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Tsu-Pei Chiu

Observed name: Chiu, Tsu-Pei
ORCID: 0000-0002-2472-6557
Observed ORCID: 0000-0002-2472-6557
OpenAlex ID: A5047776299
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding
2015 · Tsu-Pei Chiu, Federico Comoglio, et al. · Bioinformatics · 162
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DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo
2016 · Anthony Mathelier, Beibei Xin, et al. · Cell Systems · 135
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Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator
2015 · Zengqin Deng, Qing Wang, et al. · Nature Communications · 116
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Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding
2017 · Jinsen Li, Jared M. Sagendorf, et al. · Nucleic Acids Research · 101
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Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding
2018 · Satyanarayan Rao, Tsu-Pei Chiu, et al. · Epigenetics & Chromatin · 94
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Genome-wide prediction of minor-groove electrostatic potential enables biophysical modeling of protein–DNA binding
2017 · Tsu-Pei Chiu, Satyanarayan Rao, et al. · Nucleic Acids Research · 80
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Predicting DNA structure using a deep learning method
2024 · Jinsen Li, Tsu-Pei Chiu, et al. · Nature Communications · 79
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Geometric deep learning of protein–DNA binding specificity
2024 · Raktim Mitra, Jinsen Li, et al. · Nature Methods · 73
GBshape: a genome browser database for DNA shape annotations
2014 · Tsu-Pei Chiu, Lin Yang, et al. · Nucleic Acids Research · 61
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Macrophages activated by hepatitis B virus have distinct metabolic profiles and suppress the virus via IL-1β to downregulate PPARα and FOXO3
2022 · Yumei Li, Yanwen Zhu, et al. · Cell Reports · 43
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TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites
2019 · Tsu-Pei Chiu, Beibei Xin, et al. · Nucleic Acids Research · 39
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Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria
2020 · Xiaolin Wu, Bo Cao, et al. · Proceedings of the National Academy of Sciences · 34
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Experimental maps of DNA structure at nucleotide resolution distinguish intrinsic from protein-induced DNA deformations
2018 · Robert N Azad, Dana Zafiropoulos, et al. · Nucleic Acids Research · 29
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It is in the flanks: Conformational flexibility of transcription factor binding sites
2022 · Tsu-Pei Chiu, Jinsen Li, et al. · Biophysical Journal · 28
Physicochemical models of protein–DNA binding with standard and modified base pairs
2023 · Tsu-Pei Chiu, Satyanarayan Rao, et al. · Proceedings of the National Academy of Sciences · 26
Feruloyl-l-arabinose attenuates migration, invasion and production of reactive oxygen species in H1299 lung cancer cells
2013 · Hsin-Yu Fang, Hui-Min Wang, et al. · Food and Chemical Toxicology · 22
DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum
2024 · Victoria A Bonnell, Yuning Zhang, et al. · Nucleic Acids Research · 15
Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox–DNA binding
2023 · Yibei Jiang, Tsu-Pei Chiu, et al. · Biophysical Journal · 8
Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics
2022 · Brendon H Cooper, Tsu-Pei Chiu, et al. · Bioinformatics · 6
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Macrophages activated by hepatitis B virus have distinct metabolic profiles and suppress the virus via IL-1β to downregulate PPARα and FOXO3
2022 · Yumei Li, Yanwen Zhu, et al. · Cell Reports · 4
28 GBshape: a genome browser database for DNA shape annotations
2015 · Tsu-Pei Chiu, Lin Yang, et al. · Journal of Biomolecular Structure and Dynamics · 2
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Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes
2026 · Yibei Jiang, Alexandra M. Shewchuk, et al. · Biophysical Journal · 1
DNAdesign: feature-aware in silico design of synthetic DNA through mutation
2025 · Yingfei Wang, Jinsen Li, et al. · Bioinformatics · 1
Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancer
2024 · Yuanzhong Pan, Tsu-Pei Chiu, et al. · bioRxiv (Cold Spring Harbor Laboratory) · 1
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Quantitative modulation of a spatial enhancer through the biophysical properties of a transcription factor binding site
2026 · Conrad Fallon, Liucong Ling, et al. · Science Advances
Works count: 32
Citation count: 1,161
H-index: 16
I10-index: 17
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