Ali Mortazavi

Picture of Ali Mortazavi
Professor, Developmental & Cell Biology
School of Biological Sciences
Ph.D., California Institute of Technology, 2008, Biology
M.S., California State University, Los Angeles, 2004, Chemistry (Biochemistry)
B.S., California Institute of Technology, 1993, Engineering and Applied Science (Computer Science)
Phone: (949) 824-6762
University of California, Irvine
2218 Biological Sciences III
Mail Code: 2300
Irvine, CA 92697
Research Interests
Transcriptional Regulation, Genomics, Long-range chromatin interactions, ChIP-seq, RNA-seq
Academic Distinctions
2004 CSULA Chemistry and Biochemistry Graduate Student Award
2008 Caltech Lawrence L. and Audrey W. Ferguson Prize for outstanding doctoral thesis in biology
2013 NIH New Innovator Award
2014 UC Irvine Distinguished Assistant Professor Award for Research
2008 – 2011 Gordon and Betty Moore Cell Center Postdoctoral Fellowship, Caltech
2009 – 2011 Beckman Institute Postdoctoral Fellowship, Caltech
Research Abstract
Applications of genomics, computation, and sequencing technologies to the analysis of transcriptional regulation in development.

My laboratory explores how gene regulatory networks that underlie development are encoded in the human genome and we seek to understand their “grammar” and dynamics using both laboratory and computational methods. We focus on how tissue-specific transcriptional enhancers work, and whether their expression levels and target genes can be predicted from in vivo protein-DNA interactions (as measured using ChIP-seq), open chromatin (from DNase-seq) and RNA expression (from RNA-seq) of both normal and perturbed differentiation time courses. No reliable computational methods yet exist to link distal enhancers to their target genes (which can be many genes and up to a megabase-pair away in mammals) using sequence, expression or ChIP-data alone. While this identification problem is extremely difficult when considering large and complex genomes linearly, it would be a relatively easy problem if we could capture the three-dimensional interaction of the looping enhancers with their target promoters. We are, therefore, working with techniques that capture long-range chromatin interactions globally, such as ChIA-PET, in developmental time courses in order to integrate these long-range data with ChIP-seq, DNase-seq, and RNA-seq into testable gene regulatory networks. We are also interested in what fraction of these long-range interactions account for phenotypic variation between individuals and whether they are more likely to be conserved in vertebrates.
R Murad, A Macias-Muñoz, A Wong, X Ma, A Mortazavi (2021) Coordinated gene expression and chromatin regulation during Hydra head regeneration
Genome Biology and Evolution
Chen GT, Tifrea DF, Murad R, Habowski AN, Lyou Y, Duong MR, Hosohama L, Mortazavi A, Edwards RA, Waterman ML (2021) Disruption of beta-catenin dependent Wnt signaling in colon cancer cells remodels the microenvironment to promote tumor invasion
Mol Cancer Res
Chan D, Feng C, England WE, Wyman D, Flynn RA, Wang X, Shi Y, Mortazavi A, Spitale RC (2021) Diverse functional elements in RNA predicted transcriptome-wide by orthogonal RNA structure probing
Nucleic Acids Res
Forner S, Kawauchi S, Balderrama-Gutierrez G, Kramár EA, Matheos DP, Phan J, Javonillo DI, Tran KM, Hingco E, da Cunha C, Rezaie N, Alcantara JA, Baglietto-Vargas D, Jansen C, Neumann J, Wood MA, MacGregor GR, Mortazavi A, Tenner AJ, LaFerla FM, Green KN (2021) Systematic phenotyping and characterization of the 5xFAD mouse model of Alzheimer’s disease
Scientific Data
Rebboah E, Reese F, Williams K, Balderrama-Gutierrez G, McGill C, Rodriguez I, Liang H, Wold BJ, Mortazavi A (2021) Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
Genome Biology
Ionkina AA, Balderrama-Gutierrez G, Ibanez KJ, Phan SHD, Cortez AN, Mortazavi A, Prescher JA (2021) Transcriptome analysis of heterogeneity in mouse model of breast cancer
Breast Cancer Res.
