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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>Mehran's GitHub Page</title>
<!-- Bootstrap -->
<link href="css/bootstrap-4.4.1.css" rel="stylesheet">
</head>
<body>
<nav class="navbar navbar-expand-lg navbar-dark bg-dark">
<a class="navbar-brand" href="#">Quick access</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarSupportedContent" aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarSupportedContent">
<ul class="navbar-nav mr-auto">
<li class="nav-item active">
<a class="nav-link" href="#">Home <span class="sr-only">(current)</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="#class.presentation">Class presentations</a>
</li>
<li class="nav-item dropdown">
<a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Section
</a>
<div class="dropdown-menu" aria-labelledby="navbarDropdown">
<a class="dropdown-item" href="#select.publication">Select publications</a>
<a class="dropdown-item" href="#latest.work">Latest work</a>
<a class="dropdown-item" href="#class.presentation">Class presentations</a>
<a class="dropdown-item" href="#contact">Contact</a>
</div>
</li>
</ul>
</div>
</nav>
<section>
<div class="jumbotron text-center mt-2">
<div class="container">
<div class="row">
<div class="col-12">
<h1>Mehran Karimzadeh's GitHub Page</h1>
<p>I am currently a Staff Scientist at Exai Bio and am based in Seattle, WA.</p>
<p> Previously, I was a CIHR post-doctoral fellow co-supervised by Dr. Hani Goodarzi at UCSF and Dr. Bo Wang at Vector Institute for Artificial Intelligene and University Health Network.
I did my Ph.D. with Dr. Michael Hoffman at University of Toronto. I am interested in developing deep learning models for detection of disease phenotypes using high-throughput genomic datasets. </p>
<p><a class="btn btn-primary btn-lg" href="KARIMZADEH_CV.pdf" target="_blank" role="button">Mehran's CV »</a></p>
</div>
</div>
</div>
</div>
</section>
<section>
<div class="container">
<div class="row">
<div class="col-12 text-center">
<h1 id="select.publication">Select publications </h1>
<p>The list includes peer-reviewed as well as non-peer-reviewed items where Mehran is the first or co-first author</p>
</div>
</div>
</div>
</section>
<section>
<div class="container mt-2">
<div class="row">
<div class="col-md-4 col-12">
<ul class="list-unstyled">
<li class="media">
<img class="mr-3" src="images/pubmed-meta-image.png" alt="Generic placeholder image">
<div class="media-body">
<h5 class="mt-0 mb-1"><a href="https://doi.org/10.1016/j.xgen.2023.100272" target="_blank">Multi-modal single-cell atlas of the human breast upon androgen therapy</a></h5>
The molecular consequences of androgen activity in the human breast. Cell Genomics, 2023.
</div>
</li>
</ul>
</div>
<div class="col-md-4 col-12">
<ul class="list-unstyled">
<li class="media">
<img class="mr-3" src="images/pubmed-meta-image.png" alt="Generic placeholder image">
<div class="media-body">
<h5 class="mt-0 mb-1"><a href="https://doi.org/10.1186/s13059-023-02926-9" target="_blank">HPV Epigenomics</a></h5>
Viral integration transforms chromatin to drive oncogenesis. Genome Biology, 2023.
</div>
</li>
</ul>
</div>
<div class="col-md-4 col-12">
<ul class="list-unstyled">
<li class="media">
<img class="mr-3" src="images/pubmed-meta-image.png" alt="Generic placeholder image">
<div class="media-body">
<h5 class="mt-0 mb-1"><a href="https://doi.org/10.1186/s13059-022-02690-2" target="_blank">Transcription factor prediction</a></h5>
Virtual ChIP-seq: predicting transcription factor binding by learning from the transcriptome. <i>Genome Biology</i> 2022.
</div>
</li>
</ul>
</div>
<div class="col-md-4 col-12">
<ul class="list-unstyled">
<li class="media">
<img class="mr-3" src="images/pubmed-meta-image.png" alt="Generic placeholder image">
<div class="media-body">
<h5 class="mt-0 mb-1"><a href="https://doi.org/10.1093/nar/gky677" target="_blank">Methylome mappability</a></h5>
Umap and Bismap: quantifying genome and methylome mappability. Nucleic Acids Research 2018.
