Publications

  • Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks
    Adler R Dillman, Marissa Macchietto, Camille F Porter, Alicia Rogers, Brian Williams, Igor Antoshechkin, Ming-Min Lee, Zane Goodwin, Xiaojun Lu, Edwin E Lewis, Heidi Goodrich-Blair, S Patricia Stock, Byron J Adams, Paul W Sternberg, Ali Mortazavi
    Genome Biology, 2015
  • Better together: multiplexing samples to improve the preparation and reliability of gene expression studies
    A Mortazavi
    Nature Methods, 2015
  • A comparative encyclopedia of DNA elements in the mouse genome
    F Yue, et al.
    Nature, 2014
  • Extensive transcriptional response associated with seasonal plasticity of butterfly wing patterns
    EV Daniels, R Murad, A Mortazavi, RD Reed
    Molecular Ecology, 2014
  • Comparative analysis of the transcriptome across distant species
    Gerstein MB, et al.
    Nature, 2014
  • The common ground of genomics and systems biology
    Conesa A, Mortazavi A
    BMC Systems Biology, 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
  • 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
  • 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
  • Assessment of transcript reconstruction methods for RNA-seq
    Steiger T, et al.
    Nature Methods, 2013
  • 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