متابعة
Tsu-Pei Chiu
Tsu-Pei Chiu
Assistant Professor (Teaching), University of Southern California
بريد إلكتروني تم التحقق منه على usc.edu - الصفحة الرئيسية
عنوان
عدد مرات الاقتباسات
عدد مرات الاقتباسات
السنة
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding‏
TP Chiu, F Comoglio, T Zhou, L Yang, R Paro, R Rohs‏
Bioinformatics 32 (8), 1211-1213, 2016‏
1692016
DNA shape features improve transcription factor binding site predictions in vivo‏
A Mathelier, B Xin, TP Chiu, L Yang, R Rohs, WW Wasserman‏
Cell systems 3 (3), 278-286. e4, 2016‏
1672016
Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator‏
Z Deng, Q Wang, Z Liu, M Zhang, ACD Machado, TP Chiu, C Feng, ...‏
Nature communications 6 (1), 7642, 2015‏
1262015
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding‏
J Li, JM Sagendorf, TP Chiu, M Pasi, A Perez, R Rohs‏
Nucleic acids research 45 (22), 12877-12887, 2017‏
1002017
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding‏
S Rao, TP Chiu, JF Kribelbauer, RS Mann, HJ Bussemaker, R Rohs‏
Epigenetics & chromatin 11, 1-11, 2018‏
902018
Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding‏
TP Chiu, S Rao, RS Mann, B Honig, R Rohs‏
Nucleic acids research 45 (21), 12565-12576, 2017‏
852017
GBshape: a genome browser database for DNA shape annotations‏
TP Chiu, L Yang, T Zhou, BJ Main, SCJ Parker, SV Nuzhdin, TD Tullius, ...‏
Nucleic acids research 43 (D1), D103-D109, 2015‏
662015
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites‏
TP Chiu, B Xin, N Markarian, Y Wang, R Rohs‏
Nucleic acids research 48 (D1), D246-D255, 2020‏
372020
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria‏
X Wu, B Cao, P Aquino, TP Chiu, C Chen, S Jiang, Z Deng, S Chen, ...‏
Proceedings of the National Academy of Sciences 117 (25), 14322-14330, 2020‏
332020
Feruloyl-L-arabinose attenuates migration, invasion and production of reactive oxygen species in H1299 lung cancer cells‏
HY Fang, HM Wang, KF Chang, HT Hu, LJ Hwang, TF Fu, YC Lin, ...‏
Food and Chemical Toxicology 58, 459-466, 2013‏
292013
Macrophages activated by hepatitis B virus have distinct metabolic profiles and suppress the virus via IL-1β to downregulate PPARα and FOXO3‏
Y Li, Y Zhu, S Feng, Y Ishida, TP Chiu, T Saito, S Wang, DK Ann, JJ Ou‏
Cell reports 38 (4), 2022‏
262022
Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations‏
RN Azad, D Zafiropoulos, D Ober, Y Jiang, TP Chiu, JM Sagendorf, ...‏
Nucleic acids research 46 (5), 2636-2647, 2018‏
262018
Predicting DNA structure using a deep learning method‏
J Li, TP Chiu, R Rohs‏
Nature communications 15 (1), 1243, 2024‏
242024
Physicochemical models of protein–DNA binding with standard and modified base pairs‏
TP Chiu, S Rao, R Rohs‏
Proceedings of the National Academy of Sciences 120 (4), e2205796120, 2023‏
162023
Geometric deep learning of protein–DNA binding specificity‏
R Mitra, J Li, JM Sagendorf, Y Jiang, AS Cohen, TP Chiu, CJ Glasscock, ...‏
Nature Methods 21 (9), 1674-1683, 2024‏
132024
It is in the flanks: Conformational flexibility of transcription factor binding sites‏
TP Chiu, J Li, Y Jiang, R Rohs‏
Biophysical Journal 121 (20), 3765-3767, 2022‏
122022
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum‏
VA Bonnell, Y Zhang, AS Brown, J Horton, GA Josling, TP Chiu, R Rohs, ...‏
Nucleic acids research 52 (17), 10161-10179, 2024‏
52024
Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox–DNA binding‏
Y Jiang, TP Chiu, R Mitra, R Rohs‏
Biophysical Journal 123 (2), 248-259, 2024‏
42024
Deep DNAshape: Predicting DNA shape considering extended flanking regions using a deep learning method‏
J Li, TP Chiu, R Rohs‏
bioRxiv, 2023.10. 22.563383, 2023‏
22023
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics‏
BH Cooper, TP Chiu, R Rohs‏
Bioinformatics 38 (22), 5121-5123, 2022‏
22022
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مقالات 1–20