Yuchen Yang Group @ SYSU

Yang Group's publications

Lab Member;     †: Co-first authors;     §: Corresponding authors.

Preprint

  1. Giusti-Rodríguez, P.†, Lu, L.†, Yang, Y.†, ..., Sullivan, P. (2022+) Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits. bioRxiv. <link>

2024

  1. Liu, Y., Xia, X., Ren, W., Hong, X., Tang, X., Pang, H., Yang, Y.§ (2024) Alternative splicing perspective to prey preference of environmentally friendly biological agent Cryptolaemus montrouzieri. BMC Genomics, 25, 967. PMID: 39407100. <link>
  1. Zhang, Y., Zhang, J., Chen, Z., Huang, Y., Liu, J., Liu, Y., Yang, Y., Jin, X., Yang, Y.§, Chen, Y.§ (2024) Comparison of organelle genomes between endangered mangrove plant Dolichandrone spathacea to terrestrial relative provides insights into its origin and adaptative evolution. Frontiers in Plant Science, 15, 1442178. PMID: 39376234. <link>
  1. Zhao, C.†, Liu, Y.†, Zhang, P., Xia, X., Yang, Y.§ (2024) Alternative splicing plays a nonredundant role in greater amberjack (Seriola dumerili) in acclimation to ambient salinity fluctuations. Marine Environmental Research, 198, 106549. PMID: 38733739. <link>
  1. Garbutt, T., Wang, Z., Ma, H., …, Yang, Y.§, Qian, L.§, Liu, J.§ (2024) Epigenetic regulation of cardiac maturation by arginine methyltransferase CARM1. Circulation, 149(19):1501–1515. PMID: 38223978. <link>
  1. Wang, Y., Hu, M., Li, S., Yang, Y., McCabe, E., Zhang, L., Withrow, A., Ting, J., Liu. R. (2024) Universal STING mimic boosts antitumour immunity via preferential activation of tumour control signalling pathways . Nature Nanotechnology, 19: 856–866. PMID: 38480836. <link></span>
  1. Yang Y.†, Alves, T.†, Miao, M.Z., Wu, Y., Li, G., Lou, J., Hasturk, H., Van Dyke, T.E., Kantarci, A.§, Wu, D.§ (2023) Single-cell transcriptomic analysis of dental pulp and periodontal ligament stem cells. Journal of Dental Research, 103: 71-80. PMID: 37982164. <link>
  1. He, M., Han, X., Qin, X., Bao, J., Li, H., Xie, Q., Yang, Y.§, Jin, X.§ (2023) Comparative chloroplast genome analyses provide new insights into phylogeny of Taraxacum and molecular markers for distinguishing rubber producing dandelions from their weedy relatives. Industrial Crops & Products, 207: 117712. <link>

2023

  1. Zhang, Y.†, Yang Y.†, He, M., …, Wang, W., Jin, X. (2024) Comparative chloroplast genome analyses provide insights into evolutionary history of Rhizophoraceae mangroves. PeerJ, 11: e16400. <link>
  1. Xie, Y.†, Wang, Q.†, Yang, Y.†, …, Liu, J., Qian, L. (2023) Translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition. Nature Cardiovascular Research, 2: 1060–1077. <link>
  1. Miao, M.Z., Su, Q.P., Cui, Y., …, Yang, Y., …, Loeser, R.F. (2023) Redox-active endosomes mediate α5β1 integrin signaling and promote chondrocyte matrix metalloproteinase production in osteoarthritis. Science Signaling. 16: eadf8299. PMID: 37906629. <link>
  1. Xia, X., Hao, L., Sun, Y., …, Zhang, Y.§, Yang, Y.§ (2023) Unravelling Chilling-stress Resistance Mechanisms in Endangered Mangrove Plant Lumnitzera littorea (Jack) Voigt. Marine Environmental Research, 192, 106210. PMID: 37788964. <link>
  1. Wang, J.†, Xia, X.†, Qin, G., …, Yang, Y.§, Qian, J.§ (2023) Somatic Embryogenesis and Plant Regeneration from Stem Explants of Pomegranate. Horticulturae, 9: 1038. <link>
  1. Yang, Y.§ (2023) Editorial: Molecular Dissection of the Genetic Basis Underlying Plant Complex Traits. Frontiers in Genetics, 14: 1256218. PMID: 37576551. <link>
  1. Liu, Y., Yang Y.§, Qin, R., Peng, Y., Huang, Y., Zhu, C., Li, G., Jiang, D., Shi, H.§ (2023) Divergent Molecular Responses of Greater Amberjack (Seriola dumerili) to Acute Salinity Stress Revealed by Comparative Transcriptome Analysis. Frontiers in Marine Science, 10: 1185015. <link>
  1. Zhang, S.†, Liu, Y.†, Wang B., Zhou J., Yang Y.§, Zhang, Y.§, Liu, Q.§ (2023) Unraveling molecular mechanisms underlying low-temperature adaptation in Laguncularia racemosa. Plant Physiology and Biochemistry, 199: 107747. PMID: 37182276. <link>
  1. Xia, X., Fan, M., Liu, Y., Chang, X., Wang, J., Qian, J., Yang Y.§ (2023) Genome-wide Alternative Polyadenylation Dynamics Underlying Plant Growth Retardant-induced Dwarfing of Pomegranate. Frontiers in Plant Science, 14: 1189456. PMID: 37223801. <link>
  1. Xu, S., Guo, Z., Feng, X., Shao, S., Yang, Y., Li, J., Zhong, C., He, Z., Shi, S. (2022) Where whole-genome duplication is most beneficial - Adaptation of mangroves to a wide salinity range between land and sea. Molecular Ecology. 32, 460-475. PMID: 34882881. <link>

