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

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

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)

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline. - Qian Qin; Shenglin Mei; Qiu Wu; Hanfei Sun; Lewyn Li; Len Taing; Sujun Chen; Fugen Li; Tao Liu 022; Chongzhi Zang; Han Xu; Yiwen Chen; et al. (BMC 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 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)

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)

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)

Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data. - Sehi L'Yi; Mark S. Keller; Ariaki Dandawate; Len Taing; Chen-Hao Chen; Myles Brown; Clifford A. Meyer; Nils Gehlenborg (Bioinform., 2023)