C
Chen-Hao Chen
Researcher at Harvard University
Publications - 21
Citations - 2143
Chen-Hao Chen is an academic researcher from Harvard University. The author has contributed to research in topics: CRISPR & Cas9. The author has an hindex of 11, co-authored 19 publications receiving 1393 citations.
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Journal ArticleDOI
Sequence determinants of improved CRISPR sgRNA design
Han Xu,Tengfei Xiao,Chen-Hao Chen,Wei Li,Clifford A. Meyer,Qiu Wu,Qiu Wu,Di Wu,Le Cong,Le Cong,Feng Zhang,Feng Zhang,Jun Liu,Myles Brown,Myles Brown,X. Shirley Liu +15 more
TL;DR: This work derived a new sequence model for predicting sgRNA efficiency in CRISPR/Cas9 knockout experiments and suggested new features including a preference for cytosine at the cleavage site that facilitate the genome-wide design of improved sg RNA for both knockout and CRISpri/a studies.
Journal ArticleDOI
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,X. Shirley Liu,X. Shirley Liu +11 more
TL;DR: The Cistrome DB has a new Toolkit module with several features that allow users to better utilize the large-scale ChIP-seq, DNase-seq and ATAC-seq data, and the new tools will greatly benefit the biomedical research community.
Journal ArticleDOI
Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR-Cas9 library.
Shiyou Zhu,Wei Li,Jingze Liu,Chen-Hao Chen,Qi Liao,Ping Xu,Han Xu,Tengfei Xiao,Zhongzheng Cao,J. J. Peng,Pengfei Yuan,Myles Brown,Myles Brown,Xiaole Shirley Liu,Wensheng Wei +14 more
TL;DR: A high-throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library is reported, which identified 51 lnc RNAs that can positively or negatively regulate human cancer cell growth.
Journal ArticleDOI
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR
Wei Li,Johannes Köster,Han Xu,Chen-Hao Chen,Tengfei Xiao,Jun Liu,Myles Brown,Myles Brown,X. Shirley Liu,X. Shirley Liu +9 more
TL;DR: MAGeCK-VISPR defines a set of QC measures to assess the quality of an experiment, and includes a maximum-likelihood algorithm to call essential genes simultaneously under multiple conditions to iteratively estimate sgRNA knockout efficiency and gene essentiality.
Journal ArticleDOI
Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute.
Binbin Wang,Mei Wang,Wubing Zhang,Tengfei Xiao,Chen-Hao Chen,Alexander C. Wu,Feizhen Wu,Nicole Traugh,Xiaoqing Wang,Ziyi Li,Shenglin Mei,Yingbo Cui,Sailing Shi,Jesse J. Lipp,Matthias Hinterndorfer,Johannes Zuber,Myles Brown,Wei Li,Wei Li,X. Shirley Liu,X. Shirley Liu +20 more
TL;DR: This protocol explains how to use MAGeCKFlute to perform quality control (QC), normalization, batch effect removal, copy-number bias correction, gene hit identification and downstream functional enrichment analysis for CRISPR screens.