A suite of web-based programs to search for transcriptional regulatory motifs. - Yueyi Liu; Liping Wei; Serafim Batzoglou; Douglas L. Brutlag; Jun S. Liu; Xiaole Shirley Liu (Nucleic Acids Res., 2004)

A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. - Wei Li 036; Clifford A. Meyer; Xiaole Shirley Liu (ISMB (Supplement of Bioinformatics), 2005)

A boosting approach for motif modeling using ChIP-chip data. - Pengyu Hong; Xiaole Shirley Liu; Qing Zhou; Xin Lu; Jun S. Liu; Wing Hung Wong (Bioinform., 2005)

CEAS: cis-regulatory element annotation system. - Xuwo Ji; Wei Li 036; Jun Song; Liping Wei; Xiaole Shirley Liu (Nucleic Acids Res., 2006)

xMAN: extreme MApping of oligoNucleotides. - Wei Li 036; Jason S. Carroll; Myles Brown; Xiaole Shirley Liu (BIOCOMP, 2007)

Microarray blob-defect removal improves array analysis. - Jun S. Song; Kaveh Maghsoudi; Wei Li 036; Edward Fox; John Quackenbush; Xiaole Shirley Liu (Bioinform., 2007)

Getting Started in Tiling Microarray Analysis. - Xiaole Shirley Liu (PLoS Comput. Biol., 2007)

CEAS: cis-regulatory element annotation system. - Hyunjin Shin; Tao Liu 022; Arjun K. Manrai; Xiaole Shirley Liu (Bioinform., 2009)

BINOCh: binding inference from nucleosome occupancy changes. - Clifford A. Meyer; Housheng H. He; Myles Brown; Xiaole Shirley Liu (Bioinform., 2011)

CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. - Qingyi Cao; Meng Zhou; Xujun Wang; Clifford A. Meyer; Yong Zhang 006; Zhi Chen; Cheng Li; Xiaole Shirley Liu (Nucleic Acids Res., 2011)

GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data. - Jianxing Feng; Clifford A. Meyer; Qian Wang; Jun S. Liu; Xiaole Shirley Liu; Yong Zhang 006 (Bioinform., 2012)

DiNuP: a systematic approach to identify regions of differential nucleosome positioning. - Kai Fu; Qianzi Tang; Jianxing Feng; Xiaole Shirley Liu; Yong Zhang 006 (Bioinform., 2012)

CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human. - Bo Qin; Meng Zhou; Ying Ge; Len Taing; Tao Liu 022; Qian Wang; Su Wang; Junsheng Chen; Lingling Shen; Xikun Duan; Sheng'en Hu; Wei Li 036; et al. (Bioinform., 2012)

CistromeFinder for ChIP-seq and DNase-seq data reuse. - Hanfei Sun; Bo Qin; Tao Liu 022; Qixuan Wang; Jing Liu; Juan Wang; Xueqiu Lin; Yulin Yang; Len Taing; Prakash K. Rao; Myles Brown; Yong Zhang 006; et al. (Bioinform., 2013)

Computational methodology for ChIP-seq analysis. - Hyunjin Shin; Tao Liu 022; Xikun Duan; Yong Zhang 006; Xiaole Shirley Liu (Quant. Biol., 2013)

CR Cistrome: a ChIP-Seq database for chromatin regulators and histone modification linkages in human and mouse. - Qixuan Wang; Jinyan Huang; Hanfei Sun; Jing Liu; Juan Wang; Qian Wang; Qian Qin; Shenglin Mei; Chengchen Zhao; Xiaoqin Yang; Xiaole Shirley Liu; Yong Zhang 006 (Nucleic Acids Res., 2014)

Comparative analysis of metazoan chromatin organization Open. - Joshua Wing Kei Ho; Youngsook L. Jung; Tao Liu 022; Burak Han Alver; Soohyun Lee; Kohta Ikegami; Kyung-Ah Sohn; Aki Minoda; Michael Y. Tolstorukov; Alex Appert; Stephen C. J. Parker; Tingting Gu; et al. (Nat., 2014)

Meeting report on YBPW 2014 (the 3rd Young Bioinformatics PIs Workshop). - Mengyi Sun; Bingyu Yan; Chengkun Wu; Xiaole Shirley Liu (Quant. Biol., 2014)

