Tsu-Pei Chiu
Tsu-Pei Chiu
Postdoctoral Associate, University of Southern California
Verified email at usc.edu - Homepage
Title
Cited by
Cited by
Year
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
1102016
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
982016
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), 1-12, 2015
792015
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
532015
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
452017
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), 1-11, 2018
442018
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
382017
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
202013
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
132020
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
132018
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
52020
Modeling of protein-DNA binding with a multi-module deep learning framework
TP Chiu, S Rao, ACD Machado, R Rohs
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 37, 81-81, 2019
2019
Genome-Wide Studies of Protein-DNA Binding: Beyond Sequence towards Biophysical and Physicochemical Models
TP Chiu
University of Southern California, 2018
2018
Structural analysis and quantitative modeling of protein-DNA interactions
R Rohs, J Sagendorf, TP Chiu
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 254, 2017
2017
Integration of electrostatics and solvation into statistical machine learning approaches for the quantitative modeling of protein-DNA binding affinities
TP Chiu, R Rohs
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 252, 2016
2016
High-throughput prediction of minor groove electrostatic potential in studies of protein-DNA recognition
TP Chiu, R Rohs
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 251, 2016
2016
ACCEPTED ORAL PRESENTATIONS
A Mathelier, L Yang, TP Chiu, R Rohs, W Wasserman
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