Xiaole Shirley Liu
Xiaole Shirley Liu
Professor, Data Science, Dana-Farber and Harvard University
No verified email - Homepage
Title
Cited by
Cited by
Year
Model-based analysis of ChIP-Seq (MACS)
Y Zhang, T Liu, CA Meyer, J Eeckhoute, DS Johnson, BE Bernstein, ...
Genome biology 9 (9), 1, 2008
97632008
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ...
Genome research 22 (9), 1813-1831, 2012
16662012
Genome-wide analysis of estrogen receptor binding sites
JS Carroll, CA Meyer, J Song, W Li, TR Geistlinger, J Eeckhoute, ...
Nature genetics 38 (11), 1289-1297, 2006
14742006
Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1
JS Carroll, XS Liu, AS Brodsky, W Li, CA Meyer, AJ Szary, J Eeckhoute, ...
Cell 122 (1), 33-43, 2005
13882005
TIMER: a web server for comprehensive analysis of tumor-infiltrating immune cells
T Li, J Fan, B Wang, N Traugh, Q Chen, S Liu, B Li, XS Liu
Cancer Res 77 (1), e108-110, 2017
13122017
Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2
M Ko, Y Huang, AM Jankowska, UJ Pape, M Tahiliani, HS Bandukwala, ...
Nature 468 (7325), 839-843, 2010
12722010
BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.
X Liu, DL Brutlag, JS Liu
Pacific symposium on biocomputing 6, 127-138, 2001
10692001
Identifying ChIP-seq enrichment using MACS
J Feng, T Liu, B Qin, Y Zhang, XS Liu
Nature protocols 7 (9), 1728-1740, 2012
9822012
Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project
MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng, BI Arshinoff, T Liu, ...
Science 330 (6012), 1775-1787, 2010
9522010
FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription
M Lupien, J Eeckhoute, CA Meyer, Q Wang, Y Zhang, W Li, JS Carroll, ...
Cell 132 (6), 958-970, 2008
9412008
Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer
Q Wang, W Li, Y Zhang, X Yuan, K Xu, J Yu, Z Chen, R Beroukhim, ...
Cell 138 (2), 245-256, 2009
9052009
Promoter-specific binding of Rap1 revealed by genome-wide maps of protein–DNA association
JD Lieb, X Liu, D Botstein, PO Brown
Nature genetics 28 (4), 327-334, 2001
8762001
An algorithm for finding protein–DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
XS Liu, DL Brutlag, JS Liu
Nature biotechnology 20 (8), 835-839, 2002
8312002
Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells
WA Pastor, UJ Pape, Y Huang, HR Henderson, R Lister, M Ko, ...
Nature 473 (7347), 394-397, 2011
8302011
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens
LXS Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M
Genome Biol 15 (12), 554, 2014
826*2014
The JAK2/STAT3 signaling pathway is required for growth of CD44+CD24 stem cell–like breast cancer cells in human tumors
LLC Marotta, V Almendro, A Marusyk, M Shipitsin, J Schemme, SR Walker, ...
The Journal of clinical investigation 121 (7), 2723-2735, 2011
8092011
Comprehensive analyses of tumor immunity: implications for cancer immunotherapy
B Li, E Severson, JC Pignon, H Zhao, T Li, J Novak, P Jiang, H Shen, ...
Genome biology 17 (1), 1-16, 2016
8012016
Chromatin structure analyses identify miRNA promoters
F Ozsolak, LL Poling, Z Wang, H Liu, XS Liu, RG Roeder, X Zhang, ...
Genes & development 22 (22), 3172-3183, 2008
7472008
PPARγ and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale
MI Lefterova, Y Zhang, DJ Steger, M Schupp, J Schug, A Cristancho, ...
Genes & development 22 (21), 2941-2952, 2008
7392008
Differential chromatin marking of introns and expressed exons by H3K36me3
P Kolasinska-Zwierz, T Down, I Latorre, T Liu, XS Liu, J Ahringer
Nature genetics 41 (3), 376, 2009
7092009
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Articles 1–20