Works by Liu, X. Shirley

Results: 92

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer.

Published in:

Nature Structural & Molecular Biology, 2013, v. 20, n. 7, p. 908, doi. 10.1038/nsmb.2591

By:

Du, Zhou;
Fei, Teng;
Verhaak, Roel G W;
Su, Zhen;
Zhang, Yong;
Brown, Myles;
Chen, Yiwen;
Liu, X Shirley

Publication type:

Article

Reply to “Evidence against a genomic code for nucleosome positioning”.

Published in:

Nature Structural & Molecular Biology, 2010, v. 17, n. 8, p. 920, doi. 10.1038/nsmb0810-920

By:

Yong Zhang;
Moqtaderi, Zarmik;
Rattner, Barbara P.;
Euskirchen, Ghia;
Snyder, Michael;
Kadonaga, James T.;
Liu, X. Shirley;
Struhl, Kevin

Publication type:

Article

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Published in:

Nature Structural & Molecular Biology, 2009, v. 16, n. 8, p. 847, doi. 10.1038/nsmb.1636

By:

Yong Zhang;
Moqtaderi, Zarmik;
Rattner, Barbara P.;
Euskirchen, Ghia;
Snyder, Michael;
Kadonaga, James T.;
Liu, X. Shirley;
Struhl, Kevin

Publication type:

Article

CistromeFinder for ChIP-seq and DNase-seq data reuse.

Published in:

Bioinformatics, 2013, v. 29, n. 10, p. 1352, doi. 10.1093/bioinformatics/btt135

By:

Sun, Hanfei;
Qin, Bo;
Liu, Tao;
Wang, Qixuan;
Liu, Jing;
Wang, Juan;
Lin, Xueqiu;
Yang, Yulin;
Taing, Len;
Rao, Prakash K.;
Brown, Myles;
Zhang, Yong;
Long, Henry W.;
Liu, X. Shirley

Publication type:

Article

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.

Published in:

Bioinformatics, 2012, v. 28, n. 21, p. 2782, doi. 10.1093/bioinformatics/bts515

By:

Feng, Jianxing;
Meyer, Clifford A.;
Wang, Qian;
Liu, Jun S.;
Shirley Liu, X.;
Zhang, Yong

Publication type:

Article

DiNuP: a systematic approach to identify regions of differential nucleosome positioning.

Published in:

Bioinformatics, 2012, v. 28, n. 15, p. 1965, doi. 10.1093/bioinformatics/bts329

By:

Fu, Kai;
Tang, Qianzi;
Feng, Jianxing;
Liu, X. Shirley;
Zhang, Yong

Publication type:

Article

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human.

Published in:

Bioinformatics, 2012, v. 28, n. 10, p. 1411, doi. 10.1093/bioinformatics/bts157

By:

Qin, Bo;
Zhou, Meng;
Ge, Ying;
Taing, Len;
Liu, Tao;
Wang, Qian;
Wang, Su;
Chen, Junsheng;
Shen, Lingling;
Duan, Xikun;
Hu, Sheng'en;
Li, Wei;
Long, Henry;
Zhang, Yong;
Liu, X. Shirley

Publication type:

Article

BINOCh: binding inference from nucleosome occupancy changes.

Published in:

Bioinformatics, 2011, v. 27, n. 13, p. 1867, doi. 10.1093/bioinformatics/btr279

By:

Meyer, Clifford A.;
He, Housheng H.;
Brown, Myles;
Liu, X. Shirley

Publication type:

Article

CEAS: cis-regulatory element annotation system.

Published in:

Bioinformatics, 2009, v. 25, n. 19, p. 2605, doi. 10.1093/bioinformatics/btp479

By:

Hyunjin Shin;
Tao Liu;
Manrai, Arjun K.;
X. Shirley Liu

Publication type:

Article

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology.

