Posts Tagged ‘from_mrs’

interesting perspective on cancer research in wsj + upcoming book

Wednesday, October 9th, 2019

The focus is on improving detection vs. treatment of late stage disease.

https://www.wsj.com/articles/cancer-is-still-beating-uswe-need-a-new-start-11570206319

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)

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay: Cell

Thursday, August 18th, 2016

Identification of…expr.-Modulating Variants using #MPRA, by @sabeti_lab http://www.cell.com/cell/fulltext/S0092-8674(16)30421-4 Some w. allelic skew related to PWM change

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences: Cell

Sunday, April 24th, 2016

Learning the…Determinants of Alternative #Splicing [in a largely linear model] from Millions of Random Sequences
http://www.cell.com/cell/abstract/S0092-8674(15)01271-4

** Rosenberg et al Cell. 2015

Builds a model of splicing using a library of randomized sequence Also, builds a generalized model for predicting effect of a SNP in the Geuvadis RNAseq
7mer model does well with lots of data