1. Tu SQ, Li MS, Tan FX, Chen HJ, Xu J, Waxman DJ, Zhang Y, Shao S*. MAnorm2 for quantitatively comparing groups of ChIP-seq samples. Genome Research 2021, 31:131-145.
    Link to Genome Research

  2. Wang YT#, Dai GY#, Gu ZL#, Liu GP#, Tang K, Pan YH, Chen YJ, Lin X, Wu N, Chen HS, S, Qiu S, Sun HD, Li Q, Xu C, Mao YN, Zhang YW, Khaitovich P, Wang YL, Liu QX, Han JD, Shao Z, Wei G, Xu C, Jing NH and Li HP*. Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchy. Cell Research 2020, 30 (5), 408-420.

  3. Li KL#, Zhang YN#, Liu X#, Liu Y#, Gu ZM, Cao H, Dickerson KE, Chen MY, Chen WN, Shao Z, Ni M and Xu J*. Noncoding variants connect enhancer dysregulation with nuclear receptor signaling in hematopoietic malignancies. Cancer Discovery 2020, 10 (5), 724-745.

  4. Li MS#, Tu SQ#, Li ZJ, Tan FX, Liu J, Wang Q, Zhang YN, Xu J, Zhang Y, Zhou F and Shao Z*. MAP: model-based analysis of proteomic data to detect proteins with significant abundance changes. Cell Discovery 2019, 5, 40.
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  5. Yu D#, Dong L#, Yan F#, Mu H#, Tang B#, Yang X, Zeng T, Zhou Q, Gao F, Wang Z, Hao Z, Kang H, Zheng Y, Huang H, Wei Y, Pan W, Xu Y, Zhu J, Zhao S, Wang C, Wang P, Dai L, Li MS, Lan L, Wang Y, Chen H, Li YX, Fu YX, Shao Z, Bao Y, Zhao F, Chen LN, Zhang GQ*, Zhao WM* and Li HP*. eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses. National Science Review 2019, 6 (5), 867-869.

  6. Wang X#, Kang JY#, Wei L#, Yang X#, Sun HD, Yang S, Lu L, Yan M, Bai M, Chen Y, Long J, Li N, Li D, Huang J, Lei M, Shao S, Yuan W*, Zuo E*, Lu K*, Liu MF* and Li J*. PHF7 is a novel histone H2A E3 ligase prior to histone-to-protamine exchange during spermiogenesis. Development 2019, 146 (13), dev175547.

  7. Liu Y#, Fu Y#, Wang Q, Li MS, Zhou Z, Dabbagh D, Fu C, Zhang H, Li S, Zhang T, Gong J, Kong X, Zhai W, Su J, Sun J, Zhang Y, Yu XF, Shao Z, Zhou F*, Wu Y* and Tan X*. Proteomic profiling of HIV-1 infection of human CD4+ T cells identifies PSGL-1 as an HIV restriction factor. Nature Microbiology 2019, 4, 813C825.

  8. 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.

  9. Sun HD#, Wang JW#, Gong ZH#, Yao JY#, Wang YG, Xu J, Yuan GC, Zhang Y* and 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.
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  10. Vo LT, Kinney MA, Liu X, Zhang Y, Barragan J, Sousa PM, Jha DK, Han A, Cesana M, Shao Z, North TE, Orkin SH, Doulatov S, Xu J, Daley GQ*. Regulation of embryonic haematopoietic multipotency by EZH1. Nature 2018, 553, 506-510.

  11. 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, 170(5), 1028-1043.
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  12. Li T#, Zhao H#, Han X#, Yao JY, Zhang L, Guo Y, Shao Z, Jin Y*, Lai D*. The spontaneous differentiation and chromosome loss in iPSCs of human trisomy 18 syndrome. Cell Death & Disease 2017, 8: e3149.

  13. Xia M, Chen K, Yao X, Xu YC, Yao JY, Yan J, Shao Z, Wang G*. Mediator MED23 Links Pigmentation and DNA Repair through the Transcription Factor MITF. Cell Reports 2017, 20(8), 1794-1804.

