An Error Occurred:
javax.el.ELException: /programs/metagenomes/left-side.xhtml @40,76 value="#{metagenomes_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.MetagenomesHome$Proxy$_$$_WeldClientProxy
javax.faces.FacesException: javax.el.ELException: /programs/metagenomes/left-side.xhtml @40,76 value="#{metagenomes_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.MetagenomesHome$Proxy$_$$_WeldClientProxy
at javax.faces.component.UIOutput.getValue(UIOutput.java:176)
at com.sun.faces.renderkit.html_basic.HtmlBasicInputRenderer.getValue(HtmlBasicInputRenderer.java:189)
at com.sun.faces.renderkit.html_basic.HtmlBasicRenderer.getCurrentValue(HtmlBasicRenderer.java:320)
at com.sun.faces.renderkit.html_basic.HtmlBasicRenderer.encodeEnd(HtmlBasicRenderer.java:200)
at javax.faces.component.UIComponentBase.encodeEnd(UIComponentBase.java:836)
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:896)
at javax.faces.component.UIComponent.encodeAll(UIComponent.java:892)
at com.sun.facelets.FaceletViewHandler.renderView(FaceletViewHandler.java:592)
at gov.doe.jgi.portal.view.common.DefaultViewHandler.renderView(DefaultViewHandler.java:284)
at org.ajax4jsf.application.ViewHandlerWrapper.renderView(ViewHandlerWrapper.java:100)
at org.ajax4jsf.application.AjaxViewHandler.renderView(AjaxViewHandler.java:176)
at com.sun.faces.lifecycle.RenderResponsePhase.execute(RenderResponsePhase.java:106)
at com.sun.faces.lifecycle.LifecycleImpl.phase(LifecycleImpl.java:251)
at com.sun.faces.lifecycle.LifecycleImpl.render(LifecycleImpl.java:144)
at javax.faces.webapp.FacesServlet.service(FacesServlet.java:245)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.ajax4jsf.webapp.BaseXMLFilter.doXmlFilter(BaseXMLFilter.java:206)
at org.ajax4jsf.webapp.BaseFilter.handleRequest(BaseFilter.java:295)
at org.ajax4jsf.webapp.BaseFilter.processUploadsAndHandleRequest(BaseFilter.java:393)
at org.ajax4jsf.webapp.BaseFilter.doFilter(BaseFilter.java:520)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at gov.doe.jgi.portal.view.log.LogFilter.doFilter(LogFilter.java:82)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at gov.doe.jgi.portal.view.common.StaticContentFilter.doFilter(StaticContentFilter.java:167)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at gov.doe.jgi.portal.framework.data.EntityManagerFilter.doFilter(EntityManagerFilter.java:31)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at gov.doe.jgi.portal.framework.config.ConfigFilter.doFilter(ConfigFilter.java:27)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at gov.doe.jgi.portal.tomcat.SessionInvalidateValve.invoke(SessionInvalidateValve.java:74)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:298)
at org.apache.jk.server.JkCoyoteHandler.invoke(JkCoyoteHandler.java:190)
at org.apache.jk.common.HandlerRequest.invoke(HandlerRequest.java:291)
at org.apache.jk.common.ChannelSocket.invoke(ChannelSocket.java:774)
at org.apache.jk.common.ChannelSocket.processConnection(ChannelSocket.java:703)
at org.apache.jk.common.ChannelSocket$SocketConnection.runIt(ChannelSocket.java:896)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:690)
at java.lang.Thread.run(Thread.java:722)
Caused by: javax.el.ELException: /programs/metagenomes/left-side.xhtml @40,76 value="#{metagenomes_home.latestReleases}": Error reading 'latestReleases' on type gov.doe.jgi.portal.view.pages.MetagenomesHome$Proxy$_$$_WeldClientProxy
at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:76)
at javax.faces.component.UIOutput.getValue(UIOutput.java:173)
... 48 more
Caused by: java.lang.NullPointerException
at java.util.regex.Matcher.getTextLength(Matcher.java:1233)
at java.util.regex.Matcher.reset(Matcher.java:308)
at java.util.regex.Matcher.<init>(Matcher.java:228)
at java.util.regex.Pattern.matcher(Pattern.java:1088)
at gov.doe.jgi.portal.framework.config.PortalConfig.getOrganismsMatching(PortalConfig.java:1012)
at gov.doe.jgi.portal.view.pages.ProgramHome$ProgramHomeData.init(ProgramHome.java:124)
at gov.doe.jgi.portal.view.pages.ProgramHome$ProgramHomeData.check(ProgramHome.java:114)
at gov.doe.jgi.portal.view.pages.ProgramHome$ProgramHomeData.getLatestReleases(ProgramHome.java:74)
at gov.doe.jgi.portal.view.pages.ProgramHome.getLatestReleases(ProgramHome.java:224)
at gov.doe.jgi.portal.view.pages.MetagenomesHome$Proxy$_$$_WeldClientProxy.getLatestReleases(MetagenomesHome$Proxy$_$$_WeldClientProxy.java)
at sun.reflect.GeneratedMethodAccessor2367.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:601)
at javax.el.BeanELResolver.getValue(BeanELResolver.java:62)
at javax.el.CompositeELResolver.getValue(CompositeELResolver.java:54)
at com.sun.faces.el.FacesCompositeELResolver.getValue(FacesCompositeELResolver.java:64)
at org.apache.el.parser.AstValue.getValue(AstValue.java:123)
at org.apache.el.ValueExpressionImpl.getValue(ValueExpressionImpl.java:186)
at org.jboss.weld.el.WeldValueExpression.getValue(WeldValueExpression.java:50)
at com.sun.facelets.el.TagValueExpression.getValue(TagValueExpression.java:71)
... 49 more