2022

  1. Chen, J., Liu, W., Luo, T., …, Yang, Y., Li, Y. (2022) A comprehensive comparison on cell-type composition inference for spatial transcriptomics data. Briefings in Bioinformatics, 23: bbac245. PMID: 35753702. <link>
  1. Huang, L.†, Yang, Y.†, Li, G., Jiang, M., Wen, J., Abnousi, A., Rosen, J., Hu, M., Li, Y. (2022) A systematic evaluation of Hi-C data enhancement methods for enhancing PLAC-seq and HiChIP data. Briefings in Bioinformatics, 23: bbac145. PMID: 35488276. <link>
  1. Zhao, B., Li, T., Smith, S., ..., Yang, Y., ..., Zhu, H. (2022) Common variants contribute to intrinsic human brain functional networks. Nature Genetics, 54: 508-517. PMID: 35393594. <link>
  1. Qian, J.†, Wang, N.†, Ren, W.†, Zhang, R., Hong, X., Chen, L., Zhang, K., Shu, Y., Hu, N., Yang, Y.§ (2022) Molecular dissection unveiling dwarfing effects of plant growth retardants on pomegranate. Frontiers in Plant Science, 13: 866193. PMID: 35360308. <link>
  1. Janghorban, M.†, Yang, Y.†, Zhao, N., Hamor, C., Nguyen, T., Zhang, X., Rosen, J. (2022) Single Cell Analysis Unveils the Role of the Tumor Immune Microenvironment and Notch Signaling in Dormant Minimal Residual Disease. Cancer Research, 82: 885–899. PMID: 34965936. <link>
  1. Wen, J., Taylor, L., Sun, Q., Yang, Y., Chen, J., Harigaya, Y., Ulirsch, J., Sankaran, V., Hu, M., Reiner, A., Raffield, L., Li, Y. (2022) Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types. PLOS Genetics, 18: e1009984. PMID: 35100265. <link>
  1. Tang, X., Huang Y., Li, H., …, Yang, Y., Pang, H. (2022) Genomic insight into the scale specialization of the biological control agent Novius pumilus (Weise, 1892). BMC Genomics, 23: 90. PMID: 35100986. <link>
  1. Yang, Y., Sun, Q., Huang, L., Broome, J., Correa, A., Reiner, A., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Raffield, L.§, Yang, Y.§, Li, Y.§ (2022) eSCAN: Scan Regulatory Regions for Aggregate Association Testing using Whole Genome Sequencing Data. Briefings in Bioinformatics, 23: bbab497. PMID: 34882196. <link>
  1. Wang, H.†, Yang, Y.†, Qian, Y., Liu, J., Qian, L. (2022) Delineating Chromatin Accessibility Re-patterning at Single Cell Level during Early Stage of Direct Cardiac Reprogramming. Journal of Molecular and Cellular Cardiology, 162: 62-71. PMID: 34509499. <link>
  1. Wang, L.†, Yang, Y.†, Ma, H., ...., Liu, J., Qian, L. (2022) Single Cell Dual-Omics Reveals the Transcriptomic and Epigenomic Diversity of Cardiac Non-myocytes. Cardiovascular Research, 118: 1548–1563. PMID: 33839759. <link>

