Posts Tagged ‘encode’

Insights & Outcomes: a new spin on quantum research, and the biology of sex | YaleNews

August 3, 2020

https://news.yale.edu/2020/07/30/insights-outcomes-new-spin-quantum-research-and-biology-sex
QT:{{”
ENCODE and the dance between genes and DNA/RNA
Since 2003, the lab of Yale’s Mark Gerstein has played a major role in an international effort to catalog data on the complex interactions between genes and the segments of DNA and RNA that regulate their functions. The latest findings of the ENCODE project were published July 29 in 30 papers, four spearheaded by Gerstein’s lab, in a variety of scientific journals. Jing Zhang and Donghoon Lee from Gerstein’s lab have created a video illustrating science’s evolving understanding of the complex regulatory networks that can contribute to cancer and other diseases. The latest findings by the Gerstein lab and other major ENCODE contributors can be found on the Gerstein lab website. “}}

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. – PubMed – NCBI

June 15, 2019

https://www.ncbi.nlm.nih.gov/pubmed/30612741

crisprQTL

crisprQTL mapping as a genome-wide association framework for cellular genetic screens
Molly Gasperini, Andrew J. Hill, José L. McFaline-Figueroa, Beth Martin, Cole Trapnell, Nadav Ahituv, Jay Shendure
doi: https://doi.org/10.1101/314344

Untangling the Formation of DNA Loops – Scientific American

April 3, 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

February 2, 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

August 12, 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

March 17, 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

January 5, 2018

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

Software Tools – ENCODE

September 30, 2017

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

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 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.”
“}}