Posts Tagged ‘encode’

Untangling the Formation of DNA Loops – Scientific American

Wednesday, April 3rd, 2019

SCIENTIFIC AMERICAN MARCH 2019

Untangling the Formation of DNA Loops

New discoveries on ancient loops in DNA offer clues into gene regulation

By Erez Lieberman Aiden

https://www.scientificamerican.com/article/untangling-the-formation-of-dna-loops/

The effects of death and post-mortem cold ischemia on human tissue transcriptomes | Nature Communications

Saturday, February 2nd, 2019

Changes in gene activity may one day reveal…time of death
https://www.ScienceMag.org/news/2018/02/changes-gene-activity-may-one-day-reveal-time-death-crime-victims Discusses paper by @RodericGuigo (“Effects of death & post-mortem cold ischemia on….#transcriptomes,”
https://www.Nature.com/articles/s41467-017-02772-x). Obvious forensic interest but maybe a #privacy angle as well

Changes in gene activity may one day reveal the time of death for crime victims

genome-wide starr-seq + sources of experimental bias

Monday, August 13th, 2018

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)

ncdriver and ENCODE

Saturday, March 17th, 2018

Received: 13 November 2017 Revised: 22 November 2017 Accepted: 29 November 2017 https://www.nature.com/articles/s41525-017-0040-5.pdf

George Church Medical Info

Saturday, January 6th, 2018

https://my.pgp-hms.org/profile/hu43860C
George Church discloses a lot of his medical records

Software Tools – ENCODE

Sunday, October 1st, 2017

https://www.encodeproject.org/software/

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

Monday, July 10th, 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

Saturday, July 1st, 2017

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.”
“}}

Journal Club Paper

Sunday, June 18th, 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
https://www.Nature.com/nmeth/journal/v12/n10/full/nmeth.3547.html Trained w #ENCODE data

The dark side of the human genome : Nature : Nature Research

Sunday, November 27th, 2016

Dark side of the..genome
http://www.Nature.com/nature/journal/v538/n7624/full/538275a.html QT: NextGen..has been..the tech engine of #ENCODE..but..hi-res livecell imaging [is coming]

Has figure from Khurana et al. Nat. Rev. Genet. (’16)

QT:{{”
“Next-generation sequencing has been — and still is — the
technological engine of ENCODE. But looking ahead, researchers might be able to roll out high-resolution live-cell imaging on a large scale to watch the state of the genome change in real time using specific markers. This technology could be disruptive. “If we had a better microscope, we wouldn’t be sequencing anymore,” says
Stamatoyannopoulos”
“}}