Posts Tagged ‘ncvarg’

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data | Nature Genetics

March 18, 2018

Fast, scalable prediction of deleterious #noncoding variants from functional & population genomic data LINSIGHT, by @ASiepel et al., combines DNAse & conservation information

Yi-Fei Huang, Brad Gulko & Adam Siepel
Nature Genetics 49, 618–624 (2017)
Published online:
13 March 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

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

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

February 24, 2017

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 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—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 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 new popstarr assay
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
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
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