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Article
Open AccessSpecies-aware DNA language models capture regulatory elements and their evolution
The rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory instructions. To this end, new algorithms are needed that can leverage conserva...
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Article
Open AccessViral genome sequencing to decipher in-hospital SARS-CoV-2 transmission events
The SARS-CoV-2 pandemic has highlighted the need to better define in-hospital transmissions, a need that extends to all other common infectious diseases encountered in clinical settings. To evaluate how whole ...
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Article
Open AccessCurrent sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers
The largest sequence-based models of transcription control to date are obtained by predicting genome-wide gene regulatory assays across the human genome. This setting is fundamentally correlative, as those mod...
