 22:S1674-2052(22)00192-7.

3. Cui D#, Zhou H#, Ma X#, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng XW, He H*, Han L*. Genomic insights on the contribution of introgressions from Xian/indica to the genetic improvement of Geng/japonica rice cultivars. Plant Comm. 2022 May 9;3(3):100325.

2021
1. Li G#, Wang L#, Yang J#*, He H#, Jin H#, Li X#, Ren T#, Ren Z, Li F, Han X, Zhao X, Dong L, Li Y, Song Z, Yan Z, Zheng N, Shi C, Wang Z, Yang S, Xiong Z, Zhang M, Sun G, Zheng X, Gou M, Ji C, Du J, Zheng H, Dolezel J, Deng XW, Stein N, Yang Q*, Zhang K*, Wang D*. A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes. Nature Genetics. 2021 Mar 18.

2020
1. Lin Z, Qin P, Zhang X, Fu C, Deng H, Fu X, Huang Z, Jiang S, Li C, Tang X, Wang X, He G, Yang Y*, He H*, Deng XW*. Divergent selection and genetic introgression shape the genome landscape of heterosis in hybrid rice. Proc Natl Acad Sci U S A. 2020 Mar 3;117(9):4623-4631.

2. Sun L, Jing Y, Liu X, Li Q, Xue Z, Cheng Z, Wang D, He H*, Qian W*. Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis. Nature Commun. 2020 Apr 20;11(1):1886.

3. Wang B, Lin Z, Li X, Zhao Y, Zhao B, Wu G, Ma X, Wang H, Xie Y, Li Q, Song G, Kong D, Zheng Z, Wei H, Shen R, Wu H, Chen C, Meng Z, Wang T, Li Y, Li X, Chen Y, Lai J, Hufford MB, Ross-Ibarra J, He H*, Wang H*. Genome-wide selection and genetic improvement during modern maize breeding. Nature Genetics. 2020 Apr 27.

2019
1. Han X, Chang X, Zhang Z, Chen H, He H*, Zhong B*, Deng XW*. Origin and Evolution of Core Components Responsible for Monitoring Light Environment Changes during Plant Terrestrialization. Molecular Plant. 2019 Jun 3;12(6):847-862.

2018
1. Xia M#, Han X#, He H#, Yu R, Zhen G, Jia X, Cheng B*, Deng XW*. Improved de novo genome assembly and analysis of the Chinese cucurbit Siraitia grosvenorii, also known as monk fruit or luo-han-guo. Gigascience. 2018 Jun 1;7(6).

2017
1. Wang Z, Li J, Chen S, Heng Y, Chen Z, Yang J, Zhou K, Pei J, He H*, Deng XW*, Ma L*. Poaceae-specific MS1 encodes a phospholipid-binding protein for male fertility in bread wheat. Proc Natl Acad Sci U S A. 2017 Nov 6.

2. Zhen G, Qin P, Liu KY, Nie DY, Yang YZ*, Deng XW*, He H*. Genome-wide dissection of heterosis for yield traits in two-line hybrid rice populations. Sci Rep. 2017 Aug 9;7(1):7635.

3. Yan W, Chen Z, Lu J, Xu C, Xie G, Li Y, Deng XW*, He H*, Tang X*., Simultaneous Identification of Multiple Causal Mutations in Rice. Front Plant Sci. 2017 Jan 17;7:2055.

4. Chen S, Lin Z, Zhou D, Wang C, Li H, Yu R, Deng H, Tang X, Zhou S, Wang Deng X, He H*. Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement. Sci Rep. 2017 Apr 4;7:45685.

2016
1. Yu R, Yan W, Liang M, Dai X, Chen H, Sun Y, Deng XW*, Chen X, He H*, Chen L*., Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay. Sci China Life Sci. 2016 Jul;59(7):700-8.

2015
1. Liu Y, Zhou M, Gao Z, Ren W, Yang F, He H*, Zhao J*., RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in Maize. PLoS One. 2015 Nov 24;10(11):e0143128.

2. The IC4R Project Consortium (as Co-corresponding author)., Information Commons for Rice (IC4R)., Nucl. Acids Res., 2015, Oct; doi: 10.1093/nar/gkv1141.

3. Zhen G, Zhang L, Du Y, Yu R, Liu X, Cao F, Chang Q, Deng XW*, Xia M*, He H*., De novo assembly and comparative analysis of root transcriptomes from different varieties of Panax ginseng C. A. Meyer grown in different environments., Sci China Life Sci., 2015, Nov; 58(11):1099-110.

4. Zhou D, Chen W, Lin Z, Chen H, Wang C, Li H, Yu R, Zhang F, Zhen G, Yi J, Li K, Liu Y, Terzaghi W, Tang X, He H*, Zhou S*, Deng XW*., Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding., Plant Biotechnol Journal, 2015 Jun 10. doi: 10.1111/pbi.12409.

2014
1. Chen S, He H*, Deng XW*., Allele-specific DNA methylation analyses associated with siRNAs in Arabidopsis hybrids, Sci China Life Sci, 2014, 57(5):519-25.

2013
1. Chen W, Chen H, Zheng T, Yu R, Terzaghi WB, Li Z, Deng XW, Xu J*, He H*., Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing., Theor Appl Genet, 2013, 10.1007/s00122-013-2218-2.

2. Chen H#, Xie W#, He H#, Yu H#, Chen W, Li J, Yu R, Yao Y, Zhang W, He Y, Tang X, Zhou F, Deng XW, Zhang Q., A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding., Molecular Plant, 2013, 10.1093/mp/sst135.

3. He G, He H, Deng XW., Epigenetic variations in plant hybrids and their potential roles in heterosis., J Genet Genomics, 2013, 40(5):205-10.

4. Chen H, He H, Zhou F, Yu H, Deng XW., Development of genomics-based genotyping platforms and their applications in rice breeding., Curr Opin Plant Biol., 2013, 16(2):247-54.

2012
1. Shen H#, He H#, Li J, Chen W, Wang X, Guo L, Peng Z, He G, Zhong S, Qi Y, Terzaghi W, Deng XW., Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids., Plant Cell, 2012, 24(3):875-92.

2011
1. Chen H#, He H#, Zou Y#, Chen W, Yu R, Liu X, Yang Y, Gao YM, Xu JL, Fan LM, Li Y, Li ZK, Deng XW. , Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.)., Theor Appl Genet, 2011, 123(6):869-79.

2. Zhang H, He H, Wang X, Wang X, Yang X, Li L, Deng XW., Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation., Plant Journal, 2011, 65(3):346-58.

Before 2011
1. He H, Zhang H, Wang X, Wu N, Yang X, Chen R, Li Y, Deng XW, Li L., Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression., Genomics, 2010, 96(5):308-15.

2. Charron JB#, He H#, Ellinga AA, Deng XW., Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis., Plant Cell, 2009, 21(12):3732-48.

3. Li L#, He H#, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW., Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays., Genome Biology, 2008, 9(3):R57.

4. Zhang HY#, He H#, Chen LB, Li L, Liang MZ, Wang XF, Liu XG, He GM, Chen RS, Ma LG, and Deng XW., A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids., Molecular Plant, 2008, 1(5):720-31.

5. Wang X#, He H#, Li L, Chen R, Deng XW, Li S., NMPP: a user-customized NimbleGen microarray data processing pipeline., Bioinformatics, 2006, 22(23):2955-7.