Presenting ENCODE

  title={Presenting ENCODE},
  author={Magdalena Skipper and Ritu Dhand and Philip Campbell},
C O V ER IL LU ST R AT IO N ( P R EV IO U S P A G E) : C A R L D ET O R R ES CONTENTS 2001 WILL ALWAYS BE REMEMBERED AS THE YEAR OF THE HUMAN GENOME. The availability of its sequence transformed biology, and the exemplary way in which hundreds of researchers came together to form a public consortium paved the way for ‘big science’ in biology. It was an incredible achievement but it was always clear that knowing the ‘code’ was only the beginning. To understand how cells interpret the information… 
EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era
A new promoter viewer is introduced which enables users to explore promoter-defining experimental evidence in a UCSC genome browser window and chromatin signatures are started to use in addition to mRNA 5′tags to locate promoters of weekly expressed genes.
It Is Imperative to Establish a Pellucid Definition of Chimeric RNA and to Clear Up a Lot of Confusion in the Relevant Research
It is proposed that only those RNAs that are formed by joining two RNA transcripts together without a fusion gene as a genomic basis should be regarded as authentic chimeras, whereas thoseRNAs transcribed as, and cis-spliced from, single transcripts should not be deemed as chimers.
To Know How a Gene Works, We Need to Redefine It First but then, More Importantly, to Let the Cell Itself Decide How to Transcribe and Process Its RNAs
Genomic DNA (gDNA) should be more cautious in the use of cDNA and in the explanation of data resulting from cDNA, and should make delivery of gDNA into cells routine in determination of genes' functions, although this demands some technology renovation.
DEEP: a general computational framework for predicting enhancers
DEEP, a novel ensemble prediction framework that integrates three components with diverse characteristics that streamline the analysis of enhancer's properties in a great variety of cellular conditions, is developed and results indicate that DEEP performs better than four state-of-the-art methods on the ENCODE data.
Living Organisms Author Their Read-Write Genomes in Evolution
The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
Transcriptional-Readthrough RNAs Reflect the Phenomenon of “A Gene Contains Gene(s)” or “Gene(s) within a Gene” in the Human Genome, and Thus Are Not Chimeric RNAs
There are probably no authentic chimeras in humans, after readthrough and fusion-gene derived RNAs are all put back into the group of ordinary RNAs and whether trans-splicing truly exists is doubted.
Hypothesis: Artifacts, Including Spurious Chimeric RNAs with a Short Homologous Sequence, Caused by Consecutive Reverse Transcriptions and Endogenous Random Primers
This essay proposes a hypothesis of “consecutive reverse transcriptions (RTs)”, i.e. another RT reaction following the previous one, for how most spurious chimeric RNAs, especially those containing a short homologous sequence, may be generated during RT, especially in RNA-sequencing wherein RNAs are fragmented.
RCytoscape: tools for exploratory network analysis
Network visualization reveals previously unreported patterns in the data suggesting heterogeneous signaling mechanisms active in GBM Proneural tumors, with possible clinical relevance.
Progress and challenges in bioinformatics approaches for enhancer identification
A general framework for computational identification of enhancers is described, relevant data types are presented and possible computational solutions are discussed, while pragmatic guidelines for development of more efficient computational enhancer prediction methods are suggested.