PubRank

X Shirley Liu

Author PubWeight™ 334.84‹?›

Top papers

Rank Title Journal Year PubWeight™‹?›
1 Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008 51.63
2 Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006 18.63
3 Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1. Cell 2005 14.32
4 FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription. Cell 2008 14.18
5 Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A 2006 13.68
6 Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science 2010 9.78
7 ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 2012 9.13
8 Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature 2010 8.87
9 Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 2009 8.11
10 Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells. Nature 2011 7.43
11 Model-based analysis of two-color arrays (MA2C). Genome Biol 2007 7.28
12 Androgen receptor regulates a distinct transcription program in androgen-independent prostate cancer. Cell 2009 7.09
13 A hierarchical network of transcription factors governs androgen receptor-dependent prostate cancer growth. Mol Cell 2007 5.99
14 Nucleosome dynamics define transcriptional enhancers. Nat Genet 2010 5.94
15 A circadian rhythm orchestrated by histone deacetylase 3 controls hepatic lipid metabolism. Science 2011 5.91
16 Chromatin structure analyses identify miRNA promoters. Genes Dev 2008 5.40
17 High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 2007 5.24
18 PPARgamma and C/EBP factors orchestrate adipocyte biology via adjacent binding on a genome-wide scale. Genes Dev 2008 4.83
19 Integrating regulatory motif discovery and genome-wide expression analysis. Proc Natl Acad Sci U S A 2003 4.74
20 Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol 2009 4.64
21 The JAK2/STAT3 signaling pathway is required for growth of CD44⁺CD24⁻ stem cell-like breast cancer cells in human tumors. J Clin Invest 2011 4.41
22 CEAS: cis-regulatory element annotation system. Bioinformatics 2009 4.26
23 Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 2011 4.13
24 Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res 2008 4.08
25 EZH2 oncogenic activity in castration-resistant prostate cancer cells is Polycomb-independent. Science 2012 3.74
26 Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat Genet 2012 3.67
27 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC. Proc Natl Acad Sci U S A 2010 3.37
28 CEAS: cis-regulatory element annotation system. Nucleic Acids Res 2006 3.15
29 A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics 2005 3.06
30 Integrative analysis of HIF binding and transactivation reveals its role in maintaining histone methylation homeostasis. Proc Natl Acad Sci U S A 2009 2.95
31 Androgen receptor gene expression in prostate cancer is directly suppressed by the androgen receptor through recruitment of lysine-specific demethylase 1. Cancer Cell 2011 2.86
32 Differentiation-specific histone modifications reveal dynamic chromatin interactions and partners for the intestinal transcription factor CDX2. Dev Cell 2010 2.84
33 Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol 2013 2.84
34 Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res 2004 2.84
35 Evolutionarily conserved multisubunit RBL2/p130 and E2F4 protein complex represses human cell cycle-dependent genes in quiescence. Mol Cell 2007 2.74
36 Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 2008 2.66
37 Chromatin signature of embryonic pluripotency is established during genome activation. Nature 2010 2.64
38 DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res 2008 2.48
39 Genome-wide and organ-specific landscapes of epigenetic modifications and their relationships to mRNA and small RNA transcriptomes in maize. Plant Cell 2009 2.39
40 Broad chromosomal domains of histone modification patterns in C. elegans. Genome Res 2010 2.36
41 Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods 2012 2.31
42 Targeting androgen receptor in estrogen receptor-negative breast cancer. Cancer Cell 2011 2.23
43 Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 2006 2.21
44 MYC regulation of a "poor-prognosis" metastatic cancer cell state. Proc Natl Acad Sci U S A 2010 2.21
45 Transcriptional role of cyclin D1 in development revealed by a genetic-proteomic screen. Nature 2010 2.20
46 Growth factor stimulation induces a distinct ER(alpha) cistrome underlying breast cancer endocrine resistance. Genes Dev 2010 1.92
47 Cell-type selective chromatin remodeling defines the active subset of FOXA1-bound enhancers. Genome Res 2009 1.89
48 Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics. Genome Res 2012 1.85
49 Tet3 CXXC domain and dioxygenase activity cooperatively regulate key genes for Xenopus eye and neural development. Cell 2012 1.76
50 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 1.60
51 Genome-wide map of nuclear protein degradation shows NCoR1 turnover as a key to mitochondrial gene regulation. Cell 2013 1.55