Arreola MA, Soni N, Crapser JD, Hohsfield LA, Elmore MRP, Matheos DP, Wood MA, Swarup V, Mortazavi A, Green KN (2021) Microglial dyshomeostasis drives perineuronal net and synaptic loss in a CSF1R+/- mouse model of ALSP, which can be rescued via CSF1R inhibitors
Science Advances
Murad R, Avanes A, Ma X, Geng S, Mortazavi A, Momand J (2021) Transcriptome and chromatin landscape changes associated with trastuzumab resistance in HER2+ breast cancer cells
Macias-Munoz A, Mortazavi A (2021) A Bioinformatics pipeline for investigating molecular evolution and gene expression using RNA-seq
Baglietto-Vargas D, Forner S, Cai L, Martini AC, Laura Trujillo-Estrada, Swarup V, Nguyen MMT, Huynh KD, Javonillo DI, Tran KM, Phan J, Jiang S, Kramár EA, Nuñez-Diaz C, Balderrama-Gutierrez G, Garcia F, Childs J, Rodriguez-Ortiz CJ, Garcia-Leon JA, Kitazawa M, Shahnawaz M, Matheos DP, Ma X, Cunha CD, Walls KC, Ager RR, Soto C, Gutierrez A, Moreno-Gonzalez I, Mortazavi A, Tenner AJ, MacGregor GR, Wood M, Green KN, LaFerla FM (2021) Generation of a humanized aβ expressing mouse demonstrating aspects of Alzheimer’s disease-like pathology
Nature Communications
Naciri I, Lin B, Webb CH, Jiang S, Carmona S, Liu W, Mortazavi A, Sun S (2021) Linking Chromosomal Silencing with Xist Expression from Autosomal Integrated Transgenes
Frontiers in Cell and Developmental Biology
Balderrama-Gutierrez G, Milovic A, Cook VJ, Islam MN, Zhang Y, Kiaris H, Belisle JT, Mortazavi A, Barbour AG (2021) An Infection-Tolerant Mammalian Reservoir for Several Zoonotic Agents Broadly Counters the Inflammatory Effects of Endotoxin
Chau, J., Kong, X., Nguyen, N. V., Williams, K., Tawil, R., Kiyono, T., Mortazavi A, Yokomori, K (2021) Relationship of DUX4 and target gene expression in FSHD myocytes
Human Mutation
Bolton JL, Schulmann A, Garcia-Curran MM, Regev L, Chen Y, Kamei N, Shao M, Singh-Taylor A, Jiang S, Noam Y, Molet J, Mortazavi A, Baram TZ (2020) Unexpected Transcriptional Program Contribute to Hipppocampal Memory Deficits and Neuronal Stunting after Early-Life Adversity
Cell Reports
Oblak AL, Forner S, Territo PR, Sasner M, Carter GW, Howell GR, Sukoff-Rizzo SJ, Logsdon BA, Mangravite LM, Mortazavi A, Baglietto-Vargas D, Green KN, MacGregor GR, Wood MA, Tenner AJ, LaFerla FM, Lamb BT, The MODEL-AD (2020) Model organism development and evaluation for late-onset Alzheimer’s disease: MODEL-AD
Translational Research & Clinical Interventions
Hultgren NW, Fang JS, Ziegler ME, Ramirez RN, Phan DT, Hatch M, Welch-Reardon KM, Paniagua AE, Kim LS, Shon NN, Williams DS, Mortazavi A, Hughes CW (2020) Slug regulates the Dll4-Notch-VEGFR2 axis to control endothelial cell activation and angiogenesis
Nature Communications
Reese F, Mortazavi, A (2020) Swan: a library for the analysis and visualization of long-read transcriptomes
Chang D, Serra L, Lu D, Mortazavi, A, Dillman A (2020) A revised Adaptation of the Smart-seq2 Protocol for Single-Nematode RNA-Seq
RNA Abundance Analysis
ENCODE Project Consortium (2020) Expanded encyclopedias of DNA elements in the human and mouse genomes
Partridge EC, Chhetri SB, Prokop JW, Ramaker RC, Jansen CS, Goh ST, Mackiewicz M, Newberry KM, Brandsmeier LA, Meadows SK, Messer CL, Hardigan AA, Coppola CJ, Dean EC, Jiang S, Savic D, Mortazavi, A, Wold BJ, Myers RM, Mendenhall EM (2020) Occupancy maps of 208 chromatin-associated proteins in one human cell type
Jiang S, Williams K, Kong X, Zeng W, Nguyen NV, Ma X, Tawil R, Yokomori K, Mortazavi, A (2020) Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei
PLoS Genetics