- <AjaxViewRoot id="_viewRoot" immediate="false" locale="en_US" renderKitId="HTML_BASIC" renderRegionOnly="false" rendered="true" selfRendered="false" submitted="false" transient="false" viewId="/programs/metagenomes/publications_genomes.xhtml">
- <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" >
- <html xmlns="http://www.w3.org/1999/xhtml" xmlns:t="http://myfaces.apache.org/tomahawk">
<head>
- <HtmlOutputText escape="false" id="j_id2" rendered="true" transient="false" value="<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/>
<link href="/css/genome2.css" rel="stylesheet" type="text/css"/>
<!--[if lt IE 8]><script src="/js/IE8.js" type="text/javascript"></script><![endif]--><script type="text/javascript" src="/js/ie_workarounds.js"></script><!--[if IE 6]><link type="text/css" rel="stylesheet" href="/css/ie6.css"><![endif]--><script type="text/javascript">var _gaq = _gaq || [];_gaq.push(['_setAccount', 'UA-23422913-1']);_gaq.push(['_trackPageview']);_gaq.push(['_setCustomVar',3,'Looged-In','No',2]);(function() {var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);})();</script>"/>
- <script type="text/javascript" src="/js/jquery.js"/>
<script type="text/javascript" src="/js/treeUtils.js"/>
<script type="text/javascript" src="/js/preload.js"/>
<script type="text/javascript" src="/js/superfish.js"/>
<script type="text/javascript" src="/js/supersubs.js"/>
<script type="text/javascript">
<!--
jQuery.noConflict();
var g_selectOrg = null;
var g_wasInitialized = false;
function gotoOrganism() {
if( !g_wasInitialized )
initOrgSelectionBoxes();
var selectLocation = document.getElementById('selectLocation');
var encodedString = g_selectOrg.options[g_selectOrg.selectedIndex].value;
var loc = selectLocation.options[selectLocation.selectedIndex].value;
var url = "error";
if( loc == "home" )
url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/$2');
else if( loc == "browse" )
url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/cgi-bin/browserLoad?db=$2&position=$3');
else if( loc == "blast" )
url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/pages/blast.jsf?db=$2');
else if( loc == "download" )
url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/$2/$2.download.html');
else if( loc == "annotation" )
url = encodedString.replace(/(.*),(.*),(.*),(.*)/,'/$2/$2.annotation.html');
//alert('redirecting to ' + url);
top.location.href = url;
}
function emailCollaborator() {
var selectEmail = document.getElementById("selectEmail");
var emailObj = selectEmail.options[ selectEmail.selectedIndex ];
location.href = "mailto:" + emailObj.value.replace(/\+/g, "%20") + "?subject=" + escape(emailObj.text);
}
function filterOrganisms() {
if( !g_wasInitialized )
initOrgSelectionBoxes();
var category = jQuery("#selectCategory").val();
var selectOrg;
if( category == "all" )
selectOrg = jQuery( "#selectOrg" );
else if( category == "Bacteria" )
selectOrg = jQuery( "#selectOrgBacteria" );
else if( category == "Eukaryota" )
selectOrg = jQuery( "#selectOrgEukaryota" );
else if( category == "Archaea" )
selectOrg = jQuery( "#selectOrgArchaea" );
else if( category == "Microbiome" )
selectOrg = jQuery( "#selectOrgMicrobiomes" );
g_selectOrg = selectOrg[0];
selectOrg[0].selectedIndex = 0;
jQuery(".orgSelectBox").hide();
selectOrg.show();
filterLocations(selectOrg[0]);
}
function filterLocations(selectOrg) {
if( !g_wasInitialized )
initOrgSelectionBoxes();
var sel = selectOrg.options[selectOrg.selectedIndex];
var isEuk = sel.value.indexOf("Eukaryota") == 0;
var selectedLocation = jQuery( "#selectLocation" )[0];
if( !isEuk ) {
var showAnnotation = sel.value[sel.value.length - 1] == '1';
if( showAnnotation ) {
selectedLocation.options[1].text = "Annotation";
selectedLocation.options[1].value = "annotation";
selectedLocation.options[1].disabled = false;
} else {
if( selectedLocation.selectedIndex == 1 ) // Browse
selectedLocation.selectedIndex = 0; // Home
var browseLoc = selectedLocation.options[1];
browseLoc.disabled = true;
}
} else {
selectedLocation.options[1].text = "Browse";
selectedLocation.options[1].value = "browse";
selectedLocation.options[1].disabled = false;
}
}
function initOrgSelectionBoxes() {
var selectCategory = jQuery( "#selectCategory" );
if( selectCategory.length == 0 ) // if the page is rendered without the organism drop-downs, then selectOrg.length will be 0
return;
g_wasInitialized = true;
jQuery("#selectCategory").change( function () { filterOrganisms(); });
jQuery(".orgSelectBox").change( function () { filterLocations(this); });
filterOrganisms(); // initialize
}
jQuery(document).ready(function(){
jQuery("ul.sf-menu").supersubs({
minWidth: 12, // minimum width of sub-menus in em units
maxWidth: 20, // maximum width of sub-menus in em units
extraWidth: 1 // extra width can ensure lines don't sometimes turn over
// due to slight rounding differences and font-family
}).superfish(); // call supersubs first, then superfish, so that subs are
// not display:none when measuring. Call before initialising
// containing tabs for same reason.
});
var treeOfLife = new Object;
function showTreeOfLifeNodeMenu(nodeName, nodeLabel) {
var url = '/ext-api/tree-of-life/metagenome-node/' + nodeName;
// The 'menu' array will be filled in with data during the eval(data) call below.