52 A boosting approach for motif modeling using ChIP-chip data. Bioinformatics 2005 1.53
53 Mapping the C. elegans noncoding transcriptome with a whole-genome tiling microarray. Genome Res 2007 1.46
54 Gene expression profiling of human breast tissue samples using SAGE-Seq. Genome Res 2010 1.41
55 Systematic Curation of miRBase Annotation Using Integrated Small RNA High-Throughput Sequencing Data for C. elegans and Drosophila. Front Genet 2011 1.38
56 ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer. J Clin Invest 2013 1.38
57 Alu elements mediate MYB gene tandem duplication in human T-ALL. J Exp Med 2007 1.37
58 Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3'-end formation. Proc Natl Acad Sci U S A 2010 1.37
59 NOTCH1-RBPJ complexes drive target gene expression through dynamic interactions with superenhancers. Proc Natl Acad Sci U S A 2013 1.34
60 TCF4 and CDX2, major transcription factors for intestinal function, converge on the same cis-regulatory regions. Proc Natl Acad Sci U S A 2010 1.32
61 A suite of web-based programs to search for transcriptional regulatory motifs. Nucleic Acids Res 2004 1.29
62 Coactivator function defines the active estrogen receptor alpha cistrome. Mol Cell Biol 2009 1.29
63 Essential and redundant functions of caudal family proteins in activating adult intestinal genes. Mol Cell Biol 2011 1.25
64 Target analysis by integration of transcriptome and ChIP-seq data with BETA. Nat Protoc 2013 1.24
65 MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol 2014 1.22
66 Analyzing 'omics data using hierarchical models. Nat Biotechnol 2010 1.21
67 Transcriptional regulatory networks downstream of TAL1/SCL in T-cell acute lymphoblastic leukemia. Blood 2006 1.17
68 Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium. PLoS Genet 2011 1.15
69 Intestinal master transcription factor CDX2 controls chromatin access for partner transcription factor binding. Mol Cell Biol 2012 1.15
70 Gene regulatory networks mediating canonical Wnt signal-directed control of pluripotency and differentiation in embryo stem cells. Stem Cells 2013 1.14
71 A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments. Biometrics 2007 1.14
72 Molecular profiling of human mammary gland links breast cancer risk to a p27(+) cell population with progenitor characteristics. Cell Stem Cell 2013 1.14
73 SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas. J Clin Invest 2014 1.10
74 Amplitude modulation of androgen signaling by c-MYC. Genes Dev 2013 1.08
75 Altered antisense-to-sense transcript ratios in breast cancer. Proc Natl Acad Sci U S A 2010 1.08
76 CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. Bioinformatics 2012 1.07
77 Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription. Genome Res 2006 1.06
78 Canonical nucleosome organization at promoters forms during genome activation. Genome Res 2013 1.05
79 A high-resolution map of nucleosome positioning on a fission yeast centromere. Genome Res 2008 1.04
80 More synergetic cooperation of Yamanaka factors in induced pluripotent stem cells than in embryonic stem cells. Cell Res 2009 1.04
81 Target gene-specific regulation of androgen receptor activity by p42/p44 mitogen-activated protein kinase. Mol Endocrinol 2008 1.03
82 BINOCh: binding inference from nucleosome occupancy changes. Bioinformatics 2011 0.96
83 CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. Nucleic Acids Res 2013 0.95
84 Identification of human STAT5-dependent gene regulatory elements based on interspecies homology. J Biol Chem 2006 0.95
85 CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res 2010 0.94
86 Genome-wide analysis of histone modifications: H3K4me2, H3K4me3, H3K9ac, and H3K27ac in Oryza sativa L. Japonica. Mol Plant 2013 0.91
87 DiNuP: a systematic approach to identify regions of differential nucleosome positioning. Bioinformatics 2012 0.90
88 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 0.89
89 Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells. Proc Natl Acad Sci U S A 2012 0.86
90 CistromeFinder for ChIP-seq and DNase-seq data reuse. Bioinformatics 2013 0.86
91 Computational inference of mRNA stability from histone modification and transcriptome profiles. Nucleic Acids Res 2012 0.85
92 Computational dissection of Arabidopsis smRNAome leads to discovery of novel microRNAs and short interfering RNAs associated with transcription start sites. Genomics 2011 0.81
93 The role of Notch receptors in transcriptional regulation. J Cell Physiol 2015 0.81
94 Minireview: applications of next-generation sequencing on studies of nuclear receptor regulation and function. Mol Endocrinol 2012 0.80
95 Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.". Nat Struct Mol Biol 2010 0.80
96 Genomics in 2011: challenges and opportunities. Genome Biol 2011 0.75
97 Addendum: REST and stress resistance in ageing and Alzheimer's disease. Nature 2016 0.75