2021

  1. Rosen, J., Yang, Y., Abnousi, A., Chen, J., Song, M., Jones, I., Shen, Y., Hu, M., Li, Y. (2021) HPRep: Quantifying Reproducibility in HiChIP and PLAC-seq Datasets. Current Issues in Molecular Biology, 43: 1156-1170. PMID: 34563051. <link>
  1. Ma, H.†, Liu, Z.†, Yang, Y.†, ..., Liu, J. (2021) Coordinated transcriptome and cell state dynamics of non-myocytes in heart regeneration. EMBO reports, 22: e52901. PMID: 34523214. <link>
  1. Li, G., Luan, C., Dong, Y., …, Li, Y.§, Yang, Y.§ (2021) ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-cardiomyocyte Cells. International Journal of Molecular Sciences, 22: 8943. PMID: 34445647. <link>
  1. Yang, Y., Sun, H., Zhang, Y., …, Yang, Y., Wu, D., Yu, D. (2021) Dimensionality reduction by UMAP reinforces sample heterogeneity analysis in bulk transcriptomic data. Cell Reports, 36: 109442. PMID: 34320340. <link>
  1. Yu, M., Abnousi, A., Zhang, Y., ..., Yang, Y., ..., Ren, B., Hu, M. (2021) SnapHiC: a computational pipeline to identify chromatin loops from single cell Hi-C data. Nature Methods, 18: 1056–1059. PMID: 34446921. <link>
  1. Liu, W.†, Yang, Y.†, Abnousi, A., Zhang, Q., Kubo, N., Martin Beem, J., Li, Y., Hu, M. (2021) MUNIn: a statistical framework for identifying long-range chromatin interactions from multiple samples. Human Genetics and Genomics Advances, 2: 100036. PMID: 34485947. <link>
  1. Yang, Y., Li, G., Xie, Y., Wang, L., Lagler, T., Yang, Y., Liu, J., Qian, L., Li, Y. (2021) iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement. Briefings in Bioinformatics, 22: bbab122. PMID: 33839756. <link>
  1. Yu, C., Littleton S., Giroux, N., ..., Yang, Y., ..., Shen, X., Saban, D. (2021) Mucosal Associated Invariant T (MAIT) Cell Responses Differ by Sex in COVID-19. Med, 2: 755-772. PMID: 33870241. <link>
  1. Jiang, Y., Li, W., Lindsey-Boltz, L., Yang, Y., Li, Y., Sancar, A. (2021) Super-hotspots and -coldspots in the repair of UV-induced DNA damage in the human genome. Journal of Biological Chemistry, 296: 100581. PMID: 33771559. <link>
  1. Jiang, W., Yang, Y., Mercer-Smith, A., ..., Hingtgen S. (2021) Development of next-generation tumor-homing induced neural stem cells to enhance treatment of metastatic cancers. Science Advances, 7: eabf1526. PMID: 34108203. <link>
  1. Wang, H., Yang, Y., Liu, J., Qian, L. (2021) Direct cell reprogramming: approaches, mechanisms and progress. Nature Reviews Molecular Cell Biology, 22: 410–424. PMID: 33619373. <link>
  1. Bruinsma, R., Fajgenbaum, K., Yang, Y., del Mar Melendez-Gonzalez, M., Mohlke, K., Li, Y., Sayed, C. (2021) Assessment of Familial Risk in Patients with Hidradenitis Suppurativa. British Journal of Dermatology, 184: 753-754. PMID: 33152101. <link>
  1. Lagler, T., Abnousi, A., Hu, M., Yang, Y.§, Li, Y.§ (2021) HiC-ACT: improved chromatin interactions from Hi-C data via aggregated Cauchy test. American Journal of Human Genetics, 108: 257-268. PMID: 33545029. <link>
  1. Crowley, C., Yang, Y.§, Qiu, Y., ..., Hu, M.§, Li, Y.§ (2021) FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data. Computational and Structural Biotechnology Journal, 19: 355-362. PMID: 33489005. <link>
  1. Yang, Y.†, Li, G.†, Qian, H., Wilhelmsen, K., Shen, Y., Li., Y. (2021) SMNN: Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection. Briefings in Bioinformatics, 22: bbaa097. PMID: 32591778. <link>

