Posts Tagged ‘ncvarg’

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

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
https://www.Nature.com/nmeth/journal/v12/n10/full/nmeth.3547.html Trained w #ENCODE data

Detecting overlapping protein complexes in protein-protein interaction networks : Nature Methods : Nature Research

February 24, 2017

http://www.nature.com/nmeth/journal/v9/n5/abs/nmeth.1938.html

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human: Cell

February 24, 2017

FissionNet: Proteome-wide [pombe] Interactome Reveals #Network Evolution Principles
http://www.Cell.com/cell/abstract/S0092-8674(15)01556-1 Involving ~1300 soluble proteins

2016 News Feature: NIH supports new approaches to discovering DNA differences in the genome’s regulatory regions that affect disease – National Human Genome Research Institute (NHGRI)

October 7, 2016

https://www.genome.gov/27566612/2016-news-feature-nih-supports-new-approaches-to-discovering—dna-differences-in-the-genomes-regulatory-regions-that-affect-disease-/

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

August 18, 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

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort. – PubMed – NCBI

February 15, 2016

Massively parallel quantification of…regulatory effects of #noncoding…variation in a…cohort
http://genome.cshlp.org/content/25/8/1206.long new popstarr assay

http://www.ncbi.nlm.nih.gov/pubmed/26084464
Genome Res. 2015 Aug;25(8):1206-14. doi: 10.1101/gr.190090.115. Epub 2015 Jun 17.
Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort.
Vockley CM1, Guo C2, Majoros WH3, Nodzenski M4, Scholtens DM4, Hayes MG5, Lowe WL Jr5, Reddy TE6.

“The Race” to Clone BRCA1

April 25, 2015

The Race to Clone #BRCA1 http://www.sciencemag.org/content/343/6178/1462.abstract
Lessons on #LOF mutations, synthetic lethality, silly gene names & the 2-hit hypothesis

synthetic lethality (PARP inhibitors), gene names (RING fingers)

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus : Nature : Nature Publishing Group

March 23, 2015

From noncoding variant to phenotype…at…#cholesterol locus http://www.nature.com/nature/journal/v466/n7307/full/nature09266.html
Gold standard ex of #SNP functional effect: LDL changes

Kiran Musunuru,
Alanna Strong,
Maria Frank-Kamenetsky,
et al.

Nature 466, 714–719 (05 August 2010) doi:10.1038/nature09266

Changes LDL level

PLOS Genetics: A Massively Parallel Pipeline to Clone DNA Variants and Examine Molecular Phenotypes of Human Disease Mutations

February 7, 2015

Massively Parallel Pipeline to Clone DNA Variants & Examine…Disease
Mutations http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004819 CloneSeq leverages NextGen sequencing

With the advance of sequencing technologies, tens of millions of genomic variants have been discovered in the human population. However, there is no available method to date that is capable of determining the functional impact of these variants on a large scale, which has increasingly become a huge bottleneck for the development of population genetics and personal genomics. Clone-seq and comparative interactome-profiling pipeline is a first to address this issue.

Can be coupled to many readouts.