Genomics, computation and sequencing

Mortazavi Lab at UC Irvine


There are many diverse projects going on in the lab

Cellular Differentiation

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.

Gene Regulatory Networks

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.

Long-read Transcriptomics

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.

Non-model Organisms

We also use functional genomics in order to study animals such as nematodes, hydra, or the deer mouse to understand their developmental adaptations.

Model AD

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.


We are using functional genomics to understand the mechanisms driving the pathology of Facioscapulohumeral muscular dystrophy using single-cell and single-nucleus techniques.


Software produced by the lab used to analyze genomics data


Transcriptome analysis and visualization


Long-read RNA-seq annotator


Long-read RNA-seq error correction


High-dimensional data clustering with SOMs


What's happening in the lab?

  • Spring 2020


    We celebrate the graduation of three of our PhD students this spring! Congratulations to Drs. Dana Wyman, Sorena Rahmanian, and Lorrayne Serra Clague! Best of luck to all of you.

  • May 2020

    snRNA-seq FSHD2 publication

    Kate and Mandy’s single-nucleus FSHD2 study, entitled “Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei”, was published in PLoS Genetics. Read it here.

  • March 2020

    Narges joins the lab!

    Narges, an MCSB PhD student, has officially joined the lab! Welcome! She is currently working as a bioinformatician working on the Model AD project.

  • December 2019

    Hydra vulgaris opsin gene evolution and expression publication

    Aide’s Hydra opsin gene study, “Molecular evolution and expression of opsin genes in Hydra vulgaris”, was published in BMC Genomics. You can read it here.

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    November 2019

    Gene regulatory networks from scATAC and scRNA-seq linked SOM publication

    Camden’s gene-regulatory network study that uses linked SOMs on scATAC and scRNA-seq, “Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps”, has been published in PLoS Computational Biology. You can read it here.


Ali Mortazavi, PhD

Principal Investigator

Christina Wilcox Thai

Dev Cell PhD Student

Elisabeth Rebboah

MCSB PhD Student

Fairlie Reese

Dev Cell PhD Student

Gabriela Balderrama-Gutierrez

Dev Cell PhD Student

Heidi Liang

Lab Technician / Sequencing Specialist

Jasmine Sakr

Pharmaceutical Sciences PhD Student

Katherine Williams

Dev Cell PhD Student

Klebea Carvalho

Pharmaceutical Sciences PhD Student

Magdalena Gantuz

Lab Technician / Sequencing Specialist

Muhammed Hasan Celik

MCSB PhD Student

Narges Rezaie

MCSB PhD Student

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