Functional Genomics Resource Center
Selected Publications


  • ChIP-seq guidelines and practices used by the ENCODE and modENCODE consortia. Genome Research (2012) Landt SG*, Marinov GK*, Kundaje A*, el al.
  • High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation. Genome Research (2011). Anil Ozdemir*, Katherine I. Fisher-Aylor*, Shirley Pepke, Manoj Samanta, Leslie Dunipace, Kenneth McCue, Lucy Zeng, Nobuo Ogawa, Barbara J. Wold, and Angelike Stathopoulos.
  • Computation for ChIP-seq and RNA-seq studies. Nature Methods (2009) Shirley Pepke, Barbara Wold and Ali Mortazavi.
  • Genome-wide mapping of in-vivo protein-DNA interactions. Science (2007) Johnson DS*, Mortazavi A*, Myers RM, and Wold B. J.


  • Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology (2010) Trapnell C, Williams BA, Porta G, Mortazavi A , Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L.
  • Mapping and quantifying mammalian transcriptomes by RNA-seq. Nature Methods. (2008) Ali Mortazavi, Brian A Williams, Kenneth McCue, Lorian Schaeffer and Barbara Wold.

Integrated Analysis

  • Global integration of ChIP-seq and DNAse-seq ENCODE data using Self-Organizing Maps: the chromatin landscape of cell-type specificity, Genome Research in preparation. Ali Mortazavi*, Shirley Pepke*, Georgi Marinov, Barbara Wold
  • An Integrated Encyclopedia of DNA Elements in the Human Genome. Nature (2012 in press) The ENCODE Consortium
  • Transcription factor redundancy and tissue specific regulation: evidence from functional and physical network connectivity. Genome Research (2012) Steven G. Kuntz, Brian A. Williams, Paul W. Sternberg, Barbara J. Wold
  • Dynamic transformations of epigenetic marking and genome-wide transcriptional regulation establish T cell identity. Cell. (2012) Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV
  • Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Research. (2012) 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.
  • The ENCODE Project Consortium, A User's Guide to the Encyclopedia of DNA Elements (ENCODE) PLoS Biology (2011) The ENCODE Consortium
  • Computation for ChIP-seq and RNA-seq studies. Nature Methods (2009) Shirley Pepke, Barbara Wold and Ali Mortazavi