Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

Xiaole (Shirley) Liu, Ph.D.

Co-Author

This page shows the publications co-authored by Xiaole (Shirley) Liu and Clifford Meyer.
Connection Strength

4.814
  1. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet. 2014 Nov; 15(11):709-21.
    View in: PubMed
    Score: 0.606
  2. Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function. Mol Endocrinol. 2012 Oct; 26(10):1651-9.
    View in: PubMed
    Score: 0.526
  3. BINOCh: binding inference from nucleosome occupancy changes. Bioinformatics. 2011 Jul 01; 27(13):1867-8.
    View in: PubMed
    Score: 0.480
  4. ChIP-Chip: algorithms for calling binding sites. Methods Mol Biol. 2009; 556:165-75.
    View in: PubMed
    Score: 0.408
  5. Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. Nucleic Acids Res. 2017 01 04; 45(D1):D658-D662.
    View in: PubMed
    Score: 0.175
  6. ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. BMC Bioinformatics. 2016 Oct 03; 17(1):404.
    View in: PubMed
    Score: 0.175
  7. Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles. Genome Res. 2016 10; 26(10):1417-1429.
    View in: PubMed
    Score: 0.172
  8. High-dimensional genomic data bias correction and data integration using MANCIE. Nat Commun. 2016 Apr 13; 7:11305.
    View in: PubMed
    Score: 0.169
  9. Sequence determinants of improved CRISPR sgRNA design. Genome Res. 2015 Aug; 25(8):1147-57.
    View in: PubMed
    Score: 0.159
  10. MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol. 2014 Aug 07; 15(8):419.
    View in: PubMed
    Score: 0.150
  11. Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc. 2013 Dec; 8(12):2502-15.
    View in: PubMed
    Score: 0.143
  12. A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer. BMC Genomics. 2013 Oct 04; 14:680.
    View in: PubMed
    Score: 0.142
  13. Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res. 2012 Jun; 22(6):1015-25.
    View in: PubMed
    Score: 0.128
  14. Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res. 2012 Aug; 40(14):6414-23.
    View in: PubMed
    Score: 0.128
  15. Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol. 2011 Aug 22; 12(8):R83.
    View in: PubMed
    Score: 0.122
  16. MM-ChIP enables integrative analysis of cross-platform and between-laboratory ChIP-chip or ChIP-seq data. Genome Biol. 2011; 12(2):R11.
    View in: PubMed
    Score: 0.118
  17. Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res. 2010 Dec; 20(12):1730-9.
    View in: PubMed
    Score: 0.116
  18. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res. 2011 Jan; 39(Database issue):D968-74.
    View in: PubMed
    Score: 0.116
  19. Nucleosome dynamics define transcriptional enhancers. Nat Genet. 2010 Apr; 42(4):343-7.
    View in: PubMed
    Score: 0.111
  20. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137.
    View in: PubMed
    Score: 0.100
  21. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A. 2006 Aug 15; 103(33):12457-62.
    View in: PubMed
    Score: 0.086
  22. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics. 2005 Jun; 21 Suppl 1:i274-82.
    View in: PubMed
    Score: 0.080
  23. Response and resistance to BET bromodomain inhibitors in triple-negative breast cancer. Nature. 2016 Jan 21; 529(7586):413-417.
    View in: PubMed
    Score: 0.041
  24. Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification. Nat Methods. 2014 Jan; 11(1):73-78.
    View in: PubMed
    Score: 0.036
  25. Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell. 2010 Nov 16; 19(5):713-26.
    View in: PubMed
    Score: 0.029
  26. Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes Dev. 2010 Oct 01; 24(19):2219-27.
    View in: PubMed
    Score: 0.029
  27. MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A. 2010 Feb 23; 107(8):3698-703.
    View in: PubMed
    Score: 0.028
  28. Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature. 2010 Jan 21; 463(7279):374-8.
    View in: PubMed
    Score: 0.027
  29. Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery. Genome Res. 2009 Nov; 19(11):1963-73.
    View in: PubMed
    Score: 0.027
  30. Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell. 2009 Jul 23; 138(2):245-56.
    View in: PubMed
    Score: 0.027
  31. Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol. 2009 Jun; 29(12):3413-23.
    View in: PubMed
    Score: 0.026
  32. Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res. 2009 Mar; 19(3):372-80.
    View in: PubMed
    Score: 0.026
  33. FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell. 2008 Mar 21; 132(6):958-70.
    View in: PubMed
    Score: 0.024
  34. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006 Nov; 38(11):1289-97.
    View in: PubMed
    Score: 0.022
  35. Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res. 2006 Jul; 16(7):912-21.
    View in: PubMed
    Score: 0.021
  36. Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell. 2005 Jul 15; 122(1):33-43.
    View in: PubMed
    Score: 0.020
  37. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells. Genome Biol. 2005; 6(8):R64.
    View in: PubMed
    Score: 0.020
Connection Strength
The connection strength for co-authors is the sum of the scores for each of their shared publications.

Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.