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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="Genomics lab at UCI">
<meta name="author" content="Fairlie Reese, Narges Rezaie">
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<title>Mortazavi Lab</title>
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<a class="navbar-brand js-scroll-trigger" href="#">Mortazavi Lab</a>
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<ul class="navbar-nav text-uppercase ml-auto"><li class="nav-item"><a class="nav-link js-scroll-trigger" href="#services">Research</a></li>
<li class="nav-item"><a class="nav-link js-scroll-trigger" href="#portfolio">Software</a></li>
<li class="nav-item"><a class="nav-link js-scroll-trigger" href="#timeline">News</a></li>
<li class="nav-item"><a class="nav-link js-scroll-trigger" href="Dr_Mortazavi.html#Dr_Mortazavi">Dr. Mortazavi</a></li>
<li class="nav-item"><a class="nav-link js-scroll-trigger" href="#team">People</a></li>
<li class="nav-item"><a class="nav-link js-scroll-trigger" href="past_members.html#past_members">Past Members</a></li>
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<div class="intro-text"><div class="intro-lead-in"><p>Genomics, computation and sequencing</p>
</div><div class="intro-heading text-uppercase"><p>Mortazavi Lab at UC Irvine</p>
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<h2 class="section-heading text-uppercase">Research</h2>
<h3 class="section-subheading text-muted">There are many diverse projects going on in the lab</h3>
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<h4 class="service-heading"><p>Long-read Transcriptomics</p>
</h4>
<div class="text-muted"><p>We are leveraging the PacBio and Oxford Nanopore platforms to sequence full-length transcripts in order to characterize the true extent of alternative splicing. We are both sequencing transcriptomes as well as developing tools to enable these analyses.</p>
</div>
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<h4 class="service-heading"><p>IGVF</p>
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<div class="text-muted"><p>XXXX</p>
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<h4 class="service-heading"><p>Model AD</p>
</h4>
<div class="text-muted"><p>We are part of a NIA Consortium to build better late-onset Alzheimer’s Disease models in mouse. Our part includes both bioinformatics as well as single-cell transcriptomics in these new models.</p>
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<h4 class="service-heading"><p>FSHD</p>
</h4>
<div class="text-muted"><p>We are using functional genomics to understand the mechanisms driving the pathology of Facioscapulohumeral muscular dystrophy using single-cell and single-nucleus techniques.</p>
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<h4 class="service-heading"><p>Gene Regulatory Networks</p>
</h4>
<div class="text-muted"><p>We are building models of gene regulatory networks using either bulk or single-cell RNA-seq, and ATAC-seq in human, rodents, and other vertebrates in order to discover how the logic of development is encoded in the genome.</p>
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<h4 class="service-heading"><p>Cellular Differentiation</p>
</h4>
<div class="text-muted"><p>We study myogenesis and macrophage differentiation using functional genomics assays such RNA-seq, microRNA-seq, ATAC-seq, and ChIP-seq in order to understand how gene expression and chromatin states change in time courses of differentiation.</p>
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<h2 class="section-heading text-uppercase"><p>Software</p>
</h2>
<h3 class="section-subheading text-muted"><p>Software produced by the lab used to analyze genomics data</p>
</h3>
</div>
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<h4>PyWGCNA</h4>
<p class="text-muted">Weighted Gene Correlation Network Analysis</p>
</div>
</div>
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<h4>Lapa</h4>
<p class="text-muted">Alternative polyadenylation detection</p>
</div>
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<h4>Swan</h4>
<p class="text-muted">Transcriptome analysis and visualization</p>
</div>
</div>
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<h4>TALON</h4>
<p class="text-muted">Long-read RNA-seq annotator</p>
</div>
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</a>
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<h4>TranscriptClean</h4>
<p class="text-muted">Long-read RNA-seq error correction</p>
</div>
</div>
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<h4>SOMatic</h4>
<p class="text-muted">High-dimensional data clustering with SOMs</p>
</div>
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</div>
</div>
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<!-- Project Details Go Here -->
<h2 class="text-uppercase">PyWGCNA</h2>
<p class="item-intro text-muted">Python library designed to do weighted gene correlation network analysis (WGCNA)</p>
<img class="img-fluid d-block mx-auto" src="assets/img/portfolio/PyWGCNA.png" alt="PyWGCNA_workflow">
