{"id":94,"date":"2020-06-09T11:57:28","date_gmt":"2020-06-09T16:57:28","guid":{"rendered":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/?page_id=94"},"modified":"2024-08-27T09:40:37","modified_gmt":"2024-08-27T14:40:37","slug":"publications","status":"publish","type":"page","link":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<p>Lab members are <span style=\"text-decoration: underline\">underlined.<\/span><\/p>\n<p><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020 <\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">denotes\u00a0equal contribution \u00a0<\/span><\/span>\u00a0* denotes co-corresponding authors.<\/p>\n<p>used Xin Maizie Zhou (X. M. Zhou) for publications after 2022.<\/p>\n<h4>Preprints\/under review<\/h4>\n<p><span style=\"color: #333399\">Brain structure and activity predicting cognitive maturation in adolescence. <\/span><\/p>\n<p>J. Zhu, C. M. Garin, X.-L. Qi, A. Machado, Z. Wang, S. B. Hamed, T. R. Stanford, E. Salinas, C. T. Whitlow, A. W. Anderson,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span>, F. Calabro, B. Luna, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.08.23.608315v1\">bioRxiv<\/a>\u00a0(2024)<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">stDyer enables spatial domain clustering with dynamic graph embedding. <\/span><\/p>\n<p>K. Xu, Y. Xu, Z. Wang,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong>,<\/span><\/span><span style=\"color: #000000\"> L.\u00a0<\/span><span style=\"color: #000000\">Zhang.<\/span><\/p>\n<p><span style=\"color: #0000ff\"><em><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.05.08.593252v2\">bioRxiv<\/a>\u00a0(2024)<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Leveraging cross-source heterogeneity to improve the performance of bulk gene expression deconvolution.<\/span><\/p>\n<p>W. Shen*, C. Liu, <span style=\"text-decoration: underline\">Y. Hu<\/span>, Y. Lei, H-S. Wong, S. Wu*,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span><span style=\"color: #000000\">*<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.04.07.588458v1\">bioRxiv<\/a>\u00a0(2024)<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">CNVeil enables accurate and robust tumor subclone identification and copy number estimation from single-cell DNA sequencing data.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">W. Yuan<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020,<\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u00a0\u00a0<\/span><\/span><span style=\"text-decoration: underline\">C. Luo<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span><span style=\"text-decoration: underline\">,<\/span>\u00a0<span style=\"text-decoration: underline\">Y. Hu<\/span>, L. Zhang, Z.-H. Wen, <span style=\"text-decoration: underline\">Y. H. Liu<\/span>, X. Mallory, <span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.02.21.581409v1\">bioRxiv<\/a> (2024)<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">MaskGraphene: Advancing joint embedding, clustering, and batch correction for spatial transcriptomics using graph-based self-supervised learning.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. Hu<\/span>, <span style=\"text-decoration: underline\">Y. Li<\/span>, <span style=\"text-decoration: underline\">M. Xie<\/span>, <span style=\"text-decoration: underline\">M. Rao<\/span>, <span style=\"text-decoration: underline\">Y. H. Liu<\/span>,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2024.02.21.581387v1\">bioRxiv<\/a> (2023)<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Large indel detection in region-based phased diploid assemblies from linked-reads.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">C. Luo,<\/span> B. A. Peters,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em><a style=\"color: #0000ff\">BMC genomics\u00a0(2024) (under revision) (<\/a>accepted by ISBRA 2021) (acceptance rate: 17.6%)<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<h4>Peer-reviewed Publications<\/h4>\n<h3><strong><span style=\"color: #993300\">2024<\/span><\/strong><\/h3>\n<p><span style=\"color: #333399\">VolcanoSV enables accurate and robust structural variant calling in diploid genomes from single-molecule long read sequencing.