Education

• 1998: BS, Hangzhou University (now, Zhejiang University), Zhejiang, China
• 2001: MS, Zhejiang University, Zhejiang, China
• 2005: Ph.D. Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
• 2005-2008:Postdoctoral fellow, National Cancer Institute, NIH, MD, USA

Biography

Appointment and Position

02/2008-05/2012: Research Scientist University of Virginia, Charlottesville, VA, USA 
06/2012-09/2022: Senior Bioinformatics scientist, National Institute of Environmental Health Sciences, NIH, NC, USA
09/2022-Present: Associate Professor, Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 

Research

1. Develop new bioinformatics algorithms and pipelines. New tools are made to design, integrate and interpret large molecular data sets, including next generation sequencing, single cell RNA-seq and spatial transcriptome data. Last couple of years, we focused on the cutting-edge computational tools to analyze single-cell genomic sequencing data and have published several papers on high profile journals (e.g., Nature Biotechnology and Brief in Bioinformatics) through collaboration. My recent research focuses on new algorithms and software to analyze spatial transcriptome/proteomics data and multi-omics single cell data, including scRNA-seq, scATAC-seq, CITE-Seq, TCR/BCR-seq, Perturb-seq and Spatial Transcriptomics.
    
2. Application of bioinformatics algorithms and pipelines. We will use in-house and public tools and pipelines to study how cellular heterogeneity (temporal and spatial) encodes the molecular structure, function, and regulation of complex biological systems. We are happy to collaborate with both basic and clinical research scientists to investigate different biology questions. We are working on more than 30 projects using single cell sequencing technology and got more than 15 papers published last three years. Recently, we are applying powerful tools in statistical inference and machine-learning (AI) to Spatial Transcriptomics and spatial proteomics data, especially pathology and disease/clinical data.