<p><p>PyWGCNA is a Python library designed to do weighted correlation network analysis (WGCNA). It can be used for finding clusters (modules) of highly correlated genes, for summarizing such clusters using the module eigengene, for relating modules to one another and to external sample traits (using eigengene network methodology), and for calculating module membership measures. Users can also compare WGCNA networks from different datasets, or to external gene lists, to assess the conservation or functional enrichment of each module.</p>
<p>Author: Narges Rezaie</p>
<ul class="list-inline">
<li><a href="https://www.biorxiv.org/content/10.1101/2022.08.22.504852v1.abstract">PyWGCNA manuscript</a></li>
<li><a href="https://mortazavilab.github.io/PyWGCNA/html/index.html">PyWGCNA website</a></li>
<li><a href="https://github.com/mortazavilab/PyWGCNA">PyWGCNA GitHub</a></li>
</ul>
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<h2 class="text-uppercase">LAPA</h2>
<p class="item-intro text-muted">Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.</p>
<img class="img-fluid d-block mx-auto" src="assets/img/portfolio/lapa.jpg" alt="lapa">
<p><p>Alternative polyadenylation (APA) is a major mechanism that increases transcriptional diversity and regulates mRNA abundance. Existing computational tools to analyze APA have low precision because these tools are designed for short-read RNA-seq, which is a suboptimal data source to study APA. Long-read RNA-seq (LR-RNA-seq) accurately detects complete transcript isoforms with poly(A)-tails, providing an ideal data source to study APA. However, current computational tools are incompatible with LR-RNA-seq.</p>
<p>Author: Muhammed Hasan Celik</p>
<ul class="list-inline">
<li><a href="https://www.biorxiv.org/content/10.1101/2022.11.08.515683v1.abstract">LAPA manuscript</a></li>
<li><a href="https://github.com/mortazavilab/lapa">LAPA GitHub</a></li>
</ul>
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<h2 class="text-uppercase">Swan</h2>
<p class="item-intro text-muted">Graph-based visualization and analysis tools for transcriptomes</p>
<img class="img-fluid d-block mx-auto" src="assets/img/portfolio/swan.png" alt="swangraph">
<p><p>Swan is a Python library for analyzing and visualizing transcriptomes, with long-read transcriptomes in mind. Swan can find differentially-expressed genes and transcripts, isoform-switching genes, and novel exon skipping and intron retention events.</p>
<p>Author: Fairlie Reese</p>
<ul class="list-inline">
<li><a href="https://academic.oup.com/bioinformatics/article/37/9/1322/5912931?login=true">Swan manuscript</a></li>
<li><a href="https://freese.gitbook.io/swan/">Swan website</a></li>
<li><a href="https://github.com/mortazavilab/swan_vis">Swan GitHub</a></li>
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<h2 class="text-uppercase">TALON</h2>
<p class="item-intro text-muted">Technology-agnostic long-read RNA-seq annotation</p>
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<p><p>TALON (<strong>T</strong>echnology-<strong>A</strong>gnostic <strong>Lon</strong>g-read) annotation software is designed to associate transcript identities to reads from long-read RNA-seq datasets. It works equally well for both PacBio and Oxford Nanopore data. It has currently be implemented by <a href="http://encodeproject.org/">ENCODE</a> as a part of their uniform data-processing pipeline.</p>
<p>Author: Dana Wyman, PhD</p>
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<li><a href="https://www.biorxiv.org/content/10.1101/672931v2">TALON manuscript</a></li>
<li><a href="https://github.com/mortazavilab/TALON">TALON GitHub</a></li>
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<h2 class="text-uppercase">TranscriptClean</h2>
<p class="item-intro text-muted">Variant-aware long-read RNA-seq error correction</p>
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<p><p>TranscriptClean is a tool used to correct mismatches, microindels, and noncanonical splice junctions in long reads in a variant-aware manner. It can be used to recover otherwise unusable reads in long read datasets.</p>
<p>Author: Dana Wyman, PhD</p>
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<li><a href="https://pubmed.ncbi.nlm.nih.gov/29912287/">TranscriptClean publication</a></li>
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<h2 class="text-uppercase">SOMatic</h2>
<p class="item-intro text-muted">High-dimensional data clustering with SOMs</p>
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<p><p>SOMatic can be used to cluster high-dimensional data from multiple data modalities into associated modules. Visualization tools enable the user to understand the data in different contexts.</p>
<p>Author: Camden Jansen, PhD</p>
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<li><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855564/">SOM publication</a></li>
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<h2 class="text-uppercase">Ali Mortazavi, PhD</h2>
<p class="item-intro text-muted">Principal Investigator, </p>