2020

  1. Qian, J., Zhang, X., Yan, Y., Wang, N., Ge, W., Zhou, Q.§, Yang, Y.§ (2020) Unravelling the molecular mechanisms of Abscisic acid-mediated drought-stress alleviation in pomegranate (Punica granatum L.). Plant Physiology and Biochemistry, 157: 211-218. PMID: 33120112. <link>
  1. Wang, L., Ma, H., Huang, P., ..., Yang, Y., ..., Qian, L. (2020) Down-regulation of Beclin1 promotes direct cardiac reprogramming. Science Translational Medicine, 12(566): eaay7856. PMID: 33087505. <link>
  1. Yang, Y., Li, Y., Sancar, A., Oztas, O. (2020) The circadian clock shapes the Arabidopsis transcriptome through regulating alternative splicing and alternative polyadenylation. Journal of Biological Chemistry, 295: 7608-7619. PMID: 32303634. <link>
  1. Feng, X., Xu, S., Li, J., Yang, Y., Chen, Q., Lyu, H., Zhong, C., He, Z., Shi, S. (2020) Molecular adaptation to salinity fluctuation in tropical intertidal environments of a mangrove tree Sonneratia alba. BMC Plant Biology, 20: 178. PMID: 32321423. <link>
  1. Johnson, N., Huang, L., Li, R., ..., Yang, Y., ..., Conneely, K. (2020) Age-related DNA hydroxymethylation is enriched for gene expression and immune system processes in human peripheral blood. Epigenetics, 15: 294-306. PMID: 31506003. <link>
  1. Huh, R.†, Yang, Y.†, Jiang, Y., Shen, Y., Li, Y. (2020) SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble. Nucleic Acids Research, 48: 86-95. PMID: 31777938. <link>

2019

  1. Li, G., Yang, Y., Van Buren, E., Li, Y. (2019) Dropout Imputation and Batch Effect Correction for Single-Cell RNA-seq Data. Journal of Bio-X Research, 2: 169-177. <link>
  1. Giusti-Rodriguez, P., Lu, L, Yang, Y., ..., Sullivan, P. (2019) SA72A HIGH-RESOLUTION MAP OF CHROMATIN INTERACTIONS IN ADULT AND FETAL CORTEX. European Neuropsychopharmacology, 29: S1227. <link>
  1. Yang, Y., Huh, R., Culpepper, H., Lin, Y., Love, M., Li, Y. (2019) SAFE-clustering: Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data. Bioinformatics, 35: 1269-1277. PMID: 30202935. <link>
  1. Zhou Q.†, Yang Y.†, Yang Z. (2019) Molecular dissection of cadmium-responsive transcriptome profile in a low-cadmium-accumulating cultivar of Brassica parachinensis. Ecotoxicology and Environmental Safety, 176: 85-94. PMID: 30921700. <link>
  1. Juric I., Yu M., Abnousi A., ..., Yang Y., ..., Bing Ren B., Hu M. (2019) MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments. PLOS Computational Biology, 15(4): e1006982. PMID: 30986246. <link>

2018

  1. Yang, Y., Guo, W., Shen, X., Li, J., Yang, S., Chen, S., He, Z., Zhou R., Shi, S. (2018) Identification and characterization of evolutionarily conserved alternative splicing events in a mangrove genus Sonneratia. Scientific Reports, 8: 4425. PMID: 29535339. <link>
  1. Guo, Z., Li, X., He, Z., Yang, Y., Wang, W., Zhong, C., Greenberg, A.J., Wu, C-I, Duke N.C., Shi, S. (2018) Extremely low genetic diversity across mangrove taxa reflects past sea level changes and hints at poor future responses. Global Change Biology, 24: 1741–1748. PMID: 29087007. <link>