if( typeof menu[nodeName + ".menuindex"] != 'number' || typeof menu[nodeName + ".Name"] != 'string' || menu[nodeName + ".menuindex"] < 1) {
jQuery.get(url, function(data) {
treeOfLife[nodeName] = 1;
eval(data);
multitool( x, y, nodeName, nodeLabel );
});
} else {
multitool( x, y, nodeName, nodeLabel );
}
}
-->
</script>
<script type="text/javascript">
function init() {
MM_preloadImages('/images/closeBtn_over.gif','/images/questionBtn_over.gif');
initOrgSelectionBoxes();
}
</script>
<link href="/css/tree.css" rel="stylesheet" type="text/css"/>
<link href="/css/search.css" rel="stylesheet" type="text/css"/>
<link href="/css/metagenome.css" rel="stylesheet" type="text/css"/>
<link rel="stylesheet" media="screen" href="/css/superfish.css"/>
<link rel="stylesheet" media="screen" href="/css/superfish_metagenome.css"/>
- <title>Metagenomic Publications of Genomes</title>
</head>
<body onload="init();">
- <HtmlOutputText escape="false" id="j_id5" rendered="true" transient="false" value="<div class="header_wrap">
<div class="header_top"><div id="subnavleft"><a class="skipnav" href="#skipnav" accesskey="S"><img src="/images/clear.gif" alt="skip navigation" width="1" height="1" border="0" /></a><ul id="subnavicons"><li><a target="_parent" href="http://www.jgi.doe.gov" alt=""> <img class="header_image" alt="DOE Joint Genome Institute logo" style="padding-right: 2em" src="/images/jgiLogo_icon.gif"/></a></li><li><a target="_parent" href="/"><img border="0" alt="Genome Portal icon" src="/images/tree_icon.gif"/></a></li>
<li><a class="textlink" target="_parent" href="/">Home</a></li>
<li><a target="_parent" href="/genome-projects/"><img border="0" alt="Genome Projects icon" src="/images/genomeProjects_icon.gif"/></a></li>
<li><a class="textlink" target="_parent" href="/genome-projects/">Project List</a></li>
<li><a href="javascript: if(top.window.location.href.search('accessDenied')==-1) { document.cookie='jgi_return=' + escape(top.window.location.href) + '; domain=.jgi-psf.org; path=/;'; } top.window.location.href='https://signon2.jgi-psf.org/signon';"><img border="0" alt="Login icon" src="/images/login_icon.gif"/></a></li><li><a class="textlink" target="_parent" href="javascript: if(top.window.location.href.search('accessDenied')==-1) { document.cookie='jgi_return=' + escape(top.window.location.href) + '; domain=.jgi-psf.org; path=/;'; } top.window.location.href='https://signon2.jgi-psf.org/signon';">Login</a></li></ul></div></div></div>
<a name="skipnav"></a>
"/>
- <!--ui:define name="body"-->
<!-- div id="toolmenudiv" style="position: absolute; left: 100px; top: 100px; visibility: visible; overflow: auto;" / -->
<div id="toolmenudiv" style="position: absolute; padding:0;margin:0; left: 100px; top: 100px; visibility: visible; overflow: auto;" onmouseover="window.clearTimeout(timeoutId);" onmouseout="timeoutId = window.setTimeout('divoff(\'toolmenudiv\')', APP_TIMEOUT);"/>
<!--Main content section-->
<div id="container">
<!--navigation and top banner-->
- <div id="nav">
<ul class="sf-menu">
<li class="#{pagetype=='home'?'selected':''}"><a href="/programs/metagenomes/index.jsf" title="Back to home page" class="topmenu" id="home">Home</a></li>
<li class="#{pagetype=='project_list'?'selected':''}"><a href="/programs/metagenomes/metagenomic-projects.jsf" class="topmenu" title="Projects sequenced at JGI" id="project_list">Project List</a>
</li>
<li class="#{pagetype=='user_programs'?'selected':''}"><a href="http://www.jgi.doe.gov/CSP/index.html" title="Community Sequencing Program" class="topmenu" id="user_programs">User Programs</a></li>
<li class="#{pagetype=='science'?'selected':''}"><a href="/programs/metagenomes/publications_genomes.jsf" class="topmenu" title="Metagenome Projects and Publications" id="science">Science</a>
<ul class="submenu">
<li><a class="sf-with-ul" href="/programs/metagenomes/poplar_biomass.jsf">Projects<span class="sf-sub-indicator"> »</span></a>
<ul>
<li><a href="http://genomebiology.jgi-psf.org/Content/Metagenomic_analysis.htm">Metagenome Analysis</a></li>
<li><a href="/programs/metagenomes/poplar_biomass.jsf">Poplar Biomass</a></li>
<li><a href="/programs/metagenomes/CowRumenMetagenome.pdf">Cow Rumen Metagenome</a></li>
</ul>
</li>
<li><a class="sf-with-ul" href="/programs/metagenomes/publications_genomes.jsf">Publications</a>
</li>
</ul>
</li>
<li class="#{pagetype=='informatics'?'selected':''}"><a href="/programs/metagenomes/informatics_publications.jsf" class="topmenu" title="Informatics" id="informatics">Informatics</a>
<ul class="submenu">
<li><a class="sf-with-ul" href="/programs/metagenomes/systems.jsf">Systems<span class="sf-sub-indicator"> »</span></a>
<ul>
<li><a href="http://img.jgi.doe.gov/">IMG/M</a></li>
<li><a href="http://www.genomesonline.org/">GOLD</a></li>
</ul>
</li>
<li><a class="sf-with-ul" href="/programs/metagenomes/methods.jsf">Methods<span class="sf-sub-indicator"> »</span></a>
<ul>
<li><a href="/programs/metagenomes/assembly.jsf">Assembly</a></li>
<li><a href="http://journals.sfu.ca/sigen/index.php/sigen/article/viewFile/sigs.632/sigs632.pdf">Annotation Pipeline</a></li>
<li><a href="http://clams.jgi-psf.org/">CLaMS</a></li>
<li><a href="http://coal.jgi-psf.org/CoverageServer/">GammaCov</a></li>
<li><a href="http://pyrotagger.jgi-psf.org/cgi-bin/index.pl">PyroTagger</a></li>
</ul>
</li>
<li><a class="sf-with-ul" href="/programs/metagenomes/benchmarks.jsf">Benchmarks</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/data_reduction.jsf">Projects<span class="sf-sub-indicator"> »</span></a>
<ul>
<li><a href="http://fames.jgi-psf.org/">FAMeS</a></li>
<li><a href="/programs/metagenomes/data_reduction.jsf">Data Reduction</a></li>
<li><a href="/programs/metagenomes/binning.jsf">Binning</a></li>
<li><a href="/programs/metagenomes/cow_rumen_analysis.jsf">Cow Rumen Metagenome Data Analysis</a></li>
</ul>
</li>
<li><a class="sf-with-ul" href="/programs/metagenomes/informatics_publications.jsf">Publications</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/credits.jsf">Credits</a></li>
</ul>
</li>
<li class="#{pagetype=='outreach'?'selected':''}"><a href="/programs/metagenomes/workshops.jsf" class="topmenu" title="Metagenomics workshops and Meetings" id="outreach">Outreach</a>
<ul class="submenu">
<li><a class="sf-with-ul" href="/programs/metagenomes/workshops.jsf">Workshops</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/meetings.jsf">Meetings</a></li>
</ul>
</li>