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model. - Naiqian Zhang; Haiyun Wang; Yun Fang; Jun Wang; Xiaoqi Zheng; Xiaole Shirley Liu (PLoS Comput. Biol., 2015)

CRISPR-DO for genome-wide CRISPR design and optimization. - Jian Ma; Johannes Köster; Qian Qin; Shengen Hu; Wei Li 035; Chenhao Chen; Qingyi Cao; Jinzeng Wang; Shenglin Mei; Qi Liu; Han Xu; Xiaole Shirley Liu (Bioinform., 2016)

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. - Shenglin Mei; Qian Qin; Qiu Wu; Hanfei Sun; Rongbin Zheng; Chongzhi Zang; Muyuan Zhu; Jiaxin Wu; Xiaohui Shi; Len Taing; Tao Liu 022; Myles Brown; et al. (Nucleic Acids Res., 2017)

Improved design and analysis of CRISPR knockout screens. - Chen-Hao Chen; Tengfei Xiao; Han Xu; Peng Jiang 006; Clifford A. Meyer; Wei Li 035; Myles Brown; Xiaole Shirley Liu (Bioinform., 2018)

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis. - MacIntosh Cornwell; Mahesh Vangala; Len Taing; Zachary Herbert; Johannes Köster; Bo Li; Hanfei Sun; Taiwen Li; Jian Zhang; Xintao Qiu; Matthew Pun; Rinath Jeselsohn; et al. (BMC Bioinform., 2018)

A Bayesian model for single cell transcript expression analysis on MERFISH data. - Johannes Köster; Myles Brown; Xiaole Shirley Liu (Bioinform., 2019)

Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. - Shaojuan Li; Changxin Wan; Rongbin Zheng; Jingyu Fan; Xin Dong 013; Clifford A. Meyer; Xiaole Shirley Liu (Nucleic Acids Res., 2019)

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis. - Rongbin Zheng; Changxin Wan; Shenglin Mei; Qian Qin; Qiu Wu; Hanfei Sun; Chen-Hao Chen; Myles Brown; Xiaoyan Zhang; Clifford A. Meyer; Xiaole Shirley Liu (Nucleic Acids Res., 2019)

CRISPR Screens Identify Essential Cell Growth Mediators in BRAF Inhibitor-resistant Melanoma. - Ziyi Li 005; Binbin Wang; Shengqing Gu; Peng Jiang 006; Avinash Das Sahu; Chen-Hao Chen; Tong Han; Sailing Shi; Xiaoqing Wang; Nicole Traugh; Hailing Liu; Yin Liu; et al. (Genom. Proteom. Bioinform., 2020)

TIMER2.0 for analysis of tumor-infiltrating immune cells. - Taiwen Li; Jingxin Fu; Zexian Zeng; David Cohen; Jing Li; Qianming Chen; Bo Li; Xiaole Shirley Liu (Nucleic Acids Res., 2020)

CoBRA: Containerized Bioinformatics Workflow for Reproducible ChIP/ATAC-seq Analysis. - Xintao Qiu; Avery S. Feit; Ariel Feiglin; Yingtian Xie; Nikolas Kesten; Len Taing; Joseph Perkins; Shengqing Gu; Yihao Li; Paloma Cejas; Ningxuan Zhou; Rinath Jeselsohn; et al. (Genom. Proteom. Bioinform., 2021)

Neural network architecture search with AMBER. - Yi Zhang 055; Yang Liu; X. Shirley Liu (Nat. Mach. Intell., 2021)

TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. - Zexian Zeng; Cheryl J. Wong; Lin Yang; Nofal Ouardaoui; Dian Li; Wubing Zhang; Shengqing Gu; Yi Zhang 055; Yang Liu; Xiaoqing Wang; Jingxin Fu; Liye Zhou; et al. (Nucleic Acids Res., 2022)

Machine Learning Modeling of Protein-intrinsic Features Predicts Tractability of Targeted Protein Degradation. - Wubing Zhang; Shourya S. Roy Burman; Jiaye Chen; Katherine A. Donovan; Yang Cao; Chelsea Shu; Boning Zhang; Zexian Zeng; Shengqing Gu; Yi Zhang 055; Dian Li; Eric S. Fischer; et al. (Genom. Proteom. Bioinform., 2022)