Ali Mortazavi, Ph.D.
2218 Biological Sciences III
University of California Irvine
Irvine, CA 92697-2300
Tel: (949) 824-6762
Fax: (949) 824-4709
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” 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) 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 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.
- 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, In press
- 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, In press
- The common ground of genomics and systems biology
Conesa A, Mortazavi A
BMC Systems Biology, 2013, In press
- 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
- Park E, Williams B, Wold B, Mortazavi A (2012) RNA Editing in the ENCODE RNA-seq data. Genome Research.
- The ENCODE Consortium (2012) An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature.
- Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, et al. (2012) Landscape of transcription in human cells. Nature.
- 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. Cell.
- 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) Extensive Promoter-centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation. Cell.
- 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. (2012) Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Research.
- The ENCODE Project Consortium, A User’s Guide to the Encyclopedia of DNA Elements (ENCODE)(2011), PLoS Biology.
- 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.
- 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.
- Pepke S, Wold B, Mortazavi A (2009). Computation for ChIP-seq and RNA-seq studies. 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.
- Mortazavi A*, Williams BA*, McCue K, Schaeffer L, Wold B(2008). Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods.
- Johnson DS*, Mortazavi A*, Myers RM, Wold B (2007). In-vivo Protein-DNA Interactions. Science.
- 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 repertoir. 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.
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