Genome regulation, cell circuitry, and epigenomics

Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma.

Yang J, Wang C, Fu D, et al. Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma. Nature communications. 2025;16(1):8151. doi:10.1038/s41467-025-62878-5Google Scholar DOI PubMed

DNA methylation insulates genic regions from CTCF loops near nuclear speckles.

Roseman SA, Siegenfeld AP, Lee C, Lue NZ, Waterbury AL, Liau BB. DNA methylation insulates genic regions from CTCF loops near nuclear speckles. eLife. 2025;13. doi:10.7554/eLife.102930Google Scholar DOI PubMed

Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.

Kim IS, Wu J, Rahme GJ, et al. Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies. Cell Rep. 2020;33(1):108222. doi:10.1016/j.celrep.2020.108222Google Scholar DOI PubMed

Expanded encyclopaedias of DNA elements in the human and mouse genomes.

ENCODE Project Consortium, Moore JE, Purcaro MJ, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020;583(7818):699-710. doi:10.1038/s41586-020-2493-4Google Scholar DOI PubMed

Perspectives on ENCODE.

ENCODE Project Consortium, Snyder MP, Gingeras TR, et al. Perspectives on ENCODE. Nature. 2020;583(7818):693-698. doi:10.1038/s41586-020-2449-8Google Scholar DOI PubMed

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs.

Flavahan WA, Drier Y, Johnstone SE, et al. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Nature. 2019;575(7781):229-233. doi:10.1038/s41586-019-1668-3Google Scholar DOI PubMed

Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors.

Cejas P, Drier Y, Dreijerink KMA, et al. Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors. Nat Med. 2019;25(8):1260-1265. doi:10.1038/s41591-019-0493-4Google Scholar DOI PubMed

Resolving medulloblastoma cellular architecture by single-cell genomics.

Hovestadt V, Smith KS, Bihannic L, et al. Resolving medulloblastoma cellular architecture by single-cell genomics. Nature. 2019;572(7767):74-79. doi:10.1038/s41586-019-1434-6Google Scholar DOI PubMed

Single-molecule decoding of combinatorially modified nucleosomes.

Shema E, Jones D, Shoresh N, Donohue L, Ram O, Bernstein BE. Single-molecule decoding of combinatorially modified nucleosomes. Science. 2016;352(6286):717-21. doi:10.1126/science.aad7701Google Scholar DOI PubMed

An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma.

Drier Y, Cotton MJ, Williamson KE, et al. An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nat Genet. 2016;48(3):265-72. doi:10.1038/ng.3502Google Scholar DOI PubMed