Highlights-Immunomics lab

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Wang L, Zhang W, Lin L, Li X, Saksena NK, Wu J, Wang S, Joyce JG, Zhang X, Yang H, Wang J, Wang IM, Liu X.

A Comprehensive Analysis of the T and B Lymphocytes Repertoire Shaped by HIV Vaccines. Front Immunol. 2018 Sep 26;9:2194.

DOI: 10.3389/fimmu.2018.02194.

Liu X, Wu J.

History, applications, and challenges of immune repertoire research. Cell Biol Toxicol. 2018 Dec;34(6):441-457.

DOI: 10.1007/s10565-018-9426-0.

Wei Z, Qiang F, Changxi W, Xiaojing Z, Yuanping D, Liya L, Jinghua W, Longfei F, Kai Y, Xiaoying X, Hanshi X, Yi Z, Xuemei L, Ursula Huber Schoenauer, Andreas Stadlmayr, Nitin K. Saksena, Herbert Tilg, Christian Datz and Xiao L.

Characterization of BCR repertoire in the intestinal mucosa and of tumor-infiltrating lymphocytes in colorectal adenoma and carcinoma. J Immunol May 1, 2017, 198 (9) 3719-3728.

DOI: https://doi.org/10.4049/jimmunol.1602039

Wang T, Wang C, Wu J, He C, Zhang W, Liu J, Zhang R, Lv Y, Li Y, Zeng X, Cao H, Zhang X, Xu X, Huang C, Wang L, Liu X.

The Different T-cell Receptor Repertoires in Breast Cancer Tumors, Draining Lymph Nodes, and Adjacent Tissues. Cancer Immunol Res. 2017 Feb;5(2):148-156.

DOI: 10.1158/2326-6066.CIR-16-0107.

Wu J, Jia S, Wang C, Zhang W, Liu S, Zeng X, Mai H, Yuan X, Du Y, Wang X, Hong X, Li X, Wen F, Xu X, Pan J, Li C, Liu X.

Minimal Residual Disease Detection and Evolved IGHClones Analysis in Acute B Lymphoblastic Leukemia Using IGH Deep Sequencing. Front Immunol. 2016 Oct 4;7:403.

DOI: 10.3389/fimmu.2016.00403.

Zhang W, Wang IM, Wang C, Lin L, Chai X, Wu J, Bett AJ, Dhanasekaran G, Casimiro DR, Liu X.

IMPre: An Accurate and Efficient Software for Prediction of T- and B-Cell Receptor Germline Genes and Alleles from Rearranged Repertoire Data. Front Immunol. 2016 Nov 4;7:457.

DOI: 10.3389/fimmu.2016.00457.

Fu L, Li X, Zhang W, Wang C, Wu J, Yang H, Wang J, Liu X.

A comprehensive profiling of T- and B-lymphocyte receptor repertoires from a Chinese-origin rhesus macaque by high-throughput sequencing. PLoS One. 2017 Aug 16;12(8):e0182733.

DOI: 10.1371/journal.pone.0182733.

Zhao LH, Liu X, Yan HX, Li WY, Zeng X, Yang Y, Zhao J, Liu SP, Zhuang XH, Lin C, Qin CJ, Zhao Y, Pan ZY, Huang G, Liu H, Zhang J, Wang RY, Yang Y, Wen W, Lv GS, Zhang HL, Wu H, Huang S, Wang MD, Tang L, Cao HZ, Wang L, Lee TL, Jiang H, Tan YX, Yuan SX, Hou GJ, Tao QF, Xu QG, Zhang XQ, Wu MC, Xu X, Wang J, Yang HM, Zhou WP, Wang HY.

Genomic and oncogenic preference of HBV integration in hepatocellular carcinoma. Nat Commun. 2016 Oct 5;7:12992.

DOI: 1038/ncomms12992.

Su Z, Zhang J, Kumar C, Molony C, Lu H, Chen R, Stone DJ, Ling F, Liu X.

Species specific exome probes reveal new insights in positively selected genes in nonhuman primates. Sci Rep. 2016 Sep 23;6:33876.

DOI: 10.1038/srep33876.

Li X, Duan X, Yang K, Zhang W, Zhang C, Fu L, Ren Z, Wang C, Wu J, Lu R, Ye Y, He M, Nie C, Yang N, Wang J, Yang H, Liu X, Tan W.

Comparative Analysis of Immune Repertoires between Bactrian Camel's Conventional and Heavy-Chain Antibodies. PLoS One. 2016 Sep 2;11(9):e0161801.