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">C. Luo<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020,\u00a0<\/span><\/span><span style=\"text-decoration: underline\">Y. H. Liu<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span><span style=\"text-decoration: underline\">,<\/span>\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Nature Communications (2024) 15:6956.\u00a0https:\/\/doi.org\/10.1038\/s41467-024-51282-0<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Benchmarking clustering, alignment, and integration methods for spatial transcriptomics.<br \/>\n<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. Hu<\/span>,\u00a0<span style=\"text-decoration: underline\">M. Xie<\/span>,\u00a0<span style=\"text-decoration: underline\">Y. Li<\/span>,\u00a0<span style=\"text-decoration: underline\">M. Rao<\/span>, W. Shen, <span style=\"text-decoration: underline\">C. Luo<\/span>, <span style=\"text-decoration: underline\">H. Qin<\/span>, <span style=\"text-decoration: underline\">J. Baek<\/span>,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Genome Biology (2024) 25:212.\u00a0https:\/\/doi.org\/10.1186\/s13059-024-03361-0<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">SCCNAInfer: a robust and accurate tool to infer the absolute copy number on scDNA-seq data.<\/span><\/p>\n<p><span style=\"color: #000000\">L. Zhang,\u00a0<strong><span style=\"text-decoration: underline\">X. M. Zhou<\/span><\/strong>, X. Mallory.<\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Bioinformatics (2024) 40(7),\u00a0 btae454. https:\/\/doi.org\/10.1093\/bioinformatics\/btae454<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Parallel signatures of cognitive maturation in primate antisaccade performance and prefrontal activity.<\/span><\/p>\n<p><span style=\"color: #000000\">J. Zhu,\u00a0<strong><span style=\"text-decoration: underline\">X. M. Zhou<\/span><\/strong>, C. Constantinidis, E. Salinas, T. R. Stanford.<\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>iScience (2024)\u00a027(8):110488. doi: https:\/\/doi.org\/10.1016\/j.isci.2024.110488.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Tradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. H. Liu<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span>,\u00a0<span style=\"text-decoration: underline\">C. Luo<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020,<\/span><\/span> <span style=\"text-decoration: underline\">S. G. Goldin<\/span>g,\u00a0<span style=\"text-decoration: underline\">J. B. Ioffe,<\/span>\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Nature Communications (2024) 15:2447.\u00a0https:\/\/doi.org\/10.1038\/s41467-024-46614-z<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<h3><strong><span style=\"color: #993300\">2023<\/span><\/strong><\/h3>\n<p><span style=\"color: #333399\">Laminar pattern of adolescent development changes in working memory neuronal activity.<\/span><\/p>\n<p><span style=\"color: #000000\">J. Zhu, B. Hammond,\u00a0<strong><span style=\"text-decoration: underline\">X. M. Zhou<\/span><\/strong>, C. Constantinidis.<\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>J. Neurophysiology (2023)\u00a0130(4):980-989.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Editorial: predicting high-risk individuals for common diseases using multi-omics and epidemiological data, volume II.\u00a0<\/span><\/p>\n<p>W. P. Veldsman, <span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. M. Zhou<\/strong><\/span><\/span>, Y. Zhang, B. Li, L. Zhang.<\/p>\n<p><span style=\"color: #0000ff\"><em>Front. Genet. (2023) 14:1280648.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">ADEPT: autoencoder with differentially expressed genes and imputation for robust spatial transcriptomics clustering.