Macias-Munoz A, Murad R, Mortazavi, A (2019) Molecular evolution and expression of opsin genes in Hydra vulgaris
BMC Genomics
Jansen C, Ramirez RN, El-Ali NC, Gomez-Cabrero D, Tegner J, Merkenschlager M, Conesa A, Mortazavi, A (2019) Building gene regulatory networks from scATAC-seq and scRNA-seq using Linked Self Organizing Maps
PLoS Computational Biology
Gomez-Cabrero D., Tarazona S., Ferreirós-Vidal I., Ramirez R.N., Company C., Schmidt A, Reijmers T, Paul VVS, Marabita F, Rodríguez-Ubreva J, Garcia-Gomez A, Carroll T, Cooper L, Liang Z, Dharmalingam G, van der Kloet F, Harms AC, Balzano-Nogueira L, Lagani V, Tsamardinos I, Lappe M, Maier D, Westerhuis JA, Hankemeier T, Imhof A, Ballestar E, Mortazavi, A, Merkenschlager M, Tegner J, Conesa A (2019) STATegra, a comprehensive multi-omics dataset of B-cell differentiation in mouse
Scientific Data
Rahmanian S, Murad R, Breschi A, Zeng W, Mackiewicz M, Williams B, Davis CA, Roberts B, Meadows S, Moore D, Trout D, Zaleski C, Dobin A, Sei LH, Drenkow J, Scavelli A, Gingeras TR, Wold BJ, Myers RM, Guigó R, Mortazavi, A (2019) Dynamics of microRNA expression during mouse prenatal development
Genome Research
Mortazavi, A, Baram TZ (2019) Intra-individual changes in methylome profiles: an epigenetic ‘scar’ of early-life adversity ?
Long AD, Baldwin-Brown J, Tao Y, Cook VJ, Balderrama-Gutierrez G, Corbett-Detig R, Mortazavi A, Barbour AG (2019) The genome of Peromyscus leucopus, natural host for Lyme disease and other emerging infections
Science Advances
Jansen CS, Mortazavi, A (2019) Progressive Clustering and Characterization of Increasingly Higher Dimensional Datasets with Living Self-Organizing Maps
WSOM 2019
Serra L, Macchietto M, Macias-Muñoz A, McGill CJ, Rodriguez IM, Rodriguez B, Murad R, Mortazavi, A (2019) Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome
Chang DZ, Serra L, Lu D, Mortazavi, A, Dillman AR (2019) A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema
PLoS Pathogens
Fung L, Guzman H, Sevrioukov E, Idica A, Park E, Bochnakian A, Daugaard I, Jury D, Mortazavi, A, Zisoulis DG, Pedersen IM (2019) miR-128 Restriction of LINE-1 (L1) Retrotransposition is Dependent on Targeting hnRNPA1 mRNA
Int J Mol Sci
Ferreirós-Vidal I, Carroll T, Zhang T, Lagani V, Ramirez RN, Ing-Simmons E, Gómez-Valadés AG, Cooper L, Liang Z, Papoutsoglou G, Dharmalingam G, Guo Y, Tarazona S, Fernandes SJ, Noori P, Silberberg G, Fisher AG, Tsamardinos I, Mortazavi, A., Lenhard B, Conesa A, Tegner J, Merkenschlager M, Gomez-Cabrero D. (2019) Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation.
PLoS Biology
Jiang S, Kamei N, Bolton JL, Ma X, Stern HS, Baram TZ, Mortazavi A (2019) Intra-individual methylomics detects the impact of early-life adversity
Life Science Alliance
Najafi AR, Crapser J, Jiang, S, Ng W, Mortazavi, A, West BL, Green KN (2018) A limited capacity for microglial repopulation in the adult brain
Wyman DE, Mortazavi A (2018) TranscriptClean: Variant-aware correction of indels, mismatches and splice junctions in long-read transcripts
Nguyen K, Aggarwal MB, Feng C, Balderrama G, Fazio M, Mortazavi A, Spitale RC (2018) Spatially restricting biorthogonal nucleoside biosynthesis enables selective metabolic labeling of the mitochondrial transcriptome
ACS Chemical Biology
Jiang S, Mortazavi A (2018) Integrating ChIP-seq with other functional genomics data.
Briefings in Functional Genomics
Serra L, Chang DZ, Macchietto M, Williams K, Murad R, Lu D, Dillman AR, Mortazavi A (2018) Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq.
Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, del Risco H, Ferrell M, Mellado M, Macchietto M, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A (2018) SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.
Genome Research
Sierra RA, Hoverter NP, Ramirez RN, Vuong LM, Mortazavi A, Merrill BJ, Waterman ML, Donovan PJ (2018) TCF7L1 suppresses primitive streak gene expression to support human embryonic stem cell pluripotency.
Guerrero-Juarez CF, Astrowski, AA, Murad, R, Dang, CT, Shatrova, VO, Astrowskaja, A, Lim CH, Ramos R, Wang X, Liu Y, Lee HL, Pham KT, Hsi TC, Oh JW, Crocker D, Mortazavi A, Ito M, Plikus MV (2018) Wound regeneration deficit in rats correlates with low morphogenetic potential and distinct transcriptome profile of epidermis.
Journal of Investigative Dermatology
Rodríguez-Ubreva J, Català-Moll F, Obermajer N, Álvarez-Errico D, Ramirez RN, Company C, Vento-Tormo R, Moreno-Bueno G, Edwards RP, Mortazavi A, Kalinski P, Ballestar E (2017) Prostaglandin E2 Leads to the Acquisition of DNMT3A-Dependent Tolerogenic Functions in Human Myeloid-Derived Suppressor Cells.
Cell Reports
Macchietto M, Angdembey D, Heidarpour N, Rodriguez B, Serra L, El-Ali N, Mortazavi A (2017) Comparative transcriptomics of Steinernema and Caenorhabditis single embryos reveals orthologous gene expression convergence during late embryogenesis.
Genome Biology and Evolution
Hernandez MX, Jiang S, Cole TA, Chu SH, Fonseca MI, Fang MJ, Hohsfield LA, Torres MD, Green KN, Wetsel RA, Mortazavi A, Tenner AJ (2017) Prevention of C5aR1 signaling delays microglial inflammatory polarization, favors clearance pathways and suppresses cognitive loss.
Molecular Neurodegeneration
Longabaugh WJR, Zeng W, Zhang JA, Hosokawa H, Jansen CS, Li L, Romero-Wolf M, Liu P, Kueh HY, Mortazavi A, Rothenberg EV (2017) Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network.
Lu D, Macchietto M, Chang D, Barros MM, Baldwin J, Mortazavi A, Dillman AR (2017) Activated entomopathogenic nematode infective juveniles release lethal venom proteins.
PLoS Pathogens
Abud EM, Ramirez RN, 17 authors, Mortazavi A, Carson MJ, Poon WW, Blurton-Jones M (2017) iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
Ramirez RN, El-Ali NC, Mager MA, Wyman D, Conesa A, Mortazavi A (2017) Dynamic Gene Regulatory Networks of Human Myeloid Differentiation.
Cell Systems
Plikus MV, Guerrero-Juarez CF, …21 authors…, Ramirez RN, Murad R, Offermanns S, Metzger D, Chambon P, Widgerow AD, Tuan TL, Mortazavi A, Gupta RK, Hamilton BA, Millar SE, Seale P, Pear WS, Lazar MA, Cotsarelis G (2017) Regeneration of fat cells from myofibroblasts during wound healing. Science
Singh-Taylor A, Molet J, Jiang S, Korosi A, Bolton JL, Noam Y, Simeone K, Cope J, Chen Y, Mortazavi A, Baram TZ (2017) NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience.
Molecular Psychiatry
Zeng W, Jiang S, Kong X, El-Ali N, Ball AR Jr, MA CI, Hashimoto N, Yokomori K, Mortazavi A (2016) Single-nucleus RNA-seq of differentiating myoblasts reveals the extent of fate heterogeneity
Nucleic Acids Research
Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szczesniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A (2016) A survey of best practices for RNA-seq data analysis.
Genome Biology
Dillman AR, Macchietto M, Porter CF, Rogers A, Williams B, Antoshechkin I, Lee MM, Goodwin Z, Lu X, Lewis EE, Goodrich-Blair H, Stock SP, Adams BJ, Sternberg PW, Mortazavi A (2015) Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks.
Genome Biology
Mortazavi A (2015) Better together: multiplexing samples to improve the preparation and reliability of gene expression studies.
Nature Methods
Daniels EV, Murad R, Mortazavi A, Reed RD (2014) Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns.
