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* : Co-first author

Kan S, Liao X, Lan L, Kong J, Wang J, Nie L, Zou J, An H, Wu Z (2024). Cytonuclear interactions and subgenome dominance shape the evolution of organelle-targeted genes in the Brassica triangle of U. Molecular Biology and Evolution. msae043

An H, Pires JC, Conant GC (2024). Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. PLoS Computational Biology. 20(1): e1011803

Huang X, Wang J, Chen S, Liu S, Li ZH, Wang ZH, Zhang Y, Wu J, Yang X, Xie Q, Li F, An H, Huang J, Li H, Liu CH, Wu X, Liu D, Yang X, Zhou G, Zhang T (2023). Rhabdovirus encoded glycoprotein induces and harnesses host antiviral autophagy for maintaining its compatible infection. Autophagy. https://doi.org/10.1080/15548627.2023.2252273

Thomas SK*, An H * , Pires JC (2023). Mangroves and Multiplications: Influence of genome duplications on salt tolerance. Molecular Ecology. https://doi.org/10.1111/mec.16796

Huang F, Chen P, Tang X, Zhong T, Yang T, Nwafor CC, Yang C, Ge X, An H, Li Z, Cahoon EB, Zhang C (2023). Genome Assembly of the Brassicaceae Diploid Orychophragmus violaceus Reveals Complex Whole Genome Duplication and Evolution of Dihydroxy Fatty Acid Metabolism. Plant Communications. https://doi.org/10.1016/j.xplc.2022.100432

Yim WC, Swain ML, Ma D, An H, Bird K, Crudie DD, Wang S, Ham HD, Luzuriaga-Neira A, Kirkwood JS, Hur M, Solomon JKQ, Harper JF, Kosma DK, Alvarez-Ponce D, Cushman JC, Edger PP, Mason AS, Pires JC, Tang H, Zhang X (2022). The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome. Plant Cell. koac249, https://doi.org/10.1093/plcell/koac249

An H, Xiao Q, Jia Z, Pires JC, Yi B (2022). Contigs scaffolding with Hi-C for plant genomes. Bio-101. e4475. DOI: 10.21769/BioProtoc.4475

Hu J, Chen B, Zhao J, Zhang F, Xie T, Xu K, Gao G, Yan G, Li H, Li L, Ji G, An H, Li H, Huang Q, Zhang M, Wu J, Song W, Zhang X, Luo Y, Pires JC, Batley J, Tian S, Wu X (2022). Genomic selection and genetic architecture of agronomic traits during modern rapeseed breeding. Nature Genetics. 10.1038/s41588-022-01055-6

Zhao Y, Cao X, Zhong W, Zhou S, Li Z, An H, Liu X, Wu Rm Bohora S, Wu Y, Liang Zm Chen J, Yang X, Zhou G, Zhang T (2022). A viral protein orchestrates rice ethylene signaling to coordinate viral infection and insect vector-mediated transmission. Molecular Plant. 15, 689–705

Kang L, Qian L, Zheng M, Chen L, Chen H, Yang L, You L, Yang B, Yan M, Gu Y, Wang T, Schiessl SV, An H, Paul B, Liu X, Lu H, Zhang D, Rao Y, Jia D, Zhou D, Xiao H, Wang Y, Xiong X, Mason SA, Pires JC, Snowdon R, Hua W, Liu Z (2021). Genomic insights into the origin, domestication and diversification of Brassica juncea. Nature Genetics. 53, 1392–1402 (2021)

Mabry ME, Turner SD, Gallagher EY, McAlvay AC, An H, Edger PP, Moore JD, Pink DAC, Teakle GR, Stevens CJ, Barker G, Labate J, Fuller DG, Alibi RG, Beissinger TM, Decker JE, Gore MA, Pires JC (2021). The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae). Molecular Biology and Evolution. msab183

McAlvay AC, Ragsdale AP, Mabry ME, Qi X, Bird K, Velasco P, An H, Pires JC, Emshwiller E (2021). Brassica rapa domestication: untangling wild and feral forms and convergence of crop morphotypes. Molecular Biology and Evolution. Volume 38, Issue 8, August 2021, Pages 3358–3372