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. Hu<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span>, Y. Zhao<span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span>, <span style=\"text-decoration: underline\">C. T. Schunk<\/span>, <span style=\"text-decoration: underline\">Y. Ma<\/span>, T. Derr*,\u00a0<span style=\"color: #000000\"><strong><span style=\"text-decoration: underline\">X. M. Zhou<\/span><\/strong>*<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>RECOMB-Seq 2023, iScience\u00a0 (2023) 26(6):106792.\u00a0<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Haplotyping-assisted diploid assembly and variant detection with linked-reads.\u00a0<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. Hu<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span>, C. Yang<span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span>, L. Zhang*,\u00a0<span style=\"color: #000000\"><strong><span style=\"text-decoration: underline\">X. Zhou<\/span><\/strong>*<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Methods Mol Biol (2023) 2590:161-182. doi: 10.1007\/978-1-0716-2819-5_1. PMID: 36335499.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<h3><strong><span style=\"color: #993300\">2022<\/span><\/strong><\/h3>\n<p><span style=\"color: #333399\">Haplotype-phasing of long-read HiFi data to enhance structural variant detection through a Skip-Gram model.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">C. Luo<\/span>, <span style=\"text-decoration: underline\">P. A. Datar<\/span>, <span style=\"text-decoration: underline\">Y. H. Liu<\/span>, <span style=\"color: #000000\"><strong><span style=\"text-decoration: underline\">X. Zhou<\/span>.<\/strong><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Las Vegas, NV, USA, 2022, pp. 2326-2333, doi: 10.1109\/BIBM55620.2022.9995293.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants.<\/span><\/p>\n<p>C. Wang, J. Zhang, <span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span>, L. Zhang.<\/p>\n<p><span style=\"color: #0000ff\"><em>Briefings in Bioinformatics\u00a0(2022) bbac552.\u00a0https:\/\/doi.org\/10.1093\/bib\/bbac552<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Automated filtering of genome-wide large deletions through an ensemble deep learning framework.\u00a0<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. Hu<\/span>, <span style=\"text-decoration: underline\">S. Mangal<\/span>, L. Zhang,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Methods (2022) 206, 77-86.\u00a0 https:\/\/doi.org\/10.1016\/j.ymeth.2022.08.001<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Graphing cell relations in spatial transcriptomics.<\/span><\/p>\n<p><span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span>.<\/p>\n<p><span style=\"color: #0000ff\"><em>Nature Computational Science (2022) 2, 354-355.\u00a0\u00a0https:\/\/doi.org\/10.1038\/s43588-022-00269-2<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Identification of cell types in multiplexed in situ images by combining protein expression and spatial information using CELESTA reveals novel spatial biology.<\/span><\/p>\n<p>W. Zhang, I. Li, N. E. Reticker-Flynn, Z. Good, S. Chang, N. Samusik, S. Saumyaa, Y. Li, <span style=\"text-decoration: underline\"><strong><span style=\"color: #000000;text-decoration: underline\">X. Zhou<\/span><\/strong><\/span>, et al.<\/p>\n<p><span style=\"color: #0000ff\"><em>Nature Methods (2022) 9, 759\u2013769.\u00a0\u00a0<\/em><em>https:\/\/doi.org\/10.1038\/s41592-022-01498-z<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Strong gamma frequency oscillations in the adolescent prefrontal cortex.<\/span><\/p>\n<p>Z. Wang, B. Singh, <span style=\"color: #000000\"><strong><span style=\"text-decoration: underline\">X. Zhou<\/span><\/strong>*<\/span>, C. Constantinidis*.\u00a0 \u00a0<span style=\"color: #000000\">(* co-corresponding and co-senior authors)<\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Journal of Neuroscience (2022) 42 (14) 2917-2929.