<li class="#{pagetype=='about_program'?'selected':''}"><a href="/programs/metagenomes/mission.jsf" title="about program, mission, organization, advisory_committee" class="topmenu" id="about_program">About Program</a>
<ul class="submenu">
<li><a class="sf-with-ul" href="/programs/metagenomes/mission.jsf">Mission</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/organization.jsf">Organization</a></li>
<li><a class="sf-with-ul" href="/programs/metagenomes/advisory_committee.jsf">Advisory Committee</a></li>
</ul>
</li>
</ul>
</div>
<img src="/images/metagenome/metagenome_banner.png" width="" height="" border="0" usemap="#logomap" class="banner" alt="banner with logo of Metagenomics program"/>
<map name="logomap" id="logomap">
<area shape="rect" coords="10,0,350,72" href="/programs/metagenomes/index.jsf" alt="Metagenomics Program at JGI, Home"/>
</map>
<a name="skipnav" id="skipnav"/>
- <!--end of navigation and top banner-->
<!-- content section-->
<div id="content">
<!--left side panel -->
- <div id="leftside"><!--section navigation --> <!-- <div id="sectionnav">
<a href="/pages/fungi/about_program.jsf"><h2 class="list_title" >Genomic Encyclopedia of Fungi</h2></a>
<ul>
<li><a class="list_header_feedstock" href="/pages/fungi/about_program.jsf#feedstock">Plant Feedstock Health</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#symbiosis">Mycorrhizal Symbiosis</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#pathogenicity">Plant Pathogenicity</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#biocontrol">Biocontrol</a></li>
<li><a class="list_header_biorefinery" href="/pages/fungi/about_program.jsf#biorefinery">Biorefinery</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#biorefinery">Lignocellulose Degradation</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#biorefinery">Sugar Fermentation</a></li>
<li><a class="list_subheader" href="/pages/fungi/about_program.jsf#biorefinery">Industrial Organisms</a></li>
<li><a class="list_header_diversity" href="/pages/fungi/about_program.jsf#diversity">Fungal Diversity</a></li>
</ul>
</div>--> <!--end of section navigation -->
<div class="clear"/>
<!--Announcements -->
<div id="announcements">
<h2 class="red">Announcements</h2>
<ul>
<li><span class="date">January 23-24, 2012 <br/>
</span><a href="http://www.jgi.doe.gov/meetings/csp-pi-workshop/">CSP 2012 PI Workshop</a>, Walnut Creek, CA
</li>
</ul>
</div>
<a class="link_arrow" href="/programs/metagenomes/workshops.jsf">more</a>
<div class="grey_divider"/>
<!--end of Announcements -->
<div class="clear"/>
<!--New Releases -->
<div id="new_releases">
<h2 class="red">Releases</h2>
- <HtmlOutputText escape="false" id="j_id10" rendered="true" transient="false"/>
- <a class="link_arrow" href="/programs/metagenomes/genome-releases.jsf">more</a>
<!--end of New Releases -->
<div class="grey_divider"/>
</div>
</div>
- <!--end of left side panel -->
<!--right side panel -->
<div id="rightside">
<h1>Metagenomic Publications of Genomes</h1>
<ul class="outlines">
<li><a href="#2011">2011</a></li>
<li><a href="#2010">2010</a></li>
<li><a href="#2009">2009</a></li>
<li><a href="#2008">2008</a></li>
<li><a href="#2007">2007</a></li>
<li><a href="#2006">2006</a></li>
<li><a href="#2005">2005</a></li>
<li><a href="#2004">2004</a></li>
</ul>
<h2 class="subheader_with_bg"><a name="2011"/>2011</h2>
<ol class="publications">
<li>Deep metagenome sequencing illuminates permafrost response to thaw. Mackelprang R et al. <b> Nature.</b> In press.</li>
<li>IMG/M: the integrated metagenome data management and comparative analysis system. Markowitz V et al. <b> Nucleic Acids Res.</b> In press.</li>
<li>Metagenomics, metatranscriptomics and single cell sequencing reveal bacterial response to the Gulf oil spill. Mason OU et al. <b> Nature. </b> In press.</li>
<li>ClaMS: A Classifier for Metagenomic Sequences. Standards in Genomic Sciences. Pati A et al. <b/> In press. </li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/22030673">Individual genome assembly from complex community short-read metagenomic datasets</a>. Luo C et al<b>. ISME J. </b> 2011 Oct 27. doi: 10.1038/ismej.2011.147. [Epub ahead of print]</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/22004549">Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome</a>. Berg Miller ME et al<b>. Environ Microbiol. </b>2011 Oct 17. doi: 10.1111/j.1462-2920.2011.02593.x. [Epub ahead of print]</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21938024">Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows </a>. Godoy-Vitorino F et al<b>. ISME J. </b>2011 Sep 22. doi: 10.1038/ismej.2011.131. [Epub ahead of print]</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21885783">Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean </a>. Swan BK et al<b>. Science. </b>2011 Sep 2;333(6047):1296-300.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21724886">Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass </a>. Gladden JM et al<b>. Appl Environ Microbiol. </b>2011 Aug;77(16):5804-12. Epub 2011 Jul 1.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21719642">Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies</a>. Pope PB et al.<b>. Science. </b>2011 Jul 29;333(6042):646-8. Epub 2011 Jun 30.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21552244">Isolation of Succinivibrionaceae Implicated in Low Methane Emissions from Tammar Wallabies</a>. Pope PB et al.<b>. Science. </b>2011 Jul 29;333(6042):646-8. Epub 2011 Jun 30.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21552244">Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications</a>. Yilmaz P et al.<b>. Nat Biotechnol </b>2011 May;29(5):415-20.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21625595">Phage Encoded H-NS: A Potential Achilles Heel in the Bacterial Defence System</a>. Skennerton CT et al. <b>PLoS One </b>2011;6(5):e20095. Epub 2011 May 18.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21520015">Bioenergy feedstock-specific enrichment of microbial populations during high-solids thermophilic deconstruction</a>. Reddy AP et al. <b>Biotechnol Bioeng. </b>2011 Sep;108(9):2088-98. doi: 10.1002/bit.23176. Epub 2011 May 2.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21559391">Characterization of trapped lignin-degrading microbes in tropical forest soil.</a> DeAngelis KM et al. <b>PLoS One. </b>2011 Apr 29;6(4):e19306.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21368904">Cellulose-degrading bacteria associated with the invasive woodwasp Sirex noctilio</a>. Adams AS et al. <b>ISME J. </b>2011 Aug;5(8):1323-31. doi: 10.1038/ismej.2011.14. Epub 2011 Mar 3.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21194740">Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma</a>. Huang YJ et al. <b>J Allergy Clin Immunol.</b> 2011 Feb;127(2):372-381.e1-3. Epub 2010 Dec 30.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21273488">Metagenomic discovery of biomass-degrading genes and genomes from cow rumen</a>. Hess M et al. <b>Science.</b> 2011 Jan 28;331(6016):463-7. </li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20613792">Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome</a>. Burnum KE et al. <b>ISME J.</b> 2011 Jan;5(1):161-4. </li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21514469">Genomics for key players in the N cycle from Guinea pigs to the next frontier</a>. Chain PS et al. <b>Methods Enzymol.</b> 2011;496:289-318. </li>