Published in:

Nature Reviews Genetics, 2014, v. 15, n. 11, p. 709, doi. 10.1038/nrg3788

By:

Meyer, Clifford A.;
Liu, X. Shirley

Publication type:

Article

Integrative analyses of single-cell transcriptome and regulome using MAESTRO.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-02116-x

By:

Wang, Chenfei;
Sun, Dongqing;
Huang, Xin;
Wan, Changxin;
Li, Ziyi;
Han, Ya;
Qin, Qian;
Fan, Jingyu;
Qiu, Xintao;
Xie, Yingtian;
Meyer, Clifford A.;
Brown, Myles;
Tang, Ming;
Long, Henry;
Liu, Tao;
Liu, X. Shirley

Publication type:

Article

Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data.

Published in:

Genome Biology, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s13059-020-1934-6

By:

Qin, Qian;
Fan, Jingyu;
Zheng, Rongbin;
Wan, Changxin;
Mei, Shenglin;
Wu, Qiu;
Sun, Hanfei;
Brown, Myles;
Zhang, Jing;
Meyer, Clifford A.;
Liu, X. Shirley

Publication type:

Article

Big data mining yields novel insights on cancer.

Published in:

Nature Genetics, 2015, v. 47, n. 2, p. 103, doi. 10.1038/ng.3205

By:

Jiang, Peng;
Liu, X Shirley

Publication type:

Article

Chromatin marks identify critical cell types for fine mapping complex trait variants.

Published in:

Nature Genetics, 2013, v. 45, n. 2, p. 124, doi. 10.1038/ng.2504

By:

Trynka, Gosia;
Sandor, Cynthia;
Han, Buhm;
Xu, Han;
Stranger, Barbara E;
Liu, X Shirley;
Raychaudhuri, Soumya

Publication type:

Article

Nucleosome dynamics define transcriptional enhancers.

Published in:

Nature Genetics, 2010, v. 42, n. 4, p. 343, doi. 10.1038/ng.545

By:

Housheng Hansen He;
Meyer, Clifford A.;
Hyunjin Shin;
Bailey, Shannon T.;
Gang Wei;
Qianben Wang;
Yong Zhang;
Kexin Xu;
Min Ni;
Lupien, Mathieu;
Mieczkowski, Piotr;
Lieb, Jason D.;
Zhao, Keji;
Brown, Myles;
X. Shirley Liu

Publication type:

Article

Differential chromatin marking of introns and expressed exons by H3K36me3.

Published in:

Nature Genetics, 2009, v. 41, n. 3, p. 376, doi. 10.1038/ng.322

By:

Kolasinska-Zwierz, Paulina;
Down, Thomas;
Latorre, Isabel;
Tao Liu;
Liu, X. Shirley;
Ahringer, Julie

Publication type:

Article

Genome-wide analysis of estrogen receptor binding sites.

Published in:

Nature Genetics, 2006, v. 38, n. 11, p. 1289, doi. 10.1038/ng1901

By:

Carroll, Jason S.;
Meyer, Clifford A.;
Jun Song;
Wei Li;
Geistlinger, Timothy R.;
Eeckhoute, Jérôme;
Brodsky, Alexander S.;
Keeton, Erika Krasnickas;
Fertuck, Kirsten C.;
Hall, Giles F.;
Qianben Wang;
Bekiranov, Stefan;
Sementchenko, Victor;
Fox, Edward A.;
Silver, Pamela A.;
Gingeras, Thomas R.;
Liu, X. Shirley;
Brown, Myles

Publication type:

Article

xMAN: extreme MApping of OligoNucleotides.

Published in:

BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-S1-S20

By:

Wei Li;
Carroll, Jason S.;
Brown, Myles;
Liu, X. Shirley

Publication type:

Article

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.

Published in:

Bioinformatics, 2005, v. 21, p. i274

By:

Li, Wei;
Meyer, Clifford A.;
Liu, X. Shirley

Publication type:

Article

A boosting approach for motif modeling using ChIP-chip data.

Published in:

Bioinformatics, 2005, v. 21, n. 11, p. 2636, doi. 10.1093/bioinformatics/bti402

By:

Pengyu Hong;
X. Shirley Liu;
Qing Zhou;
Xin Lu;
Jun S. Liu;
Wing H. Wong

Publication type:

Article

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences.

Published in:

Bioinformatics, 2005, v. 21, n. 1, p. i274

By:

X. Shirley Liu

Publication type:

Article

Vasodilation Effects and Action Mechanisms of TMB-8 on Basilar Artery in Rabbits.