\u00a0 https:\/\/doi.org\/10.1523\/JNEUROSCI.1604-21.2022<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<div class=\"gs_gray\"><span style=\"color: #333399\">Benchmarking challenging small variants with linked and long reads.\u00a0<\/span><\/div>\n<p>J. Wagner, N. D. Olson\u2026,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span>,\u2026, J. Zook.<\/p>\n<p><em><span style=\"color: #0000ff\">Cell Genomics (2022) 2(5), 100128.\u00a0 \u00a0https:\/\/doi.org\/10.1016\/j.xgen.2022.100128<\/span><\/em><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Neural mechanisms of working memory accuracy revealed by recurrent neural networks.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. Xie<\/span>, <span style=\"text-decoration: underline\">Y. H. Liu<\/span>, C. Constantinidis, <span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Front. Syst. Neurosci. (2022)\u00a016:760864. https:\/\/doi.org\/10.3389\/fnsys.2022.760864<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">A Bayesian factorization method to recover single-cell RNA sequencing data.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Z.-H. Wen<\/span>, <span style=\"text-decoration: underline\">J. L. Langsam<\/span>, L. Zhang, W. Shen*,\u00a0<span style=\"color: #000000\"><strong><span style=\"text-decoration: underline\">X. Zhou<\/span><\/strong>*<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Cell Reports Methods (2022) 2, 100133. https:\/\/doi.org\/10.1016\/j.crmeth.2021.100133<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<h3><strong><span style=\"color: #993300\">2021<\/span><\/strong><\/h3>\n<p><span style=\"color: #333399\">An ensemble deep learning framework to refine large deletions in linked-reads.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. Hu<\/span>, <span style=\"text-decoration: underline\">S. V. Mangal<\/span>, L. Zhang,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (2021), pp. 288-295, doi: 10.1109\/BIBM52615.2021.9669571.\u00a0 (acceptance rate: 19.3%)<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p class=\"p1\"><span style=\"color: #333399\">The epithelial and stromal immune microenvironment in gastric cancer: a comprehensive analysis reveals prognostic factors with digital cytometry.<\/span><\/p>\n<p>W. Shen, G. Wang, <span style=\"text-decoration: underline\">G. R. Cooper<\/span>, Y. Jiang,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>Cancers (Basel) (2021) 13(21):5382. https:\/\/doi.org\/10.3390\/cancers13215382<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p class=\"p1\"><span style=\"color: #333399\">Emergence of prefrontal neuron maturation properties by training recurrent neural networks in cognitive tasks.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y. H. Liu<\/span>, J. Zhu, C. Constantinidis,\u00a0<span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.<\/span><\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>iScience (2021) 24(10):103178. https:\/\/doi.org\/10.1016\/j.isci.2021.103178<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Editorial: predicting high-risk individuals for common diseases using multi-omics and epidemiological data.<\/span><\/p>\n<p>D. Chowdhury, <span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span>, B. Li, Y. Zhang, W. K. Cheung, A. Lyu, L. Zhang.<\/p>\n<p><span style=\"color: #0000ff\"><em>Front. Genet. (2021) 12:737598.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-Seq Data.<\/span><\/p>\n<p>J. Chen, C. Cheong, L. Lan, <span style=\"text-decoration: underline\"><span style=\"color: #000000;text-decoration: underline\"><strong>X. Zhou<\/strong><\/span><\/span>, J. Liu, A. Lyu, W. K. Cheung, L. Zhang.<\/p>\n<p><span style=\"color: #0000ff\"><em>Briefings in Bioinformatics (2021), 22(6):bbab325. https:\/\/doi.org\/10.1093\/bib\/bbab325<br \/>\n<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Text mining of gene-phenotype associations reveals new phenotypic profiles of autism-associated genes.