Genomics: The ENCODE project

@article{Souza2012GenomicsTE,
  title={Genomics: The ENCODE project},
  author={Natalie de Souza},
  journal={Nature Methods},
  year={2012},
  volume={9},
  pages={1046-1046}
}
The second, genome-wide phase of the Encyclopedia of DNA Elements (ENCODE) project is being reported. 
Correction to: The coding and noncoding transcriptome of Neurospora crassa
After publication of the original article [1], the authors noted that Additional files 6, 8 and 9 and their legends were incorrect.
High‐wire act: the poised genome and cellular memory
TLDR
This review focuses on two crucial mechanisms of gene poising: bivalent chromatin marks and RNA polymerase II stalling, which are critical for recapitulating developmental choices, leading to regenerative function.
Molecular Functions of Long Non-Coding RNAs in Plants
TLDR
The current understanding of long ncRNA functions in plants is reviewed and the challenges in functional characterization of plantlong ncRNAs are discussed.
Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases
TLDR
The predictive and analytical power of the Manteia system is demonstrated to predict candidate genes responsible for human genetic diseases.
A cytosine-thymine (CT)-rich haplotype in intron 4 of SNCA confers risk for Lewy body pathology in Alzheimer's disease and affects SNCA expression
TLDR
It is shown that tagging single‐nucleotide polymorphisms across the SNCA locus were significantly associated with increased risk for Lewy body pathology in Alzheimer's disease cases, but the actual genetic variant(s) that underlie the observed associations remain elusive.
Predicting Gene Expression from DNA Sequence using Residual Neural Network
TLDR
A deep residual network model is developed, named ExpResNet, to predict gene expression directly from DNA sequence, and it is demonstrated that this model outperforms the three existing models across four tissues tested.
Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
TLDR
Novel linkage-based droplet digital PCR assays on 20 inversions showing clear signs of being recurrent and validating gene expression differences reported before for two inversions and finding new candidate associations are tested, highlighting the importance of direct genotyping to assess their potential consequences and clinical implications.
The role of long noncoding RNAs in cancer metastasis
TLDR
In this review, this review highlights the specific role lncRNAs have in promoting the metastatic cascade across a number of epithelial cancer models.
Computational solutions for omics data
TLDR
This Review samples the algorithmic landscape, focusing on state-of-the-art techniques, the understanding of which will aid the bench biologist in analysing omics data.
Cross-cell DNA methylation annotation and analysis for pan-cancer study
TLDR
The online curated resource of DNA methylation annotation knowledgebase was utilized, to implement the cross-cell interrogation of pan-cancer study of breast cancer, which revealed genome-wide differentially-methylated loci and regions by the reduced representation bisulfite sequencing profiling.
...
1
2
3
4
...

References

An Integrated Encyclopedia of DNA Elements in the Human Genome
TLDR
The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.