Genomics, computation and sequencing

Mortazavi Lab at UC Irvine


There are many diverse projects going on in the lab

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.



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.

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.

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.


Software produced by the lab used to analyze genomics data


Reproducible latent dirichlet allocation (LDA) for single cell epigenomics data


Weighted Gene Correlation Network Analysis


Alternative polyadenylation detection


Transcriptome analysis and visualization


Long-read RNA-seq annotator


Long-read RNA-seq error correction


High-dimensional data clustering with SOMs


Ali Mortazavi, PhD

Principal Investigator

Elisabeth Rebboah

MCSB PhD Student

Fairlie Reese

Dev Cell PhD Student

Heidi Liang

Lab Technician / Sequencing Specialist

Jasmine Sakr

Pharmaceutical Sciences PhD Student

Narges Rezaie

MCSB PhD Student

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