The ENCODE project: Missteps overshadowing a success

2013/04/01 by Sean R. Eddy · 1 voice · 100 citations
Biochemistry, Genetics and Molecular Biology · Psychology · #Biology #Cognitive science #ENCODE #Gene #Genetics #Genetics, Bioinformatics, and Biomedical Research #Genomics and Chromatin Dynamics #Literature #Narrative #Psychology #RNA and protein synthesis mechanisms

paper · pdf · doi:10.1016/j.cub.2013.03.023

published in Current Biology 23(7), R259-R261 (Elsevier BV)

openalex publication_date 2013/04/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28

Cited by

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• Life Before Earth
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• Beyond the ENCODE project: using genomics and epigenomics strategies to study enhancer evolution. [europepmc]
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• Comparative population genomics: power and principles for the inference of functionality. [europepmc]
• Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. [europepmc]
• Genomic data integration for ecological and evolutionary traits in non-model organisms. [europepmc]
• A method for calculating probabilities of fitness consequences for point mutations across the human genome. [europepmc]
• Non-coding RNA: what is functional and what is junk? [europepmc]
• Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. [europepmc]
• Transforming Big Data into Cancer-Relevant Insight: An Initial, Multi-Tier Approach to Assess Reproducibility and Relevance. [europepmc]
• CRISPR Screens to Discover Functional Noncoding Elements. [europepmc]
• DNA methylation and DNA methyltransferases. [europepmc]
• Ten things you should know about transposable elements. [europepmc]
• An evolutionary framework for measuring epigenomic information and estimating cell-type-specific fitness consequences. [europepmc]
• A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel's second law. [europepmc]
• Getting clear about the F-word in genomics. [europepmc]
• Modular Organization of Cis -regulatory Control Information of Neurotransmitter Pathway Genes in Caenorhabditis elegans . [europepmc]
• Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts. [europepmc]
• Non-Darwinian Molecular Biology. [europepmc]
• Identification and Characterization of Polymorphisms in piRNA Regions. [europepmc]
• Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges. [europepmc]
• Synthetic reversed sequences reveal default genomic states. [europepmc]
• Pervasive Transcription in the Human Genome Exceeds Background Noise. [europepmc]
• Transposon Ecology and the Octopus Genome. [europepmc]
• “Dark” or “Junk”? Functional Roles of Pervasive Transcription in the Human Genome [europepmc]

Discussions

• In 2012 the ENCODE project claimed that most of our genome 🧬 wasn't junk after all on the basis that most of it was active in some way 🧪 In response, @cryptogenomicon.bsky.social proposed the rando [bsky, 15 points, 2 comments]