Here’s a quick list of recently published modENCODE C. elegans papers:

Science
Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project.
Science 24 December 2010: Vol. 330 no. 6012 pp. 1775-1787
DOI: 10.1126/science.1196914

Genome Research
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.113050.110

A global analysis of C. elegans trans-splicing
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.113811.110

Broad chromosomal domains of histone modification patterns in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.115519.110

Diverse transcription factor binding features revealed by genome-wide ChIP-seq in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.114587.110

High nucleosome occupancy is encoded at X-linked gene promoters in C. elegans
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.115931.110

Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
Genome Res. Published in Advance December 22, 2010
doi:10.1101/gr.108845.110

Genome-wide analysis of alternative splicing in Caenorhabditis elegans
Genome Res. gr.114645.110 Published in Advance December 22, 2010
doi:10.1101/gr.114645.110

A Spatial and Temporal Map of C. elegans Gene Expression
Genome Res. gr.114595.110 Published in Advance December 22, 2010
doi:10.1101/gr.114595.110

Prediction and characterization of non-coding RNAs in C. elegans by integrating conservation, secondary structure and high throughput sequencing and array data
Genome Res. gr.110189.110 Published in Advance December 22, 2010
doi:10.1101/gr.110189.110