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<h2 class="text-uppercase">Elisabeth Rebboah</h2>
<p class="item-intro text-muted">MCSB PhD Student, </p>
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<p><p><strong>Research Interests:</strong> <br />
I am interested in NGS-focused biotechnology and currently work on integrating bulk & single-cell/single-nucleus RNA-seq and ATAC-seq in an in vitro model of skeletal muscle differentiation.</p><br />
<br />
<p><strong>Links:</strong> <br />
<a href="http://orcid.org/0000-0003-2273-0189"><strong>ORCID</strong></a> <br />
<a href="https://www.linkedin.com/in/elisabeth-rebboah-a33923104/"><strong>LinkedIn</strong></a> <br />
<a href="https://github.com/erebboah"><strong>GitHub</strong></a></p><br />
<br />
<p><strong>Personal Interests:</strong> <br />
I enjoy watching anime and getting takeout when I’m not working.</p><br />
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<p><strong>Contact:</strong> <br />
erebboah {at} uci.edu</p><br />
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<h2 class="text-uppercase">Fairlie Reese</h2>
<p class="item-intro text-muted">Dev Cell PhD Student, Bioinformatician</p>
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<p><p><strong>Research Interests:</strong> <br />
I currently work on long-read transcriptomes, and am specifically focused on developing tools for their analysis.</p><br />
<br />
<p><strong>Software:</strong> <br />
<a href="https://freese.gitbook.io/swan/"><strong>Swan:</strong></a> a Python library for visualizing and analyzing transcriptomes <br />
<a href="https://github.com/mortazavilab/TALON"><strong>TALON:</strong></a> Technology-agnostic long-read annotation and quantification pipeline</p><br />
<br />
<p><strong>Links:</strong> <br />
<a href="https://fairliereese.github.io/"><strong>Personal Website</strong></a> <br />
<a href="https://scholar.google.com/citations?user=SgA5IcgAAAAJ&hl=en"><strong>Google Scholar</strong></a> <br />
<a href="http://orcid.org/0000-0002-9240-0102"><strong>ORCID</strong></a> <br />
<a href="https://www.linkedin.com/in/fairlie-reese-a930a5b7/"><strong>LinkedIn</strong></a> <br />
<a href="https://github.com/fairliereese"><strong>GitHub</strong></a></p><br />
<br />
<p><strong>Personal Interests:</strong> <br />
When I’m not working (and there’s not a pandemic going on) you can find me at the beach, at rock concerts, or eating Mexican food. At home, I like to play video games, Dungeons and Dragons, and hang out with my cats.</p><br />
<br />
<p><strong>Contact:</strong> <br />
freese {at} uci.edu</p><br />
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<h2 class="text-uppercase">Heidi Liang</h2>
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<p class="item-intro text-muted">Pharmaceutical Sciences PhD Student, </p>
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<p><p><strong>Research Interests:</strong> <br />
I am currently working on different metabolic labeling strategies and long-read sequencing to study the mRNA transcription.</p><br />
<br />
<p><strong>Links:</strong> <br />
<a href="https://orcid.org/0000-0002-4470-3192"><strong>ORCID</strong></a> <br />
<a href="https://www.linkedin.com/in/jasmine-sakr/"><strong>LinkedIn</strong></a></p><br />
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<p><strong>Contact:</strong> <br />
jsakr {at} uci.edu</p><br />
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<h2 class="text-uppercase">Narges Rezaie</h2>
<p class="item-intro text-muted">MCSB PhD Student, </p>
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<p><p><strong>Research Interests:</strong> <br />
As a person with a computer science background, I’ve always been interested in machine learning methods, network analysis and their applications. Currently, I find the brain as an interesting organ, so I’m trying to identify and classify every functional part of the genome in the brain.</p><br />
<br />
<p><strong>Links:</strong> <br />
<a href="https://nargesr.github.io/"><strong>Personal Website</strong></a> <br />
<a href="https://scholar.google.com/citations?user=xS23yQUAAAAJ&hl=en"><strong>Google Scholar</strong></a> <br />
<a href="https://orcid.org/0000-0001-9326-9954"><strong>ORCID</strong></a> <br />
<a href="https://www.linkedin.com/in/narges-rezaie-ab9710b8/"><strong>LinkedIn</strong></a> <br />
<a href="https://github.com/nargesr"><strong>GitHub</strong></a></p><br />
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<p><strong>Personal Interests:</strong> <br />
I consider myself as an outgoing person, I like camping and adventure. Most weekends, I go hiking with my friends. At home, I like cooking, playing board games and playing guitar.</p><br />
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<p><strong>Contact:</strong> <br />
nargesr {at} uci.edu</p><br />
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<h2 class="text-uppercase">Katherine Williams</h2>
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<p><p><strong>Research Interests:</strong> <br />