DOI: 10.1371/journal.pone.0161801.

Liu X, Zhang W, Zeng X, Zhang R, Du Y, Hong X, Cao H, Su Z, Wang C, Wu J, Nie C, Xu X, Kristiansen K.

Systematic Comparative Evaluation of Methods for Investigating the TCRβ Repertoire. PLoS One. 2016 Mar 28;11(3):e0152464.

DOI: 10.1371/journal.pone.0152464.

Liu X, Li Z, Su Z, Zhang J, Li H, Xie J, Xu H, Jiang T, Luo L, Zhang R, Zeng X, Xu H, Huang Y, Mou L, Hu J, Qian W, Zeng Y, Zhang X, Xiong C, Yang H, Kristiansen K, Cai Z, Wang J, Gui Y.

Novel Y-chromosomal microdeletions associated with non-obstructive azoospermia uncovered by high throughput sequencing of sequence-tagged sites (STSs). Sci Rep. 2016 Feb 24;6:21831.

DOI: 10.1038/srep21831.

Zhang W, Du Y, Su Z, Wang C, Zeng X, Zhang R, Hong X, Nie C, Wu J, Cao H, Xu X, Liu X.

IMonitor: A Robust Pipeline for TCR and BCR Repertoire Analysis. Genetics. 2015 Oct;201(2):459-72.

DOI: 10.1534/genetics.115.176735.

Zhuang X, Li Y, Cao H, Wang T, Chen J, Liu J, Lin L, Ye R, Li X, Liu S, Li W, Lv Y, Zhang J, He C, Xu X, Wang Z, Huang C, Liu X, Wang L.

Case report of a Li-Fraumeni syndrome-like phenotype with a de novo mutation in CHEK2. Medicine (Baltimore). 2016 Jul;95(29):e4251.

DOI: 10.1097/MD.0000000000004251.

Sung WK, Zheng H, Li S, Chen R, Liu X, Li Y, Lee NP, Lee WH, Ariyaratne PN, Tennakoon C, Mulawadi FH, Wong KF, Liu AM, Poon RT, Fan ST, Chan KL, Gong Z, Hu Y, Lin Z, Wang G, Zhang Q, Barber TD, Chou WC, Aggarwal A, Hao K, Zhou W, Zhang C, Hardwick J, Buser C, Xu J, Kan Z, Dai H, Mao M, Reinhard C, Wang J, Luk JM.

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet. 2012 May 27;44(7):765-9.

DOI: 10.1038/ng.2295.

Kan Z, Zheng H, Liu X, Li S, Barber TD, Gong Z, Gao H, Hao K, Willard MD, Xu J, Hauptschein R, Rejto PA, Fernandez J, Wang G, Zhang Q, Wang B, Chen R, Wang J, Lee NP, Zhou W, Lin Z, Peng Z, Yi K, Chen S, Li L, Fan X, Yang J, Ye R, Ju J, Wang K, Estrella H, Deng S, Wei P, Qiu M, Wulur IH, Liu J, Ehsani ME, Zhang C, Loboda A, Sung WK, Aggarwal A, Poon RT, Fan ST, Wang J, Hardwick J, Reinhard C, Dai H, Li Y, Luk JM, Mao M.

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Res. 2013 Sep;23(9):1422-33.

DOI: 10.1101/gr.154492.113.

Hong JY, Liu X, Mao M, Li M, Choi DI, Kang SW, Lee J, La Choi Y.

Genetic aberrations in imatinib-resistant dermatofibrosarcoma protuberans revealed by whole genome sequencing. PLoS One. 2013 Jul 29;8(7):e69752.

DOI: 10.1371/journal.pone.0069752.

Wang CX, Xu HS, Li XF, Lu J, Hu XX, Liu X.

The complete mitochondrial genome of the white-tailed tropicbird, Phaethon lepturus. Mitochondrial DNA A DNA Mapp Seq Anal. 2016 Nov;27(6):42594260.

DOI: 10.3109/19401736.2015.1053076. Epub 2016 May 20.

Nelson MR, Wegmann D, Ehm MG, Kessner D, St Jean P, Verzilli C, Shen J, Tang Z, Bacanu SA, Fraser D, Warren L, Aponte J, Zawistowski M, Liu X, Zhang H, Zhang Y, Li J, Li Y, Li L, Woollard P, Topp S, Hall MD, Nangle K, Wang J, Abecasis G, Cardon LR, Z?llner S, Whittaker JC, Chissoe SL, Novembre J, Mooser V.

An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science. 2012 Jul 6;337(6090):100-4.

