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08/2018 - Detecting repeated cancer evolution from multi-region tumor sequencing data

Recurrent successions of genomic changes, both within and between patients, reflect repeated evolutionary processes that are valuable for the anticipation of cancer progression. Multi-region sequencing allows the temporal order of some genomic changes in a tumor to be inferred, but the robust identification of repeated evolution across patients remains a challenge. We developed a machine-learning […]

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08/2018 - Human iPSC-derived trigeminal neurons lack constitutive TLR3-dependent immunity that protects cortical neurons from HSV-1 infection

Herpes simplex virus type 1 (HSV-1) encephalitis (HSE) is the most common sporadic viral encephalitis in Western countries. Some HSE children carry inborn errors of the Toll-like receptor 3 (TLR3)-dependent IFN-α/β– and -λ–inducing pathway. Induced pluripotent stem cell (iPSC)-derived cortical neurons with TLR3 pathway mutations are highly susceptible to HSV-1, due to impairment of cell-intrinsic […]

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06/2018 - The memory of science: Inflation, myopia, and the knowledge network

Scientific production is steadily growing, exhibiting 4% annual growth in publications and 1.8% annual growth in the number of references per publication, together producing a 12-year doubling period in the total supply of references, i.e. links in the science citation network. This growth has far-reaching implications for how academic knowledge is connected, accessed and evaluated. […]

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06/2018 - Quantification of subclonal selection in cancer from bulk sequencing data

Subclonal architectures are prevalent across cancer types. However, the temporal evolutionary dynamics that produce tumor subclones remain unknown. Here we measure clone dynamics in human cancers by using computational modeling of subclonal selection and theoretical population genetics applied to high-throughput sequencing data. Our method determined the detectable subclonal architecture of tumor samples and simultaneously measured […]

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