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                            <h2>
                                TCGA Genome Data Analysis Center (GDAC) for <br/>Systems Analysis of the Cancer Regulome
                                <small>
                                    <p>
                                        <a href="http://www.systemsbiology.org" target="_blank">Institute for Systems Biology</a> and
                                        <a href="http://www.mdanderson.org" target="_blank">MD Anderson Cancer Center</a>
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                        <p>
                            <a href="http://cancergenome.nih.gov" target="_blank">The Cancer Genome Atlas</a> (TCGA) provides an unprecedented opportunity to
                            take an integrated approach toward a systems level understanding of regulatory disruptions in cancer. Such disruptions and their
                            consequences are intertwined within complex dynamical networks through a multitude of interactions among different types of
                            molecules. Understanding such relationships requires multivariate analysis methods that can be effective in the context of highly
                            heterogeneous data, measurement uncertainty, and missing data.
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                                    <p>The cover of Cancer Cell features: <br/>
                                        <a href="http://www.sciencedirect.com/science/article/pii/S1535610813000032" target="_blank"><strong>"Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer"</strong></a>
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                                    <p><a href="http://explorer.cancerregulome.org/all_pairs/" target="_blank"><strong>Regulome Explorer</strong></a>: Explore, mine, and visualize complex datasets</p>
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                                    <p><a href="http://explorer.cancerregulome.org/pubcrawl/" target="_blank"><strong>Pubcrawl</strong></a>: Dynamic network topologies created from literature distances</p>
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                                    <p><a href="http://explorer.cancerregulome.org/crc_agg/" target="_blank"><strong>CRC Aggressiveness</strong></a>: Explore features related to colorectal cancer aggressiveness</p>
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                                    <p><a href="http://genespot.org" target="_blank"><strong>GeneSpot</strong></a>: Explore TCGA data from a gene-centric point-of-view</p>
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                            <h2>Research</h2>

                            <p>Development of novel computational approaches for analyzing large-scale heterogeneous data.</p>

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                            <h2>Cancer Studies</h2>

                            <p>Actively participating and contributing to several TCGA tumor Analysis Working Groups.</p>

                            <p><a class="btn" href="cancerstudies.html">View Details &raquo;</a></p>
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                            <h2>Software</h2>

                            <p>Web-based interactive visualization and exploratory tools, and computational infrastructure that promotes collaborative research.</p>