Publications

1. Yi Fang, Wei Fan, Xiaojiang Xu, Agnes Janoshazi, David Fargo, and Xiaoling Li. SIRT1 regulates cardiomyocyte alignment during maturation. J of Cell Science, 2022
2. Anchang B, Mendez-Giraldez R, Xu X, Archer TK, Chen Q, Hu G, Plevritis SK, Motsinger-Reif AA, Li JL. Visualization, benchmarking and characterization of nested single-cell heterogeneity as dynamic forest mixtures. Brief In Bioinformatics. 2022 Feb 22:bbac017. doi: 10.1093/bib/bbac017.
3. Felipe A. Olave, Felipe I. Aguayo, Luciano Román-Albasini, Wladimir A. Corrales, Juan P. Silva, Pablo I. González, Sara Lagos, María A. García, Matías Alarcón-Mardones, Paulina S. Rojas, Xiaojiang Xu, John A. Cidlowski, Esteban Aliaga, Jenny Fiedler, Chronic restraint stress produces sex-specific behavioral and molecular outcomes in the dorsal and ventral rat hippocampus, Neurobiology of Stress, 2022, https://doi.org/10.1016/j.ynstr.2022.100440
4. Fang Y, Xu X, Ding J, Yang L, Doan MT, Karmaus PWF, Snyder NW, Zhao Y, Li JL, Li X. Histone crotonylation promotes mesoendodermal commitment of human embryonic stem cells. Cell Stem Cell. 2021 Jan 8:S1934-5909(20)30593-2. doi: 10.1016/j.stem.2020.12.009.
5. Yu Wang^*, Yiyi Liang^*, Haiyan Xu^*, et. al. Xiaojiang Xu^#, Jing Xue^#, Liwei Wang^#_. Single-cell analysis of pancreatic ductal adenocarcinoma identifies a novel fibroblast subtype associated with poor prognosis but better immunotherapy response. Cell Discov 7, 36 (2021). https://doi.org/10.1038/s41421-021-00271-4
6. Wu B, Zhang S, Guo Z, Bi Y, Zhou M, Li P, Seyedsadr M, Xu X, Li JL, Markovic-Plese S, Wan YY. The TGF-β superfamily cytokine Activin-A is induced during autoimmune neuroinflammation and drives pathogenic Th17 cell differentiation. Immunity. 2021 Jan 4. pii: S1074-7613(20)30538-0. doi: 10.1016/j.immuni.2020.12.010
7. Zhang S, Takaku M, Zou L, Gu AD, Chou WC, Zhang G, Wu B, Kong Q, Thomas SY, Serody JS, Chen X, Xu X, Wade PA, Cook DN, Ting JPY, Wan YY. Reversing SKI-SMAD4-mediated suppression is essential for T(H)17 cell differentiation. Nature. 2017 Nov 2;551(7678):105-109.
8. Fan W, Tang S, Fan X, Fang Y, Xu X, Li L, Xu J, Li JL, Wang Z, Li X. SIRT1 regulates sphingolipid metabolism and neural differentiation of mouse embryonic stem cells through c-Myc- SMPDL3B. Elife. 2021 May 27;10:e67452. doi: 10.7554/eLife.67452. Epub ahead of print. PMID: 34042046.
9. Shuang Tang, Zhan Zhang, Robert H. Oakley, Wenling Li, Weijing He, Xiaojiang Xu, Ming Ji, Qing Xu, Liang Chen, Alicia S. Wellman, Qingguo Li, Leping Li, Jian-Liang Li, Xinxiang Li, John A. Cidlowski, Xiaoling Li Intestinal epithelial glucocorticoid receptor promotes chronic inflammation-associated colorectal cancer. JCI insight, Nov. 16, 2021, https://doi.org/10.1172/jci.insight.151815.
10. Busada JT, Peterson KN, Khadka S, Xu X, Oakley RH, Cook DN, Cidlowski JA. Glucocorticoids and Androgens Protect From Gastric Metaplasia by Suppressing Group 2 Innate Lymphoid Cell Activation. Gastroenterology. 2021 May 7:S0016-5085(21)00750-2. doi: 10.1053/j.gastro.2021.04.075. Epub ahead of print. PMID: 33971182.
11. Robert H. Oakley, Shannon D. Whirledge, Maria G. Petrillo, Natallia V. Riddick, Xiaojiang Xu, Sheryl S. Moy, John A. Cidlowski, Combinatorial actions of glucocorticoid and mineralocorticoid stress hormone receptors are required for preventing neurodegeneration of the mouse hippocampus, Neurobiology of Stress,2021. https://doi.org/10.1016/j.ynstr.2021.100369.
12. WanqiuChen^*, Yongmei Zhao^*, Xin Chen^*, Xiaojiang Xu^*, Zhaowei Yang^* al. Charles Wang^#. A Comprehensive Multi-Center Cross-platform Benchmarking Study of Single-cell RNA Sequencing Using Reference Samples. BioRxiv March 27^th2020. doi: https://doi.org/10.1101/2020.03.27.010249; Nature Biotechnology. 2020 Dec 21. doi: 10.1038/s41587-020-00748-9
13. Igor Shats, Jason G. Williams, Juan Liu, Leesa J. Deterding, Chaemin Lim, Xiaojiang Xu, Ethan Lee, Wei Fan, Jian-Liang Li, Marina Sokolsky, Alexander V. Kabanov, Jason W. Locasale and Xiaoling Li. Bacteria boost mammalian host NAD metabolism by engaging the deamidated biosynthesis pathway. Cell Metabolism Mar 3;31(3):564-579.e7
14. Wang, Z., Xu, X.^# scRNA-seq Profiling of Human Testes Reveals the Presence of the ACE2 Receptor, A Target for SARS-CoV-2 Infection in Spermatogonia, Leydig and Sertoli Cells. Cells. 2020, 9, 920.