DOI: 10.1126/science.1217876. Epub 2012 May 17.

Zhou HW, Li DF, Tam NF, Jiang XT, Zhang H, Sheng HF, Qin J, Liu X, Zou F.

BIPES, a cost-effective high-throughput method for assessing microbial diversity. ISME J. 2011 Apr;5(4):741-9.

DOI: 10.1038/ismej.2010.160. Epub 2010 Oct 21.

Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, Nie X, Wu H, Zhao M, Cao H, Zou J, Shan Y, Li S, Yang Q, Asan, Ni P, Tian G, Xu J, Liu X, Jiang T, Wu R, Zhou G, Tang M, Qin J, Wang T, Feng S, Li G, Huasang, Luosang J, Wang W, Chen F, Wang Y, Zheng X, Li Z, Bianba Z, Yang G, Wang X, Tang S, Gao G, Chen Y, Luo Z, Gusang L, Cao Z, Zhang Q, Ouyang W, Ren X, Liang H, Zheng H, Huang Y, Li J, Bolund L, Kristiansen K, Li Y, Zhang Y, Zhang X, Li R, Li S, Yang H, Nielsen R, Wang J, Wang J.

Sequencing of 50 human exomes reveals adaptation to high altitude. Science. 2010 Jul 2;329(5987):75-8.

DOI: 10.1126/science.1190371.

Li Y, Vinckenbosch N, Tian G, Huerta-Sanchez E, Jiang T, Jiang H, Albrechtsen A, Andersen G, Cao H, Korneliussen T, Grarup N, Guo Y, Hellman I, Jin X, Li Q, Liu J, Liu X, Spars? T, Tang M, Wu H, Wu R, Yu C, Zheng H, Astrup A, Bolund L, Holmkvist J, J?rgensen T, Kristiansen K, Schmitz O, Schwartz TW, Zhang X, Li R, Yang H, Wang J, Hansen T, Pedersen O, Nielsen R, Wang J.

Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet. 2010 Nov;42(11):969-72.

DOI: 10.1038/ng.680. Epub 2010 Oct 3.

Guo G, Gui Y, Gao S, Tang A, Hu X, Huang Y, Jia W, Li Z, He M, Sun L, Song P, Sun X, Zhao X, Yang S, Liang C, Wan S, Zhou F, Chen C, Zhu J, Li X, Jian M, Zhou L, Ye R, Huang P, Chen J, Jiang T, Liu X, Wang Y, Zou J, Jiang Z, Wu R, Wu S, Fan F, Zhang Z, Liu L, Yang R, Liu X, Wu H, Yin W, Zhao X, Liu Y, Peng H, Jiang B, Feng Q, Li C, Xie J, Lu J, Kristiansen K, Li Y, Zhang X, Li S, Wang J, Yang H, Cai Z, Wang J.

Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet. 2011 Dec 4;44(1):17-9.

DOI: 10.1038/ng.1014.

Li R, Fan W, Tian G, Zhu H, He L, Cai J, Huang Q, Cai Q, Li B, Bai Y, Zhang Z, Zhang Y, Wang W, Li J, Wei F, Li H, Jian M, Li J, Zhang Z, Nielsen R, Li D, Gu W, Yang Z, Xuan Z, Ryder OA, Leung FC, Zhou Y, Cao J, Sun X, Fu Y, Fang X, Guo X, Wang B, Hou R, Shen F, Mu B, Ni P, Lin R, Qian W, Wang G, Yu C, Nie W, Wang J, Wu Z, Liang H, Min J, Wu Q, Cheng S, Ruan J, Wang M, Shi Z, Wen M, Liu B, Ren X, Zheng H, Dong D, Cook K, Shan G, Zhang H, Kosiol C, Xie X, Lu Z, Zheng H, Li Y, Steiner CC, Lam TT, Lin S, Zhang Q, Li G, Tian J, Gong T, Liu H, Zhang D, Fang L, Ye C, Zhang J, Hu W, Xu A, Ren Y, Zhang G, Bruford MW, Li Q, Ma L, Guo Y, An N, Hu Y, Zheng Y, Shi Y, Li Z, Liu Q, Chen Y, Zhao J, Qu N, Zhao S, Tian F, Wang X, Wang H, Xu L, Liu X, Vinar T, Wang Y, Lam TW, Yiu SM, Liu S, Zhang H, Li D, Huang Y, Wang X, Yang G, Jiang Z, Wang J, Qin N, Li L, Li J, Bolund L, Kristiansen K, Wong GK, Olson M, Zhang X, Li S, Yang H, Wang J, Wang J.

