Genomic context sensitizes regulatory elements to genetic disruption.

Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT*. Molecular Cell (2024). doi: 10.1101/2023.07.02.547201

Genomic Analysis of a Synthetic Reversed Sequence Reveals Default Chromatin States in Yeast and Mammalian Cells.

Camellato B, Brosh R, Ashe HJ, Maurano MT, and Boeke JD. Nature 628:373-380 (2024).

The genetic basis of tail-loss evolution in humans and apes.

Xia B, Zhang W, Zhao G, Zhang X, Bai J, Brosh R, Wudzinska A, Huang E, Ashe H, Ellis G, Pour M, Zhao Y, Coelho C, Zhu Y, Miller A, Dasen JS, Maurano MT, Kim SY, Boeke JD, Yanai I. Nature 626: 1042–1048 (2024).

Mouse genome rewriting and tailoring of three important disease loci.

Zhang W, Golynker I, Brosh R, Fajardo A, Zhu Y, Wudzinska AM, Ordoñez R, Ribeiro-dos-Santos AM, Carrau L, Damani-Yokota P, Yeung S, Khairallah C, Gardner AV, Chalhoub N, Huang E, Ashe H, Khanna KM, Maurano MT, Kim SY, tenOever BR, and Boeke JD. Nature 623: 423–431 (2023).

Synthetic regulatory genomics uncovers enhancer context dependence at the Sox2 locus.

Brosh R, Coelho C, Ribeiro-dos-Santos AM, Ellis G, Hogan MS, Ashe HJ, Somogyi N, Ordoñez R, Luther R, Huang E, Boeke JD, Maurano MT*. Molecular Cell 83: 1140-1152.e7 (2023).

Synthetic genomic reconstitution reveals principles of mammalian Hox cluster regulation

Pinglay S, Bulajić M, Rahe DP, Huang E, Brosh R, German S, Cadley JA, Rieber L, Easo N, Mahony S, Maurano MT, Holt LJ, Mazzoni EO, Boeke JD. Science, 377: eabk2820 (2022).

Genomic context sensitivity of insulator function

Ribeiro-dos-Santos AM, Hogan MS, Luther RD, Brosh R, Maurano MT*. Genome Research. doi: 10.1101/gr.276449.121 (2022).

An Effector Index to Predict Causal Genes at GWAS Loci

Forgetta V, Jiang L, Vulpescu NA, Hogan MS, Chen S, Morris JA, Grinek S, Benner C, McCarthy MI, Fauman E, Greenwood CM*, Maurano MT*, and Richards JB*. Human Genetics. doi: 10.1101/2020.06.28.171561 (2022).

De novo mutations in childhood cases of sudden unexplained death that disrupt intracellular Ca²⁺ regulation

Halvorsen M, Gould L, Wang X, Grant G, Moya R, Rabin R, Ackerman MJ, Tester DJ, Lin PT, Pappas JG, Maurano MT, Goldstein DB, Tsien RW, Devinsky O. PNAS 118:e2115140118 (2021).

Tissue context determines the penetrance of regulatory DNA variation

Halow J, Byron R, Hogan MS, Ordonez R, Groudine M, Bender MA, Stamatoyannopoulos JA*, and Maurano MT*. Nat. Communications. doi: 10.1038/s41467-021-23139-3 (2021).

A versatile platform for locus-scale genome rewriting and verification

Brosh R, Laurent JM, Ordoñez R, Huang E, Hogan MS, Hitchcock AM, Mitchell LA, Pinglay S, Cadley JA, Luther RD, Truong DM, Boeke JD, Maurano MT. PNAS. 118:e2023952118 (2021).

Sequencing Identifies Multiple Early Introductions of SARS-CoV-2 to the New York City Region

Maurano MT*, Ramaswami S, Westby G, Zappile P, Dimartino D, Shen G, Feng X, Ribeiro-Dos-Santos AM, Vulpescu NA, Black M, Hogan M, Marier C, Meyn P, Zhang Y, Cadley J, Ordonez R, Luther R, Huang E, Guzman E, Serrano A, Belovarac B, Gindin T, Lytle A, Pinnell J, Vougiouklakis T, Boytard L, Chen J, Lin LH, Rapkiewicz A, Raabe V, Samanovic-Golden MI, Jour G, Osman I, Aguero-Rosenfeld M, Mulligan MJ, Cotzia P, Snuderl M*, and Heguy A*. Genome Research. doi: 10.1101/gr.266676.120 (2020)

Large-scale identification of functional variants impacting human transcription factor occupancy in vivo

Maurano MT*, Haugen E, Sandstrom R, Vierstra J, Kaul R, and Stamatoyannopoulos JA*. Nature Genetics 47: 1393–1401 (2015).

Role of DNA Methylation in Modulating Transcription Factor Occupancy

Maurano MT*, Wang H, John S, Shafer A, Canfield T, Lee K, and Stamatoyannopoulos JA*. Cell Reports 12: 1184–1195 (2015).

Genomic discovery of highly potent chromatin insulators for human gene therapy

Liu M, Maurano MT, Wang H, Song CZ, Navas PA, Emery DW, Stamatoyannopoulos JA and Stamatoyannopoulos G. Nature Biotech. 33: 198-203 (2015).

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, and Stamatoyannopoulos JA. Science 337: 1190–1195 (2012)

Widespread Plasticity in CTCF Occupancy Linked to DNA Methylation

Wang H, Maurano MT, Qu H, Varley KE, Gertz J, Pauli F, Lee K, Canfield T, Weaver M, Sandstrom R, Thurman RE, Kaul R, Myers RM, and Stamatoyannopoulos JA. Genome Research 22: 1680–1688 (2012).

The Accessible Chromatin Landscape of the Human Genome

Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, Haugen E, Sheffield NC, Stergachis AB, Wang H, Vernot B, Garg K, John S, Sandstrom R, Bates D, Boatman L, Canfield TK, Diegel M, Dunn D, Ebersol AK, Frum T, Giste E, Johnson AK, Johnson EM, Kutyavin T, Lajoie B, Lee B-K, Lee K, London D, Lotakis D, Neph S, Neri F, Nguyen ED, Qu H, Reynolds AP, Roach V, Safi A, Sanchez ME, Sanyal A, Shafer A, Simon JM, Song L, Vong S, Weaver M, Yan Y, Zhang Z, Zhang Z, Lenhard B, Tewari M, Dorschner MO, Hansen RS, Navas PA, Stamatoyannopoulos G, Iyer VR, Lieb JD, Sunyaev SR, Akey JM, Sabo PJ, Kaul R, Furey TS, Dekker J, Crawford GE, and Stamatoyannopoulos JA. Nature 489: 75–82 (2012).

An Expansive Human Regulatory Lexicon Encoded in Transcription Factor Footprints

Neph S, Vierstra J, Stergachis AB, Reynolds AP, Haugen E, Vernot B, Thurman RE, John S, Sandstrom R, Johnson AK, Maurano MT, Humbert R, Rynes E, Wang H, Vong S, Lee K, Bates D, Diegel M, Roach V, Dunn D, Neri J, Schafer A, Hansen RS, Kutyavin T, Giste E, Weaver M, Canfield T, Sabo P, Zhang M, Balasundaram G, Byron R, MacCoss MJ, Akey JM, Bender MA, Groudine M, Kaul R, and Stamatoyannopoulos JA. Nature 489: 83–90 (2012).

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

Maurano MT, Wang H, Kutyavin T, and Stamatoyannopoulos JA. PLoS Genetics 8: e1002599 (2012)