15. Wu B, Zhang G, Guo Z, Wang G, Xu X, Li JL, Whitmire JK, Zheng J, Wan YY. The SKI proto-oncogene restrains the resident CD103(+) CD8(+) T cell response in viral clearance. Cell Mol Immunol. 2020 Jul 1. doi: 10.1038/s41423-020-0495-7
16. MengqiuMa,  al., Dachun Xu^#, Xiaojiang Xu^#. Single-cell Transcriptome Analysis Indicates New Potential Regulation Mechanism of ACE2 and NPs signaling among heart failure patients infected with SARS-CoV-2. MedRxiv.  April 30^th 2020. Front. Cardiovasc. Med., 2021 February 23; 8:103   https://doi.org/10.3389/fcvm.2021.628885
17. Wang Z, Xu X, Li JL, Palmer C, Maric D, Dean J. Sertoli cell-only phenotype and scRNA-seq define PRAMEF12 as a factor essential for spermatogenesis in mice. Nat Commun. 2019 Nov 15;10(1):5196
18. Grimm SA, Shimbo T, Takaku M, Thomas JW, Auerbach S, Bennett BD, Bucher JR, Burkholder AB, Day F, Du Y, Duncan CG, French JE, Foley JF, Li J, Merrick BA, Tice RR, Wang T, Xu X, NISC Comparative Sequencing Program., Bushel PR, Fargo DC, Mullikin JC, et al. DNA methylation in mice is influenced by genetics as well as sex and life experience. Nat Commun. 2019 Jan 18; 10(1):305.
19. Phillips BT, Williams JG, Atchley DT, Xu X, Li JL, Adams AL, Johnson KL, Hall TMT. Mass spectrometric identification of candidate RNA-binding proteins associated with Transition Nuclear Protein mRNA in the mouse testis. Science Report 2019 Sep 20;9(1)
20. Robert H. Oakley, Diana Cruz-Topete, Bo He, Julie F. Foley, Page H. Myers, Xiaojiang Xu, Celso E. Gomez-Sanchez, Pierre Chambon, Monte S. Willis, and John A. Cidlowski, Cardiomyocyte glucocorticoid and mineralocorticoid receptors directly and antagonistically regulate heart disease in mice. Science Signaling.  16^th Apr 2019, Vol. 12, Issue 577
21. Busada JT, Ramamoorthy S, Cain DW, Xu X, Cook DN, Cidlowski JA. Endogenous glucocorticoids prevent gastric metaplasia by suppressing spontaneous inflammation. J Clin Invest. 2019 Mar 1;129(3):1345-1358.
22. Quinn MA, McCalla A, He B, Xu X, Cidlowski JA. Silencing of maternal hepatic glucocorticoid receptor is essential for normal fetal development in mice. Biol. 2019 Mar 15; 2:104.
23. Cruz‐Topete, Oakley R.H, Carroll N, He B, Myers P.H , Xu X , Cidlowski J.A. Deletion of the Cardiomyocyte Glucocorticoid Receptor Leads to Sexually Dimorphic Changes in Cardiac Gene Expression and Progression to Heart Failure. JAHA 2019 July
24. Quinn MA, Xu X, Ronfani M, Cidlowski JA. Estrogen Deficiency Promotes Hepatic Steatosis via a Glucocorticoid Receptor-Dependent Mechanism in Mice. Cell Report. 2018 Mar 6;22(10):2690-2701.
25. Thomas SY, Whitehead GS, Takaku M, Ward JM, Xu X, Nakano K, Lyons-Cohen MR,Nakano H, Gowdy KM, Wade PA, Cook DN. MyD88-dependent dendritic and epithelial cell crosstalk orchestrates immune responses to allergens. Mucosal Immunol. 2018 May;11(3):796-810.
26. Tang S, Fang Y, Huang G, Xu X, Padilla-Banks E, Fan W, Xu Q, Sanderson SM, Foley JF, Dowdy S, McBurney MW, Fargo DC, Williams CJ, Locasale JW, Guan Z, Li X. Methionine metabolism is essential for SIRT1-regulated mouse embryonic stem cell maintenance and embryonic development. EMBO J. 2017 36(21):3175-3193.
27. MicroRNA Profiling and Bioinformatics Target Analysis in Dorsal Hippocampus of Chronically Stressed Rats: Relevance to Depression Pathophysiology. Muñoz-Llanos M, García-Pérez MA, Xu X, Tejos-Bravo M, Vidal EA, Moyano TC,Gutiérrez RA, Aguayo FI, Pacheco A, García-Rojo G, Aliaga E, Rojas PS, Cidlowski JA, Fiedler JL. Frontiers in Molecular Neuroscience. 2018 Aug 6; 11: 251
28. Olivares-Morales MJ, De La Fuente MK, Dubois-Camacho K, Parada D, Diaz-Jiménez D, Torres-Riquelme A, Xu X, Chamorro-Veloso N, Naves R, Gonzalez MJ, Quera R,Figueroa C, Cidlowski JA, Vidal RM, Hermoso MA. Glucocorticoids Impair Phagocytosis and Inflammatory Response Against Crohn's Disease-Associated Adherent-Invasive Escherichia coli. Front Immunol. 2018 May 16;9:1026.
29. Whirledge SD, Jewell CM, Barber LM, Xu X, Katen KS, Garantziotis S, Cidlowski JA. Generating diversity in human glucocorticoid signaling through a racially diverse polymorphism in the beta isoform of the glucocorticoid receptor. Lab Invest. 2017 97(11):1282-1295.
