<div dir="ltr"><div><div class="gmail_default"><font color="#000000" face="arial, helvetica, sans-serif">When:     Wednesday, February 1st at 11:00 am </font></div><div class="gmail_default"><font color="#000000" face="arial, helvetica, sans-serif"><br></font></div><div class="gmail_default"><font color="#000000" face="arial, helvetica, sans-serif">Where:    <span class="gmail-m_-6569105212788927681m_9067904842688472155gmail-m_3071693547520408192gmail-il">TTIC</span>, 6045 S Kenwood Avenue, 5th Floor, Room 526</font></div><div class="gmail_default"><font color="#000000" face="arial, helvetica, sans-serif"><br></font></div><div><font color="#000000" face="arial, helvetica, sans-serif">Who:       Wei Zhang, University of Minnesota</font></div></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><div><font face="arial, helvetica, sans-serif"><br></font></div><p class="MsoNormal"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif">Title: Computational
Analysis of Transcript Interactions and Variants in Cancer</font></span></p><p class="MsoNormal"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif"><br></font></span></p>

<p class="MsoNormal"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif">Abstract: Gene
expression and gene isoforms in cancer transcriptome are informative for
phenotype prediction.<span class="gmail-apple-converted-space"> Network-based learning
models are playing increasing role in cancer transcriptome analysis. These
methods integrate large scale patient transcriptome data with structural
information in biological networks to improve phenotype prediction accuracy,
model robustness and biological interpretation of results. In this talk, I will
present two such reliable network-based methods.  First, I will introduce a Network-based
method for RNA-Seq-based Transcript Quantification (Net-RSTQ), which integrates
protein domain-domain interaction information with RNA-Seq short read
alignments for transcript abundance estimation under the assumption that the
abundances of the neighboring transcripts by domain-domain interactions in
transcript interaction network are positively correlated. Second, I will
present a Network-based Cox regression model (Net-Cox), which integrates gene
network information into the Cox’s proportional hazard model to explore the
co-expression or functional relation among high-dimensional gene expression features
in a gene network. In the experiments of studying the cancer trasnscriptome data
in The Cancer Genome Atlas (TCGA), it was observed that both models can improve
cancer treatment outcome prediction. Throughout the talk, I will also talk
about my future research direction.<span></span></span></font></span></p><p class="MsoNormal"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif"><span class="gmail-apple-converted-space"><br></span></font></span></p>

<p class="MsoNormal"><font face="arial, helvetica, sans-serif"><span class="gmail-apple-converted-space"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial">Bio: Dr. Wei Zhang is a Research Associate in Computer
Science and Engineering at the University of Minnesota Twin Cities. His
research interests include computational biology and machine learning. His
research has centered around developing network-based algorithms to better
understand three specific topics in cancer transcriptome: alternative splicing,
alternative polyadenylation and interactions. He received his PhD and MS from University
of Minnesota Twin Cities in 2015 and 2011, BS from Hebei University of Technology
in 2009, all in computer science.</span></span><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><span></span></span></font></p><p class="MsoNormal"><span class="gmail-apple-converted-space"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif"><br></font></span></span></p><p class="MsoNormal"><span class="gmail-apple-converted-space"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif"><br></font></span></span></p><p class="MsoNormal"><span class="gmail-apple-converted-space"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif">Host: <a href="mailto:j3xu@ttic.edu">Jinbo Xu</a></font></span></span></p><p class="MsoNormal"><span class="gmail-apple-converted-space"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif"><br></font></span></span></p><p class="MsoNormal"><span class="gmail-apple-converted-space"><span style="line-height:107%;color:rgb(51,51,51);background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><font face="arial, helvetica, sans-serif"><br></font></span></span></p><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><font face="arial, helvetica, sans-serif">Mary C. Marre</font><div><font face="arial, helvetica, sans-serif">Administrative Assistant</font></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6"><b>Toyota Technological Institute</b></font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">6045 S. Kenwood Avenue</font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Room 504</font></i></div><div><i><font face="arial, helvetica, sans-serif" color="#3d85c6">Chicago, IL  60637</font></i></div><div><i><font face="arial, helvetica, sans-serif">p:(773) 834-1757</font></i></div><div><i><font face="arial, helvetica, sans-serif">f: (773) 357-6970</font></i></div><div><b><i><a href="mailto:mmarre@ttic.edu" target="_blank"><font face="arial, helvetica, sans-serif">mmarre@ttic.edu</font></a></i></b></div></div></div></div></div></div></div></div></div></div>
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