Ali Mortazavi, PhD

Applications of genomics, computation, and sequencing technologies to the analysis of transcriptional regulation in development. My research interests are in the application of genomic methods to answer fundamental questions in the transcriptional regulation of development using a combination of functional sequencing assays and computational methods. I am particularly interested in understanding how homologous gene regulatory networks are encoded in the human and mouse genomes. I have also a separate interest in comparative genomics and development of nematode parasites with a particular focus on the genus Steinernema. My lab combines experimental work and computational analysis primarily in hematopoietic, skeletal muscle, and embryonic stem cells in human, mouse, and other mammals to understand which regulatory elements are conserved, which elements are not conserved but functional, and which elements regulates what genes. My laboratory has focused over the last six years on doing comparative analyses of regulatory elements and their long-range interactions in human and mouse using a combination of ChIP-seq, DNA methylation, ATAC-seq and RNA-seq using ever lower amounts of starting material down to single cells when practical. My long term goals are (a) to develop models that take into account the complex interplay of promoters and enhancers in controlling gene expression and (b) to understand the common and species-specific parts of the human and mouse Gene Regulatory Networks for homologous cell types and tissues in order to translate seamlessly results between human and mouse models of disease. I have actively participated in ENCODE since 2008, first at Caltech and now in my own lab at UCI.