Molecular Ecology
Yue F, ….60 authors …, Jansen C, …65 authors…, Mortazavi A, … 9 authors (2014) A comparative encyclopedia of DNA elements in the mouse genome.
Gerstein MB, Rozowsky J, … 56 authors…, Mortazavi A, Murad R, … 36 authors (2014) Comparative analysis of the transcriptome across distant species.
Zeng W, Chen YY, Newkirk DA, Wu B, Balog J, Kong X, Ball AR, Zanotti S, Tawil R, Hasimoto N, Mortazavi A, van der Maarel K, Yokomori K (2014) Genetic and Epigenetic Characteristics of FSHD-Associated 4q and 10q D4Z4 that are distinct from Non-4q/10q D4Z4 Homologs.
Human Mutation
Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Hamidane HB, Graumann J, Mortazavi A, Nadeau JH, Davidson NO (2014) Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver.
Genome Biology
Conesa A, Mortazavi A (2014) The common ground of genomics and systems biology.
BMC Systems Biology
Steijger T, Abril JF, Engström PG, Kokocinski F; The RGASP Consortium, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P, Bohnert R, Bucher P, Cloonan N, Derrien T, Djebali S, Du J, Dudoit S, Gerstein M, Gingeras TR, Gonzalez D, Grimmond SM, Guigó R, Habegger L, Harrow J, Hubbard TJ, Iseli C, Jean G, Kahles A, Lagarde J, Leng J, Lefebvre G, Lewis S, Mortazavi A, and 26 more authors (2013) Assessment of transcript reconstruction methods for RNA-seq.
Nature Methods
Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison R, Myers RM, Wold B (2013) Integrating and mining the chromatin landscape of cell type specificity using Self-Organizing Maps.
Genome Research
Srinivasan J, Dilman AR, Macchietto MG, Heikkinen L, Lakso M, Fracchia KM, Antoshechkin I, Mortazavi A, Wong G, Sternberg PW (2013) The Draft Genome and Transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle.
Park E, Williams B, Wold B, Mortazavi A (2012) RNA Editing in the human ENCODE RNA-seq data.
Genome Research.
The ENCODE Consortium (2012) An Integrated Encyclopedia of DNA Elements in the Human Genome.
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, et al. (2012) Landscape of transcription in human cells.
Zeng W, Mortazavi A (2012) Technical considerations for functional sequencing assays.
Nature Immunology
The Mouse ENCODE Consortium (2012) An Encyclopedia of Mouse DNA Elements (Mouse ENCODE).
Genome Biology
Dilman AR, Mortazavi A, Sternberg PW (2012) Incorporating Genomics into the Toolkit of Nematology.
Journal of Nematology
Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV (2012) Dynamic transformations of epigenetic marking and genome-wide transcriptional regulation establish T cell identity.
The ENCODE Project Consortium. (2011). A user's guide to the Encyclopedia of DNA Elements (ENCODE).
PLoS Biol.
Trapnell C, Williams BA, Porta G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter B. (2010) Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation.
Nature Biotech
Mortazavi A*, Schwarz EM*, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW. (2010) Scaffolding a de novo nematode genome with RNA-seq.
Genome Research.
Pepke S, Wold B, Mortazavi A. (2009). Computation for ChIP-seq and RNA-seq studies.
Nature Methods.
Mortazavi A*, Williams BA*, McCue K, Schaeffer L, Wold B. (2008). Mapping and quantifying mammalian transcriptomes by RNA-seq.
Nature Methods.
Berghella L, De Angelis L, De Buysscher T, Mortazavi A, Biressi S, Forcales SV, Sirabella D, Cossu G, Wold BJ. (2008) A highly conserved molecular switch binds MSY-3 to regulate myogenin repression in postnatal muscle.
Genes and Development.
*Johnson, D. S., *Mortazavi, A., Myers, R. M. and Wold, B. (2007). Genome-wide mapping of in vivo protein DNA interactions.
Science. (*co-first authors).
Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B. (2006). Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire.
Genome Research.
Roden JC, King BW, Trout D, Mortazavi A, Wold BJ, Hart CE. (2006). Mining gene expression data by interpreting principal components.
BMC Bioinformatics.
Professional Societies
Genetics Society of America
Society for Neuroscience
Other Experience
Associate Editor
BMC Bioinformatics 2010
Graduate Programs
Cellular and Molecular Biosciences
Mathematical and Computational Biology
Research Centers
Center for Complex Biological Systems
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