Now showing items 21-24 of 24

    • A suite of web-based programs to search for transcriptional regulatory motifs 

      Liu, Y.; Wei, L.; Batzoglou, S.; Brutlag, D. L.; Liu, Jun; Liu, Xiaole (Shirley) Shirley (Oxford University Press (OUP), 2004)
      The identification of regulatory motifs is important for the study of gene expression. Here we present a suite of programs that we have developed to search for regulatory sequence motifs: (i) BioProspector, a Gibbs-sampling-based ...
    • Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila 

      Wang, Xiangfeng; Liu, Xiaole Shirley (Frontiers Research Foundation, 2011)
      MicroRNAs (miRNAs) are a class of 20–23 nucleotide small RNAs that regulate gene expression post-transcriptionally in animals and plants. Annotation of miRNAs by the miRNA database (miRBase) has largely relied on computational ...
    • Systematic Evaluation of Factors Influencing ChIP-Seq Fidelity 

      Negre, Nicolas; Li, Qunhua; Mieczkowska, Joanna O.; Slattery, Matthew; Kim, Tae-Kyung; Zieba, Jennifer; Ruan, Yijun; Bickel, Peter J.; Wold, Barbara J.; Lieb, Jason D.; Chen, Yiwen; Liu, Tao; Zhang, Yong; He, Housheng H; Myers, Richard M.; White, Kevin P.; Liu, Xiaole Shirley (Nature Publishing Group, 2012)
      We performed a systematic evaluation of how variations in sequencing depth and other parameters influence interpretation of Chromatin immunoprecipitation (ChIP) followed by sequencing (ChIP-seq) experiments. Using Drosophila ...
    • TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions 

      Verzi, M. P.; Hatzis, Phillip Evangelos; Sulahian, R.; Philips, J.; Schuijers, J.; Shin, H.; Freed, E.; Lynch, J. P.; Dang, D. T.; Brown, Myles A.; Clevers, H.; Liu, Xiaole (Shirley) Shirley; Shivdasani, Ramesh Arjun (Proceedings of the National Academy of Sciences, 2010)
      Surprisingly few pathways signal between cells, raising questions about mechanisms for tissue-specific responses. In particular, Wnt ligands signal in many mammalian tissues, including the intestinal epithelium, where ...