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">S. Li<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span>, <span style=\"text-decoration: underline\">Z. Guo<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">\u2020<\/span><\/span>, <span style=\"text-decoration: underline\">J. B. Ioffe<\/span>, <span style=\"text-decoration: underline\">Y. Hu<\/span>, Y. Zhen*,\u00a0<span style=\"color: #000000\"><strong><span style=\"text-decoration: underline\">X. Zhou<\/span><\/strong>*<\/span><span style=\"color: #993366\"><span style=\"color: #000000\">.\u00a0 \u00a0 \u00a0 \u00a0<\/span><\/span><span style=\"color: #993366\"><span style=\"color: #000000\">(<strong>\u2020<\/strong> equal contribution)<\/span><\/span><\/p>\n<p><em><span style=\"color: #0000ff\">Scientific Reports (2021) 11(1):15269.\u00a0https:\/\/doi.org\/10.1038\/s41598-021-94742-z<\/span><\/em><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-reads.<\/span><\/p>\n<p><span style=\"text-decoration: underline\">Y.H. Liu<\/span>, <span style=\"text-decoration: underline\">G. L. Grubbs<\/span>, L. Zhang, X. Fang, D. L. Dill, A. Sidow, <span style=\"color: #000000\"><span style=\"text-decoration: underline\"><strong>X. Zhou<\/strong><\/span>.<\/span><\/p>\n<p><em><span style=\"color: #0000ff\">Bioinformatics Advances (2021) 1, vbab007. https:\/\/doi.org\/10.1093\/bioadv\/vbab007<\/span><\/em><\/p>\n<p>&nbsp;<\/p>\n<div>\n<p>&nbsp;<\/p>\n<h3><strong><span style=\"color: #993300\">2020 and earlier<\/span><\/strong><\/h3>\n<\/div>\n<p><span style=\"color: #333399\">Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked-reads.\u00a0<\/span><\/p>\n<div>\n<p><span style=\"color: #993366\"><span style=\"color: #000000\"><span style=\"text-decoration: underline\"><strong>X. Zhou<\/strong><\/span>*<\/span><\/span>, L. Zhang,\u00a0 Z. Weng, D. L. Dill, A. Sidow*.\u00a0 <span style=\"color: #000000\">\u00a0(*\u00a0co-corresponding authors)<\/span><\/p>\n<p><em><span style=\"color: #0000ff\">Nature Communications (2021) 12:1077.<\/span><\/em><\/p>\n<p>&nbsp;<\/p>\n<\/div>\n<div>\n<p class=\"p1\"><span class=\"s1\" style=\"color: #333399\">A comprehensive investigation of metagenome assembly by linked-read sequencing.<\/span><\/p>\n<p class=\"p2\"><span class=\"s1\">L. Zhang, X. Fang, H. Liao, Z. Zhang, <\/span><span class=\"s2\" style=\"color: #000000\"><b>X. Zhou<\/b><\/span><span class=\"s1\">, L. Han, Y. Chen, Q. Qiu, S. C. Li.<\/span><\/p>\n<p class=\"p3\"><span class=\"s1\" style=\"color: #0000ff\"><i>Microbiome (2020) 8(1), 1-11.<\/i><\/span><\/p>\n<\/div>\n<div>\n<p>&nbsp;<\/p>\n<\/div>\n<div class=\"gs_gray\"><span style=\"color: #333399\">A diploid assembly-based benchmark for variants in the major histocompatibility complex.\u00a0<\/span><\/div>\n<p>C. Chin, J. Wagner,\u2026,\u00a0<span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>,\u2026, J. Zook.<\/p>\n<p><em><span style=\"color: #0000ff\">Nature Communications (2020)\u00a011:4794.<\/span><\/em><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">De novo diploid genome assembly for genome-wide structural variant detection.\u00a0<\/span><\/p>\n<p>L. Zhang<span style=\"color: #000000\"><span style=\"color: #993366\"><span style=\"color: #333333\">\u2020<\/span><\/span><\/span>,\u00a0<span style=\"color: #993366\"><strong><span style=\"color: #000000\">X. Zhou<\/span><\/strong><span style=\"color: #000000\">\u2020<\/span><span style=\"color: #000000\">,<\/span><\/span> Z. Weng, A. Sidow.\u00a0 \u00a0 \u00a0 \u00a0<span style=\"color: #000000\">(<span style=\"color: #333333\"><strong>\u2020<\/strong><\/span> equal contribution)<\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>NAR Genomics and Bioinformatics (2020)<\/em>\u00a0<em>2(1)1-10.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Plasticity of persistent activity and its constraints.<\/span><\/p>\n<p>S. Li, <span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, C. Constantinidis, X.-L. Qi.<\/p>\n<p><em><span style=\"color: #0000ff\">Frontiers in Neural Circuits (2020)\u00a014: 15.