</ol>
<h2 class="subheader_with_bg"><a name="2010"/>2010</h2>
<ol class="publications">
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/19725865">Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates</a>. Kunin V, Engelbrektson A, Ochman H and Hugenholtz P. <b>Environ Microbiol.</b> 2010 Jan; 12 (1): 118-23</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20008478">Estimating DNA coverage and abundance in metagenomes using a gamma approximation</a>. Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN and Kyrpides NC. <b>Bioinformatics.</b> 2010 Feb 1; 26 (3): 295-301</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20182523">Metagenomic insights into evolution of a heavy metal-contaminated groundwater microbial community</a>. Hemme CL, Deng Y, Gentry TJ, Fields MW, Wu L, Barua S, Barry K, Tringe SG, Watson DB, He Z, Hazen TC, Tiedje JM, Rubin EM and Zhou J. <b>ISME J.</b> 2010 May; 4 (5): 660-72</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20148930">Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge</a>. He S, Kunin V, Haynes M, Martin HG, Ivanova N, Rohwer F, Hugenholtz P and McMahon KD. <b>Environ Microbiol.</b> 2010 Feb 9; </li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20090784">Experimental factors affecting PCR-based estimates of microbial species richness and evenness</a>. Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H and Hugenholtz P. <b>ISME J.</b> 2010 May; 4 (5): 642-7</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20421484">Enigmatic, ultrasmall, uncultivated Archaea</a>. Baker BJ, Comolli LR, Dick GJ, Hauser LJ, Hyatt D, Dill BD, Land ML, Verberkmoes NC, Hettich RL and Banfield JF. <b>Proc Natl Acad Sci U S A.</b> 2010 May 11; 107 (19): 8806-11</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20098679">Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost community</a>. Allgaier M, Reddy A, Park JI, Ivanova N, D'Haeseleer P, Lowry S, Sapra R, Hazen TC, Simmons BA, VanderGheynst JS and Hugenholtz P. <b>PLoS One.</b> 2010 5 (1): e8812</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20653767">A call for standardized classification of metagenome projects</a>. Ivanova, N., Tringe, S.G., Liolios, K., Liu, W.T., Morrison, N., Hugenholtz, P., Kyrpides, N.C. <b>Environmental Microbiology</b> 12: 1803-1805, 2010</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20668243">Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores</a>. Pope, P.B., Denman, S.E., Jones, M., Tringe, S.G., Barry, K., Malfatti, S.A., McHardy, A.C., Cheng, J.-F., Hugenholtz, P., McSweeney, C.S., Morrison, M. <b>Proceedings of the National Academy of Sciences </b>107: 14793-14798, 2010.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20668244">Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton</a>. Cuvelier, M.L., Allen, A.E., Monier, A., McCrow, J.P., Messie, M., Tringe, S.G., Woyke, T., Welsh, R.M., Ishoey, T., Lee, J.-H., Binder, B.J., Latasa, M., Guigand, C., Buck, K.R., DuPont, C.L., Hilton, J.A., Thiagarajan, M., Caler, E., Lasken, R., Chavez, F.P., Worden, A.Z. <b>Proceedings of the National Academy of Sciences </b>107: 14679-14684, 2010</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20676626">Structure and dynamics of the microbial communities underlying the carboxylate platform for biofuel production</a>. Hollister, E.B., Forrest, A.K., Wilkinson, H.H., Ebbole, D.J., Malfatti, S.A., Tringe, S.G., Holtzapple, M.T., Gentry, T.J. <b>Applied Microbiology and Biotechnology</b> 88: 389-99, 2010.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20686509">Multiple syntrophic interactions in a terephthalate-degrading methanogenic consortium</a>. Lykidis, A., Chen, C.-L., Tringe, S.G., McHardy, A., Copeland, A., Kyrpides, N., Hugenholtz, P., and Liu, W.-T. <b>ISME Journal</b>, published online Aug 5 2010.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20852648">Validation of two ribosomal RNA removal methods for microbial metatranscriptomics</a>. He, S., Wurtzel, O., Singh, K., Froula, J.L., Yilmaz, S., Tringe, S.G., Wang, Z., Chen, F., Lindquist, E.A., Sorek, R., Hugenholtz, P. <b>Nature Methods</b> 7: 807-12, 2010.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20885794">An insect herbivore microbiome with high plant biomass-degrading capacity</a>. Suen, G., Scott, J.J., Aylward, F.O., Adams, S.M., Tringe, S.G., Pinto-Tomás, A.A., Foster, C.E., Pauly, M., Weimer, P.J., Barry, K.W., Goodwin, L.A., Bouffard, P., Li, L., Osterberger, J., Harkins, T.T., Slater, S.C., Donahue, T.J., Currie, C.R. <b>PLoS Genetics</b> 6: e1001129, 2010.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/19914934">The Genomes OnLine Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata</a>. Liolios, K., Chen, I-MA., Mavromatis, K., Tavernarakis, N., Hugenholtz, P., Markowitz, VM., and Kyrpides, N.C. <b>Nucleic Acids </b> Res. 38:D346-54.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21116242">Multiple displacement amplification compromises quantitative analysis of metagenomes</a>. Yilmaz S, Allgaier M, Hugenholtz P. <b>Nature Methods </b> 7(12):943-4.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/21103409">Evolutionary relationships of wild hominids recapitulated by gut microbial communities</a>. Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, Hugenholtz P. <b>PLoS Biology </b> 2011 Jan;5(1):161-4. Epub 2010 Jul 8.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20613792">Proteome insights into the symbiotic relationship between a captive colony of Nasutitermes corniger and its hindgut microbiome</a>. Burnum KE, Callister SJ, Nicora CD, Purvine SO, Hugenholtz P, Warnecke F, Scheffrahn RH, Smith RD, Lipton MS. <b>ISME J. </b> 8(11):e1000546.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20505753">Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations</a>. Yilmaz S, Haroon MF, Rabkin BA, Tyson GW, Hugenholtz P. <b>ISME J. </b> 2010 Oct;4(10):1352-6. Epub 2010 May 27.</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/20090784">Experimental factors affecting PCR-based estimates of microbial species richness and evenness</a>. Engelbrektson A, Kunin V, Wrighton KC, Zvenigorodsky N, Chen F, Ochman H, Hugenholtz P. <b>ISME J. </b> May;4(5):642-7. Epub 2010 Jan 21.</li>