The sequence and de novo assembly of the giant panda genome. Nature. 2010 Jan 21;463(7279):311-7.

DOI: 10.1038/nature08696. Epub 2009 Dec 13. Erratum in: Nature. 2010 Feb 25;463(7284):1106.

Xu X, Hou Y, Yin X, Bao L, Tang A, Song L, Li F, Tsang S, Wu K, Wu H, He W, Zeng L, Xing M, Wu R, Jiang H, Liu X, Cao D, Guo G, Hu X, Gui Y, Li Z, Xie W, Sun X, Shi M, Cai Z, Wang B, Zhong M, Li J, Lu Z, Gu N, Zhang X, Goodman L, Bolund L, Wang J, Yang H, Kristiansen K, Dean M, Li Y, Wang J.

Single-cell exome sequencing reveals single-nucleotide mutation characteristics of a kidney tumor. Cell. 2012 Mar 2;148(5):886-95.

DOI: 10.1016/j.cell.2012.02.025.

Shao H, Bellos E, Yin H, Liu X, Zou J, Li Y, Wang J, Coin LJ.

A population model for genotyping indels from next-generation sequence data. Nucleic Acids Res. 2013 Feb 1;41(3):e46.

DOI: 10.1093/nar/gks1143. Epub 2012 Dec 5.

Li W, Zeng X, Lee NP, Liu X, Chen S, Guo B, Yi S, Zhuang X, Chen F, Wang G, Poon RT, Fan ST, Mao M, Li Y, Li S, Wang J, Jianwang, Xu X, Jiang H, Zhang X.

HIVID: an efficient method to detect HBV integration using low coverage sequencing. Genomics. 2013 Oct;102(4):338-44.

DOI: 10.1016/j.ygeno.2013.07.002.

Xu Z, Chen M, Ren Z, Zhang N, Xu H, Liu X, Tian G, Song L, Yang H.

Deep sequencing identifies regulated small RNAs in Dugesia japonica. Mol Biol Rep. 2013 Jun;40(6):4075-81.

DOI: 10.1007/s11033-012-2485-z. Epub 2013 Jan 12.

Asan, Xu Y, Jiang H, Tyler-Smith C, Xue Y, Jiang T, Wang J, Wu M, Liu X, Tian G, Wang J, Wang J, Yang H, Zhang X.

Comprehensive comparison of three commercial human whole-exome capture platforms. Genome Biol. 2011 Sep 28;12(9):R95.

DOI: 10.1186/gb-2011-12-9-r95.

Li Z, Xia J, Jiang L, Tan Y, An Y, Zhu X, Ruan J, Chen Z, Zhen H, Ma Y, Jie Z, Xiao L, Yang H, Wang J, Kristiansen K, Xu X, Jin L, Nie C, Krutmann J, Liu X, Wang J.

Characterization of the human skin resistome and identification of two microbiota cutotypes. Microbiome. 2021 Feb 17;9(1):47.

DOI: 10.1186/s40168-020-00995-7.

Liu X, Xu H, Xu H, Geng Q, Mak WH, Ling F, Su Z, Yang F, Zhang T, Chen J, Yang H, Wang J, Zhang X, Xu X, Jia H, Zhang Z, Liu X, Zhong S.

New genetic variants associated with major adverse cardiovascular events in patients with acute coronary syndromes and treated with clopidogrel and aspirin. Pharmacogenomics J. 2021 Dec;21(6):664-672.

DOI: 10.1038/s41397-021-00245-5.

Wu J, Wang X, Lin L, Li X, Liu S, Zhang W, Luo L, Wan Z, Fang M, Zhao Y, Wang X, Mai H, Yuan X, Wen F, Li C, Liu X.

Developing an Unbiased Multiplex PCR System to Enrich the TRB Repertoire Toward Accurate Detection in Leukemia. Front Immunol. 2020 Aug 6;11:1631.

DOI: 10.3389/fimmu.2020.01631.

Jiang X, Wang S, Zhou C, Wu J, Jiao Y, Lin L, Lu X, Yang B, Zhang W, Xiao X, Li Y, Wu X, Wang X, Chen H, Zhao L, Fei Y, Yang H, Zhang W, Zhang F, Chen H, Zhang J, Li B, Yang H, Wang J, Liu X, Zhang X.

Comprehensive TCR repertoire analysis of CD4+ T-cell subsets in rheumatoid arthritis. J Autoimmun. 2020 May;109:102432.

DOI: 10.1016/j.jaut.2020.102432.