Published in:

1996

By:

Xiao, Jigao;
Liu, Shirley X. L.;
Chen, Zhou;
Chiou, George C. Y.;
Xiao, J;
Liu, SX;
Chen, Z;
Chiou, GC

Publication type:

journal article

Genetic fusions favor tumorigenesis through degron loss in oncogenes.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26871-y

By:

Liu, Jing;
Tokheim, Collin;
Lee, Jonathan D.;
Gan, Wenjian;
North, Brian J.;
Liu, X. Shirley;
Pandolfi, Pier Paolo;
Wei, Wenyi

Publication type:

Article

Fast alignment and preprocessing of chromatin profiles with Chromap.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-26865-w

By:

Zhang, Haowen;
Song, Li;
Wang, Xiaotao;
Cheng, Haoyu;
Wang, Chenfei;
Meyer, Clifford A.;
Liu, Tao;
Tang, Ming;
Aluru, Srinivas;
Yue, Feng;
Liu, X. Shirley;
Li, Heng

Publication type:

Article

Genome-wide identification and characterization of Notch transcription complex–binding sequence-paired sites in leukemia cells.

Published in:

Science Signaling, 2017, v. 10, n. 477, p. 1, doi. 10.1126/scisignal.aag1598

By:

Severson, Eric;
Arnett, Kelly L.;
Hongfang Wang;
Chongzhi Zang;
Len Taing;
Hudan Liu;
Pear, Warren S.;
Liu, X. Shirley;
Blacklow, Stephen C.;
Aster, Jon C.

Publication type:

Article

A closer look into DNase I hypersensitivity.

Published in:

2013

By:

Housheng Hansen He;
Meyer, Clifford A.;
Long, Henry;
Liu, X. Shirley;
Brown, Myles

Publication type:

Conference Paper/Materials

Polycomb-independent activity of EZH2 in castration resistant prostate cancer.

Published in:

2013

By:

Kexin Xu;
Wu, Zhenhua Jeremy;
Groner, Anna C.;
Housheng Hansen He;
Changmeng Cai;
Stack, Edward C.;
Loda, Massimo;
Tao Liu;
Morrissey, Colm;
Vessella, Robert L.;
Kantoff, Philip W.;
Balk, Steven P.;
Liu, X. Shirley;
Brown, Myles

Publication type:

Conference Paper/Materials

MetaTiME integrates single-cell gene expression to characterize the meta-components of the tumor immune microenvironment.

Published in:

Nature Communications, 2023, p. 1, doi. 10.1038/s41467-023-38333-8

By:

Zhang, Yi;
Xiang, Guanjue;
Jiang, Alva Yijia;
Lynch, Allen;
Zeng, Zexian;
Wang, Chenfei;
Zhang, Wubing;
Fan, Jingyu;
Kang, Jiajinlong;
Gu, Shengqing Stan;
Wan, Changxin;
Zhang, Boning;
Liu, X. Shirley;
Brown, Myles;
Meyer, Clifford A.

Publication type:

Article

Large-scale public data reuse to model immunotherapy response and resistance.

Published in:

Genome Medicine, 2020, v. 12, n. 1, p. 1, doi. 10.1186/s13073-020-0721-z

By:

Fu, Jingxin;
Li, Karen;
Zhang, Wubing;
Wan, Changxin;
Zhang, Jing;
Jiang, Peng;
Liu, X. Shirley

Publication type:

Article

Immune receptor repertoires in pediatric and adult acute myeloid leukemia.

Published in:

Genome Medicine, 2019, v. 11, n. 1, p. N.PAG, doi. 10.1186/s13073-019-0681-3

By:

Zhang, Jian;
Hu, Xihao;
Wang, Jin;
Sahu, Avinash Das;
Cohen, David;
Song, Li;
Ouyang, Zhangyi;
Fan, Jingyu;
Wang, Binbin;
Fu, Jingxin;
Gu, Shengqing;
Sade-Feldman, Moshe;
Hacohen, Nir;
Li, Wuju;
Ying, Xiaomin;
Li, Bo;
Liu, X. Shirley

Publication type:

Article

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline.

