H
Hongkai Ji
Researcher at Johns Hopkins University
Publications - 146
Citations - 11350
Hongkai Ji is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Gene & Regulation of gene expression. The author has an hindex of 39, co-authored 137 publications receiving 9358 citations. Previous affiliations of Hongkai Ji include Johns Hopkins University School of Medicine & Tsinghua University.
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Journal ArticleDOI
Initial sequence of the chimpanzee genome and comparison with the human genome
Tarjei S. Mikkelsen,LaDeana W. Hillier,Evan E. Eichler,Michael C. Zody,David B. Jaffe,Shiaw-Pyng Yang,Wolfgang Enard,Ines Hellmann,Kerstin Lindblad-Toh,Tasha K. Altheide,Nicoletta Archidiacono,Peer Bork,Jonathan Butler,Jean L. Chang,Ze Cheng,Asif T. Chinwalla,Pieter J. de Jong,Kimberley D. Delehaunty,Catrina Fronick,Lucinda L. Fulton,Yoav Gilad,Gustavo Glusman,Sante Gnerre,Tina Graves,Toshiyuki Hayakawa,Karen E. Hayden,Xiaoqiu Huang,Hongkai Ji,W. James Kent,Mary Claire King,Edward J. Kulbokasl,Ming K. Lee,Ge Liu,Carlos López-Otín,Kateryna D. Makova,Orna Man,Elaine R. Mardis,Evan Mauceli,Tracie L. Miner,William E. Nash,Joanne O. Nelson,Svante Pääbo,Nick Patterson,Craig Pohl,Katherine S. Pollard,Kay Prüfer,Xose S. Puente,David Reich,Mariano Rocchi,Kate R. Rosenbloom,Maryellen Ruvolo,Daniel J. Richter,Stephen F. Schaffner,Arian F.A. Smit,Scott M. Smith,Mikita Suyama,James E. Taylor,David Torrents,Eray Tüzün,Ajit Varki,Gloria Velasco,Mario Ventura,John W. Wallis,Michael C. Wendl,Richard K. Wilson,Eric S. Lander,Robert H. Waterston +66 more
TL;DR: It is found that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles.
Journal ArticleDOI
FoxOs are lineage-restricted redundant tumor suppressors and regulate endothelial cell homeostasis
Jihye Paik,Ramya Kollipara,Gerald C. Chu,Hongkai Ji,Yonghong Xiao,Zhihu Ding,Lili Miao,Zuzana Tothova,James W. Horner,Daniel R. Carrasco,Shan Jiang,D. Gary Gilliland,Lynda Chin,Wing Hung Wong,Diego H. Castrillon,Diego H. Castrillon,Ronald A. DePinho +16 more
TL;DR: The role of the mammalian FoxO transcription factor family (FoxO1, FoxO3, and FoxO4) in PI3K-AKT signaling appears to be an obligate event in the development of cancer.
Journal ArticleDOI
Integration of Brassinosteroid Signal Transduction with the Transcription Network for Plant Growth Regulation in Arabidopsis
Yu Sun,Xiying Fan,Xiying Fan,Dong Mei Cao,Wenqiang Tang,Kun He,Jia Ying Zhu,Jun-Xian He,Ming-Yi Bai,Ming-Yi Bai,Shengwei Zhu,Eunkyoo Oh,Sunita Patil,Tae-Wuk Kim,Hongkai Ji,Wing H. Wong,Seung Y. Rhee,Zhi-Yong Wang +17 more
TL;DR: This work uses transcript profiling and chromatin-immunoprecipitation microarray experiments to identify 953 BR-regulated BZR1 target (BRBT) genes and reveals a regulatory network that integrates hormonal and light-signaling pathways for plant growth regulation.
Journal ArticleDOI
An integrated software system for analyzing ChIP-chip and ChIP-seq data.
TL;DR: CisGenome is a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data designed to meet all basic needs of ChIP data analyses, including visualization, data normalization, peak detection, false discovery rate computation, gene-peak association, and sequence and motif analysis.
Journal ArticleDOI
TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis
Zhicheng Ji,Hongkai Ji +1 more
TL;DR: TSCAN is a software tool developed to better support in silico pseudo-Time reconstruction in Single-Cell RNA-seq ANalysis and quantitative measures are developed to objectively evaluate and compare different pseudo-time reconstruction methods.