2017

  1. Yang, Y., Li, J., Yang, S., Li, X., Fang, L., Zhong, C., Duke, N., Zhou, R., Shi, S. (2017) Effects of Pleistocene sea-level fluctuations on mangrove population dynamics: A lesson from Sonneratia alba. BMC Evolutionary Biology, 17: 22. PMID: 28100168. <link>
  1. Li, J., Yang, Y., Yang, S., Zhang, Z., Chen, S., Zhong, C., Zhou, R., Shi, S. (2017) Comparative transcriptome analyses of a mangrove tree Sonneratia caseolaris and its non-mangrove relatives, Trapa bispinosa and Duabanga grandiflora. Marine Genomics, 31: 13-15. PMID: 27810366. <link>
  1. Zhou, Q., Yang, Y., Shen, C., He, C., Yuan, J., Yang, Z. (2017) Comparative analysis between low- and high-cadmium-accumulating cultivars of Brassica parachinensis to identify difference of cadmium-induced microRNA and their targets. Plant and Soil, 420: 223-237. <link>
  1. Du, Y., Martin, J., McGee, J., Yang, Y., Liu, E., Sun, Y., Geihs, M., Kong, X., Zhou, E., Li, Y., Huang, J. (2017) A SNP panel and online tool for checking genotype concordance through comparing QR codes. PLoS ONE, 12(9): e0182438. PMID: 28926565. <link>

2016

  1. Yang, Y., Duke, N.C., Peng, F., Li, J., Yang, S., Zhong, C., Zhou, R., Shi, S. (2016) Ancient geographical barriers drive differentiation among Sonneratia caseolaris. populations and recent divergence from S. lanceolata. Frontiers in Plant Science, 7: 1618. PMID: 27833634. <link>
  1. Li, J., Yang, Y., Chen, Q., ..., Zhou R., Shi. S. (2016) Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses. Scientific Reports, 6: 29486. PMID: 27380895. <link>
  1. Fang, L., Yang, Y., Guo, W., Li, J., Zhong, C., Huang, Y., Zhou, R., Shi, S. (2016) De novo assembly of the transcriptome of Aegiceras corniculatum, a mangrove species in the Indo-West Pacific region. Marine Genomics, 28: 49–52. PMID: 27296448. <link>
  1. Li, X., Duke, N., Yang, Y., Huang, L., Zhu, Y., Zhang, Z., Zhou, R., Zhong, C., Huang, Y., Shi, S. (2016) Re-Evaluation of Phylogenetic Relationships among Species of the Mangrove Genus Avicennia from Indo-West Pacific Based on Multilocus Analyses. PLoS ONE, 11(10): e0164453. PMID: 27716800. <link>
  1. Wang, S., Chen, Y., Yang, Y., Wu, W., Liu, Y., Fan, Q., Zhou, R. (2016) Phylogenetic relationships and natural hybridization in Triadica inferred from nuclear and chloroplast DNA analyses. Biochemical Systematics and Ecology, 64: 142-148. <link>
  1. Zhang, Z., He, Z., Xu, S., Li, X., Guo, W., Yang, Y., Zhong, C., Zhou, R., Shi, S. (2016) Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum. Scientific Reports, 6: 35634. PMID: 27782130. <link>
  1. Shi, L., Li, N., Wang, S., Zhou, Y., Huang, W., Yang, Y., Ma, Y., Zhou, R. (2016) Molecular Evidence for the Hybrid Origin of Ilex dabieshanensis (Aquifoliaceae). PLoS ONE, 11(1): e0147825. PMID: 26808531. <link>

2015

  1. Yang Y., Yang, S., Li, J., Deng, Y., Zhang, Z., Xu, S., Guo, W., Zhong, C., Zhou, R., Shi, S. (2015) Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones. BMC Genomics, 16: 605. PMID: 26272068. <link>
  1. Yang, Y., Yang, S., Li, J., Li, X., Zhong, C., Huang, Y., Zhou, R., Shi, S. (2015) De novo assembly of the transcriptomes of two yellow mangroves, Ceriops tagal and C. zippeliana , and one of their terrestrial relatives, Pellacalyx yunnanensis. Marine Genomics, 23: 33-36. PMID: 25899405. <link>
  1. Yang, Y., Yang, S., Fang, L., Li, J., Zhong, C., Zhou, R., Shi, S. (2015) Phylogenetic position of Sonneratia griffithii based on sequences of the nuclear ribosomal internal transcribed spacer and 13 nuclear genes. Journal of Systematics and Evolution, 53(1): 47-52. <link>

2014

  1. 杨宇晨, 李建芳, 郭无瑕, 钟才荣, 周仁超, 施苏华. (2014) 植物物种形成的模式与机制. 生命科学, 26: 138-143.

2011

  1. 钟才荣, 李诗川, 杨宇晨, 张影, 林作武. (2011) 红树植物拉关木的引种效果调查研究. 福建林业科技, 38: 96-99.
  1. 杨宇晨, 施苏华. (2011) 亟待保护的中国红树林. 生命世界, 265: 84-87.