Published in:

BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1274-4

By:

Qian Qin;
Shenglin Mei;
Qiu Wu;
Hanfei Sun;
Lewyn Li;
Len Taing;
Sujun Chen;
Fugen Li;
Tao Liu;
Chongzhi Zang;
Han Xu;
Yiwen Chen;
Meyer, Clifford A.;
Yong Zhang;
Brown, Myles;
Long, Henry W.;
Liu, X. Shirley

Publication type:

Article

Getting Started in Tiling Microarray Analysis.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 10, p. e183, doi. 10.1371/journal.pcbi.0030183

By:

Liu, X. Shirley

Publication type:

Article

SOX2 and p63 colocalize at genetic loci in squamous cell carcinomas.

Published in:

Journal of Clinical Investigation, 2014, v. 124, n. 4, p. 1636, doi. 10.1172/JCI71545

By:

Hideo Watanabe;
Qiuping Ma;
Shouyong Peng;
Adelmant, Guillaume;
Swain, Danielle;
Wenyu Song;
Fox, Cameron;
Francis, Joshua M.;
Chandra Sekhar Pedamallu;
DeLuca, David S.;
Brooks, Angela N.;
Su Wang;
Jianwen Que;
Rustgi, Anil K.;
Kwok-kin Wong;
Ligon, Keith L.;
Liu, X. Shirley;
Marto, Jarrod A.;
Meyerson, Matthew;
Bass, Adam J.

Publication type:

Article

ERG induces androgen receptor-mediated regulation of SOX9 in prostate cancer.

Published in:

Journal of Clinical Investigation, 2013, v. 123, n. 3, p. 1109, doi. 10.1172/JCI66666

By:

Changmeng Cai;
Hongyun Wang;
Housheng Hansen He;
Sen Chen;
Lingfeng He;
Fen Ma;
Mucci, Lorelei;
Qianben Wang;
Fiore, Christopher;
Sowalsky, Adam G.;
Loda, Massimo;
Liu, X. Shirley;
Brown, Myles;
Balk, Steven P.;
Xin Yuan

Publication type:

Article

NF-E2, FLI1 and RUNX1 collaborate at areas of dynamic chromatin to activate transcription in mature mouse megakaryocytes.

Published in:

Scientific Reports, 2016, p. 30255, doi. 10.1038/srep30255

By:

Zang, Chongzhi;
Luyten, Annouck;
Chen, Justina;
Liu, X. Shirley;
Shivdasani, Ramesh A.

Publication type:

Article

An Integrative Pharmacogenomic Approach Identifies Two-drug Combination Therapies for Personalized Cancer Medicine.

Published in:

Scientific Reports, 2016, p. 22120, doi. 10.1038/srep22120

By:

Liu, Yin;
Fei, Teng;
Zheng, Xiaoqi;
Brown, Myles;
Zhang, Peng;
Liu, X. Shirley;
Wang, Haiyun

Publication type:

Article

CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments.

Published in:

PLoS ONE, 2017, v. 12, n. 9, p. 1, doi. 10.1371/journal.pone.0184281

By:

Cao, Qingyi;
Ma, Jian;
Chen, Chen-Hao;
Xu, Han;
Chen, Zhi;
Li, Wei;
Liu, X. Shirley

Publication type:

Article

Analyzing 'omics data using hierarchical models.

Published in:

Nature Biotechnology, 2010, v. 28, n. 4, p. 337, doi. 10.1038/nbt.1619

By:

Ji, Hongkai;
Liu, X. Shirley

Publication type:

Article

High-throughput mapping of the chromatin structure of human promoters.

Published in:

Nature Biotechnology, 2007, v. 25, n. 2, p. 244, doi. 10.1038/nbt1279

By:

Ozsolak, Fatih;
Song, Jun S.;
Liu, X. Shirley;
Fisher, David E.

Publication type:

Article

An algorithm for finding protein?DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Published in:

Nature Biotechnology, 2002, v. 20, n. 8, p. 835, doi. 10.1038/nbt717

By:

Liu, X. Shirley;
Brutlag, Douglas L.;
Liu, Jun S.

Publication type:

Article

Regulation of Chromatin Assembly and Cell Transformation by Formaldehyde Exposure in Human Cells.