</ol>
<h2 class="subheader_with_bg"><a name="2009"/>2009</h2>
<ol class="publications">
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/19900896">Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones</a>. Walsh DA, Zaikova E, Howes CG, Song YC, Wright JJ, Tringe SG, Tortell PD and Hallam SJ. <b>Science.</b> 2009 Oct 23; 326 (5952): 578-82</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/19352371">Getting to the core of the gut microbiome</a>. Tschop MH, Hugenholtz P and Karp CL. <b>Nat Biotechnol.</b> 2009 Apr; 27 (4): 344-6</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/19696045">ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes</a>. Kristiansson E, Hugenholtz P and Dalevi D. <b>Bioinformatics.</b> 2009 Oct 15; 25 (20): 2737-8</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/19921923">Biocorrosive thermophilic microbial communities in Alaskan North Slope oil facilities</a>. Duncan KE, Gieg LM, Parisi VA, Tanner RS, Tringe SG, Bristow J and Suflita JM. <b>Environ Sci Technol.</b> 2009 Oct 15; 43 (20): 7977-84</li>
</ol>
<h2 class="subheader_with_bg"><a name="2008"/>2008</h2>
<ol class="publications">
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18769460">A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells</a>. Wrighton KC, Agbo P, Warnecke F, Weber KA, Brodie EL, DeSantis TZ, Hugenholtz P, Andersen GL and Coates JD. <b>ISME J.</b> 2008 Nov; 2 (11): 1146-56</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18976703">Prokaryotic community profiles at different operational stages of a Greek solar saltern</a>. Tsiamis G, Katsaveli K, Ntougias S, Kyrpides N, Andersen G, Piceno Y and Bourtzis K. <b>Res Microbiol.</b> 2008 Nov-Dec; 159 (9-10): 609-27</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18382653">The airborne metagenome in an indoor urban environment</a>. Tringe SG, Zhang T, Liu X, Yu Y, Lee WH, Yap J, Yao F, Suan ST, Ing SK, Haynes M, Rohwer F, Wei CL, Tan P, Bristow J, Rubin EM and Ruan Y. <b>PLoS One.</b> 2008 3 (4): e1862</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18817891">A renaissance for the pioneering 16S rRNA gene</a>. Tringe SG and Hugenholtz P. <b>Curr Opin Microbiol.</b> 2008 Oct; 11 (5): 442-6</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18441115">Assembly of viral metagenomes from yellowstone hot springs</a>. Schoenfeld T, Patterson M, Richardson PM, Wommack KE, Young M and Mead D. <b>Appl Environ Microbiol.</b> 2008 Jul; 74 (13): 4164-74</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18643843">Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal</a>. Peterson SB, Warnecke F, Madejska J, McMahon KD and Hugenholtz P. <b>Environ Microbiol.</b> 2008 Oct; 10 (10): 2692-703</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18643843">Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of biological phosphorus removal</a>. Peterson SB, Warnecke F, Madejska J, McMahon KD and Hugenholtz P. <b>Environ Microbiol.</b> 2008 Oct; 10 (10): 2692-703</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17932063">IMG/M: a data management and analysis system for metagenomes</a>. Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P and Kyrpides NC. <b>Nucleic Acids Res.</b> 2008 Jan; 36 (Database issue): D534-8</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18523433">Millimeter-scale genetic gradients and community-level molecular convergence in a hypersaline microbial mat</a>. Kunin V, Raes J, Harris JK, Spear JR, Walker JJ, Ivanova N, von Mering C, Bebout BM, Pace NR, Bork P and Hugenholtz P. <b>Mol Syst Biol.</b> 2008 4 198</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18077539">A bacterial metapopulation adapts locally to phage predation despite global dispersal</a>. Kunin V, He S, Warnecke F, Peterson SB, Garcia Martin H, Haynes M, Ivanova N, Blackall LL, Breitbart M, Rohwer F, McMahon KD and Hugenholtz P. <b>Genome Res.</b> 2008 Feb; 18 (2): 293-7</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/19052320">A bioinformatician's guide to metagenomics</a>. Kunin V, Copeland A, Lapidus A, Mavromatis K and Hugenholtz P. <b>Microbiol Mol Biol Rev.</b> 2008 Dec; 72 (4): 557-78, Table of Contents</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18711340">High-resolution metagenomics targets specific functional types in complex microbial communities</a>. Kalyuzhnaya MG, Lapidus A, Ivanova N, Copeland AC, McHardy AC, Szeto E, Salamov A, Grigoriev IV, Suciu D, Levine SR, Markowitz VM, Rigoutsos I, Tringe SG, Bruce DC, Richardson PM, Lidstrom ME and Chistoserdova L. <b>Nat Biotechnol.</b> 2008 Sep; 26 (9): 1029-34</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18818648">Microbiology: metagenomics</a>. Hugenholtz P and Tyson GW. <b>Nature.</b> 2008 Sep 25; 455 (7212): 481-3</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18416669">Habitat-Lite: a GSC case study based on free text terms for environmental metadata</a>. Hirschman L, Clark C, Cohen KB, Mardis S, Luciano J, Kottmann R, Cole J, Markowitz V, Kyrpides N, Morrison N, Schriml LM and Field D. <b>OMICS.</b> 2008 Jun; 12 (2): 129-36</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18564916">Toward a standards-compliant genomic and metagenomic publication record</a>. Garrity GM, Field D, Kyrpides N, Hirschman L, Sansone SA, Angiuoli S, Cole JR, Glockner FO, Kolker E, Kowalchuk G, Moran MA, Ussery D and White O. <b>OMICS.</b> 2008 Jun; 12 (2): 157-60</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18535141">A korarchaeal genome reveals insights into the evolution of the Archaea</a>. Elkins JG, Podar M, Graham DE, Makarova KS, Wolf Y, Randau L, Hedlund BP, Brochier-Armanet C, Kunin V, Anderson I, Lapidus A, Goltsman E, Barry K, Koonin EV, Hugenholtz P, Kyrpides N, Wanner G, Richardson P, Keller M and Stetter KO. <b>Proc Natl Acad Sci U S A.