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Genome regulation, cell circuitry, and epigenomics

Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.
Kim ISoo, 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.2020.108222.
Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Moore JE, Purcaro MJ, Pratt HE, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020;583(7818):699-710. doi:10.1038/s41586-020-2493-4.
Perspectives on ENCODE.
Snyder MP, Gingeras TR, Moore JE, et al. Perspectives on ENCODE. Nature. 2020;583(7818):693-698. doi:10.1038/s41586-020-2449-8.
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/s41586-019-1668-3.
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/s41586-019-1434-6.
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/s41591-019-0493-4.
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.aad7701.
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.3502.
Insulator dysfunction and oncogene activation in IDH mutant gliomas.
Flavahan WA, Drier Y, Liau BB, et al. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2016;529(7584):110-4. doi:10.1038/nature16490.
A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes.
van Galen P, Viny AD, Ram O, et al. A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Mol Cell. 2016;61(1):170-80. doi:10.1016/j.molcel.2015.11.003.
Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.
Rotem A, Ram O, Shoresh N, et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015;33(11):1165-72. doi:10.1038/nbt.3383.
Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma.
Ryan RJH, Drier Y, Whitton H, et al. Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discov. 2015;5(10):1058-71. doi:10.1158/2159-8290.CD-15-0370.
FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.
Claussnitzer M, Dankel SN, Kim K-H, et al. FTO Obesity Variant Circuitry and Adipocyte Browning in Humans. N Engl J Med. 2015;373(10):895-907. doi:10.1056/NEJMoa1502214.
Dissecting neural differentiation regulatory networks through epigenetic footprinting.
Ziller MJ, Edri R, Yaffe Y, et al. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015;518(7539):355-9. doi:10.1038/nature13990.
Genetic and epigenetic fine mapping of causal autoimmune disease variants.
Farh KKai-How, Marson A, Zhu J, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015;518(7539):337-43. doi:10.1038/nature13835.
Integrative analysis of 111 reference human epigenomes.
Kundaje A, Meuleman W, Ernst J, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317-30. doi:10.1038/nature14248.
Transcription factor binding dynamics during human ES cell differentiation.
Tsankov AM, Gu H, Akopian V, et al. Transcription factor binding dynamics during human ES cell differentiation. Nature. 2015;518(7539):344-9. doi:10.1038/nature14233.
Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis.
Kang S, Tsai LT, Zhou Y, et al. Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis. Nat Cell Biol. 2015;17(1):44-56. doi:10.1038/ncb3080.
Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells.
Suvà ML, Rheinbay E, Gillespie SM, et al. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell. 2014;157(3):580-94. doi:10.1016/j.cell.2014.02.030.
An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia.
Knoechel B, Roderick JE, Williamson KE, et al. An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nat Genet. 2014;46(4):364-70. doi:10.1038/ng.2913.
Locus-specific editing of histone modifications at endogenous enhancers.
Mendenhall EM, Williamson KE, Reyon D, et al. Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol. 2013;31(12):1133-6. doi:10.1038/nbt.2701.
Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.
Gifford CA, Ziller MJ, Gu H, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013;153(5):1149-63. doi:10.1016/j.cell.2013.04.037.
An integrated encyclopedia of DNA elements in the human genome.
An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489(7414):57-74. doi:10.1038/nature11247.