30. Wellman AS, Metukuri MR, Kazgan N, Xu X, Xu Q, Ren NSX, Czopik A, Shanahan MT,Kang A, Chen W, Azcarate-Peril MA, Gulati AS, Fargo DC, Guarente L, Li X. Intestinal Epithelial Sirtuin 1 Regulates Intestinal Inflammation During Aging in Mice by Altering the Intestinal Microbiota. Gastroenterology. 2017 153(3):772-786.
31. Tian H, Ketova T, Hardy D, Xu X, Gao X, Zijlstra A, Blobe GC. Endoglin Mediates Vascular Maturation by Promoting Vascular Smooth Muscle Cell Migration and Spreading. Arterioscler Thromb Vasc Biol. 2017 37(6):1115-1126.
32. Lu J, Xu Q, Ji M, Guo X, Xu X, Fargo DC, Li X. The phosphorylation status of T522 modulates tissue-specific functions of SIRT1 in energy metabolism in mice. EMBO Rep. 2017 18(5):841-857.
33. Ren NSX, Ji M, Tokar EJ, Busch EL, Xu X, Lewis D, Li X, Jin A, Zhang Y, Wu WKK,Huang W, Li L, Fargo DC, Keku TO, Sandler RS, Li X. Haploinsufficiency of SIRT1 Enhances Glutamine Metabolism and Promotes Cancer Development. Curr Biol. 2017 27(4):483-494.
34. Kadmiel M, Janoshazi A, Xu X, Cidlowski JA. Glucocorticoid action in human corneal epithelial cells establishes roles for corticosteroids in wound healing and barrier function of the eye. Exp Eye Res. 2016 152:10-33.
35. Cruz-Topete D, He B, Xu X, Cidlowski JA. Krüppel-like Factor 13 Is a Major Mediator of Glucocorticoid Receptor Signaling in Cardiomyocytes and Protects These Cells from DNA Damage and Death. J Biol Chem. 2016 291(37):19374-86.
36. Chen J, Xiao Y, Gai Z, Li R, Zhu Z, Bai C, Tanguay RL, Xu X, Huang C, Dong Q. Reproductive toxicity of low level bisphenol A exposures in a two-generation zebrafish assay: Evidence of male-specific effects. Aquat Toxicol. 2015 169:204-14.
37. Wamsley JJ, Kumar M, Allison DF, Clift SH, Holzknecht CM, Szymura SJ, Hoang SA,Xu X, Moskaluk CA, Jones DR, Bekiranov S, Mayo MW. Activin upregulation by NF-κB is required to maintain mesenchymal features of cancer stem-like cells in non-small cell lung cancer. Cancer Res. 2015 Jan 15;75(2):426-35.
38. Tang S, Huang G, Fan W, Chen Y, Ward JM, Xu X, Xu Q, Kang A, McBurney MW, Fargo DC, Hu G, Baumgart-Vogt E, Zhao Y, Li X. SIRT1-mediated deacetylation of CRABPII regulates cellular retinoic acid signaling and modulates embryonic stem cell differentiation. Mol Cell. 2014 55(6):843-855.
39. Cohen JN, Tewalt EF, Rouhani SJ, Buonomo EL, Bruce AN, Xu X, Bekiranov S, Fu YX, Engelhard VH. Tolerogenic properties of lymphatic endothelial cells are controlled by the lymph node microenvironment. PLoS One. 2014 9(2):e87740.
40. Cieślik M, Hoang SA, Baranova N, Chodaparambil S, Kumar M, Allison DF, Xu X, Wamsley JJ, Gray L, Jones DR, Mayo MW, Bekiranov S. Epigenetic coordination of signaling pathways during the epithelial-mesenchymal transition. Epigenetics Chromatin. 2013 6(1):28.
41. Whirledge S, Xu X, Cidlowski JA. Global gene expression analysis in human uterine epithelial cells defines new targets of glucocorticoid and estradiol antagonism. Biol Reprod. 2013;89(3):66.
42. McCullough SD, Xu X, Dent SY, Bekiranov S, Roeder RG, Grant PA. Reelin is a target of polyglutamine expanded ataxin-7 in human spinocerebellar ataxia type 7(SCA7) astrocytes. Proc Natl Acad Sci USA. 2012 109(52):21319-24.
43. Hoang SA, Xu X, Bekiranov S. Quantification of histone modification ChIP-seq enrichment for data mining and machine learning applications. BMC Res Notes. 2011 Aug 11; 4:288.
44. Xu X.^*, Hoang S, Mayo MW, Bekiranov S. Application of machine learning methods to histone methylation ChIP-Seq data reveals H4R3me2 globally represses gene expression. BMC Bioinformatics. 2010 Jul 23;
45. Pernas FG, Allen CT, Winters ME, Yan B, Friedman J, Dabir B, Saigal K, Mundinger GS, Xu X, Morris JC, Calvo KR, Van Waes C, Chen Z. Proteomic signatures of epidermal growth factor receptor and survival signal pathways correspond to gefitinib sensitivity in head and neck cancer. Clin Cancer Res. 2009 Apr 1;15(7):2361-72.
46. Xu X.^*, Zhao Y, Simon R. Gene Set Expression Comparison kit for BRB-ArrayTools. Bioinformatics. 2008 Jan 1;24(1):137-9. Epub 2007 Nov 15.
47. Xu X.^*, Wang L, Ding D. Learning module networks from genome-wide location and expression data. FEBS Lett. 2004 Dec 17;578(3):297-304.
48. Xu XJ^*, Wang LS, Ding DF. Estimating coarse gene networks from yeast gene expression time series Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai). 2003;35(8):707‐