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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>National Resource for Network Biology</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="author" content="">
<!-- Le styles -->
<link href="assets/css/bootstrap.css" rel="stylesheet">
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<link href="assets/css/nrnb.css" rel="stylesheet">
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<body>
<div class="belt top">
<div class="container">
<div class="row top-right">
<div class="span5 offset7">
<div class="row">
<img class="logo-big" src="images/NRNB_white.svg"/>
<h2>National Resource for Network Biology</h2>
</div>
<div class="row buttons">
<a class="button-flat" href="projects.html">Research Projects</a>
<a class="button-flat" href="tools.html">Tools</a>
<a class="button-flat" href="training.html">Training</a>
<a class="button-flat btn-blue" href="outreach.html">Collaboration</a>
<a class="button-flat btn-green" href="#renewed">Funding Renewed</a>
<a class="button-flat" href="#highlights">Research Highlights</a>
</div>
</div>
</div>
</div>
</div>
<div class="belt white">
<div class="container">
<div class="row section">
<h3>What is NRNB?</h3>
</div>
<div class="row">
<div class="span4">
<iframe width="300" height="225"
src="http://www.youtube.com/embed/_nbqSe4Zaps?rel=0
&theme=light&color=white"
frameborder="0" allowfullscreen>
</iframe>
</div>
<div class="span8">
<p>
The aim of the <b>National Resource for Network Biology (NRNB)</b>
is to advance the new science of
Biological Networks through analytic tools, visualizations, databases and computing resources.
Biomedical research is increasingly dependent on knowledge of biological networks of multiple
types and
scales, including gene, protein and drug interactions, cell-cell and cell-host communication,
and vast
social networks. Our technologies enable researchers to assemble and analyze these networks and
to
use
them to better understand biological systems and, in particular, how they fail in disease. NRNB
leverages the <a href="http://www.cytoscape.org/">Cytoscape</a> Cyberinfrastructure,
a widely-used network analysis
platform which we further support through a rich set of tutorials, workshops, 24/7 help desk
assistance,
and over 100 collaboration and service projects.</p>
<p> We are developing freely available, open source software
technologies to enable network-based visualization, analysis, and
biomedical discovery. We are driving research and development <a
href="projects.html"><b>projects</b></a>, coordinating <a
href="training.html"><b>training</b></a> opportunities, and
actively seeking new <a href="outreach.html"><b>collaborations</b></a>
to develop NRNB <a href="tools.html"><b>tools</b></a> and apply
them to biomedical research.
</p>
</div>
</div>
</div>
</div>
<div id="renewed"></div>
<div class="belt white">
<div class="container">
<div class="row section">
<h3>5-Year Funding Renewal</h3>
</div>
<div class="row">
<div class="span3">
<img src="images/NRNB_black.png" alt="nrnb logo">
</div>
<div class="span9">
<p>
We have been awarded another five years of funding by <a href="http://publications.nigms.nih.gov/btrrs/
searchresultsall.asp">NIGMS</a> for the National Reseource of Network Biology. This was our first
round of competitve renewal as a resource center and thus a major test of both our track record
and our vision. We have identified <a href="./projects.html">three major themes</a> in Network Biology
that will define our <a href="./projects.html">technology research and development projects</a>. With
this renewed investment, we will also continue to pursue a broad range of <a href="./outreach">collaboration
</a> and <a href="./training.html">training</a> opportunities.
</p>
</div>
</div>
</div>
</div>
</div>
<div id="highlights"></div>
<div class="belt white">
<div class="container">
<div class="row section">
<h3>Research Highlights</h3>
</div>
<div class="row belt">
<div class="span3">
<img src="images/NeXO.png" alt="image">
</div>
<div class="span9">
<p><b>Network Approach to Building Gene Ontologies</b><br/>
<a href="http://nexontology.org/">NeXO</a> (The Network Extracted Ontology) uses a principled
computational approach which integrates evidence from hundreds of thousands of individual gene and
protein interactions to construct a complete hierarchy of cellular components and processes. This
data-derived ontology aligns with known biological machinery in the GO Database and also uncovers
many new structures.
