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<title>Integrative Genomics Laboratory</title>
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<pubDate>Tue, 22 Jul 2014 15:34:36 +0000</pubDate>
<description>Where big data meet biology.</description>
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<wp:author_display_name><![CDATA[Anna Greene]]></wp:author_display_name>
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<wp:author_login>dnicholson329@gmail.com</wp:author_login>
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<wp:author_display_name><![CDATA[David Nicholson]]></wp:author_display_name>
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<title>Home</title>
<pubDate>Tue, 03 Sep 2019 18:23:22 +0000</pubDate>
<content:encoded><![CDATA[<h1 style="text-align:center;white-space:pre-wrap;">We bring together large compendia of publicly available data to answer pressing questions in biology and medicine.</h1> <p style="text-align:center;white-space:pre-wrap;" class="">New technologies allow researchers to extensively profile biological systems, and researchers have embraced these technologies. Anyone can download more than 1.9 million genome-wide assays from <a href="http://www.ebi.ac.uk/arrayexpress/" target="_blank">Array Express</a>, a repository of such data. Now the challenge is to understand what these data reveal about underlying biology. We develop and apply methods that extract biological principles from these data, and we train the next generation of biological data scientists.</p><p style="text-align:center;white-space:pre-wrap;" class="">(<a href="https://www.flickr.com/photos/nataliejohnson/1016760060" target="_blank">donut img source</a>)</p>
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<h2 style="text-align:center;white-space:pre-wrap;"><a href="/publications">Lab Highlights</a></h2><p style="text-align:center;white-space:pre-wrap;" class="">Keep up with our latest papers, grants, and webservers.</p><p style="text-align:center;white-space:pre-wrap;" class=""><a href="/publications">Recent News →</a></p><h2 style="text-align:center;white-space:pre-wrap;"><a href="/lab-members">Meet our group</a></h2><p style="text-align:center;white-space:pre-wrap;" class="">We're a team of enthusiastic scientists who aim to bring big data to every biology lab.</p><p style="text-align:center;white-space:pre-wrap;" class=""><a href="/lab-members">Meet Us →</a></p><hr />
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<pubDate>Sun, 09 Aug 2015 14:01:59 +0000</pubDate>
<content:encoded><![CDATA[<p>Many aspects of our research are made possible through ongoing strong collaborations with outstanding research groups around the world.</p><h2>Personalized Medicine</h2><p><a href="http://www.dartmouth.edu/~sanchezlab/">Yoli Sanchez</a></p><p><a href="http://cancer.dartmouth.edu/melanoma_skin/teamprofile/53638/kerrington_d_smith_md">Kerry Smith</a></p><p><a href="http://cancer.dartmouth.edu/neuro_brain/teamprofile/785/Camilo_E_Fadul_MD">Camilo Fadul</a></p><p><a href="http://cancer.dartmouth.edu/gi_pancreatic/teamprofile/23464/Gregory_J_Tsongalis_PhD">Greg Tsongalis</a></p><h2>Ovarian Cancer</h2><p><a target="_blank" href="http://www.uci.or.ug/">Uganda Cancer Institute</a></p><p><a href="http://geiselmed.dartmouth.edu/faculty/facultydb/view.php?uid=4741">Jen Doherty</a></p><p><a href="http://cancer.dartmouth.edu/lung_thoracic/teamprofile/56703/Laura_J_Tafe_MD">Laura Tafe</a></p><p><a href="http://cancer.dartmouth.edu/surgical_oncology/teamprofile/51360/Evelyn_L_Fleming_MD">Evelyn Flemming</a></p><h2>Deep Learning of Microbial Regulatory Programs</h2><p><a href="http://www.dartmouth.edu/~hoganlab/">Deb Hogan</a></p><h2>Aging and Memory</h2><p><a href="http://www.boscogeneticslab.com/">Gio Bosco</a></p><h2>Gene Function Prediction</h2><p><a href="http://iddo-friedberg.org/">Iddo Friedberg</a></p><p><a href="http://www.informatics.indiana.edu/predrag/">Pedja Radivojac</a></p><p><a href="https://www.buckinstitute.org/mooneyLab">Sean Mooney</a></p>]]></content:encoded>
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<link>/news</link>
<title>News</title>
<pubDate>Sun, 09 Aug 2015 14:10:00 +0000</pubDate>
<content:encoded><![CDATA[<p>Keep up with our lab news by following <a target="_blank" href="http://twitter.com/GreeneLab">@GreeneLab</a> on Twitter.</p>
<a class="twitter-timeline" data-dnt="true" href="https://twitter.com/GreeneLab" data-widget-id="630379398223515648">Tweets by @GreeneLab</a>
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<wp:post_name>news</wp:post_name>
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<link>/research</link>
<title>Research</title>
<pubDate>Wed, 28 Sep 2016 18:45:07 +0000</pubDate>