Gang Y, Yi Z, Feng X Fuxiang Z, Ziyun W, Jingwan W, Xie W, Kai G, Lixia C, Xinyang L, Chen C, Yashu K, Xiu Q, Huanming Y, Jian W, Bing S, Lei C, Wei Z, Yong H, Xun X, Yinyan H, Andy Tsun, Xiao L, Bin L.

Single-cell RNA-seq unveils critical regulators of human FOXP3+ regulatory T cell stability, Science Bulletin, 2020, 65(3）: 1114-1124.

DOI:

Liu X, Zhang W, Zhao M, Fu L, Liu L, Wu J, Luo S, Wang L, Wang Z, Lin L, Liu Y, Wang S, Yang Y, Luo L, Jiang J, Wang X, Tan Y, Li T, Zhu B, Zhao Y, Gao X, Wan Z, Huang C, Fang M, Li Q, Peng H, Liao X, Chen J, Li F, Ling G, Zhao H, Luo H, Xiang Z, Liao J, Liu Y, Yin H, Long H, Wu H, Yang H, Wang J, Lu Q.

T cell receptor β repertoires as novel diagnostic markers for systemic lupus erythematosus and rheumatoid arthritis. Ann Rheum Dis. 2019 Aug;78(8):1070-1078.

DOI: 10.1136/annrheumdis-2019-215442.

Gao K, Chen L, Zhang Y, Zhao Y, Wan Z, Wu J, Lin L, Kuang Y, Lu J, Zhang X, Tian L, Liu X, Qiu X.

Germline-Encoded TCR-MHC Contacts Promote TCR V Gene Bias in Umbilical Cord Blood T Cell Repertoire. Front Immunol. 2019 Aug 30;10:2064.

DOI: 10.3389/fimmu.2019.02064.

Cao K, Wu J, Li X, Xie H, Tang C, Zhao X, Wang S, Chen L, Zhang W, An Y, Li X, Lin L, Chai R, Fang M, Yue Y, Wang X, Ding Y, Zhou L, Zhao Q, Yang H, Wang J, He S, Liu X.

eceptor repertoire data provides new evidence for hygiene hypothesis of allergic diseases. Allergy. 2020 Mar;75(3):681-683.

DOI: 10.1111/all.14014.

Zhang W, Wang L, Liu K, Wei X, Yang K, Du W, Wang S, Guo N, Ma C, Luo L, Wu J, Lin L, Yang F, Gao F, Wang X, Li T, Zhang R, Saksena NK, Yang H, Wang J, Fang L, Hou Y, Xu X, Liu X.

PIRD: Pan Immune Repertoire Database. Bioinformatics. 2020 Feb 1;36(3):897-903.

DOI: 10.1093/bioinformatics/btz614.

Zhao Y, Li X, Zhao W, Wang J, Yu J, Wan Z, Gao K, Yi G, Wang X, Fan B, Wu Q, Chen B, Xie F, Wu J, Zhang W, Chen F, Yang H, Wang J, Xu X, Li B, Liu S, Hou Y, Liu X.

Single-cell transcriptomic landscape of nucleated cells in umbilical cord blood. Gigascience. 2019 May 1;8(5):giz047.

DOI: 1093/gigascience/giz047.

Zhang W, Li X, Wang L, Deng J, Lin L, Tian L, Wu J, Tang C, Yang H, Wang J, Qiu P, Fu TM, Saksena NK, Wang IM, Liu X.

Identification of Variable and Joining Germline Genes and Alleles for Rhesus Macaque from B Cell Receptor Repertoires. J Immunol. 2019 Mar 1;202(5):1612-1622.

DOI: 10.4049/jimmunol.1800342.

Wang D, Li Y, Zhong H, Ding Q, Lin Y, Tang S, Zong Y, Wang Q, Zhang X, Yang H, Wang R, Liu X.

Alterations in the human gut microbiome associated with Helicobacter pylori infection. FEBS Open Bio. 2019 Sep;9(9):1552-1560.

DOI: 10.1002/2211-5463.12694.

Huang C, Li X, Wu J, Zhang W, Sun S, Lin L, Wang X, Li H, Wu X, Zhang P, Xu G, Wang H, Liu H, Liu Y, Chen D, Zhuo L, Li W, Yang H, Wang J, Wang L, Liu X.

The landscape and diagnostic potential of T and B cell repertoire in Immunoglobulin A Nephropathy. J Autoimmun. 2019 Feb;97:100-107.

DOI: 10.1016/j.jaut.2018.10.018.