Published in:

Environmental Health Perspectives, 2017, v. 125, n. 9, p. 1, doi. 10.1289/EHP1275

By:

Chen, Danqi;
Fang, Lei;
Mei, Shenglin;
Li, Hongjie;
Xu, Xia;
Marais, Thomas L. Des;
Lu, Kun;
Liu, X. Shirley;
Jin, Chunyuan

Publication type:

Article

Intestinal Master Transcription Factor CDX2 Controls Chromatin Access for Partner Transcription Factor Binding.

Published in:

Molecular & Cellular Biology, 2013, v. 33, n. 2, p. 291, doi. 10.1128/MCB.01185-12

By:

Verzi, Michael P.;
Shin, Hyunjin;
Romana, Adrianna K. San;
Liu, X. Shirley;
Shivdasani, Ramesh A.

Publication type:

Article

Essential and Redundant Functions of Caudal Family Proteins in Activating Adult Intestinal Genes.

Published in:

Molecular & Cellular Biology, 2011, v. 31, n. 10, p. 8, doi. 10.1128/MCB.01250-10

By:

Verzi, Michael P.;
Hyunjin Shin;
Li-Lun Ho;
Liu, X. Shirley;
Shivdasani, Ramesh A.

Publication type:

Article

Coactivator Function Defines the Active Estrogen Receptor Alpha Cistrome.

Published in:

Molecular & Cellular Biology, 2009, v. 29, n. 12, p. 16, doi. 10.1128/MCB.00020-09

By:

Lupien, Mathieu;
Eeckhoute, Jérôme;
Meyer, Clifford A.;
Krum, Susan A.;
Rhodes, Daniel R.;
Liu, X. Shirley;
Brown, Myles

Publication type:

Article

Expression of lncRNA MIR222HG co-transcribed from the miR-221/222 gene promoter facilitates the development of castration-resistant prostate cancer.

Published in:

Oncogenesis, 2018, v. 7, n. 3, p. 1, doi. 10.1038/s41389-018-0039-5

By:

Sun, Tong;
Du, Shin-Yi;
Armenia, Joshua;
Qu, Fangfang;
Fan, Jingyu;
Wang, Xiaodong;
Fei, Teng;
Komura, Kazumasa;
Liu, Shirley X.;
Lee, Gwo-Shu Mary;
Kantoff, Philip W

Publication type:

Article

Determinants of transcription factor regulatory range.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16106-x

By:

Chen-Hao Chen;
Rongbin Zheng;
Tokheim, Collin;
Xin Dong;
Jingyu Fan;
Changxin Wan;
Qin Tang;
Brown, Myles;
Liu, Jun S.;
Meyer, Clifford A.;
Liu, X. Shirley

Publication type:

Article

A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-680

By:

Haiyun Wang;
Meyer, Clifford A.;
Teng Fei;
Gang Wang;
Fan Zhang;
X Shirley Liu

Publication type:

Article

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 1, p. 1, doi. 10.1186/s12859-018-2139-9

By:

Cornwell, MacIntosh;
Vangala, Mahesh;
Taing, Len;
Herbert, Zachary;
Köster, Johannes;
Li, Bo;
Sun, Hanfei;
Li, Taiwen;
Zhang, Jian;
Qiu, Xintao;
Pun, Matthew;
Jeselsohn, Rinath;
Brown, Myles;
Liu, X. Shirley;
Long, Henry W.

Publication type:

Article

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model.

Published in:

PLoS Computational Biology, 2015, v. 11, n. 9, p. 1, doi. 10.1371/journal.pcbi.1004498

By:

Zhang, Naiqian;
Wang, Haiyun;
Fang, Yun;
Wang, Jun;
Zheng, Xiaoqi;
Liu, X. Shirley

Publication type:

Article

Strategic human resource management, institutionalization, and employment modes: an empirical study in China.

Published in:

Strategic Management Journal (Wiley-Blackwell) - 1980 to 2009, 2008, v. 29, n. 3, p. 337, doi. 10.1002/smj.655

By:

Li, Ji;
Lam, Kevin;
Sun, James J. M.;
Liu, Shirley X. Y.

Publication type:

Article