                            <p><a class="btn" href="software.html">View Details &raquo;</a></p>
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                                <h4>May 2013</h4>
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                                        New paper published in Nature on <a href="http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html" target="_blank">"Integrated genomic characterization of endometrial carcinoma"</a> as part of the <a href="http://cancergenome.nih.gov" target="_blank">TCGA network</a>.
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                                <h4>April 2013</h4>
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                                        We were awarded the first prize in the <a href="http://www.yarcdata.com/News/press/press04042013.php" target="_blank">YarcData Graph Analytics Challenge</a>. The topic of our entry was drug repurposing for cancer and uses data from <a href="http://cancergenome.nih.gov" target="_blank">TCGA</a>, PubMed, and other databases.
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                                <h4>February 2013</h4>
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                                        Investigators from our GDAC have published the discovery and characterization of FGFR3-TACC3 fusion in 8% of glioblastoma in <a href="http://www.ncbi.nlm.nih.gov/pubmed/23298836" target="_blank">"The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma"</a>.
                                    </div>
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                                        New paper published in Cancer Cell on <a href="http://www.sciencedirect.com/science/article/pii/S1535610813000032" target="_blank">"Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer"</a>
                                        as part of the <a href="http://cancergenome.nih.gov" target="_blank">TCGA network</a>.
                                        <br/><br/>
                                        The <a href="http://www.cell.com/cancer-cell/issue?pii=S1535-6108(13)X0003-0#" target="_blank">cover of Cancer Cell</a> features the article, with a graphic depicting the analysis.
                                    </div>
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                                        </a>
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                            <hr/>
                            <div>
                                <h4>November 2012</h4>
                                <div class="sideEventsCell">
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                                        Researchers at our center attended and presented at the <a href="http://www.capconcorp.com/meeting/2012/TCGASymposium" target="_blank">2nd Annual TCGA Scientific Symposium</a>. The symposium was co-chaired by <a href="http://www.systemsbiology.org/ilya-shmulevich" target="_blank">Dr <NAME></a>.
                                        <br/><br/>
                                        <a href="http://www.systemsbiology.org/brady-bernard" target="_blank"><NAME></a> and <a href="http://www.systemsbiology.org/hector-rovira" target="_blank"><NAME></a> gave a <a href="http://cancergenome.nih.gov/newsevents/multimedialibrary/videos/GeneSpotBernard2012" target="_blank">talk</a>, introducing <a href="http://www.genespot.org" target="_blank">Genespot</a>:
                                        A Portal for Interactive Gene-Centric Exploration of The Cancer Genome Atlas. <a href="http://www.systemsbiology.org/dick-kreisberg" target="_blank">Dick Kreisberg</a> presented a <a href="http://bit.ly/regex_workshop" target="_blank">workshop</a> on <a href="http://explorer.cancerregulome.org" target="_blank">Regulome Explorer</a>.
                                    </div>
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                            </div>
                            <hr/>
                            <div>
                                <h4>October 2012</h4>
                                <div class="sideEventsCell">
                                    <div class="text">
                                        New paper published in Nature on <a href="http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html" target="_blank">"Comprehensive molecular portraits of human breast tumours"</a>
                                        as a part of the <a href="http://cancergenome.nih.gov" target="_blank">TCGA network</a>.
                                        <br/><br/>
                                        An <a href="http://www.nytimes.com/2012/09/24/health/study-finds-variations-of-breast-cancer.html" target="_blank">article</a> related to the work was published in the <i><strong>New York Times</strong></i>.
                                    </div>
                                    <div class="image">
                                        <a href="http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html" target="_blank">
                                            <img src="images/pubs/nature_logo.png">
                                        </a>
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                            </div>
                            <hr/>
                            <div>
                                <h4>September 2012</h4>
                                <div class="sideEventsCell">
                                    <div class="text">
                                        The TCGA project published a Case Study on <a href="http://cancergenome.nih.gov/researchhighlights/tcgainaction/CloudMayWidenBottleneck" target="_blank">"The New Genomic Bottleneck and How the Cloud Might Widen It"</a> in which <a href="http://www.systemsbiology.org/ilya-shmulevich" target="_blank">Dr <NAME></a> is interviewed on his lab’s efforts to analyze genomic information using large computational clusters with cloud infrastructure on demand.
                                    </div>
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                            </div>
                            <hr/>
                            <div>
                                <h4>July 2012</h4>
                                <div class="sideEventsCell">
                                    <div class="text">
                                        New paper published in Nature on
                                        <a href="http://www.nature.com/nature/journal/v487/n7407/full/nature11252.html" target="_blank">"Comprehensive molecular characterization of human colon and rectal cancer"</a>
                                        as part of the <a href="http://cancergenome.nih.gov" target="_blank">TCGA network</a>.
                                        <br/><br/>
                                        An <a href="http://www.nytimes.com/2012/07/19/health/research/vast-gene-study-raises-hopes-for-colon-cancer-drugs.html" target="_blank">article</a>
                                        related to the work was featured on the home page of the <i><strong>New York Times</strong></i>.
                                    </div>
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                            <div>
                                <h4>June 2012</h4>

