Yuchen Yang @ UNC-CH

Yuchen Yang's publications

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

Preprint

  1. Taylor, L., Yang, Y., Harigaya, Y., Ulirsch, J., Sankaran, V., Hu, M., Reiner, A., Raffield, L., Wen, J., Li, Y. (2021+) Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types. bioRxiv. <link>
  1. Zhao, B., Li, T., Smith, S., ..., Yang, Y., ..., Zhu, H. (2021+) Common variants contribute to intrinsic human brain functional networks. bioRxiv. <link>
  1. Giusti-Rodríguez, P.†, Lu, L.†, Yang, Y.†, ..., Sullivan, P. (2021+) Using three-dimensional regulatory chromatin interactions from adult and fetal cortex to interpret genetic results for psychiatric disorders and cognitive traits. bioRxiv. <link>

2022

  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>

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, Accpted. <link>
  1. Yang, Y.†, Yang, Y.†, Huang, L., Broome, J., Correa, A., Reiner, A., NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Raffield, L., Li, Y. (2021) eSCAN: Scan Regulatory Regions for Aggregate Association Testing using Whole Genome Sequencing Data. Briefings in Bioinformatics, Accepted. <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. Accepted.
  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, Accepted. PMID: 34446921.
  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. Wang, L.†, Yang, Y.†, Ma, H., ...., Liu, J., Qian, L. (2021) Single Cell Dual-Omics Reveals the Transcriptomic and Epigenomic Diversity of Cardiac Non-myocytes. Cardiovascular Research, cvab134. PMID: 33839759. <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, 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>

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, G.†, Qian, H., Wilhelmsen, K., Shen, Y., Li., Y. (2020) SMNN: Batch Effect Correction for Single-cell RNA-seq data via Supervised Mutual Nearest Neighbor Detection. Briefings in Bioinformatics, bbaa097. PMID: 32591778. <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>