Posts Tagged ‘network’

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

A scored human protein-protein interaction network to catalyze genomic interpretation : Nature Methods : Nature Research

December 9, 2016

Scored…PPI #network to catalyze genomic interpretation >500k links from lit. mining; up weights small-scale expt

Spatiotemporal 16p11.2 Protein Network Implicates Cortical Late Mid-Fetal Brain Development and KCTD13-Cul3-RhoA Pathway in Psychiatric Diseases

November 15, 2016

Spatiotemporal…Protein Network Implicates Cortical…Fetal Brain Development & KCTD13…RhoA Pathway in…Diseases

dyanamic PPI w brainspan data

Spatiotemporal 16p11.2 Protein Network Implicates Cortical Late Mid-Fetal Brain Development and KCTD13-Cul3-RhoA Pathway in
Psychiatric Diseases

Guan Ning Lin1, 5,
Roser Corominas1, 5,
Irma Lemmens2,
Xinping Yang3,
Jan Tavernier2,
David E. Hill3,
Marc Vidal3,
Jonathan Sebat1, 4,
Lilia M. Iakoucheva1,

Kinome-wide Decoding of Network-Attacking Mutations Rewiring Cancer Signaling: Cell

July 2, 2016

Kinome-wide Decoding of #Network-Attacking Mutations Rewiring Cancer Mapping NAMs onto well-known signaling pathways

Computer Vision and Computer Hallucinations » American Scientist

October 21, 2015

Computer Vision
&…Hallucinations,y.2015,no.5,content.true,page.1,css.print/issue.aspx Instead of training a neural network, train an image to fit it. Dreams emerge
“The algorithm behind the deep dream images was devised by Alexander Mordvintsev, a Google software engineer in Zurich. In the blog posts he was joined by two coauthors: Mike Tyka, a biochemist, artist, and Google software engineer in Seattle; and Christopher Olah of Toronto, a software engineering intern at Google.

Here’s a recipe for deep dreaming. Start by choosing a source image and a target layer within the neural network. Present the image to the network’s input layer, and allow the recognition process to proceed normally until it reaches the target layer. Then, starting at the target layer, apply the backpropagation algorithm that corrects errors during the training process. However, instead of adjusting connection weights to improve the accuracy of the network’s response, adjust the source image to increase the amplitude of the response in the target layer. This forward-backward cycle is then repeated a number of times, and at intervals the image is resampled to increase the number of pixels.”

PLOS Genetics: Statistical Estimation of Correlated Genome Associations to a Quantitative Trait Network

December 28, 2014

Correlated Genome Associations to Quantitative Trait #Network (QTN)
Uses fused #lasso for estimation of relationships

Kim & Xing (’09) provide a new method for calculating how genetic
markers associate with phenotypes by incorporating phenotype
connectivity features into the correlation structure between markers
and phenotypes. Their model attempts to quantify pleiotropic
relationships between different phenotypes and assumes a common
genotypic origin for the existence of clusters of correlated
phenotypes, which their algorithm uses to reduce the number of
significant genetic markers. In particular, Kim and Xing present a
method for performing quantitative trait analysis that implements two
novel approaches to inferring the contribution of a
[marker/allele/SNP/gene/locus] to a quantitative trait. The first is
organization of traits into a quantitative trait network (QTN). The
second is the utilization of fused lasso, a variation of multivariate
regression that seeks to minimize the number of non-zero coefficients
and least squared error. These two approaches are combined in an
attempt to minimize noise (in the form of small coefficients for SNP’s
that don’t really make a contribution) and focus on truly relevant
SNP’s while dealing with the correlated nature of quantitative
traits. Based on two datasets – simulated HapMap data and
data from the Severe Asthma Research Program – the authors show marked
improvement in accuracy and reduction of false positives over simpler
multivariate regression methods.

VIRGO: computational prediction of gene functions

December 25, 2014

VIRGO: computational prediction of gene function Webserver propagates GO terms over PPI & gene-expression #networks

This work was said to be the first web server for gene function
annotation (not the first algorithm).
The idea is to predict gene functions from known molecular interaction
networks (such as PPI), which includes both annotated and unannotated
genes. The potential function of an unannotated gene is predicted
using a propagation diagram, which takes into account the neighbors’
functions. The weight of edge in the network is determined by user uploaded expression data. Weight = |Pearson correlation| of expression
profiles of the gene pair. Weight reflects the confidence of the edge.

Dissecting Disease Inheritance Modes in a Three-Dimensional Protein Network Challenges the “Guilt-by-Asso ciation” Principle

August 7, 2014

Inheritance Modes in… #Network Challenges… Guilt-by-Association #Diseases of recessive interface SNVs predictable

surprisingly, no positional effects on LOF mutations … significant proportion of truncation alleles give rise to functional products

“guilt by assoc works”

signif. number dom mut give rise to func products

PLOS Biology: The Ecology of Collective Behavior

July 11, 2014

#Ecology of Collective Behavior #Network structure reflects resource patchiness, operating costs & threat of rupture

Nature Genetics calls for data analysis papers

May 9, 2014

Call for… analysis papers: nice description of hypothesis generation v. validation & 3 types of #network robustness

Call for data analysis papers
Nature Genetics 46, 213 (2014) doi:10.1038/ng.2914Published online 26 February 2014
Deadline expired but maybe still relevant…