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2
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3
Multiple modes of PRC2 inhibition elicit global chromatin alterations in H3K27M pediatric glioma.
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4
Molecular heterogeneity and CXorf67 alterations in posterior fossa group A (PFA) ependymomas.
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5
SETD2-mediated crosstalk between H3K36me3 and H3K79me2 in MLL-rearranged leukemia.
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6
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7
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8
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9
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