  14. Tu SQ and Shao Z*. An introduction to computational tools for differential binding analysis with ChIP-seq data. Quantitative Biology 2017, 5(3), 226-235.
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  15. 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, 19, 626-638.
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  16. Anso E#, Weinberg SE#, Diebold LP, Thompson BJ, Malinge S, Schumacker PT, Liu X, Zhang YN, Shao Z, Steadman M, Marsh KM, Xu J, Crispino JD and Chandel NS*. The mitochondrial respiratory chain is essential for haematopoietic stem cell function. Nature Cell Biology 2017, 19, 614-625.

  17. 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, 7, 41669.
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  18. Zhao J, Sun Y, Huang Y, Song F, Huang ZS, Bao YF, Zuo J, Saffen D, Shao Z, Liu W*, and Wang YB*. Functional analysis reveals that RBM10 mutations contribute to lung adenocarcinoma pathogenesis by deregulating splicing. Scientific Reports 2017, 7, 40488.

  19. Chen Y, Breeze CE, Zhen S, Beck S, Teschendorff AE*. Tissue-independent and tissue-specific patterns of DNA methylation alteration in cancer. Epigenetics & Chromatin 2016, 9 (1), 10.

  20. 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, 36, 9-23.
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  21. Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH*. PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Reports 2015, 12 (9), 1456-1470.
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  22. 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, 57 (2), 304-316.
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  23. Maroz A, Stachorski L, Emmrich S, Reinhardt K, Xu J, Shao Z, Käbler S, Dertmann T, HITZLER J, Roberts I, Vyas P, Juban G, Hennig C, Hansen G, Li Z, Orkin SH, Reinhardt D, and Klusmann J*. GATA1s induces hyperproliferation of eosinophil precursors in Down syndrome transient leukemia. Leukemia 2014, 28, 1259-1270.
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  24. 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 Jmjd2c/Kdm4c in mouse embryonic stem cells identity. Molecular Cell 2014, 53 (1), 32-48.
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  25. Bauer DE, Kamran SC, Lessard S, Xu J, Fujiwara Y, Lin C, Shao Z, Canver MC, Smith EC, Pinello L, Sabo PJ, Vierstra J, Voit RA, Yuan GC, Porteus MH, Stamatoyannopoulos JA, Lettre G, Orkin SH*. An adult-stage erythroid enhancer of BCL11A determines fetal hemoglobin level. Science 2013, 342 (6155), 253-257.
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  26. Kerenyi M, Shao Z, Hsu Y, Guo G, Luc S, O'Brien K, Fujiwara Y, Peng C, Nguyen M and Orkin SH*. Histone demethylase Lsd1 is required to repress hematopoietic stem and progenitor cell signatures in blood cells to permit terminal differentiation. eLife 2013, 2:e00633.
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  27. 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* and Li Z*. ETV1 directs androgen metabolism and confers aggressive prostate cancer in targeted mice and patients. Gene & Development 2013, 27 (6), 683-698.
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  28. Xu J#, Shao Z#, Bauer DE, Glass K, Pinello L, Handel B, Hou S, Stamatoyannopoulos J, Mikkola H, Yuan GC* and Orkin SH*. Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. Developmental Cell 2012, 23 (4):796-811.
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  29. Shao Z#, Zhang Y#, Yuan GC, Orkin SH* and Waxman DJ*. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets. Genome Biology 2012, 13 R16.
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  30. Xu J, Peng C, Sankaran VJ, Shao Z, Esrick E, Chong B, Ippolito G, Fujiwara Y, Ebert B, Tucker P, Orkin SH*. Correction of sickle cell disease in adult mice by interference with fetal hemoglobin silencing. Science 2011, 334 993-996.
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  31. Rao S, Shao Z, Roumiantsev S, McDonald L, Yuan GC and Orkin SH*. The Role of Sall4 isoforms in Murine Embryonic Stem Cell Pluripotency. Molecular Cell Biology 2010, 30 (22):5364-80.
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  32. Liu Y#, Shao Z#, and Yuan GC*. Prediction of Polycomb target genes in mouse embryonic stem cells. Genomics 2010, 96: 17-26.
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  33. Shao Z ,and Zhou H*. Dynamics-driven evolution to structural heterogeneity in complex networks. Physica A 2008, 388, 523-528.
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  34. Shao Z ,and Zhou H*. Optimal transportation network with concave cost functions: Loop analysis and algorithms. Physics Review E 2007, 75, 066112.
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