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PUBLICATIONS

  1. Patta, I., Zand, M., Lee, L. Mishra S, Bortnick A, Lu H, Prusty A, McArdle S, Mikulski Z, Wang HY, Cheng CS, Fisch KM, Hu M, Murre C. Nuclear morphology is shaped by loop-extrusion programs. Nature 627, 196–203 (2024). https://doi.org/10.1038/s41586-024-07086-9

  2. Rickner HD*, Jiang L*, Hong R, O’Neill NK, Mojica CA, Snyder BJ, Zhang L, Shaw D, Medalla M, Wolozin B# & Cheng CS#. Single cell transcriptomic profiling of a neuron-astrocyte assembloid tauopathy model. Nature Communications 2022 Oct 21;13(1):6275. doi: 10.1038/s41467-022-34005-1.

  3. Mota A, Waxman HK, Hong R, Lagani GD, Niu S-Y, Bertherat FL, Wolfe L, Malicdan CM, Markello TC, Adams DR, Gahl WA, Cheng CS, Beffert U, Ho A. FOXR1 regulates stress response pathways and is necessary for proper brain development. PLoS Genetics 2021 Nov; 17(11):e1009854. PMID: 34723967. 

  4. Karagiannis T*, Cleary JP*, Gok B, Henderson AJ, Martin NG, Nelson EC, Yajima M, Cheng CS#. Single cell transcriptomics reveals opioid usage evokes widespread suppression of antiviral gene program. Nature Communications 2020 11, 2611 (2020).

  5. Rickner HD, Niu S-Y, Cheng CS#. An ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes. J Vis Exp. 2019 Mar 22;(145). PMID: 3095873

  6. Gate RE*, Cheng CS*#, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG,Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang SC, Durand NC, Feng T, DeJager PL, Chang HY, Aiden EL, Benoist C, Beer MA, Ye CJ#, Regev A#. Genetic determinants of co-accessible chromatin regions in activated T cells across humans. Nature genetics. 2018; 50(8):1140-1150. PMID: 29988122

  7. Quinodoz SA, Ollikainen N, Tabak B, Palla A, Schmidt JM, Detmar E, Lai MM, Shishkin AA, Bhat P, Takei Y, Trinh V, Aznauryan E, Russell P, Cheng CS, Jovanovic M, Chow A, Cai L, McDonel P, Garber M, Guttman M. Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus. Cell. 2018 Jul 26;174(3):744-757. PMCID: PMC6548320

  8. Ji Z, He L, Rotem A, Janzer A, Cheng CS, Regev A, Struhl K. Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation. Nature communications. 2018; 9(1):2068. PMID: 29802342

  9. Soto-Feliciano YM, Bartlebaugh JME, Liu Y, Sánchez-Rivera FJ, Bhutkar A, Weintraub AS, Buenrostro JD, Cheng CS, Regev A, Jacks TE, Young RA, Hemann MT. PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. Genes & development. 2017; 31(10):973-989. PMID: 28607179

  10. Fiziev P, Akdemir KC, Miller JP, Keung EZ, Samant NS, Sharma S, Natale CA, Terranova CJ, Maitituoheti M, Amin SB, Martinez-Ledesma E, Dhamdhere M, Axelrad JB, Shah A, Cheng CS, Mahadeshwar H, Seth S, Barton MC, Protopopov A, Tsai KY, Davies MA, Garcia BA, Amit I, Chin L, Ernst J, Rai K. Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression. Cell reports. 2017; 19(4):875-889. PMID: 28445736

  11. Cheng CS*, Behar MS*, Suryawanshi GW, Feldman KE, Spreafico R, Hoffmann A. Iterative Modeling Reveals Evidence of Sequential Transcriptional Control Mechanisms. Cell systems. 2017; 4(3):330-343.e5. PMID: 28237795

  12. Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng CS, Regev A, Zhang F. High-resolution interrogation of functional elements in the noncoding genome. Science. 2016; 353(6307):1545-1549. PMID: 27708104

  13. Cheng CS, Rai K, Garber M, Hollinger A, Robbins D, Anderson S, Macbeth A, Tzou A, Carneiro MO, Raychowdhury R, Russ C, Hacohen N, Gershenwald JE, Lennon N, Nusbaum C, Chin L, Regev A, Amit I. Semiconductor-based DNA sequencing of histone modification states. Nature communications. 2013; 4:2672. PMID: 24157732

  14. Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng CS, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Molecular cell. 2012; 47(5):810-22. PMID: 22940246

  15. Escoubet-Lozach L, Benner C, Kaikkonen MU, Lozach J, Heinz S, Spann NJ, Crotti A, Stender J, Ghisletti S, Reichart D, Cheng CS, Luna R, Ludka C, Sasik R, Garcia-Bassets I, Hoffmann A, Subramaniam S, Hardiman G, Rosenfeld MG, Glass CK. Mechanisms establishing TLR4-responsive activation states of inflammatory response genes. PLoS genetics. 2011; 7(12):e1002401. PMID: 22174696

  16. Cheng CS, Feldman KE, Lee J, Verma S, Huang DB, Huynh K, Chang M, Ponomarenko JV, Sun SC, Benedict CA, Ghosh G, Hoffmann A. The specificity of innate immune responses is enforced by repression of interferon response elements by NF-κB p50. Science signaling. 2011; 4(161):ra11. PMID: 21343618

  17. Ramirez-Carrozzi VR, Braas D, Bhatt DM, Cheng CS, Hong C, Doty KR, Black JC, Hoffmann A, Carey M, Smale ST. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell. 2009; 138(1):114-28. PMID: 19596239

  18. Cheng CS, Johnson TL, Hoffmann A. Epigenetic control: slow and global, nimble and local. Genes & development. 2008; 22(9):1110-4. PMID: 18451102

  19. Kwon YS, Garcia-Bassets I, Hutt KR, Cheng CS, Jin M, Liu D, Benner C, Wang D, Ye Z, Bibikova M, Fan JB, Duan L, Glass CK, Rosenfeld MG, Fu XD. Sensitive ChIP-DSL  technology reveals an extensive estrogen receptor alpha-binding program on human gene promoters. Proceedings of the National Academy of Sciences of the United States of America. 2007; 104(12):4852-7. PMID: 17360330

  20. Garcia-Bassets I, Kwon YS, Telese F, Prefontaine GG, Hutt KR, Cheng CS, Ju BG, Ohgi KA, Wang J, Escoubet-Lozach L, Rose DW, Glass CK, Fu XD, Rosenfeld MG. Histone methylation-dependent mechanisms impose ligand dependency for gene activation by nuclear receptors. Cell. 2007; 128(3):505-518. PMID: 17289570

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