I use sequencing technologies to explore epigenetics and gene expression in development of diseases and in non-model organisms. <br />
My main work in collaboration with the Yokomori lab focuses on investigating the transcriptomeand epigenome in facioscapulohumeral muscular dystrophy (FSHD). I use a variety of techniques such as single-nucleus RNA-seq from multinucleated myotubes, RRBS, and bulk RNA-seq. We aim to uncover how the misexpression of a single transcription factor results in pathogenesis. <br />
I work and collaborate on many other projects including studying the transcriptomes of mammals and nematodes. I love having the opportunity to bring new insights into our understanding of other organisms and ourselves!</p><br />
<br />
<p><strong>Links:</strong> <br />
<a href="https://scholar.google.com/citations?user=Lepe9wwAAAAJ&hl=en"><strong>Google Scholar</strong></a> <br />
<a href="http://orcid.org/0000-0001-8061-0105"><strong>ORCID</strong></a> <br />
<a href="https://www.linkedin.com/in/curlsforscience/"><strong>LinkedIn</strong></a> <br />
<a href="https://github.com/CurlsForScience"><strong>GitHub</strong></a></p><br />
<br />
<p><strong>Personal Interests:</strong> <br />
I love to dance, specifically lindy hop and east coast swing. I especially love dancing at Disneyland. Most importantly, I enjoy spending time with my dog and being out in the California sun.</p><br />
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<p><strong>Contact:</strong> <br />
kwillia4 {at} uci.edu</p><br />
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<h2 class="text-uppercase">Gabriela Balderrama-Gutierrez</h2>
<p class="item-intro text-muted">Dev Cell PhD Student, </p>
<img class="img-fluid d-block mx-auto" src="assets/img/team/gaby.jpg" width="300" height="300">
<p><p><strong>Research Interests:</strong> <br />
Working in the intersection of sequencing techologies and data analysis to understand Alzheimer’s disease. Additional collaborations include cancer biology and Biology/immunity of Peromyscus leucopus.</p><br />
<br />
<p><strong>Experience with:</strong> <br />
RNA-seq (bulk, single-cell, single-nucleus) <br />
Data analysis <br />
Metabolomics <br />
Semi-fluent in R <br />
Begginer in Python</p><br />
<br />
<p><strong>Links:</strong> <br />
<strong>Personal Website (Coming soon!)</strong> <br />
<a href="http://orcid.org/0000-0002-5794-4518"><strong>ORCID</strong></a> <br />
<a href="www.linkedin.com/in/GabyBG"><strong>LinkedIn</strong></a> <br />
<a href="https://github.com/GabyBG"><strong>GitHub</strong></a></p><br />
<br />
<p><strong>Personal Interests:</strong> <br />
Human.Controversial yet brave. In love with ballet but also taco lover. Full-time PomMom who dances to New wave music.</p><br />
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<p><strong>Contact:</strong> <br />
gbalderr {at} uci.edu</p><br />
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<h2 class="text-uppercase">Christina Wilcox Thai</h2>
<p class="item-intro text-muted">Dev Cell PhD Student, </p>
<img class="img-fluid d-block mx-auto" src="assets/img/team/christina.jpg" width="300" height="300">
<p><p><strong>Research Interests:</strong> <br />
I have three main projects. The first is my main thesis project investigating a time-series of embryonic stem cell differentiation to neuronal and endodermal lineages via RNA-seq and ATAC-seq in multiple mammalian species. The transcriptional and chromatin information gathered from these time courses are used to build and compare gene regulatory networks for each lineage and species. The second and third projects are related collaboration projects in collaboration with the Baram lab at UC Irvine. Both projects investigate early life stress (ELS) and how early life experiences can affect gene expression and contribute to mental illness in adulthood. The first of these investigates single cell transcriptomics of Corticotropin-releasing hormone (CRH) expressing neurons of the mouse hypothalamus after a model of ELS. Cells from the hypothalamus are separated via FACS and the transcriptome is analyzed via single cell RNA-seq. The second related project investigates methylation heterogeneity in human babies via buccal swabs during the first year of life to investigate a range of ELS in humans.</p><br />
<br />
<p><strong>Links:</strong> <br />
<a href="https://www.linkedin.com/in/christinawilcoxthai/"><strong>LinkedIn</strong></a></p><br />
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<h2 class="text-uppercase">Cassandra McGill</h2>
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<h2 class="text-uppercase">Dana Wyman, PhD</h2>
<p class="item-intro text-muted">Former MCSB PhD Student</p>
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<h2 class="text-uppercase">Aide Macias-Muñoz, PhD</h2>
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<h2 class="text-uppercase">Lorrayne Serra Clague, PhD</h2>
<p class="item-intro text-muted">Former Dev Cell PhD Student</p>
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<p><p>Description coming soon</p>
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