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/nbs.png" alt="image">
</div>
<div class="span9">
<p><b>Network-based stratification of tumor mutations</b><br/>
<a href="http://www.nature.com/nmeth/journal/v10/n11/full/nmeth.2651.html">NBS</a> is a method for stratification (clustering) of patients in a cancer cohort based on somatic mutations and a gene interaction network. The method uses network propagation to integrate genome wide somatic mutation profiles for each patient over a gene interaction network, and a non-negative matrix factorization based clustering approach in order to derive biologically meaningful stratification of a patient cohort.
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/cyappstore1.png" alt="image">
</div>
<div class="span9">
<p><b>Cytoscape App Store</b><br/>
The overarching goals of the <a href="http://apps.cytoscape.org">Cytoscape App Store</a> are to
highlight the important features apps add to Cytoscape, to enable researchers to find apps they
need, and for developers to promote their apps. The Cytoscape App Store highlights the important
features that apps add to Cytoscape, enable researchers to find and install apps they need, and help
developers promote their apps.
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/cBioPortal_2.png" alt="image">
</div>
<div class="span9">
<p><b>Network Analysis Tools</b><br/>
Our research programs are exploring an array of new approaches to network analysis, such as how to
use
molecular networks to stratify cancer patient genomes (Network-Based Stratification) or how to
assemble
a gene ontology of the cell directly from molecular network data (<a
href="http://www.nexontology.org/">nexontology.org</a>). In recent years
we
have released a number of widely-used network analysis resources, including the Cancer Biology
Portal
(<a href="http://www.cbioportal.org/public-portal/">cBioPortal.org</a>), the GeneMANIA network
database (<a href="http://genemania.org/">genemania.org</a>), and the Cytoscape Appstore
(<a href="http://apps.cytoscape.org/">apps.cytoscape.org</a>).
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/nrnbPNASfriendNetworks.png" alt="image">
</div>
<div class="span9">
<p><b>Correlated Genotypes in Friendship Networks </b><br/>
In his book CONNECTED, NRNB investigator James Fowler argued that "social networks are in our
nature." Then last year he published a paper showing that genes influence our social network
position -- how central we are, and how likely it is that our friends know one another. In a related
NRNB study published in PNAS this year, Fowler examined another important social network process
called "homophily" -- it's a word that literally means "love of like" and it refers to the idea that
we tend to make friends with people who resemble us -- "birds of a feather flock together."
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/SynthGeneAnalysisYeast.png" alt="image">
</div>
<div class="span9">
<p><b>Synthetic Genetic Analysis of Budding Yeast</b><br/>
NRNB investigator Gary Bader has been collaborating with scientists at the University of Toronto
(Charles Boone, Brenda Andrews) to complete the first complete genetic interaction network for a
cell and to decipher the general principles that govern this network. This reference map provides a
model for expanding genetic network analysis to higher organisms, and it will stimulate valuable
insights into gene function, drug target and mode-of-action analysis. The resulting complete map of
genetic interactions for budding yeast, with ~6000 genes, will contain 36 million quantitative
interaction pairs (18 million unique pairs). The most recent publication of roughly 20% of the
complete map was in the top 30 most cited papers of 2.2 million in 2010. The map currently is 75%
complete and continues to be analyzed.
</p>
</div>
</div>
<div class="row belt">
<div class="span3">
<img src="images/GeneNetworksDNAdamage.png" alt="image">
</div>
<div class="span9">
<p><b>Genetic Networks Remodeled by DNA Damage</b><br/>
Although cellular behaviors are dynamic, the networks that govern these behaviors have been mapped
primarily as static snapshots. To explore network dynamics, the Ideker laboratory has been
collaborating with the laboratory of Nevan Krogan at UCSF to analyze interaction networks as they
are remodeled by different cellular stresses and stimuli. This past year, they developed a new
approach called differential epistasis mapping (dE-MAP) which creates a genetic network based on the
changes in interaction strength observed between two static conditions. Using this approach, they
have mapped widespread changes in genetic interaction among yeast kinases, phosphatases, and
transcription factors as the cell responds to DNA damage. This proof-of-principle work suggests that
differential networks chart a new type of genetic landscape that will be invaluable for mapping many
different cellular responses to stimuli.
</p>
</div>
</div>
<a class="btn button-flat btn-gray pull-right"
href="http://www.citeulike.org/user/nrnb"
target="_blank">
Recent NRNB Publications
</a>
</div>
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