ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking

by Wu, George, Ji, Hongkai
Published 2013

PolyaPeak: Detecting Transcription Factor Binding Sites from ChIP-seq Using Peak Shape Information

by Wu, Hao, Ji, Hongkai
Published 2014

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

by Ji, Zhicheng, Ji, Hongkai
Published 2016

An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse

by Kim, Ryung S, Ji, Hongkai, Wong, Wing H
Published 2006

Global Mapping of Transcription Factor Binding Sites by Sequencing Chromatin Surrogates: a Perspective on Experimental Design, Data Analysis, and Open Problems

by Wei, Yingying, Wu, George, Ji, Hongkai
Published 2012

A novel DNA sequence motif in human and mouse genomes

by Zhang, Shilu, Du, Fang, Ji, Hongkai
Published 2015

Joint analysis of differential gene expression in multiple studies using correlation motifs

by Wei, Yingying, Tenzen, Toyoaki, Ji, Hongkai
Published 2015

A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors

by Ji, Hongkai, Vokes, Steven A., Wong, Wing H.
Published 2006

iASeq: integrating multiple chip-seq datasets for detecting allele-specific binding

by Wei, Yingying, Li, Xia, Wang, Qianfei, Ji, Hongkai
Published 2012

iASeq: integrative analysis of allele-specificity of protein-DNA interactions in multiple ChIP-seq datasets

by Wei, Yingying, Li, Xia, Wang, Qian-fei, Ji, Hongkai
Published 2012

Gene set bagging for estimating the probability a statistically significant result will replicate

by Jaffe, Andrew E, Storey, John D, Ji, Hongkai, Leek, Jeffrey T
Published 2013

Turning publicly available gene expression data into discoveries using gene set context analysis

by Ji, Zhicheng, Vokes, Steven A., Dang, Chi V., Ji, Hongkai
Published 2016

Dynamics of Regulatory Networks in the Developing Mouse Retina

by Hwang, Woochang, Hackler, Laszlo, Wu, George, Ji, Hongkai, Zack, Donald J., Qian, Jiang
Published 2012

Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes

by Wang, Jie, Xia, Shuli, Arand, Brian, Zhu, Heng, Machiraju, Raghu, Huang, Kun, Ji, Hongkai, Qian, Jiang
Published 2016

High temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast

by Kuang, Zheng, Cai, Ling, Zhang, Xuekui, Ji, Hongkai, Tu, Benjamin P., Boeke, Jef D.
Published 2014

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data

by Wu, George, Yustein, Jason T., McCall, Matthew N., Zilliox, Michael, Irizarry, Rafael A., Zeller, Karen, Dang, Chi V., Ji, Hongkai
Published 2013

Antagonistic effects of MYC and hypoxia in channeling glucose and glutamine into de novo nucleotide biosynthesis

by Fan, Teresa, Le, Anne, Stine, Zachary, Yang, Ye, Zeller, Karen, Zhou, Weiqiang, Ji, Hongkai, Higashi, Richard, Dang, Chi, Lane, Andrew
Published 2014

Cell-Type Independent MYC Target Genes Reveal a Primordial Signature Involved in Biomass Accumulation

by Ji, Hongkai, Wu, George, Zhan, Xiangcan, Nolan, Alexandra, Koh, Cheryl, De Marzo, Angelo, Doan, Hoang Mai, Fan, Jinshui, Cheadle, Christopher, Fallahi, Mohammad, Cleveland, John L., Dang, Chi V., Zeller, Karen I.
Published 2011

Construction of human activity-based phosphorylation networks

by Newman, Robert H, Hu, Jianfei, Rho, Hee-Sool, Xie, Zhi, Woodard, Crystal, Neiswinger, John, Cooper, Christopher, Shirley, Matthew, Clark, Hillary M, Hu, Shaohui, Hwang, Woochang, Seop Jeong, Jun, Wu, George, Lin, Jimmy, Gao, Xinxin, Ni, Qiang, Goel, Renu, Xia, Shuli, Ji, Hongkai, Dalby, Kevin N, Birnbaum, Morris J, Cole, Philip A, Knapp, Stefan, Ryazanov, Alexey G, Zack, Donald J, Blackshaw, Seth, Pawson, Tony, Gingras, Anne-Claude, Desiderio, Stephen, Pandey, Akhilesh, Turk, Benjamin E, Zhang, Jin, Zhu, Heng, Qian, Jiang
Published 2013