</b> 2008 Jun 10; 105 (23): 8102-7</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18689842">Annotation of metagenome short reads using proxygenes</a>. Dalevi D, Ivanova NN, Mavromatis K, Hooper SD, Szeto E, Hugenholtz P, Kyrpides NC and Markowitz VM. <b>Bioinformatics.</b> 2008 Aug 15; 24 (16): i7-13</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18845759">Environmental genomics reveals a single-species ecosystem deep within Earth</a>. Chivian D, Brodie EL, Alm EJ, Culley DE, Dehal PS, DeSantis TZ, Gihring TM, Lapidus A, Lin LH, Lowry SR, Moser DP, Richardson PM, Southam G, Wanger G, Pratt LM, Andersen GL, Hazen TC, Brockman FJ, Arkin AP and Onstott TC. <b>Science.</b> 2008 Oct 10; 322 (5899): 275-8</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18426903">Identification of ancient remains through genomic sequencing</a>. Blow MJ, Zhang T, Woyke T, Speller CF, Krivoshapkin A, Yang DY, Derevianko A and Rubin EM. <b>Genome Res.</b> 2008 Aug; 18 (8): 1347-53</li>
</ol>
<h2 class="subheader_with_bg"><a name="2007"/>2007</h2>
<ol class="publications">
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18033299">Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite</a>. Warnecke F, Luginbuhl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, Cayouette M, McHardy AC, Djordjevic G, Aboushadi N, Sorek R, Tringe SG, Podar M, Martin HG, Kunin V, Dalevi D, Madejska J, Kirton E, Platt D, Szeto E, Salamov A, Barry K, Mikhailova N, Kyrpides NC, Matson EG, Ottesen EA, Zhang X, Hernandez M, Murillo C, Acosta LG, Rigoutsos I, Tamayo G, Green BD, Chang C, Rubin EM, Mathur EJ, Robertson DE, Hugenholtz P and Leadbetter JR. <b>Nature.</b> 2007 Nov 22; 450 (7169): 560-5</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/18177506">Building on basic metagenomics with complementary technologies</a>. Warnecke F and Hugenholtz P. <b>Genome Biol.</b> 2007 8 (12): 231</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17272687">Quantitative phylogenetic assessment of microbial communities in diverse environments</a>. von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N and Bork P. <b>Science.</b> 2007 Feb 23; 315 (5815): 1126-30</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17303757">The Calyptogena magnifica chemoautotrophic symbiont genome</a>. Newton IL, Woyke T, Auchtung TA, Dilly GF, Dutton RJ, Fisher MC, Fontanez KM, Lau E, Stewart FJ, Richardson PM, Barry KW, Saunders E, Detter JC, Wu D, Eisen JA and Cavanaugh CM. <b>Science.</b> 2007 Feb 16; 315 (5814): 998-1000</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17179938">Accurate phylogenetic classification of variable-length DNA fragments</a>. McHardy AC, Martin HG, Tsirigos A, Hugenholtz P and Rigoutsos I. <b>Nat Methods.</b> 2007 Jan; 4 (1): 63-72</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17468765">Use of simulated data sets to evaluate the fidelity of metagenomic processing methods</a>. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy AC, Rigoutsos I, Salamov A, Korzeniewski F, Land M, Lapidus A, Grigoriev I, Richardson P, Hugenholtz P and Kyrpides NC. <b>Nat Methods.</b> 2007 Jun; 4 (6): 495-500</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17620602">Dissecting biological "dark matter" with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth</a>. Marcy Y, Ouverney C, Bik EM, Losekann T, Ivanova N, Martin HG, Szeto E, Platt D, Hugenholtz P, Relman DA and Quake SR. <b>Proc Natl Acad Sci U S A.</b> 2007 Jul 17; 104 (29): 11889-94</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17409203">Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa</a>. Flanagan JL, Brodie EL, Weng L, Lynch SV, Garcia O, Brown R, Hugenholtz P, DeSantis TZ, Andersen GL, Wiener-Kronish JP and Bristow J. <b>J Clin Microbiol.</b> 2007 Jun; 45 (6): 1954-62</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17436031">The positive role of the ecological community in the genomic revolution</a>. Field D and Kyrpides N. <b>Microb Ecol.</b> 2007 Apr; 53 (3): 507-11</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17267615">Genome dynamics in a natural archaeal population</a>. Allen EE, Tyson GW, Whitaker RJ, Detter JC, Richardson PM and Banfield JF. <b>Proc Natl Acad Sci U S A.</b> 2007 Feb 6; 104 (6): 1883-8</li>
</ol>
<h2 class="subheader_with_bg"><a name="2006"/>2006</h2>
<ol class="publications">
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16980956">Symbiosis insights through metagenomic analysis of a microbial consortium</a>. Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM and Dubilier N. <b>Nature.</b> 2006 Oct 26; 443 (7114): 950-5</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16461883">Application of sequence-based methods in human microbial ecology</a>. Weng L, Rubin EM and Bristow J. <b>Genome Res.</b> 2006 Mar; 16 (3): 316-22</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16623744">Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH)</a>. Watt M, Hugenholtz P, White R and Vinall K. <b>Environ Microbiol.</b> 2006 May; 8 (5): 871-84</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17110569">Sequencing and analysis of Neanderthal genomic DNA</a>. Noonan JP, Coop G, Kudaravalli S, Smith D, Krause J, Alessi J, Chen F, Platt D, Paabo S, Pritchard JK and Rubin EM. <b>Science.</b> 2006 Nov 17; 314 (5802): 1113-8</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16873494">An experimental metagenome data management and analysis system</a>. Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavromatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P and Kyrpides NC. <b>Bioinformatics.</b> 2006 Jul 15; 22 (14): e359-67</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16517657">Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments</a>. Imachi H, Sekiguchi Y, Kamagata Y, Loy A, Qiu YL, Hugenholtz P, Kimura N, Wagner M, Ohashi A and Harada H. <b>Appl Environ Microbiol.</b> 2006 Mar; 72 (3): 2080-91</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16533068">Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota</a>. Hallam SJ, Mincer TJ, Schleper C, Preston CM, Roberts K, Richardson PM and DeLong EF. <b>PLoS Biol.</b> 2006 Apr; 4 (4): e95</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17114289">Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum</a>. Hallam SJ, Konstantinidis KT, Putnam N, Schleper C, Watanabe Y, Sugahara J, Preston C, de la Torre J, Richardson PM and DeLong EF. <b>Proc Natl Acad Sci U S A.