quite relevant
https://www.nature.com/articles/nmeth.4534
Resolving systematic errors in widely used enhancer activity assays in human cells
Felix Muerdter
, Łukasz M Boryń
, Ashley R Woodfin
, Christoph Neumayr
, Martina Rath
, Muhammad A Zabidi
, Michaela Pagani
, Vanja Haberle
, Tomáš Kazmar
, Rui R Catarino
, Katharina Schernhuber
, Cosmas D Arnold
& Alexander Stark
Nature Methods volume 15, pages141–149 (2018)
Received: 13 November 2017 Revised: 22 November 2017 Accepted: 29 November 2017 https://www.nature.com/articles/s41525-017-0040-5.pdf
https://my.pgp-hms.org/profile/hu43860C
George Church discloses a lot of his medical records
.@Genome_Gov Extramural Grant Portfolio
https://www.Genome.Gov/27569006/july-6-2017-the-nhgri-extramural-grant-portfolio-using-different-approaches-to-fund-genomics-research Nice grid divides programs into PI-initiated/consortia & RFA-solicited v not
Genome-wide characterization of..promoters w…enhancer functions http://www.Nature.com/ng/journal/v49/n7/full/ng.3884.html Blurs distinction betw these, suggests flexibility
Genome-wide characterization of mammalian promoters with distal enhancer functions
Lan T M Dao,
Ariel O Galindo-Albarrán,
Jaime A Castro-Mondragon,
Charlotte Andrieu-Soler,
Alejandra Medina-Rivera,
Charbel Souaid,
Guillaume Charbonnier,
Aurélien Griffon,
Laurent Vanhille,
Tharshana Stephen,
Jaafar Alomairi,
David Martin,
Magali Torres,
Nicolas Fernandez,
Eric Soler,
Jacques van Helden,
Denis Puthier
& Salvatore Spicuglia
Promoting transcription over long distances
Rui R Catarino,
Christoph Neumayr
& Alexander Stark
Nature Genetics 49, 972–973 (2017) doi:10.1038/ng.3904
28 June 2017
http://www.nature.com/ng/journal/v49/n7/full/ng.3884.html
http://www.nature.com/ng/journal/v49/n7/full/ng.3904.html
QT:{{”
“Should we be surprised that promoters can function as enhancers—or better—that enhancers and promoter regions can overlap? Probably not: the habit of annotating different genomic regions with distinct labels ignores the fact that DNA sequences typically encode different genetic functions in a rather flexible manner. Enhancers and promoters are determined by the presence of short degenerate motifs, and even protein-coding regions display flexibility due to the degeneracy of the genetic code. Therefore, a single DNA sequence can encode different types of functions, including enhancer function of protein-coding regions or—as shown now—enhancer function of
promoters.”
“}}
Zhou, J. and Troyanskaya, O.G. (2015). Predicting effects of noncoding variants with deep learning–based sequence model. Nature Methods, 12, 931–934.
Predicting (& prioritizing) effects of noncoding variants w. [DeepSEA] #DeepLearning…model
https://www.Nature.com/nmeth/journal/v12/n10/full/nmeth.3547.html Trained w #ENCODE data
DNA’s secret weapon against knots & tangles http://www.Nature.com/news/dna-s-secret-weapon-against-knots-and-tangles-1.21838 Quick overview of recent models of loop extrusion w/ cohesin & CTCF
QT:{{”
“The dark proteome could be an evolutionary playground for trying out new folds
Ultimately one would expect particularly useful variations to get fixed at the genetic level. But it needn’t be where that variation begins. What’s more, organisms needn’t be quite so dependent for their molecular repertoire on their evolutionary heritage. O’Donoghue thinks that all organisms probably have a significant fraction of proteins unique just to them.
‘The fact that the dark matter of the proteome has less evolutionary constraint than the other bits of proteome may suggest that it’s under less selection,’ says Gerstein. ‘This is perhaps because it’s more flexible structurally, but also in a sense more flexible in terms of accommodating various amino-acid changes compared to the structurally inflexible and fixed parts of the crystallised proteome.’ This adds momentum to the picture of genomics as a rather more fluid affair than is suggested by the old picture of identical proteins being
mass-produced from a fixed genetic template.
Gerstein feels that studying the dark proteome opens up a host of interesting questions. For example, although known bacteria have a smaller dark proteome than eukaryotes, there’s a huge ‘dark
microbiome’ of unculturable bacteria. Might that be more full of dark proteins – perhaps useful ones?
And what about us? ‘How does the human dark proteome compare to that of eukaryotes as a whole?’ Gerstein wonders. How well, really, do we know ourselves?”
“}}
Shedding light on the dark proteome
BY PHILIP BALL13 FEBRUARY 2017
https://www.chemistryworld.com/feature/shedding-light-on-the-dark-proteome/2500392.article
#IHEC: A Blueprint for…Collab. & Discovery
http://www.Cell.com/cell/abstract/S0092-8674(16)31528-8?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416315288%3Fshowall%3Dtrue Summary bullets on heterogeneity, disease, rel. to SNPs, comp. tools