Recent Publications

  • Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network.
    Longabaugh WJR, Zeng W, Zhang JA, Hosokawa H, Jansen CS, Li L, Romero-Wolf M, Liu P, Kueh HY, Mortazavi A, Rothenberg EV.
    PNAS, 2017
  • Activated entomopathogenic nematode infective juveniles release lethal venom proteins.
    Lu D, Macchietto M, Chang D, Barros MM, Baldwin J, Mortazavi A, Dillman AR.
    PLoS Pathogens, 2017
  • iPSC-Derived Human Microglia-like Cells to Study Neurological Diseases.
    Abud EM, Ramirez RN, …17 authors…, Mortazavi A, Carson MJ, Poon WW, Blurton-Jones M.
    Neuron, 2017
  • Dynamic Gene Regulatory Networks of Human Myeloid Differentiation.
    Ramirez RN, El-Ali NC, Mager MA, Wyman D, Conesa A, Mortazavi A.
    Cell Systems, 2017
  • Regeneration of fat cells from myofibroblasts during wound healing.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.
    Science, 2017
  • NRSF-dependent epigenetic mechanisms contribute to programming of stress-sensitive neurons by neonatal experience, promoting resilience.
    Singh-Taylor A, Molet J, Jiang S, Korosi A, Bolton JL, Noam Y, Simeone K, Cope J, Chen Y, Mortazavi A, Baram TZ.
    Mol Psychiatry, 2017
  • Single-nucleus RNA-seq of differentiating myoblasts reveals the extent of fate heterogeneity
    Zeng W, Jiang S, Kong X, El-Ali N, Ball AR Jr, MA CI, Hashimoto N, Yokomori K, Mortazavi A
    Nucleic Acids Research, 2016
  • A survey of best practices for RNA-seq data analysis
    Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szczesniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A
    Genome Biology, 2016
  • Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
    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
    Genome Biology, 2015
  • Better together: multiplexing samples to improve the preparation and reliability of gene expression studies.
    Mortazavi A
    Nature Methods, 2015
  • Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns.
    Daniels EV, Murad R, Mortazavi A, Reed RD
    Molecular Ecology, 2014
  • A comparative encyclopedia of DNA elements in the mouse genome
    Yue F, ….60 authors …, Jansen C, …65 authors…, Mortazavi A, … 9 authors,
    Nature, 2014
  • Comparative analysis of the transcriptome across distant species
    Gerstein MB, Rozowsky J, … 56 authors…, Mortazavi A, Murad R, … 36 authors
    Nature, 2014
  • Genetic and Epigenetic Characteristics of FSHD-Associated 4q and 10q D4Z4 that are distinct from Non-4q/10q D4Z4 Homologs
    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
    Human Mutation, 2014
  • Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver
    Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Hamidane HB, Graumann J, Mortazavi A, Nadeau JH, Davidson NO
    Genome Biology, 2014
  • The common ground of genomics and systems biology
    Conesa A, Mortazavi A
    BMC Systems Biology, 2014
  • Assessment of transcript reconstruction methods for RNA-seq
    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.
    Nature Methods, 2013
  • Integrating and mining the chromatin landscape of cell type specificity using Self-Organizing Maps
    Mortazavi A*$, Pepke S*, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison R, Myers RM, Wold B$
    Genome Research, 2013
    *first co-authors
    $corresponding authors
  • The Draft Genome and Transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle
    Srinivasan J, Dilman AR, Macchietto MG, Heikkinen L, Lakso M, Fracchia KM, Antoshechkin I, Mortazavi A, Wong G, Sternberg PW
    Genetics 2013
  • RNA Editing in the ENCODE RNA-seq data
    Park E, Williams B, Wold B, Mortazavi A
    Genome Research 2012
  • An Integrated Encyclopedia of DNA Elements in the Human Genome
    The ENCODE Consortium
    Nature 2012
  • Landscape of transcription in human cells
    Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, et al.
    Nature 2012
  • Technical considerations for functional sequencing assays
    Zeng W,  Mortazavi A
    Nature Immunology 2012
  • An Encyclopedia of Mouse DNA Elements (Mouse ENCODE)
    The Mouse ENCODE consortium
    Genome Biology 2012
  • Incorporating genomics into the toolkit of nematology
    Dilman AR, Mortazavi A, Sternberg PW
    Journal of Nematology 2012
  • Dynamic transformations of epigenetic marking and genome-wide transcriptional regulation establish T cell identity
    Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV
    Cell 2012
  • Extensive Promoter-centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
    Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher K, Mortazavi A, Gerstein M, Gingeras T, Wold B, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y (2012)
    Cell 2012
  • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression
    Reddy TE, Gertz J, Pauli F, Kucera KS, Varley KE, Newberry KM, Marinov GK, Mortazavi A, Williams BA, Song L, Crawford GE, Wold BJ, Willard HF, Myers RM.
    Genome Research 2012
  • A User’s Guide to the Encyclopedia of DNA Elements (ENCODE)
    The ENCODE Project Consortium
    PLoS Biology 2011
  • Scaffolding a de novo nematode genome with RNA-seq
    Mortazavi A*, Schwarz EM*, Williams B, Schaeffer L, Antoshechkin I, Wold BJ, Sternberg PW
    Genome Research 2010
  • Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
    Trapnell C, Williams BA, Porta G, Mortazavi A , Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter B.
    Nature Biotech 2010
  • Computation for ChIP-seq and RNA-seq studies
    Pepke S, Wold B, Mortazavi A
    Nature Methods 2009
  • A highly conserved molecular switch binds MSY-3 to regulate myogenin repression in postnatal muscle
    Berghella L, De Angelis L, De Buysscher T, Mortazavi A, Biressi S, Forcales SV, Sirabella D, Cossu G, Wold BJ
    Genes and Development 2008
  • Mapping and quantifying mammalian transcriptomes by RNA-seq
    Mortazavi A*, Williams BA*, McCue K, Schaeffer L, Wold B
    Nature Methods 2008
  • In-vivo Protein-DNA Interactions.
    Johnson DS*, Mortazavi A*, Myers RM, Wold B
    Science 2007
  • Comparative genomics modeling of the NRSF/REST repressor network: from single conserved sites to genome-wide repertoire
    Mortazavi A, Leeper Thompson EC, Garcia ST, Myers RM, Wold B
    Genome Research 2006
  • Mining gene expression data by interpreting principal components Roden JC, King BW, Trout D, Mortazavi A, Wold BJ, Hart CE
    BMC Bioinformatics 2006

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