                                <div class="sideEventsCell">
                                    <div class="text">
                                        Our work was featured during a <a href="http://developers.google.com/compute/io" target="_blank">keynote presentation at the Google I/O
                                        2012 conference</a>.
                                        <br/><br/>
                                        The keynote, delivered by <NAME>, Senior Vice President of Infrastructure at Google,
                                        introduced Google Compute Engine. He demonstrated how
                                        <a href="http://rf-ace.googlecode.com" target="_blank">RF-ACE</a>, a machine learning
                                        algorithm that learns associations among genomic and clinical features, can be scaled to
                                        600,000 cores across Google’s global data centers and the results visualized using a version of
                                        <a href="http://explorer.cancerregulome.org" target="_blank">Regulome Explorer</a>.
                                        <br/><br/>
                                        A <a href="http://cloud.google.com/files/ComputeISBCaseStudy.pdf" target="_blank">case study</a> published by Google discusses the integration with Compute Engine.
                                    </div>
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                                        <a href="http://developers.google.com/compute/io" target="_blank">
                                            <img src="http://developers.google.com/apps/images/io/google-io-logo.png">
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                            <h2>
                                TCGA Genome Data Analysis Center (GDAC) for <br/>Systems Analysis of the Cancer Regulome
                                <small>
                                    <p>
                                        <a href="http://www.systemsbiology.org" target="_blank">Institute for Systems Biology</a> and
                                        <a href="http://www.mdanderson.org" target="_blank">MD Anderson Cancer Center</a>
                                    </p>
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                        <p>
                            <a href="http://cancergenome.nih.gov" target="_blank">The Cancer Genome Atlas</a> (TCGA) provides an unprecedented opportunity to
                            take an integrated approach toward a systems level understanding of regulatory disruptions in cancer. Such disruptions and their
                            consequences are intertwined within complex dynamical networks through a multitude of interactions among different types of
                            molecules. Understanding such relationships requires multivariate analysis methods that can be effective in the context of highly
                            heterogeneous data, measurement uncertainty, and missing data.
                        </p>
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                                    <img src="images/cancer_cell_cover.jpg" width="192" height="250" alt="Cover of Cancer Cell">
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                                    <p>The cover of Cancer Cell features: <br/>
                                        <a href="http://www.sciencedirect.com/science/article/pii/S1535610813000032" target="_blank"><strong>"Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer"</strong></a>
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                                    <p><a href="http://explorer.cancerregulome.org/all_pairs/" target="_blank"><strong>Regulome Explorer</strong></a>: Explore, mine, and visualize complex datasets</p>
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                                    <p><a href="http://explorer.cancerregulome.org/pubcrawl/" target="_blank"><strong>Pubcrawl</strong></a>: Dynamic network topologies created from literature distances</p>
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                                    <p><a href="http://explorer.cancerregulome.org/crc_agg/" target="_blank"><strong>CRC Aggressiveness</strong></a>: Explore features related to colorectal cancer aggressiveness</p>
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                                    <p><a href="http://genespot.org" target="_blank"><strong>GeneSpot</strong></a>: Explore TCGA data from a gene-centric point-of-view</p>
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                            <h2>Research</h2>

                            <p>Development of novel computational approaches for analyzing large-scale heterogeneous data.</p>

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                            <h2>Cancer Studies</h2>

                            <p>Actively participating and contributing to several TCGA tumor Analysis Working Groups.</p>

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                            <h2>Software</h2>

                            <p>Web-based interactive visualization and exploratory tools, and computational infrastructure that promotes collaborative research.</p>