</b> 2006 Nov 28; 103 (48): 18296-301</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16998472">Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities</a>. Garcia Martin H, Ivanova N, Kunin V, Warnecke F, Barry KW, McHardy AC, Yeates C, He S, Salamov AA, Szeto E, Dalin E, Putnam NH, Shapiro HJ, Pangilinan JL, Rigoutsos I, Kyrpides NC, Blackall LL, McMahon KD and Hugenholtz P. <b>Nat Biotechnol.</b> 2006 Oct; 24 (10): 1263-9</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16820507">Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB</a>. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P and Andersen GL. <b>Appl Environ Microbiol.</b> 2006 Jul; 72 (7): 5069-72</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16845035">NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes</a>. DeSantis TZ, Jr., Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R and Andersen GL. <b>Nucleic Acids Res.</b> 2006 Jul 1; 34 (Web Server issue): W394-9</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16439655">Community genomics among stratified microbial assemblages in the ocean's interior</a>. DeLong EF, Preston CM, Mincer T, Rich V, Hallam SJ, Frigaard NU, Martinez A, Sullivan MB, Edwards R, Brito BR, Chisholm SW and Karl DM. <b>Science.</b> 2006 Jan 27; 311 (5760): 496-503</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/17185602">Lineages of acidophilic archaea revealed by community genomic analysis</a>. Baker BJ, Tyson GW, Webb RI, Flanagan J, Hugenholtz P, Allen EE and Banfield JF. <b>Science.</b> 2006 Dec 22; 314 (5807): 1933-5</li>
</ol>
<h2 class="subheader_with_bg"><a name="2005"/>2005</h2>
<ol class="publications">
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16204553">Genome-directed isolation of the key nitrogen fixer Leptospirillum ferrodiazotrophum sp. nov. from an acidophilic microbial community</a>. Tyson GW, Lo I, Baker BJ, Allen EE, Hugenholtz P and Banfield JF. <b>Appl Environ Microbiol.</b> 2005 Oct; 71 (10): 6319-24</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/15845853">Comparative metagenomics of microbial communities</a>. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P and Rubin EM. <b>Science.</b> 2005 Apr 22; 308 (5721): 554-7</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/16304596">Metagenomics: DNA sequencing of environmental samples</a>. Tringe SG and Rubin EM. <b>Nat Rev Genet.</b> 2005 Nov; 6 (11): 805-14</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/15933159">Genomic sequencing of Pleistocene cave bears</a>. Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, Rabeder G, Krause J, Detter JC, Paabo S and Rubin EM. <b>Science.</b> 2005 Jul 22; 309 (5734): 597-9</li>
</ol>
<h2 class="subheader_with_bg"><a name="2004"/>2004</h2>
<ol class="publications">
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/14961025">Community structure and metabolism through reconstruction of microbial genomes from the environment</a>. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS and Banfield JF. <b>Nature.</b> 2004 Mar 4; 428 (6978): 37-43</li>
<li><a href="http://www.ncbi.nlm.nih.gov/pubmed/15353801">Reverse methanogenesis: testing the hypothesis with environmental genomics</a>. Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM and DeLong EF. <b>Science.</b> 2004 Sep 3; 305 (5689): 1457-62</li>
</ol>
</div>
<!--end of right side panel -->
<div class="clear"/>
</div>
<!-- end of content section-->
</div>
<!-- End of Main content section-->
<!-- footer -->
- <HtmlOutputText escape="false" id="j_id13" rendered="true" transient="false" value="<div class="divider"></div><div class="clear"></div><div id="footer"><div style="margin: 5px 15px 0 15px"> <div id="uclogo"><a href="http://www.ucop.edu" target="_parent"><img src="/images/uclogo.gif" width="45" height="43" alt="UC logo" border="0" /></a></div> <div id="doelogo"><a href="http://science.energy.gov/" target="_parent"><img src="/images/doe_sc_logo.gif" width="201" height="34" alt="DOE logo" border="0" /></a></div> <div id="clustrmaps" style="display:none;"><a href="http://www4.clustrmaps.com/counter/maps.php?url=http://genome.jgi-psf.org" id="clustrMapsLink"><img src="http://www4.clustrmaps.com/counter/index2.php?url=http://genome.jgi-psf.org" class="clustrmap_footer" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" /></a><script type="text/javascript">function cantload() {img = document.getElementById("clustrMapsImg");img.onerror = null;img.src = "http://www2.clustrmaps.com/images/clustrmaps-back-soon.jpg";document.getElementById("clustrMapsLink").href = "http://www2.clustrmaps.com";}img = document.getElementById("clustrMapsImg");img.onerror = cantload;</script> </div> <p> <a target="_parent" href="http://www.jgi.doe.gov" class="textlink">DOE Joint Genome Institute</a> <a target="_parent" href="/pages/credits.jsf" class="textlink">Credits</a> <a target="_parent" href="http://www.jgi.doe.gov/whoweare/disclaimer.html" class="textlink">Disclaimer</a> <a target="_parent" href="http://contact.jgi-psf.org/cgi-bin/support/contact_global.pl?inquiry=cgi" class="textlink">Comments/Questions</a> <a target="_parent" href="/pages/citeUs.jsf" class="textlink">Cite Us</a> </p> <p>© 1997-2012 The Regents of the University of California. <span class="version">Genome Portal version:6.0.294.15571 content:15571 clustering:3427 synteny:3427 gp-edge3.jgi-psf.org 22-May-2012 01:56:46.984 PDT</span></p> <div class="clear"></div></div></div>"/>
- </body>
</html>
- </AjaxViewRoot>
Request Parameters| Name | Value |
|---|
| None |
Request Attributes| Name | Value |
|---|
| ajaxContext | org.ajax4jsf.context.AjaxContextImpl@eb9d716 |
| page-scope-view-context | holding 0 instances |
| response_time_clock_start | 1337677006960 |
| scriptName | /programs/metagenomes/publications_genomes.jsf |
| serverName | http://genome.jgi-psf.org |
Session Attributes| Name | Value |
|---|
| keep-alive-scope-view-context | {/programs/metagenomes/publications_genomes.jsf=holding 1 instances} |
| keep-alive-with-queryscope-view-context | {/programs/metagenomes/publications_genomes.jsf=holding 0 instances} |
| page-scope-view-context | {/programs/metagenomes/publications_genomes.jsf=holding 0 instances} |
Application Attributes| Name | Value |
|---|
| None |
May 22, 2012 1:56:46 AM - Generated by Facelets