PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

(2009) K. D. Pruitt et al.   GENOME RESEARCH

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Models of coding sequence evolution

(2008) W. Delport et al.   BRIEFINGS IN BIOINFORMATICS

Investigating Protein-Coding Sequence Evolution with Probabilistic Codon Substitution Models

(2008) M. Anisimova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

(2008) Michael F. Lin et al.   PLoS Computational Biology

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

(2007) Michael R. Brent   NATURE REVIEWS GENETICS