Posts Tagged research

Recent papers discussing “function” in eukaryotic genomes

ENCODE Project Consortium et al. 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.

Graur D, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E. 2013. On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol. 5:578-590.

Eddy S. 2012. The C-value paradox, junk DNA and ENCODE. Curr Biol. 22:R898– R899.

Eddy SR. 2013. The ENCODE project: missteps overshadowing a success. Curr. Biol. 23: R259-61.

Eddy SR. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci U S A. 2013 Apr 2;110(14):5294-300.

Kellis M et al. 2014. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8.

Niu D-K, Jiang L. 2013. Can ENCODE tell us how much junk DNA we carry in our genome? Biochem Biophys Res Commun. 430:1340–1343.

Palazzo AF and Gregory TR. 2014. The Case for Junk DNA. PLoS Gentics 10 (5): e1004351

Doolittle, WF, Brunet TDP, Linquist S, Gregory TR (2014). Distinguishing between “function” and “effect” in genome biology. Genome Biol Evol (2014) doi: 10.1093/gbe/evu098



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Abstract word cloud from glam journals – 2013 edition.

Quick and simple post, considering it is Jan 1st and I’m still tired from last night, and the fact that I just came back from, you guessed it, the lab.

Anyway, I wanted to know what the most recurring topics were on the top two glam journals during 2013, so I obtained the 2013 PubMed-indexed abstracts from Nature and Science using EBOT and then used Wordle to generate a word cloud.

Here are the results:

1) Nature

Image2) Science

ImageCool, ah? You’ll notice that many words are shared.

It’s pretty easy to do it for any other journal or for any other query in PubMed using Ebot. If you want to do something similar for say, your country or institution and you need help, let me know.

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