<\/span><\/em><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Assessment of human diploid genome assembly with 10x Linked-Reads data.<\/span><\/p>\n<p>L. Zhang<span style=\"color: #000000\"><span style=\"color: #333333\">\u2020<\/span><\/span>,\u00a0<span style=\"color: #993366\"><strong><span style=\"color: #000000\">X. Zhou<\/span><\/strong><span style=\"color: #000000\">\u2020<\/span><\/span>, Z. Weng, A. Sidow.\u00a0 \u00a0 \u00a0<span style=\"color: #000000\">(<span style=\"color: #333333\"><strong>\u2020<\/strong><\/span> equal contribution)<\/span><\/p>\n<p><span style=\"color: #0000ff\"><em>GigaScience\u00a0(2019)<\/em>\u00a0<em>8:1-11.\u00a0<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Assessment of network module identification across complex diseases.\u00a0<\/span><\/p>\n<p>S. Choobdar et al.<\/p>\n<p><span style=\"color: #0000ff\"><em>Nature Methods\u00a0(2019)\u00a016:843-852.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\"><a style=\"color: #333399\">HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.\u00a0<\/a><\/span><\/p>\n<p><span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, S. Batzoglou, A. Sidow, L. Zhang.<\/p>\n<p><span style=\"color: #0000ff\"><a style=\"color: #0000ff\"><em>BMC genomics (2018)\u00a019 (1), 467.<\/em><\/a><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Anterior-posterior gradient of plasticity in primate prefrontal cortex.\u00a0<\/span><\/p>\n<p>M. Riley, X.-L. Qi,\u00a0<span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em>Nature Communications (2018)<\/em>\u00a0<em>9(1):3790.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Fixation target representation in prefrontal cortex during the anti-saccade task.\u00a0<\/span><\/p>\n<p><span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em>J. Neurophysiology (2017)\u00a0\u00a0<\/em><em>117:2152-2162.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Neural correlates of working memeory development in adolescent primates.\u00a0<\/span><\/p>\n<p><span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, D. Zhu, X.-L. Qi, S. H. Li, S.G. King, E. Salinas, T. R. Stanford, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em>Nature Communications (2016)<\/em>\u00a0<em>7:13423.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Behavioral response inhibition and maturation of goal representation in prefrontal cortex after puberty.<strong>\u00a0<\/strong><\/span><\/p>\n<p><span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, D. Zhu, S. G. King, C. J. Lees, A. J. Bennett, E. Salinas, T. R. Stanford, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em>Proc. Natl. Acad. Sci. USA\u00a0(2016)\u00a0<\/em><em>113(12):3353-8.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Distinct roles of the prefrontal and posterior parietal cortices in response inhibition.\u00a0<\/span><\/p>\n<p><span style=\"color: #993366\"><span style=\"color: #000000\"><strong>X. Zhou<\/strong>,<\/span><\/span> X.-L. Qi, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em>Cell Reports (2016<\/em>)\u00a0<em>14(12):2765-73.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">An evolutionary strategy for resilient cyber defense.\u00a0<\/span><\/p>\n<p>E. W. Fulp, H. D. Gage, D. J. John, M. McNiece, W. H. Turkett, and\u00a0<span style=\"color: #993366\"><strong><span style=\"color: #000000\">X. Zhou<\/span>\u00a0<\/strong><span style=\"color: #000000\">[<i>alphabetical<\/i>]<\/span><\/span>.<\/p>\n<p><span style=\"color: #0000ff\"><em>In\u00a0Proceedings of the IEEE Global Communications Conference (GLOBECOM) (2015)<\/em>.<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Age-dependent changes in prefrontal intrinsic connectivity.\u00a0<\/span><\/p>\n<p><span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span><b>,\u00a0<\/b>D. Zhu, F. Katsuki, X.-L. Qi, C. J. Lees, A. J. Bennett, E. Salinas, T. R. Stanford, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><i>Proc. Natl. Acad. Sci. USA (2014)\u00a0<\/i><em>111(10):3853-3858.