Posts Tagged ‘encode’

ncdriver and ENCODE

March 17, 2018

Received: 13 November 2017 Revised: 22 November 2017 Accepted: 29 November 2017

George Church Medical Info

January 5, 2018
George Church discloses a lot of his medical records

Software Tools – ENCODE

September 30, 2017

The Genomics Landscape: A monthly update from the NHGRI Director – July 2017

July 9, 2017

.@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

promoter/enhancer categorization and Encyclopedia

July 1, 2017

Genome-wide characterization of..promoters w…enhancer functions 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

“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

Journal Club Paper

June 18, 2017

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 Trained w #ENCODE data

DNA’s secret weapon against knots and tangles

May 7, 2017

DNA’s secret weapon against knots & tangles Quick overview of recent models of loop extrusion w/ cohesin & CTCF

Shedding light on the dark proteome

April 24, 2017

“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

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. – PubMed – NCBI

April 16, 2017

#IHEC: A Blueprint for…Collab. & Discovery Summary bullets on heterogeneity, disease, rel. to SNPs, comp. tools

whole genome assembly from Hi-C data

April 2, 2017

De novo assembly of the A aegypti genome using #HiC, by @erezaterez et al Works on human too, w. promise for #SVs

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

Olga Dudchenko1,2,3,4,
Sanjit S. Batra1,2,3,*,
Arina D. Omer1,2,3,*,
Sarah K. Nyquist1,3,
Marie Hoeger1,3,
Neva C. Durand1,2,3,
Muhammad S. Shamim1,2,3,
Ido Machol1,2,3,
Eric S. Lander5,6,7,
Aviva Presser Aiden1,2,8,9,
Erez Lieberman Aiden1,2,3,4,5,†

Science 23 Mar 2017:
DOI: 10.1126/science.aal3327

on whole genome assembly from Hi-C reads. There is also some info on chromosomal rearrangement from Hi-C.