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The modENCODE project was initiated to study the genomes of D. melanogaster and C. elegans and systematically annotate functional genomic elements of these organisms. The most significant findings of modENCODE were published in 2010 in the following integrative analysis papers: Gerstein MB, Lu ZJ, Van Nostrand EL, et al. Integrative analysis of the Caenorhabditis elegans genome by the modENCODE pr