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Hehuang Xie, Ph.D. - Publications

Affiliations: 
2003 University of Iowa, Iowa City, IA 
Area:
Genetics, Molecular Biology, Obstetrics and Gynecology
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46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Wang Z, Heid B, He J, Xie H, Reilly CM, Dai R, Ahmed SA. Egr2 Deletion in Autoimmune-Prone C57BL6/lpr Mice Suppresses the Expression of Methylation-Sensitive Dlk1-Dio3 Cluster MicroRNAs. Immunohorizons. 7: 898-907. PMID 38153351 DOI: 10.4049/immunohorizons.2300111  0.302
2022 Xu X, Johnson Z, Wang A, Padget RL, Smyth JW, Xie H. Folate regulates RNA mC modification and translation in neural stem cells. Bmc Biology. 20: 261. PMID 36424632 DOI: 10.1186/s12915-022-01467-0  0.301
2020 Wang Q, Yu G, Ming X, Xia W, Xu X, Zhang Y, Zhang W, Li Y, Huang C, Xie H, Zhu B, Xie W. Imprecise DNMT1 activity coupled with neighbor-guided correction enables robust yet flexible epigenetic inheritance. Nature Genetics. PMID 32690947 DOI: 10.1038/S41588-020-0661-Y  0.353
2019 Yin L, Luo Y, Xu X, Wen S, Wu X, Lu X, Xie H. Virtual methylome dissection facilitated by single-cell analyses. Epigenetics & Chromatin. 12: 66. PMID 31711526 DOI: 10.1186/S13072-019-0310-9  0.364
2019 Xu X, Wei X, Xie H. Advances in methods and software for RNA cytosine methylation analysis. Genomics. PMID 31678155 DOI: 10.1016/J.Ygeno.2019.10.017  0.363
2019 Sun Z, Xu X, He J, Murray A, Sun MA, Wei X, Wang X, McCoig E, Xie E, Jiang X, Li L, Zhu J, Chen J, Morozov A, Pickrell AM, ... ... Xie H, et al. EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity. Nature Communications. 10: 3892. PMID 31467272 DOI: 10.1038/S41467-019-11905-3  0.44
2019 Hazy A, Bochicchio L, Oliver A, Xie E, Geng S, Brickler T, Xie H, Li L, Allen IC, Theus MH. Divergent age-dependent peripheral immune transcriptomic profile following traumatic brain injury. Scientific Reports. 9: 8564. PMID 31189983 DOI: 10.1038/S41598-019-45089-Z  0.306
2019 Banerjee S, Wei X, Xie H. Recursive Motif Analyses Identify Brain Epigenetic Transcription Regulatory Modules. Computational and Structural Biotechnology Journal. 17: 507-515. PMID 31011409 DOI: 10.1016/J.Csbj.2019.04.003  0.522
2019 He J, Xu X, Monavarfeshani A, Banerjee S, Fox MA, Xie H. Retinal-input-induced epigenetic dynamics in the developing mouse dorsal lateral geniculate nucleus. Epigenetics & Chromatin. 12: 13. PMID 30764861 DOI: 10.1186/S13072-019-0257-X  0.416
2018 Banerjee S, Zhu H, Tang M, Feng WC, Wu X, Xie H. Identifying Transcriptional Regulatory Modules Among Different Chromatin States in Mouse Neural Stem Cells. Frontiers in Genetics. 9: 731. PMID 30697231 DOI: 10.3389/Fgene.2018.00731  0.36
2018 Ma S, de la Fuente Revenga M, Sun Z, Sun C, Murphy TW, Xie H, González-Maeso J, Lu C. Cell-type-specific brain methylomes profiled via ultralow-input microfluidics. Nature Biomedical Engineering. 2: 183-194. PMID 29963329 DOI: 10.1038/S41551-018-0204-3  0.487
2018 Luo Y, He J, Xu X, Sun MA, Wu X, Lu X, Xie H. Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells. Plos Computational Biology. 14: e1006034. PMID 29561833 DOI: 10.1371/Journal.Pcbi.1006034  0.548
2016 Sun MA, Sun Z, Wu X, Rajaram V, Keimig D, Lim J, Zhu H, Xie H. Mammalian Brain Development is Accompanied by a Dramatic Increase in Bipolar DNA Methylation. Scientific Reports. 6: 32298. PMID 27585862 DOI: 10.1038/Srep32298  0.548
2016 von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, et al. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Molecular Cell. 62: 983. PMID 27315559 DOI: 10.1016/j.molcel.2016.06.005  0.382
2016 von Meyenn F, Iurlaro M, Habibi E, Liu NQ, Salehzadeh-Yazdi A, Santos F, Petrini E, Milagre I, Yu M, Xie Z, Kroeze LI, Nesterova TB, Jansen JH, Xie H, He C, et al. Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells. Molecular Cell. PMID 27237052 DOI: 10.1016/J.Molcel.2016.04.025  0.496
