Data are available for the following papers of the ENCODE/modENCODE publication release.

Ho et al.

Comparative analysis of metazoan chromatin organization

Nature 512:449–452, 2014.  

Data Page

Boyle et al.

Comparative analysis of regulatory information and circuits across distant species

Nature 512:453–456, 2014.  

Data Page

Gerstein et al.

Comparative analysis of the transcriptome across distant species

Nature 512:445–448, 2014.  

Data Page

Members of the consortium have published several companion papers related to the three studies above.

Companion Papers


  • Brown et al., Diversity and dynamics of the Drosophila transcriptome, Nature 512:393–399, 2014. 
  • Araya et al., Regulatory analysis of the C. elegans genome with spatiotemporal resolution, Nature 512:400–405, 2014. 

Genome Research

  • Li et al., Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data, Genome Research 24:1086-1101, 2014. 
  • Lubelsky et al., DNA replication and transcription programs respond to the same chromatin cues, Genome Research 24:1102-1114, 2014. 
  • Arthur et al., Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification, Genome Research 24:1115-1124, 2014. 
  • Chen et al., Comparative validation of the D. melanogaster modENCODE transcriptome annotation, Genome Research 24:1209-1223, 2014. 
  • Slattery et al., Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster, Genome Research 24:1224-1235, 2014. 
  • Chen et al., Extreme HOT regions are CpG-dense promoters in C. elegans and humans, Genome Research 24:1138-1146, 2014. 
  • Wen et al., Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines, Genome Research 24:1236-1250, 2014. 

Genome Biology

  • Kudron et al., Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs, Genome Biology 14:R5, 2013. 
  • Yan et al., OrthoClust: An orthology-based network framework for clustering data across multiple species, Genome Biology 15:R100, 2014. doi:10.1186/gb-2014-15-8-r100. In production. (Software)
  • Lee et al., DNA copy number evolution in Drosophila cell lines, Genome Biology, in press, 2014.


  • Sturgill et al., Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki), BMC Bioinformatics 14:320, 2013. 
  • Bolye et al., Genome-guided transcript assembly by integrative analysis of RNA sequence data, Nature Biotechnolgy 32:341-6, 2014. 
  • Mohammed et al., The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution, RNA 19:1295-308, 2013. 
  • Trinh et al., Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE, BMC Genomics 14:494, 2013. 
  • Sisu et al., Comparative analysis of pseudogenes across three phyla, Proceedings of the National Academy of Sciences USA, published online ahead of print, 2014.  (Data)