<\/em><\/span><em><b><br \/>\n<\/b><\/em><\/p>\n<p>&nbsp;<\/p>\n<p><span class=\"Apple-style-span\" style=\"color: #333399\">Working memory performance and neural activity in the prefrontal cortex of peri-pubertal monkeys.\u00a0<\/span><\/p>\n<p><span class=\"Apple-style-span\"><span style=\"color: #000000\"><b><strong>X. Zhou<\/strong><\/b><\/span>, D. Zhu, X.-L. Qi, C. J. Lees, A. J. Bennett, E. Salinas, T. R. Stanford, C. Constantinidis. <\/span><\/p>\n<p><span class=\"Apple-style-span\"><span style=\"color: #0000ff\"><em>J. Neurophysiology (2013) 110:2648-2660.<\/em><\/span><b><br \/>\n<\/b><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Neurons with inverted tuning during the delay periods of working memory tasks in the dorsal prefrontal and posterior parietal cortex.\u00a0<\/span><\/p>\n<p><span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, F. Katsuki, X.-L. Qi, and C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em>J. Neurophysiology (2012) 108:31-38.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Cholinergic modulation of working memory activity in primate prefrontal cortex.\u00a0<\/span><\/p>\n<p><span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, X.-L. Qi, K. Douglas, K. Palaninathan, H. S. Kang, J. J. Buccafusco, D. T. Blake, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em>J. Neurophysiology (2011)\u00a0106:2180:8<\/em>.<\/span><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #333399\">Comparison of neural activity related to working memory in primate dorsolateral prefrontal and posterior parietal cortex.\u00a0<\/span><\/p>\n<p>X.-L. Qi, F. Katsuki, T. Meyer, J. B. Rawley,\u00a0<span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, K. Douglas, C. Constantinidis.<\/p>\n<p><span style=\"color: #0000ff\"><em>Front. Syst. Neurosci. (2010)\u00a04:12.<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<h4>Book Chapters<\/h4>\n<p><span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, E. Salinas, T. R. Stanford, C. Constantinidis. Dynamic interactions in prefrontal functional connectivity during adolescence.\u00a0<span style=\"color: #0000ff\"><em>In: Advances in Cognitive Neurodynamics (V) (2016) R. Wang and X. Pan, Editors. Springer. pp. 193-197<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n<p>X.-L. Qi,\u00a0<span style=\"color: #000000\"><strong>X. Zhou<\/strong><\/span>, C. Constantinidis. Neurophysiological mechanisms of working memory: cortical specialization &amp; plasticity.\u00a0<span style=\"color: #0000ff\"><em>In: Attention and Performance XXV (2015). Jolicoeur P., Lefebvre C. and Martinez-Trujillo J., Editors. Academic Press. pp. 171-186<\/em><\/span><\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Lab members are underlined. \u2020 denotes\u00a0equal contribution \u00a0\u00a0* denotes co-corresponding authors. used Xin Maizie Zhou (X. M. Zhou) for publications after 2022. Preprints\/under review Brain structure and activity predicting cognitive maturation in adolescence. J. Zhu, C. M. Garin, X.-L. Qi, A. Machado, Z. Wang, S. B. Hamed, T. R. Stanford, E. Salinas, C. T. Whitlow,&#8230;<\/p>\n","protected":false},"author":242,"featured_media":0,"parent":0,"menu_order":1,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"tags":[],"class_list":["post-94","page","type-page","status-publish","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/pages\/94","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/users\/242"}],"replies":[{"embeddable":true,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/comments?post=94"}],"version-history":[{"count":255,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/pages\/94\/revisions"}],"predecessor-version":[{"id":1524,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/pages\/94\/revisions\/1524"}],"wp:attachment":[{"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/media?parent=94"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/lab.dev.vanderbilt.edu\/maizie-zhou-lab\/wp-json\/wp\/v2\/tags?post=94"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}