2016 Sharif J, Endo TA, Nakayama M, Karimi MM, Shimada M, Katsuyama K, Goyal P, Brind'Amour J, Sun MA, Sun Z, Ishikura T, Mizutani-Koseki Y, Ohara O, Shinkai Y, Nakanishi M, ... Xie H, et al. Activation of Endogenous Retroviruses in Dnmt1(-/-) ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA. Cell Stem Cell. PMID 27151458 DOI: 10.1016/J.Stem.2016.03.013  0.445
2016 Tran H, Wu X, Tithi S, Sun MA, Xie H, Zhang L. A Bayesian Assignment Method for Ambiguous Bisulfite Short Reads. Plos One. 11: e0151826. PMID 27011215 DOI: 10.1371/Journal.Pone.0151826  0.472
2015 Sun MA, Velmurugan KR, Keimig D, Xie H. HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis. Advances in Bioinformatics. 2015: 760423. PMID 26798339 DOI: 10.1155/2015/760423  0.409
2015 Porter J, Sun MA, Xie H, Zhang L. Investigating bisulfite short-read mapping failure with hairpin bisulfite sequencing data. Bmc Genomics. 16: S2. PMID 26576456 DOI: 10.1186/1471-2164-16-S11-S2  0.439
2015 He J, Sun MA, Wang Z, Wang Q, Li Q, Xie H. Characterization and machine learning prediction of allele-specific DNA methylation. Genomics. PMID 26407641 DOI: 10.1016/J.Ygeno.2015.09.007  0.45
2015 Wu X, Sun MA, Zhu H, Xie H. Nonparametric Bayesian clustering to detect bipolar methylated genomic loci. Bmc Bioinformatics. 16: 11. PMID 25592753 DOI: 10.1186/S12859-014-0439-2  0.538
2015 Xie H. Personalized Epigenetics: Analysis and Interpretation of DNA Methylation Variation Personalized Epigenetics. 123-150. DOI: 10.1016/B978-0-12-420135-4.00005-X  0.464
2014 Shao X, Zhang C, Sun MA, Lu X, Xie H. Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming. Bmc Genomics. 15: 978. PMID 25404570 DOI: 10.1186/1471-2164-15-978  0.538
2014 Luo Y, Lu X, Xie H. Dynamic Alu methylation during normal development, aging, and tumorigenesis. Biomed Research International. 2014: 784706. PMID 25243180 DOI: 10.1155/2014/784706  0.538
2014 McErlean P, Favoreto S, Costa FF, Shen J, Quraishi J, Biyasheva A, Cooper JJ, Scholtens DM, Vanin EF, de Bonaldo MF, Xie H, Soares MB, Avila PC. Human rhinovirus infection causes different DNA methylation changes in nasal epithelial cells from healthy and asthmatic subjects. Bmc Medical Genomics. 7: 37. PMID 24947756 DOI: 10.1186/1755-8794-7-37  0.615
2014 Tran H, Porter J, Sun MA, Xie H, Zhang L. Objective and comprehensive evaluation of bisulfite short read mapping tools. Advances in Bioinformatics. 2014: 472045. PMID 24839440 DOI: 10.1155/2014/472045  0.325
2014 Zhao L, Sun MA, Li Z, Bai X, Yu M, Wang M, Liang L, Shao X, Arnovitz S, Wang Q, He C, Lu X, Chen J, Xie H. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation. Genome Research. 24: 1296-307. PMID 24835587 DOI: 10.1101/Gr.163147.113  0.562
2013 He J, Sun X, Shao X, Liang L, Xie H. DMEAS: DNA methylation entropy analysis software. Bioinformatics (Oxford, England). 29: 2044-5. PMID 23749987 DOI: 10.1093/Bioinformatics/Btt332  0.543
2013 Xie H, Wang M, de Andrade A, Bonaldo MF, Galat V, Arndt K, Rajaram V, Goldman S, Tomita T, Soares MB. Genome-wide quantitative assessment of variation in DNA methylation patterns Nucleic Acids Research. 41: 7184-7184. DOI: 10.1093/Nar/Gkt209  0.49
2013 McErlean P, Favoreto S, Costa F, Shen J, Biyasheva A, Bonaldo MdF, Scholtens D, Xie H, Soares MB, Avila PC. DNA Methylation Profiling in Asthmatic and Non Asthmatic Nasal Epithelial Cells During Respiratory Virus Infection Journal of Allergy and Clinical Immunology. 131: AB136. DOI: 10.1016/J.JACI.2012.12.1151  0.589
2012 Zhang X, Wallace AD, Du P, Lin S, Baccarelli AA, Jiang H, Jafari N, Zheng Y, Xie H, Soares MB, Kibbe WA, Hou L. Genome-wide study of DNA methylation alterations in response to diazinon exposure in vitro. Environmental Toxicology and Pharmacology. 34: 959-68. PMID 22964155 DOI: 10.1016/J.Etap.2012.07.012  0.702
2012 Hoxha E, Lambers E, Xie H, De Andrade A, Krishnamurthy P, Wasserstrom JA, Ramirez V, Thal M, Verma SK, Soares MB, Kishore R. Histone deacetylase 1 deficiency impairs differentiation and electrophysiological properties of cardiomyocytes derived from induced pluripotent cells. Stem Cells (Dayton, Ohio). 30: 2412-22. PMID 22915496 DOI: 10.1002/Stem.1209  0.598
