Announcing the publication of “Functional transcriptomics in the post-ENCODE era” in Genome Research.


Just a brief post to draw your attention to this article, which was made available in Genome Research as an Advance Online Article on the 30th October.  The article is Open Access.

So what is it about? It is a perspective piece in which we draw on our experience in generating the GENCODE geneset to discuss the current state of human gene annotation. We argue that this annotation remains absolutely a work in progress, and that there is in fact a large amount of work still to be done before we can confidently claim to have an understanding of the transcriptome. Efforts will proceed along two lines: firstly, we need to capture missing human transcripts and to fully extend many existing models to completion; secondly, there is an urgent need to improve the functional annotation of the transcriptome, in particular to separate those transcripts that make genuine contributions to human biology from those that do not. We appraise the various methodologies that are currently being used to meet these aims -including high-throughput experimentation, single gene studies and comparative genomics – discussing both their advantages and limitations. While the GENCODE annotation set is used for illustration, the purpose of the article is to discuss transcriptomics in a general context. In other words, it’s not about ENCODE, rather where we go from here.

So if you’ve been lying awake at night wondering…

•    What value does the concept of the gene have in modern biology?
•    How large is the human transcriptome?
•    How do I know if my favourite transcript is complete?
•    What proportion of the transcriptome is truly functional?
•    What exactly is a ‘functional’ transcript? Or a non-functional transcript?
•    What is the relationship between transcript functionality and genome functionality?
•    Is annotation causing artefacts in my genome-wide analysis?
•    Where exactly are we with lncRNAs right now?
•    Does modern high-throughput experimental biology render comparative analysis redundant?
•    Why are single gene studies still important?
•    Is proteomics still stuck in the 1970s?
•    Can knowledge of gene regulation inform transcript annotation?

… then we suggest you give it a read.



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