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1.?Gui X#, Huang J#, Ruan L#, Wu Y#, Guo X#, Cao R, Zhou S, Tan F, Zhu H, Li M, Zhang G, Zhou H, Zhan L*, Liu X*, Tu S* and Shao Z*. zMAP toolset: model-based analysis of large-scale proteomic data via a variance stabilizing z-transformation. Genome Biology?2024, 25:267.

2.?Yu J#, Gui XQ#, Zou YH#, Liu Q#, Yang ZC, An JS，Guo X, Wang KH, Guo JM, Huang MN, Zhou SH, Zuo J, Chen YM, Deng L, Yuan GW, Li N, Song Y, Jia J, Zeng J, Zhao YX, Liu XM, Du XX, Liu YS, Wang P, Zhang B, Ding L, Robles AI, Rodriguez H, Zhou H*, Shao Z*, Wu LY* and Gao DM*. A proteogenomic analysis of cervical cancer reveals therapeutic and biological insights. Nature Communications?2024, 15, 10114.

3.?Ge T#, Gui X#, Xu JX#, Xia W#, Wang CH, Yang W, Huang K, Walsh C, Umen JG, Walter J, Du YR, Chen H*, Shao Z*, and Xu GL*. DNA cytosine methylation suppresses meiotic recombination at the sex-determining region. Science?Advances?2024, 10, eadr2345.

4.?Liu G#, Li Y#, Li M#, Li S, He Q, Liu S, Su Q, Chen X, Xu M, Zhang ZN*, Shao Z*, Li W*. Charting a high-resolution roadmap for regeneration of pancreatic β cells by in vivo transdifferentiation from adult acinar cells. Science Advances 2023 May 24;9(21):eadg2183.

5.?Chen HJ#, Tu SQ#*, Yuan CZ, Tian FX, Zhang Y, Sun YH, Shao Z*. HyperChIP for identifying hypervariable signals across ChIP/ATAC-seq samples. Genome Biology 2022 Feb 28;23(1):62.

6.?Liu G#, Li YN#, Zhang TJ#, Li MS#, Li S, He Q, Liu SX, Xu ML, XiaoTH, Shao Z*, Shi WY*, Li WD*. Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells. Genomics, Proteomics &?Bioinformatics 2021 Jun;19(3):408-422.

7.?Tu SQ, Li MS, Tan FX, Chen HJ, Xu J, Waxman DJ, Zhang YJ, Shao Z*. MAnorm2 for quantitatively comparing groups of ChIP-seq samples. Genome Research?2021;31:131-145.

8.?Yuan CZ#, Chen HJ#, Tu SQ#, Huang SY#, Pan YJ, Gui XQ, Kuang MY, Shen XX, Zheng Q, Zhang Y, Cheng C, Hong H, Tao XT, Peng YZ, Yao XX, Meng FL*, Ji HB*, Shao Z*, Sun YH*. A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks. Genome Biology 2021 May 17;22(1):156.

9.?Li MS#, Tu SQ#, Li ZJ, Tan FX, Liu J, Wang Q, Zhang YN, Xu J, Zhang YJ, Zhou F, Shao Z*. MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes. Cell Discovery?2019;5:40.

10.?Sun HD#, Wang JW#, Gong ZH#, Yao JY#, Wang YG, Xu J, Yuan GC, Zhang YJ*, Shao Z*. Quantitative integration of epigenomic variation and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator at gene promoters. Cell Discovery 2018;4(1):38.

11.?Li S, Li MS, Liu XJ, Yang YY, Wei YD, Chen YH, Qiu Y, Zhou TT, Feng ZH, Ma DJ, Fang J, Ying H, Wang H, Musunuru K, Shao Z*, Zhao YX*, Ding QR*. Genetic and Chemical Screenings Identify HDAC3 as a Key Regulator in Hepatic Differentiation of Human Pluripotent Stem Cells. Stem Cell Reports 2018;11(1):22-31.

12.?Liu X#, Zhang YN#, Chen Y#, Li MS#, Zhou F#, Li KL, Cao H, Ni M, Liu YX, Gu ZM, Dickerson KE, Xie SQ, Hon GC, Xuan ZY, Zhang MQ, Shao Z, Xu J*. In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell 2017 Aug 24;170(5):1028-1043.

13.?Tu SQ, Shao Z*. An introduction to computational tools for differential binding analysis with ChIP-seq data. Quantitative Biology 2017 Aug;5(3):226-235.

14.?Liu X#, Zhang YN#, Ni M#, Cao H, Signer RAJ, Li D, Li MS, Gu ZM, Hu ZP, Dickerson KE, Weinberg SE, Chandel NS, DeBerardinis RJ, Zhou F*, Shao Z*, Xu J*. Regulation of Mitochondrial Biogenesis in Erythropoiesis by mTORC1-Mediated Protein Translation. Nature Cell Biology?2017 Jun;19(6):626-638.

15.?Tu SQ, Yuan GC, Shao Z*. The PRC2-binding long non-coding RNAs in human and mouse genomes are associated with predictive sequence features. Scientific Reports 2017 Jan 31:7:41669.

16.?Huang J#, Liu X#, Li D#, Shao Z#, Cao H, Zhang YN, Trompouki E, Bowman TV, Zon LI, Yuan GC, Stuart H. Orkin SH*, Xu J*. Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. Developmental Cell 2016 Jan 11;36(1):9-23.

17.?Xu J#, Shao Z#, Li D, Xie H, Kim W, Huang J, Taylor JE, Pinello L, Glass K, Jaffe JD, Yuan GC, Orkin SH*. Developmental control of Polycomb subunit composition by GATA factors mediates a switch to non-canonical functions. Molecular Cell 2015 Jan 22;57(2):304-316.

18.?Das PP#, Shao Z#, Beyaz S, Apostolou E, O’Brien K, Atsma JM, Ljuboja D, Guo G, Kerenyi M, Woo A, Yuan GC, Onder T, Hochedlinger K, Kim J, Orkin SH*. Distinct and combinatorial functions of Jmjd2b/Kdm4b and cells identity. Molecular Cell 2014 Jan 9;53(1):32-48.

19.?Baena E, Shao Z#, Linn D#, Glass K, Hamblen M, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho F, Bronson RT, Mucci L, Loda M, Yuan GC, Orkin SH*, Li Z*. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Gene?& Development 2013 Mar 15;27(6):683-698.

20.?Xu J#, Shao Z#, Bauer DE, Glass K, Pinello L, Handel B, Hou S, Stamatoyannopoulos J, Mikkola H, Yuan GC*, Orkin SH*. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Developmental Cell 2012 Oct 16;23(4):796-811.

21.?Shao Z#, Zhang Y#, Yuan GC, Orkin SH*, Waxman DJ*. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biology?2012 Mar 16;13(3):R16.

22.?Liu Y#, Shao Z#, Yuan GC*. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics 2010 Jul;96(1):17-26.