Zhicheng Ji

I am a second-year PhD student in Department of Biostatistics and MSE student in Department of Computer Science at Johns Hopkins University. I am working as a research assistance under the advisory of Dr. Hongkai Ji.

My primary research interest is developing novel statistical and computational methods for analyzing data from high-thoughput sequencing technologies. I am currently focused on some of the hottest topics in genomics such as big data genomics and single-cell analysis.


This website is hand coded by Zhicheng Ji. Last update: 02-05-2017.
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1. Statistical and Computational Tools for Single-Cell Analysis:

TSCAN: Pseudo-Time Reconstruction and Evaluation in Single-Cell RNA-seq Analysis. [Paper][Software]

SCRAT: Single-Cell Regulome Analysis Tool. [Software]

2. Tools for Mining Big Genomics Data:

GSCA: Gene Set Context Analysis for Turning Publicly Available Gene Expression Data into Discoveries. [Paper][Software]

3. Predicting Chromatin Accessibility Using Gene Expressions:

Genome-wide Prediction of DNase I Hypersensitivity Using Gene Expression. [Paper]

Global Prediction of Chromatin Accessibility Using RNA-seq from Small Number of Cells. [Paper]


All Publications on Google Scholar
Name Type Author Availability
GSCA: Gene Set Context Analysis R Software Package Zhicheng Ji, Hongkai Ji [Github] [Bioconductor] [Online GUI]
TSCAN: Tools for Single-Cell ANalysis R Software Package Zhicheng Ji, Hongkai Ji [Github] [Bioconductor] [Online GUI]
SEPA: Single-cell Gene Expression Pattern Analysis R Software Package Zhicheng Ji, Hongkai Ji [Github] [Bioconductor] [Online GUI]
GEOsearch: Extendable Search Engine for GEO R Software Package Zhicheng Ji, Hongkai Ji [Github] [Bioconductor] [Online GUI]
SCRAT: Single-Cell Regulome Analysis Tool R Software Package Zhicheng Ji, Weiqiang Zhou, Hongkai Ji [Github] [Online GUI]

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Office:
E3038 Department of Biostatistics
Bloomberg School of Public Health
615 North Wolfe Street
Baltimore, MD, 21205, USA

Email:
zji4@jhu.edu

Github:
https://github.com/zji90