<content:encoded><![CDATA[<p><a target="_blank" href="https://en.wikipedia.org/wiki/TL;DR"><strong>tl;dr:</strong></a> There's a lot of public data about biological systems under various perturbations. But they are also noisy. Our lab develops algorithms that integrate that data to model complex biological systems. We do this because we want to understand how biological systems work. This way when we need to intervene to improve health we aren't taking a shot in the dark. We recognize that our lab won't have all the answers, or even all of the questions, so we develop systems that any biologist can use.</p><h2>Overview</h2><p>Right now anyone can download genome-wide measurements from more than <a target="_blank" href="http://www.ebi.ac.uk/arrayexpress/">2 million assays</a> of diverse physiological conditions. We develop and apply computational methods that analyze these large and heterogeneous data compendia to provide a data-driven lens into <a target="_blank" href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002957">pathways</a>, <a target="_blank" href="http://genome.cshlp.org/content/23/11/1862.long">cell-lineages</a>, <a target="_blank" href="http://www.nature.com/ng/journal/v47/n6/full/ng.3259.html">diseases</a>, and other biological systems of interest.</p><p>Our projects are grouped into three major areas:</p><ul><li>new algorithms for noisy data,</li><li>improving the accessibility of data and methods,</li><li>and applications that span from basic biology to precision treatments for human diseases.</li></ul><p>Members of our lab work on specific research questions related to these topics, and frequently find that their research eventually touches on more than one of these core areas. We have a strong commitment to open and reproducible science: our <a href="/webservers">webservers</a> are freely available and our code is released under open source licenses on <a target="_blank" href="http://www.github.com/greenelab">github</a> and <a target="_blank" href="http://bitbucket.org/greenelab">bitbucket</a>.</p><p>Our work is funded by grants from the National Science Foundation (NSF), the <a target="_blank" href="https://www.moore.org/programs/science/data-driven-discovery/investigators">Gordon and Betty Moore Foundation</a>, and the <a target="_blank" href="http://www.cff.org/">Cystic Fibrosis Foundation</a>. In the past we have received funding from the <a target="_blank" href="http://cancer.dartmouth.edu/">Norris Cotton Cancer Center</a> and the <a target="_blank" href="http://www.cancer.org/">American Cancer Society</a>.</p>
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<![endif]--> <!--StartFragment--></h2><p>The goal of this aim is to develop algorithms that can integrate data across multiple experiments and platforms to capture useful biological patterns. We develop both supervised and unsupervised approaches. We focus on supervised methods when we know precisely what question we’d like to answer and unsupervised methods for discovery-oriented projects</p><p>We’ve developed supervised methods that address key biological challenges related to <a target="_blank" href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002957">genes’ developmental roles</a>, <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/23950145">tissue-specific expression</a>, and <a target="_blank" href="http://www.nature.com/ng/journal/v47/n6/abs/ng.3259.html">tissue-specific function</a>. We’ve developed unsupervised methods to identify the key biological patterns in <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/25592575">cancer</a> and <a target="_blank" href="http://msystems.asm.org/content/1/1/e00025-15">microbial</a> genomics data.</p><p>Many of our methods are based on “deep learning” approaches. These techniques are trendy right now. However, we adapt them because the denoising autoencoder framing works well on the types of data that we deal with, i.e. noisy data. We were the <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed/25592575">first</a> to apply these methods to genomic data integration, and we have found them to be particularly robust to cross-dataset noise. Our recent work has also demonstrated that these methods can be broadly applied, e.g. to <a target="_blank" href="http://www.greenelab.com/publications">electronic health records</a>.</p><p>In summary, we develop robust machine learning based approaches. Our methods perform well in many contexts, and we continue to devise new strategies to tackle pressing biomedical challenges.</p><p><!--EndFragment--></p><h2>Reproducible "big data" analysis for everyone <!--[if gte mso 9]><xml>
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