Hongkai Ji

发表

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

Ryung S. Kim, Wing Hung Wong, Hongkai Ji, 2006, BMC Bioinformatics.

Computational analysis of ChIP-seq data.

Hongkai Ji, Hongkai Ji, 2010, Methods in molecular biology.

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

Andrew E. Jaffe, Jeffrey T. Leek, Hongkai Ji, 2013, BMC Bioinformatics.

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

Jie Wang, Raghu Machiraju, Jiang Qian, 2016, PLoS Comput. Biol..

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

Hongkai Ji, George Wu, Hongkai Ji, 2013, BMC Bioinformatics.

TileProbe: modeling tiling array probe effects using publicly available data

Hongkai Ji, Jennifer Toolan Judy, Hongkai Ji, 2009, Bioinform..

JAMIE: joint analysis of multiple ChIP-chip experiments

Hao Wu, Hongkai Ji, Hongkai Ji, 2010, Bioinform..

Angle-insensitive multicolor display device based on phase change materials

Hongkai Ji, Xiangshui Miao, 2017 .

Computational Analysis of ChIP-chip Data

Hongkai Ji, 2011, Handbook of Statistical Bioinformatics.

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

Xia Li, Hongkai Ji, Yingying Wei, 2012, BMC Bioinformatics.

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

Matthew N. McCall, Rafael A. Irizarry, Michael J. Zilliox, 2013, Bioinform..

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

Li Chen, Hongkai Ji, George Wu, 2011, Bioinform..

AsMamDB: an alternative splice database of mammals

Qing Zhou, Xin Lu, Yanda Li, 2001, Nucleic Acids Res..

Single-cell regulome data analysis by SCRAT

Zhicheng Ji, Hongkai Ji, Weiqiang Zhou, 2017, Bioinform..

ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates

Guohua Wang, Hongkai Ji, Liyun Zhang, 2016, Nature Protocols.

TileMap: create chromosomal map of tiling array hybridizations

Wing Hung Wong, Hongkai Ji, W. Wong, 2005, Bioinform..

JAMIE: A software tool for jointly analyzing multiple ChIP-chip experiments.

Hao Wu, Hongkai Ji, Hongkai Ji, 2012, Methods in molecular biology.

Analyzing 'omics data using hierarchical models

Hongkai Ji, X Shirley Liu, Hongkai Ji, 2010, Nature Biotechnology.

Pseudotime Reconstruction Using TSCAN.

Hongkai Ji, Zhicheng Ji, Hongkai Ji, 2019, Methods in molecular biology.

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

Xuekui Zhang, Ling Cai, Hongkai Ji, 2014, Nature Structural &Molecular Biology.

Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes

Hongkai Ji, Jef D Boeke, Zhicheng Ji, 2017, Nucleic acids research.

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

Hongkai Ji, Hao Wu, Hongkai Ji, 2014, PloS one.

A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb.

Hongkai Ji, Wing H Wong, Andrew P McMahon, 2008, Genes & development.

Differential principal component analysis of ChIP-seq

Hongkai Ji, Hongkai Ji, Qianfei Wang, 2013, Proceedings of the National Academy of Sciences.

Gata6 potently initiates reprograming of pluripotent and differentiated cells to extraembryonic endoderm stem cells

Hongkai Ji, Yingying Wei, R. Sherwood, 2015, Genes & development.

Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis

Hongkai Ji, Wing H Wong, Baiyu Zhou, 2010, Proceedings of the National Academy of Sciences.

Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning

Andrew P. McMahon, Hongkai Ji, Eric H. Davidson, 2007, Development.

Why do human diversity levels vary at a megabase scale?

Hongkai Ji, Kay Prüfer, Michael C Zody, 2005, Genome research.

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

Hongkai Ji, Wing H. Wong, W. Wong, 2006, Nucleic acids research.

Using CisGenome to Analyze ChIP‐chip and ChIP‐seq Data

Wing Hung Wong, Hongkai Ji, Hui Jiang, 2011, Current protocols in bioinformatics.

FoxOs Are Lineage-Restricted Redundant Tumor Suppressors and Regulate Endothelial Cell Homeostasis

Yonghong Xiao, D. Gary Gilliland, Hongkai Ji, 2007, Cell.

Genome-wide DNA methylation associations with spontaneous preterm birth in US blacks: findings in maternal and cord blood samples

Hongkai Ji, Hui-Ju Tsai, Xiumei Hong, 2018, Epigenetics.