Posts Tagged ‘encode’

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

June 15, 2019


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

Untangling the Formation of DNA Loops – Scientific American

April 3, 2019


Untangling the Formation of DNA Loops

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

By Erez Lieberman Aiden

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 Discusses paper by @RodericGuigo (“Effects of death & post-mortem cold ischemia on….#transcriptomes,” 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

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

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