Hao Y, Mabry ME, Edger PP, Freeling M, Zheng C, Jin L, VanBuren R, Colle M, An H, Abrahams RS, Qi X, Barry K, Daum C, Shu S, Schmutz J, Sankoff D, Barker MS, Lyons E, Pires JC, Conant GC (2021). The Contributions of the Allopolyploid Parents of the Mesopolyploid Brassiceae are Evolutionarily Distinct but Functionally Compatible. Genome Research. 10.1101/gr.270033.120

Qi XS* , An H* , Hall TE, Di CL, Blischak PD, Pires JC, Barker MS (2021). Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. New Phytologist. 10.1111/nph.17194

Züst T, Strickler SR, Powell AF, Mabry ME, An H, Mirzaei M, York T, Holland CK, Kumar P, Erb M, Petschenka G, MGoméz J, Perfectti F, Müller C, Pires JC, Mueller LA, Jande G (2020). Independent evolution of ancestral and novel defenses in a genus of toxic plants (Erysimum, Brassicaceae). eLife. 9, e51712

Mabry ME, Brose JM, Blischak PD, Sutherland B, Dismukes WT, Bottoms CA, Edger PP, Washburn JD, An H, Hall JC, McKain MR, Al I-Shehbaz, Barker MS, Schranz ME, Conant GC, Pires JC (2020). Phylogeny and Multiple Independent Whole-Genome Duplication Events in the Brassicales. American Journal of Botany. 10.1002/ajb2.1514

One Thousand Plant Transcriptomes Initiative (2019). One thousand plant transcriptomes and the phylogenomics of green plants. Nature. 574, 679–685 (Cover)

An H* , Qi XS* , Gaynor MS, Hao Y, Gebken SC, Mabry ME, McAlvay AC, Teakle G, Conant GC, MS Barker, Fu TD, Yi B, Pires JC (2019). Transcriptome and organellar sequencing highlights the complex origin and diversification of allotetraploid Brassica napus. Nature Communications. 10, 2878

Zhang T, Zhao YL, Ye JJ, Cao X, Xu CH, Chen B, An H, Jiao YT, Zhang FS, Yang X, Zhou GH (2019). Establishing CRISPR/Cas13a immune system conferring RNA virus resistance in both dicot and monocot plants. Plant Biotechnology Journal. 10.1111/pbi.13095

Wang ZX, Wu XP, Wu ZX, An H, Yi B, Wen J, Ma CZ, Shen JX, Fu TD, Tu JX (2018). Genome-wide DNA methylation comparison between rapeseed genic male sterile line and its restorer line. International journal of molecular sciences. 19(9), 2689

Li M, An H, Angelovici R, Bagaza C, Batushansky A, Clark L, Coneva V, Donoghue M, (…), Chitwood DH (2018). Topological data analysis as a morphometric method: using persistent homology to demarcate a leaf morphospace. Frontiers in Plant Science. 9, 553

Zhang T, Zheng QF, Yi X, An H, Zhao YL, Ma SQ, Zhou GH (2018). Establishing RNA virus resistance in plants by harnessing CRISPR immune system. Plant Biotechnology Journal. 10.1111/pbi.12881

Qi XS* , An H* , Ragsdale AP, Hall TE, Gutenkunst RN, Pires JC, Barker MS (2017). Genomic inferences of domestication events are corroborated by written records in Brassica rapa. Molecular Ecology. 10.1111/mec.14131 (Co-first author)

Bird KA, An H, Gazave E, Gore MA, Pires JC, Robertson LD, Labate JA (2017). Population structure and phylogenetic relationships in a diverse panel of Brassica rapa L. Frontiers in Plant Science. 8, 321

Liu Z, Yang ZH, Wang X, Li KD, An H, Liu J, Yang GS, Fu TD, Yi B, and Hong DF (2016). A mitochondria-targeted PPR protein restores Polima cytoplasmic male sterility by reducing orf224 transcripts in Brassica napus. Molecular Plant. 9 (7), 1082-1084

Liu CQ, Zhang XK, Zhang K, An H, Hu KN, Wen J, Shen JX, Ma CZ, Yi B, Tu JX, Fu TD (2015). Comparative analysis of the Brassica napus root and leaf transcript profiling in response to drought stress. International journal of molecular sciences. 16 (8), 18752-18777

An H, Yang ZH, Yi B, Wen J, Shen JX, Tu JX, Ma CZ, Fu TD (2014). Comparative transcript profiling of the fertile and sterile flower buds of pol CMS in B. napus. BMC Genomics. 15 (1), 258