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A gene–environment-induced epigenetic program initiates tumorigenesis

Direna Alonso‐Curbelo, Yu-Jui Ho, Cassandra Burdziak, Jesper L.V. Mååg, John P. Morris, Rohit Chandwani, Hsuan-An Chen, Kaloyan M. Tsanov, Francisco M. Barriga, Wei Luan,

Nature · 2021 · 321 citations · 80 references

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80

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love, Wolfgang Huber, Simon Anders · Genome biology · 2014 · 100.5K citations · Full text

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony Bolger, Marc Lohse, Björn Usadel · Bioinformatics · 2014 · 69.7K citations · Full text

, , +13

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

, , +11

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha et al. · Proceedings of the National Academy of Sciences · 2005 · 56.7K citations · Full text

, , +12

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics · 2012 · 56.2K citations · Full text

, , +17