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                                <h4>May 2013</h4>
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                                        New paper published in Nature on <a href="http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html" target="_blank">"Integrated genomic characterization of endometrial carcinoma"</a> as part of the <a href="http://cancergenome.nih.gov" target="_blank">TCGA network</a>.
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                                <h4>April 2013</h4>
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                                        We were awarded the first prize in the <a href="http://www.yarcdata.com/News/press/press04042013.php" target="_blank">YarcData Graph Analytics Challenge</a>. The topic of our entry was drug repurposing for cancer and uses data from <a href="http://cancergenome.nih.gov" target="_blank">TCGA</a>, PubMed, and other databases.
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                                <h4>February 2013</h4>
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                                        Investigators from our GDAC have published the discovery and characterization of FGFR3-TACC3 fusion in 8% of glioblastoma in <a href="http://www.ncbi.nlm.nih.gov/pubmed/23298836" target="_blank">"The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma"</a>.
                                    </div>
                                    <div class="image">
                                        <a href="http://www.jci.org/articles/view/67144" target="_blank">
                                            <img src="images/pubs/jci_logo.png">
                                        </a>
                                    </div>
                                </div>
                                <p/>
                                <div class="sideEventsCell">
                                    <div class="text">
                                        New paper published in Cancer Cell on <a href="http://www.sciencedirect.com/science/article/pii/S1535610813000032" target="_blank">"Integrated Analyses Identify a Master MicroRNA Regulatory Network for the Mesenchymal Subtype in Serous Ovarian Cancer"</a>
                                        as part of the <a href="http://cancergenome.nih.gov" target="_blank">TCGA network</a>. The <a href="http://www.cell.com/cancer-cell/issue?pii=S1535-6108(13)X0003-0#" target="_blank">cover of Cancer Cell</a> features the article, with a graphic depicting the analysis.
                                    </div>
                                    <div class="image">
                                        <a href="http://www.cell.com/cancer-cell/abstract/S1535-6108(13)00003-2" target="_blank">
                                            <img src="images/cancer_cell_cover.jpg">
                                        </a>
                                    </div>
                                </div>
                            </div>
                        </div>
                        <div class="page">
                            <hr/>
                            <div>
                                <h4>November 2012</h4>
                                <div class="sideEventsCell">
                                    <div class="text">
                                        Researchers at our center attended and presented at the <a href="http://www.capconcorp.com/meeting/2012/TCGASymposium" target="_blank">2nd Annual TCGA Scientific Symposium</a>. The symposium was co-chaired by <a href="http://www.systemsbiology.org/ilya-shmulevich" target="_blank">Dr <NAME></a>.  <a href="http://www.systemsbiology.org/brady-bernard" target="_blank">Dr <NAME></a> and <a href="http://www.systemsbiology.org/hector-rovira" target="_blank"><NAME></a> gave a <a href="http://cancergenome.nih.gov/newsevents/multimedialibrary/videos/GeneSpotBernard2012" target="_blank">talk</a> <a href="http://www.genespot.org" target="_blank">Genespot</a>:
                                        A Portal for Interactive Gene-Centric Exploration of The Cancer Genome Atlas. <a href="http://www.systemsbiology.org/dick-kreisberg" target="_blank"><NAME></a> presented a <a href="http://bit.ly/regex_workshop" target="_blank">workshop</a> on <a href="http://explorer.cancerregulome.org" target="_blank">Regulome Explorer</a>.
                                    </div>
                                </div>
                            </div>
                            <hr/>
                            <div>
                                <h4>October 2012</h4>
                                <div class="sideEventsCell">
                                    <div class="text">
                                        New paper published in Nature on <a href="http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html" target="_blank">"Comprehensive molecular portraits of human breast tumours"</a>
                                        as a part of the <a href="http://cancergenome.nih.gov" target="_blank">TCGA network</a>.  An <a href="http://www.nytimes.com/2012/09/24/health/study-finds-variations-of-breast-cancer.html" target="_blank">article</a> related to the work was published in the <i><strong>New York Times</strong></i>.
                                    </div>
                                    <div class="image">
                                        <a href="http://www.nature.com/nature/journal/v490/n7418/full/nature11412.html" target="_blank">
                                            <img src="images/pubs/nature_logo.png">
                                        </a>
                                    </div>
                                </div>
                            </div>
                            <hr/>
                            <div>
                                <h4>September 2012</h4>
                                <div class="sideEventsCell">
                                    <div class="text">
                                        The TCGA project published a Case Study on <a href="http://cancergenome.nih.gov/researchhighlights/tcgainaction/CloudMayWidenBottleneck" target="_blank">"The New Genomic Bottleneck and How the Cloud Might Widen It"</a> in which <a href="http://www.systemsbiology.org/ilya-shmulevich" target="_blank">Dr <NAME></a> is interviewed on his lab’s efforts to analyze genomic information using large computational clusters with cloud infrastructure on demand.
                                    </div>
                                </div>
                            </div>
                            <hr/>
                            <div>
                                <h4>July 2012</h4>
                                <div class="sideEventsCell">
                                    <div class="text">
                                        New paper published in Nature on
                                        <a href="http://www.nature.com/nature/journal/v487/n7407/full/nature11252.html" target="_blank">"Comprehensive molecular characterization of human colon and rectal cancer"</a>
                                        as part of the <a href="http://cancergenome.nih.gov" target="_blank">TCGA network</a>. An <a href="http://www.nytimes.com/2012/07/19/health/research/vast-gene-study-raises-hopes-for-colon-cancer-drugs.html" target="_blank">article</a>
                                        related to the work was featured on the home page of the <i><strong>New York Times</strong></i>.
                                    </div>
                                </div>
                            </div>
                        </div>
                        <div class="page">
                            <div>
                                <h4>June 2012</h4>

                                <div class="sideEventsCell">
                                    <div class="text">
                                        Our work was featured during the <a href="http://developers.google.com/compute/io" target="_blank">Compute Engine keynote</a> presentation at the Google I/O 2012 conference.
                                        <br/><br/>
                                        <a href="http://developers.google.com/compute/io" target="_blank">
                                            <img src="http://developers.google.com/apps/images/io/google-io-logo.png" style="width: 50%;">
                                        </a>
                                        <br/><br/>
                                        The keynote, delivered by <NAME>, Senior Vice President of Infrastructure at Google,
                                        introduced Google Compute Engine. He demonstrated how
                                        <a href="http://rf-ace.googlecode.com" target="_blank">RF-ACE</a>, a machine learning
                                        algorithm that learns associations among genomic and clinical features, can be scaled to
                                        600,000 cores across Google’s global data centers and the results visualized using a version of
                                        <a href="http://explorer.cancerregulome.org" target="_blank">Regulome Explorer</a>. A
                                        <a href="http://cloud.google.com/files/ComputeISBCaseStudy.pdf" target="_blank">case study</a> published by Google
                                        discusses the integration with Compute Engine.
                                    </div>
                                </div>
                            </div>
                            <hr/>
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