Publications

Selected publications

Kim S, Morgunova E, Naqvi S, Goovaerts S, Bader M, Koska M, Popov A, Luong C, Pogson A, Swigut T, Claes P, Taipale J, Wysocka J. (2024). DNA-guided transcription factor cooperativity shapes face and limb mesenchyme. Cell 187:692-711. doi: 10.1016/j.cell.2023.12.032.

Kim et al_2024_DNA-guided transcription factor cooperativity shapes face and limb mesenchyme Download

Kim S, Wysocka J. (2023). Deciphering the multi-scale, quantitative cis-regulatory code. Molecular Cell 83:373-392. doi: 10.1016/j.molcel.2022.12.032. (review)

Kim_Wysocka_2023_Deciphering the multi-scale, quantitative cis-regulatory code Download

Kim S, Dunham MJ, Shendure J. (2019). A combination of transcription factors mediates inducible interchromosomal contacts. eLife 8:e42499. doi: 10.7554/eLife.42499.

All publications

Naqvi S, Kim S*, Tabatabaee S*, Pampari A, Kundaje A, Pritchard JK, Wysocka J. Transfer learning reveals sequence determinants of the quantitative response to transcription factor dosage. Cell Genomics 5:100780. doi: 10.1016/j.xgen.2025.100780.

Naqvi S, Kim S, Hoskens H, Matthews H, Spritz RA, Klein OD, Hallgrimsson B, Swigut T, Claes P, Pritchard JK, Wysocka J. (2023). Precise modulation of transcription factor levels reveals drivers of dosage sensitivity. Nature Genetics 55:841-851. doi: 10.1038/s41588-023-01366-2.

Kim S, Shendure J. (2019). Mechanisms of interplay between transcription factors and the 3D genome. Molecular Cell 76:306-319. doi: 10.1016/j.molcel.2019.08.010. (review)

Gasperini M, Hill A, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J. (2019). A genome-wide association framework for mapping regulatory interactions in cellular genetic screens. Cell 176:377-390. doi: 10.1016/j.cell.2018.11.029.

Swygert SG, Kim S, Wu X, Fu T, Hsieh T-H, Rando OJ, Eisenman RN, Shendure J, McKnight JN, Tsukiyama T. (2019). Condensin-dependent chromatin condensation represses transcription globally during quiescence. Molecular Cell 73:533-546. doi: 10.1016/j.molcel.2018.11.020.

Kim S, Liachko I, Brickner DG, Cook K, Noble WS, Brickner JH, Shendure J, Dunham MJ. (2017). The dynamic three-dimensional organization of the diploid yeast genome. eLife 6:e23623. doi: 10.7554/eLife.23623.

Palmer AC*, Toprak E*, Baym MH, Kim S, Veres A, Bershtein S, Kishony R. (2015). Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nature Communications 6:7835. doi: 10.1038/ncomms8385.

Kim S, Lieberman TD, Kishony R. (2014). Alternating antibiotic treatments constrain evolutionary paths to multi-drug resistance. PNAS 111(40):14494-9. doi: 10.1073/pnas.1409800111.