Posts Tagged ‘ncvarg’

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.

Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ, Sunyaev SR. Pooled association tests for rare variants in exon-resequencing studies. American Journal of Human Genetics (2010) 86: 832-838.

February 1, 2015

Pooled association tests for rare variants in exon-resequencing http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3032073 Simulation shows advantage of mult. rarity thresholds

Price AL, Kryukov GV, de Bakker PI, Purcell SM, Staples J, Wei LJ,
Sunyaev SR. Pooled association tests for rare variants in
exon-resequencing studies. American Journal of Human Genetics (2010)
86: 832-838.

SUMMARY

Multiple studies indicate strong association between rare variants and
resulting phenotype. This paper describes a population-genetics
simulation framework to study the influence of variant allele
frequency on the corresponding phenotype. In a prior study, causal
relationship between variants and phenotype was resolved by performing
association test on set of variants having allele frequency below a
fixed threshold. However, here it is observed that simulation
frameworks based on a variable allele frequency threshold provide
higher accuracy in association test compared to the fixed allele
frequency model. In addition, inclusion of predicted functional
effects of variants (Polyphen-2 scores) increases the accuracy of the
variable frequency threshold model. Overall, this paper describes a novel methodology, which can be
used to explore the association between rare variants and various
diseases.

NOT-OD-15-032: Update: New Biographical Sketch Format Required for NIH and AHRQ Grant Applications Submitted for Due Dates on or After May 25, 2015

January 11, 2015

http://grants.nih.gov/grants/guide/notice-files/NOT-OD-15-032.html