</div>
</li>
</ul>
</div>
<div class="col-md-4 col-12">
<ul class="list-unstyled">
<li class="media">
<img class="mr-3" src="images/pubmed-meta-image.png" alt="Generic placeholder image">
<div class="media-body">
<h5 class="mt-0 mb-1"><a href="https://dx.doi.org/10.18632%2Foncotarget.25382" target="_blank">Cancer aberration hubs</a></h5>
Aberration hubs in protein interaction networks highlight actionable targets in cancer. Oncotarget 2018.
</div>
</li>
</ul>
</div>
<div class="col-md-4 col-12">
<ul class="list-unstyled">
<li class="media">
<img class="mr-3" src="images/pubmed-meta-image.png" alt="Generic placeholder image">
<div class="media-body">
<h5 class="mt-0 mb-1"><a href="https://doi.org/10.1093/bib/bbw134" target="_blank">Bioinformatics software documentation</a></h5>
Top considerations for creating bioinformatics software documentation. Briefings in Bioinformatics 2018.
</div>
</li>
</ul>
</div>
</div>
</div>
</section>
<section>
<div class="container">
<div class="row">
<div class="col-12 text-center">
<h2 id="latest.work">Latest Work</h2>
<p>Recent publications</p>
</div>
</div>
<div class="row">
<div class="col-md-6 col-12 text-center">
<img class="img-fluid" src="images/iscience.png" alt="">
<h4>Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses</h4>
<h6>Collaboration with Mossman lab, 2021</h6>
</div>
<div class="col-md-6 col-12 text-center mt-md-0 mt-2">
<img class="img-fluid" src="images/elife.png" alt="">
<h4>Massively multiplex single-molecule oligonucleosome footprinting</h4>
<h6>Collaboration with Ramani lab, 2020</h6>
</div>
<div class="col-md-6 col-12 text-center">
<img class="img-fluid" src="images/scientific_reports.png" alt="">
<h4>Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease</h4>
<h6>Collaboration with Cyclica and Ryerson, 2020–2021</h6>
</div>
<div class="col-md-6 col-12 text-center">
<img class="img-fluid" src="images/transbreast_biorxiv.png" alt="">
<h4>The molecular consequences of androgen activity in the human breast</h4>
<h6>Collaboration with Knott lab, 2020–2022</h6>
</div>
</div>
</div>
</section>
<hr>
<section>
<div class="container">
<div class="row">
<div class="col-12 text-center">
<h1 id="class.presentation">Class presentations</h1>
<ul>
<li><a href="dnaMethylationAnalysis/dnaMethylationAnalysis_v1.1.html">DNA methylation workshop</a> for Genomic Methodologies, University of Toronto</li>
<li><a href="isoformworkshop/isoformAnalysis.html">Isoform analysis workshop</a> for Genomic Methodologies course, University of Toronto</li>
<li><a href="https://jasonlerch.github.io/MBP-stats-2018">Introduction to biostatistics</a> for Department of Medical Biophysics, University of Toronto (2018)</li>
<li><a href="https://jasonlerch.github.io/MBP-stats-2019/">Introduction to biostatistics</a> for Department of Medical Biophysics, University of Toronto (2019)</li>
<li><a href="https://docs.google.com/presentation/d/e/2PACX-1vTvcG4QneCQB8bpCzM0_FFbJaYnhQyDPTEOnD3ps1-K6yicR5KZ0K3g1apU-7PQTBsVC22HmYeKoyo1/pub">Introduction to ggplot</a> for MBP Tech talks, University of Toronto</li>
<li><a href="https://mbp-tech-talks.github.io/2017-2018/intro-to-R_mehran-karimzadeh_francis-nguyen.pdf">Introduction to R</a> for MBP Tech Talks, University of Toronto</li>
</ul>
</div>
</div>
</div>
</section>
<hr>
<div class="section">
<div class="container">
<div class="row">
<div class="col-md-4 col-12">
<h3 class="text-center" id="contact">Contact information</h3>
<p>Email: mehran dot karimzadeh at uhnresearch dot ca</p>
</div>
</div>
</div>
</div>
<hr>
<footer class="text-center">
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