Posts Tagged ‘encodec’

New study finds cell line difference across labs

Friday, August 17th, 2018

https://www.nature.com/articles/s41586-018-0409-3
QT:{{”
“… comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic
diversification. Similar results were obtained with multiple strains of 13 additional cell lines.
“}}

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)

The Cancer Genome Atlas: Creating Lasting Value beyond Its Data

Friday, June 15th, 2018

Commentary
The Cancer Genome Atlas: Creating Lasting Value beyond Its Data Carolyn Hutter + Jean Claude Zenklusen

https://www.sciencedirect.com/science/article/pii/S009286741830374X

Genome-Scale Signatures of Gene Interaction from Compound Screens Predict Clinical Efficacy of Targeted Cancer Therapies – ScienceDirect

Sunday, April 29th, 2018

Genome-Scale Signatures of Gene Interaction from #CompoundScreens Predict…Efficacy of Targeted Cancer Therapies
https://www.ScienceDirect.com/science/article/pii/S2405471218300097 How to find drug combos: Find expression response profiles associated w/ a drug target. A synergistic drug might change profiles similarly

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

Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma | Nature Genetics

Sunday, February 11th, 2018

https://www.nature.com/articles/ng.3861?WT.ec_id=NG-201706&spMailingID=54145295&spUserID=MTc2NTYxNjY4OQS2&spJobID=1164335784&spReportId=MTE2NDMzNTc4NAS2

Chromatin states define tumour-specific T cell dysfunction and reprogramming | Nature

Monday, November 20th, 2017

https://www.nature.com/articles/nature22367

STAR Methods

Friday, September 29th, 2017

Here is the STAR Methods format (Structured, Transparent, Accessible Reporting) introduced last year by Cell, marketed as a structure that “promotes transparent reporting of experimental design and
methodological details.” Details are in the links below.

Editorial: http://www.cell.com/cell/fulltext/S0092-8674(16)31072-8 Instructions: http://www.cell.com/star-authors-guide
Website: http://www.cell.com/star-methods

US cancer institute to overhaul tumour cell lines

Sunday, July 9th, 2017

QT:{{"
“The NCI will continue to supply the NCI-60 cell lines to researchers, but will eventually refocus its drug screening on newer models. It is developing hundreds of ‘patient-derived xenografts’ (PDXs), which are created by implanting small chunks of human tumours into mice. There, the tumours grow in an environment that, although not human, better mimics their native environment”
"}}