2012 Zhang X, Wallace AD, Du P, Kibbe WA, Jafari N, Xie H, Lin S, Baccarelli A, Soares MB, Hou L. DNA methylation alterations in response to pesticide exposure in vitro. Environmental and Molecular Mutagenesis. 53: 542-9. PMID 22847954 DOI: 10.1002/Em.21718  0.709
2012 Wang M, Xie H, Shrestha S, Sredni S, Morgan GA, Pachman LM. Methylation alterations of WT1 and homeobox genes in inflamed muscle biopsy samples from patients with untreated juvenile dermatomyositis suggest self-renewal capacity. Arthritis and Rheumatism. 64: 3478-85. PMID 22674142 DOI: 10.1002/Art.34573  0.354
2012 Wang D, Liu X, Zhou Y, Xie H, Hong X, Tsai HJ, Wang G, Liu R, Wang X. Individual variation and longitudinal pattern of genome-wide DNA methylation from birth to the first two years of life. Epigenetics. 7: 594-605. PMID 22522910 DOI: 10.4161/Epi.20117  0.443
2011 de Andrade A, Wang M, Bonaldo MF, Xie H, Soares MB. Genetic and epigenetic variations contributed by Alu retrotransposition. Bmc Genomics. 12: 617. PMID 22185517 DOI: 10.1186/1471-2164-12-617  0.559
2011 Xie H, Wang M, de Andrade A, Bonaldo Mde F, Galat V, Arndt K, Rajaram V, Goldman S, Tomita T, Soares MB. Genome-wide quantitative assessment of variation in DNA methylation patterns. Nucleic Acids Research. 39: 4099-108. PMID 21278160 DOI: 10.1093/Nar/Gkr017  0.704
2011 Wang M, Xie H, Stellpflug W, Rajaram V, Bonaldo Mde F, Goldman S, Tomita T, Soares MB. BTECH: a platform to integrate genomic, transcriptomic and epigenomic alterations in brain tumors. Neuroinformatics. 9: 59-67. PMID 21210251 DOI: 10.1007/S12021-010-9091-9  0.608
2010 Hamm CA, Stevens JW, Xie H, Vanin EF, Morcuende JA, Abdulkawy H, Seftor EA, Sredni ST, Bischof JM, Wang D, Malchenko S, Bonaldo Mde F, Casavant TL, Hendrix MJ, Soares MB. Microenvironment alters epigenetic and gene expression profiles in Swarm rat chondrosarcoma tumors. Bmc Cancer. 10: 471. PMID 20809981 DOI: 10.1186/1471-2407-10-471  0.715
2010 Xie H, Wang M, Bonaldo Mde F, Rajaram V, Stellpflug W, Smith C, Arndt K, Goldman S, Tomita T, Soares MB. Epigenomic analysis of Alu repeats in human ependymomas. Proceedings of the National Academy of Sciences of the United States of America. 107: 6952-7. PMID 20351280 DOI: 10.1073/Pnas.0913836107  0.695
2009 Hamm CA, Xie H, Costa FF, Vanin EF, Seftor EA, Sredni ST, Bischof J, Wang D, Bonaldo MF, Hendrix MJ, Soares MB. Global demethylation of rat chondrosarcoma cells after treatment with 5-aza-2'-deoxycytidine results in increased tumorigenicity. Plos One. 4: e8340. PMID 20019818 DOI: 10.1371/Journal.Pone.0008340  0.751
2009 Yadav AK, Renfrow JJ, Scholtens DM, Xie H, Duran GE, Bredel C, Vogel H, Chandler JP, Chakravarti A, Robe PA, Das S, Scheck AC, Kessler JA, Soares MB, Sikic BI, et al. Monosomy of chromosome 10 associated with dysregulation of epidermal growth factor signaling in glioblastomas. Jama. 302: 276-89. PMID 19602687 DOI: 10.1001/Jama.2009.1022  0.59
2009 Xie H, Wang M, Bonaldo Mde F, Smith C, Rajaram V, Goldman S, Tomita T, Soares MB. High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum. Nucleic Acids Research. 37: 4331-40. PMID 19458156 DOI: 10.1093/Nar/Gkp393  0.68
2009 Xie H, Wang M, Bischof J, Bonaldo Mde F, Soares MB. SNP-based prediction of the human germ cell methylation landscape. Genomics. 93: 434-40. PMID 19442638 DOI: 10.1016/J.Ygeno.2009.01.005  0.65
2006 Ma S, Kosorok MR, Huang J, Xie H, Manzella L, Soares MB. Robust semiparametric microarray normalization and significance analysis. Biometrics. 62: 555-61. PMID 16918920 DOI: 10.1111/J.1541-0420.2005.00452.X  0.561
2005 Wang D, Huang J, Xie H, Manzella L, Soares MB. A robust two-way semi-linear model for normalization of cDNA microarray data. Bmc Bioinformatics. 6: 14. PMID 15663789 DOI: 10.1186/1471-2105-6-14  0.549
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