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. “}}
Posts Tagged ‘encode’
Insights & Outcomes: a new spin on quantum research, and the biology of sex | YaleNews
August 3, 2020A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. – PubMed – NCBI
June 15, 2019https://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, 2019SCIENTIFIC 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, 2019Changes 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, 2018quite 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, 2018Received: 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, 2018https://my.pgp-hms.org/profile/hu43860C
George Church discloses a lot of his medical records
Software Tools – ENCODE
September 30, 2017The 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, 2017Genome-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.”
“}}
