Tsu-Pei Chiu
机构: Assistant Professor (Teaching), University of Southern California
主页: usc.edu
每年引用次数
引用次数
引用: 901
H-指数: 12
I10-指数 : 12
出版物: 27
ACCEPTED ORAL PRESENTATIONS
Anthony Mathelier , Lin Yang , Tsu‐Pei Chiu , Remo Rohs
Feruloyl-l-arabinose attenuates migration, invasion and production of reactive oxygen species in H1299 lung cancer cells
Hsin-Yu Fang , Hui-Min Wang , Kuo-Feng Chang , Huei-Ting Hu
Food and Chemical Toxicology 58 459 -466
23
2013
Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator
Zengqin Deng , Qing Wang , Zhao Liu , Manfeng Zhang
Nature Communications 6 ( 1) 7642 -7642
63
2015
GBshape: a genome browser database for DNA shape annotations
Tsu-Pei Chiu , Lin Yang , Tianyin Zhou , Bradley J. Main
Nucleic Acids Research 43 103 -109
46
2015
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding
Tsu-Pei Chiu , Federico Comoglio , Tianyin Zhou , Lin Yang
Bioinformatics 32 ( 8) 1211 -1213
99
2016
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.
Tsu-Pei Chiu , Beibei Xin , Nicholas Markarian , Yingfei Wang
Nucleic Acids Research 48
25
2019
Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations
Robert N Azad , Dana Zafiropoulos , Douglas Ober , Yining Jiang
Nucleic Acids Research 46 ( 5) 2636 -2647
12
2018
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.
Jinsen Li , Jared M. Sagendorf , Tsu-Pei Chiu , Marco Pasi
Nucleic Acids Research 45 ( 22) 12877 -12887
36
2017
Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding
Tsu-Pei Chiu , Satyanarayan Rao , Richard S. Mann , Barry Honig
Nucleic Acids Research 45 ( 21) 12565 -12576
35
2017
DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo.
Anthony Mathelier , Beibei Xin , Tsu-Pei Chiu , Lin Yang
Cell systems 3 ( 3) 278 -286
86
2016
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding
Satyanarayan Rao , Tsu-Pei Chiu , Judith F. Kribelbauer , Richard S. Mann
Epigenetics & Chromatin 11 ( 1) 1 -11
31
2018
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria.
Xiaolin Wu , Bo Cao , Patricia Aquino , Tsu-Pei Chiu
Proceedings of the National Academy of Sciences of the United States of America 117 ( 25) 14322 -14330
23
2020
It is in the flanks: conformational flexibility of transcription factor binding sites
Tsu-Pei Chiu , Jinsen Li , Yibei Jiang , Remo Rohs
Biophysical Journal 121 ( 20) 3765 -3767
8
2022
Physicochemical models of protein–DNA binding with standard and modified base pairs
Tsu-Pei Chiu , Satyanarayan Rao , Remo Rohs
Proceedings of the National Academy of Sciences USA 120 ( 4) e2205796120 -e2205796120
7
2023
Predicting DNA structure using a deep learning method
Jinsen Li , Tsu-Pei Chiu , Remo Rohs
Nature Communications 15 ( 1) 1243 -1243
4
2024
Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox–DNA binding
Yibei Jiang , Tsu-Pei Chiu , Raktim Mitra , Remo Rohs
Biophysical Journal 123 ( 2) 248 -259
2
2024
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics
Brendon H Cooper , Tsu-Pei Chiu , Remo Rohs
Bioinformatics 38 ( 22) 5121 -5123
2
2022
Deep DNAshape: predicting DNA shape considering extended flanking regions using a deep learning method
Jinsen Li , Tsu-Pei Chiu , Remo Rohs
bioRxiv 2023.10. 22.563383 -2023.10. 22.563383
1
2023
Dna Sequence Context and the Chromatin Landscape Differentiate Sequence-Specific Transcription Factor Binding in the Human Malaria Parasite Plasmodium Falciparum
Victoria A. Bonnell , Yuning Zhang , Alan S. Brown Jr. , John Horton
The Pennsylvania State University
1
2023
DeepPBS: geometric deep learning for interpretable prediction of protein-DNA binding specificity
Raktim Mitra , Jinsen Li , Jared M Sagendorf , Yibei Jiang
bioRxiv 2023.12. 15.571942 -2023.12. 15.571942
2023