Camden Jansen

Dr. Ali Mortazavi

Associate Professor

ali.mortazavi@uci.edu

Research Interests:

I have been fascinated since my days in college with the idea of development as a program encoded in DNA. I want to learn the grammar of DNA so that I can read the “book of life”. Therefore every project in my lab ultimately connects to the regulation of gene expression using different genomics techniques such as functional genomics and comparative genomics.
While in graduate school, I helped develop two now-widely adopted methods known as ChIP-seq and RNA-seq to map protein-DNA binding and gene expression genome-wide using the latest generation of short-read sequencers. These techniques are the bread and butter of my lab. I am particularly interested in understanding the wiring of cis-regulatory networks at the level of transcription factor binding using techniques such as ChIP-seq, DNAse-seq, and ATAC-seq affecting the output of these networks, as measured by RNA-seq. My long-term goals are (a) to build accurate global models of gene-regulation during cell differentiation as well as animal development and (b) understand the evolution of these networks in sister species.

Recent Publications:

  • 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
    *first co-authors
    $corresponding authors
  • 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
    Genetics 2013
  • 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. Faculty Log In inShare

Other Interests:

My main personal interests outside of biology are history, geography, economics, and politics. I am an avid fan of comedies and historical dramas. I love traveling and visiting museums.