教育經曆:

2009 - 2011 , 博士後 , 生物信息學 , 北京大學
2004 - 2009 , 理學博士 , 生物信息學 , 中科院生物物理所
2000 - 2004 , 理學學士 , 應用數學 , 北京大學

工作經曆:

2011 - 2020，副研究員，北京大學
2020 - 至今，研究員，北京大學

      1.多組學（Multi-Omics）研究
　　生物信息學是在生命科學的研究中，利用信息技術對大量而複雜的生物數據進行存儲、檢索和分析，進而揭示生物學奧秘的學科。近年來，随着基因組序列的不斷完善和各種大通量采集數據實驗方法的開發，對數據的發掘和理解也在生物研究中起到越來越重要的作用。本課題組通過長期基因組序列變異、轉錄組、表觀遺傳組及表型組的研究，建立起完善的生物信息分析平台，将不同的組學數據整合，發掘基因在不同組學數據中的關聯，形成層級或網絡的調控關系，并通過多組學方法發現新的調控因子和調控通路。

2.雜種優勢研究
　　雜交優勢是自然界普遍存在的一種複雜生物學現象，在農業生産中獲得了廣泛的應用。但是雜交優勢的分子遺傳機理迄今尚不清楚。随着分子生物學、基因組學和生物信息學研究的深入和發展，利用系統生物學手段開展雜交優勢分子機理的研究，具有重要的科學意義和實際應用價值。基因型異質的親本其雜交子一代許多性狀上不同于雙親，這必然涉及到親本基因組在雜交遺傳背景中相互作用而引起基因表達調控發生變化。目前，我們利用高通量測序技術對具有不同優勢的雜交組合的親本和子一代不同組織在不同環境條件下進行全基因組基因差異表達分析，并進一步分析造成這種差異表達基于順式作用元件和反式調控因子DNA序列多态性的遺傳機制，以及基于DNA甲基化、組蛋白修飾、染色質重塑和非編碼RNA的表觀遺傳機制，全面探索雜交優勢的可能分子機制。

3.AI育種
　　 随着AI技術在生命科學和農業生産中的發展，育種從傳統育種、分子育種、設計育種逐漸轉為AI育種。本課題組通過發掘植物基因型、多組學、表型組、環境組學的複雜關聯，建立大模型形成育種知識結構，達到理解植物基因-環境-性狀關系，預測性狀表現，開展AI育種，創制新品種和新物種。

4.數據庫與工具（Databases and Tools）
首個西瓜T2T基因組與突變體庫(The first T2T watermelon genome and the mutant library)
http://www.watermelondb.cn

猕猴桃屬T2T基因組數據庫(T2T Genomic Database for Actinidia Species)
http://8.140.245.74:6688/

拟南芥轉光發育單細胞數據庫(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.