Publications

Publications

Best 10

  1.  Lieb JD, Liu X, Botstein D, Brown PO (2001). Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet. 28(4):327-34. (cited by 353)
  2. Liu XS*, Brutlag DL, Liu JS (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments. Nat Biotechnol. 20(8):835-9. *Xiaole Liu added middle name Shirley. (cited by 300)
  3. Conlon EM*, Liu XS*, Lieb JD, Liu JS (2003). Integrating regulatory motif discovery and genome-wide expression     analysis. Proc Natl Acad Sci U S A. 100(6):3339-44. *Joint first authors. (cited by 202)
  4. Liu Y*, Liu XS*, Wei L, Altman RB, Batzoglou (2004). Conservation of eukaryotic regulatory elements and their   identification using comparative genomics. Genome Res. 14(3):451-8. *Joint first authors. (cited by 97)
  5. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS (2006). MAT: Model-based Analysis of Tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 103(33): 12457-12462. (cited by 61)
  6. Carroll JS, Meyer CA, Song J, Li W, Brodsky AS, Hall G, Geistlinger TR, Eeckhoute J, Wang QB, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS*, Brown M* (2006). Genome wide analysis of estrogen receptor binding sites. Nat Genet. 38:1289-97. *Co-corresponding authors. (cited by 146)
  7. Ozsolak F, Song JS, Liu XS*, Fisher DE* (2007). Global chromatin structure mapping of human promoters. Nat Biotechnol. 25:244-8. *Co-corresponding authors. (cited by 32)
  8. Lupien M, Eeckhoute J, Meyer CA, Wang Q, Zhang Y, Li W, Carroll JS, Liu XS, Brown M (2008). FoxA1 translates epigenetic signatures into enhancer driven lineage-specific transcription. Cell. 132(6):958-70.
  9. Johnson DS, Li W, et al., Struhl K, Myers RM, Lieb JD, Liu XS (2008). Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 18(3):393-403. (cited by 9)
  10. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein B, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9(9):R137. (cited by 2)

 

Peer Reviewed Methodology Publications

  1. Liu X, Altman RB (1998). Updating a bibliography using the related articles function within PubMed. Proc AMIA Symp. 750-4. (cited by 16)
  2. Liu X, Brutlag DL, Liu JS (2001). BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Proc Pac Symp Biocomput. 127-38. (cited by 408)
  3. Liu XS*, Brutlag DL, Liu JS (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments. Nat Biotechnol. 20(8):835-9. *Xiaole Liu added middle name Shirley. (cited by 300)
  4. Conlon EM*, Liu XS*, Lieb JD, Liu JS (2003). Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A. 100(6):3339-44. *Joint first authors. (cited by 202)
  5. Liu Y*, Liu XS*, Wei L, Altman RB, Batzoglou (2004). Conservation of eukaryotic regulatory elements and their identification using comparative genomics. Genome Res. 14(3):451-8. *Joint first authors. (cited by 97)
  6. Liu Y, Wei L, Batzoglou S, Brutlag DL, Liu JS, Liu XS (2004). A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res. 32(Web Server issue):W204-W207. (cited by 27)
  7. Li W, Meyer CA, Liu XS (2005). A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. ISMB2005 (acceptance rate 13%). Bioinformatics. 21 Suppl 1:i274-i282. (cited by 42)
  8. Ji X, Li W, Song J, Wei L, Liu XS (2006). CEAS: Cis-Elements Annotation Systems. Nucleic Acids Res. 34(Web Server issue):W551-4. (cited by 12)
  9. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS (2006). MAT: Model-based Analysis of Tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 103(33): 12457-62. (cited by 61)
  10. Carroll JS, Meyer CA, Song J, Li W, Brodsky AS, Hall G, Geistlinger TR, Eeckhoute J, Wang QB, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS*, Brown M* (2006). Genome wide analysis of estrogen receptor binding sites. Nat Genet. 38(11):1289-97. *Co-corresponding authors. (cited by 132)
  11. Ozsolak F, Song JS, Liu XS*, Fisher DE* (2007). Global chromatin structure mapping of human promoters. Nat Biotechnol. 25(2):244-8. *Co-corresponding authors. (cited by 32)
  12. Song JS, Maghsou K, Li W, Fox E, Quackenbush J, Liu XS (2007). Microarray blob-defect removal improves array analysis. Bioinformatics. 23(8):966-71. (cited by 7)
  13. Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS (2007). Model-based analysis for 2-color arrays (MA2C). Genome Biol. 8(8):R178. (cited by 6, and over 300 users worldwide)
  14. Gottardo R, Johnson WE, Li W, Liu XS (2008). A flexible and powerful Bayesian hierarchical model for ChIP-chip experiments. Biometrics. 64(2):468-78.
  15. Li W, Carroll JS, Brown M, Liu XS (2008). xMAN: extreme Mapping of OligoNucleotides. BIOCOMP’07 (acceptance rate 27%). BMC Genomics. 9(Suppl 1):S20. (cited by 5)
  16. Johnson DS, Li W, et al., Struhl K*, Myers RM*, Lieb JD*, Liu XS* (2008). Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res. 18(3):393-403. *Co-corresponding authors. (cited by 6)
  17. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein B, Nusbaum C, Myers RM, Brown M, Li W, Liu XS (2008). Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9(9):R137.
  18. Zhang Y, Shin H, Song JS, Y Lei, Liu XS (2008). Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics. 9:537.
  19. Johnson WE, Liu JS, Liu XS. Doubly-stochastic continuous hidden Markov approach for applications on genome tiling arrays. Submitted.