DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding
Chiu, Tsu-Pei, Comoglio, Federico, Zhou, Tianyin, Yang, Lin, Paro, Renato, Rohs, Remo
Published in Bioinformatics (15.04.2016)
Published in Bioinformatics (15.04.2016)
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Journal Article
TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites
Chiu, Tsu-Pei, Xin, Beibei, Markarian, Nicholas, Wang, Yingfei, Rohs, Remo
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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Journal Article
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding
Li, Jinsen, Sagendorf, Jared M, Chiu, Tsu-Pei, Pasi, Marco, Perez, Alberto, Rohs, Remo
Published in Nucleic acids research (15.12.2017)
Published in Nucleic acids research (15.12.2017)
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Journal Article
Macrophages activated by hepatitis B virus have distinct metabolic profiles and suppress the virus via IL-1β to downregulate PPARα and FOXO3
Li, Yumei, Zhu, Yanwen, Feng, Shu, Ishida, Yuji, Chiu, Tsu-Pei, Saito, Takeshi, Wang, Sean, Ann, David K., Ou, Jing-hsiung James
Published in Cell reports (Cambridge) (25.01.2022)
Published in Cell reports (Cambridge) (25.01.2022)
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Journal Article
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding
Rao, Satyanarayan, Chiu, Tsu-Pei, Kribelbauer, Judith F, Mann, Richard S, Bussemaker, Harmen J, Rohs, Remo
Published in Epigenetics & chromatin (06.02.2018)
Published in Epigenetics & chromatin (06.02.2018)
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Journal Article
Physicochemical models of protein-DNA binding with standard and modified base pairs
Chiu, Tsu-Pei, Rao, Satyanarayan, Rohs, Remo
Published in Proceedings of the National Academy of Sciences - PNAS (24.01.2023)
Published in Proceedings of the National Academy of Sciences - PNAS (24.01.2023)
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Journal Article
Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox-DNA binding
Jiang, Yibei, Chiu, Tsu-Pei, Mitra, Raktim, Rohs, Remo
Published in Biophysical journal (16.01.2024)
Published in Biophysical journal (16.01.2024)
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Journal Article
Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria
Wu, Xiaolin, Cao, Bo, Aquino, Patricia, Chiu, Tsu-Pei, Chen, Chao, Jiang, Susu, Deng, Zixin, Chen, Shi, Rohs, Remo, Wang, Lianrong, Galagan, James E., Dedon, Peter C.
Published in Proceedings of the National Academy of Sciences - PNAS (23.06.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (23.06.2020)
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Journal Article
Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator
Deng, Zengqin, Wang, Qing, Liu, Zhao, Zhang, Manfeng, Machado, Ana Carolina Dantas, Chiu, Tsu-Pei, Feng, Chong, Zhang, Qi, Yu, Lin, Qi, Lei, Zheng, Jiangge, Wang, Xu, Huo, XinMei, Qi, Xiaoxuan, Li, Xiaorong, Wu, Wei, Rohs, Remo, Li, Ying, Chen, Zhongzhou
Published in Nature communications (02.07.2015)
Published in Nature communications (02.07.2015)
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Journal Article
DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo
Mathelier, Anthony, Xin, Beibei, Chiu, Tsu-Pei, Yang, Lin, Rohs, Remo, Wasserman, Wyeth W.
Published in Cell systems (28.09.2016)
Published in Cell systems (28.09.2016)
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Journal Article
GBshape: a genome browser database for DNA shape annotations
Chiu, Tsu-Pei, Yang, Lin, Zhou, Tianyin, Main, Bradley J, Parker, Stephen C J, Nuzhdin, Sergey V, Tullius, Thomas D, Rohs, Remo
Published in Nucleic acids research (28.01.2015)
Published in Nucleic acids research (28.01.2015)
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Journal Article
Macrophages activated by hepatitis B virus have distinct metabolic profiles and suppress the virus via IL-1β to downregulate PPARα and FOXO3
Li, Yumei, Zhu, Yanwen, Feng, Shu, Ishida, Yuji, Chiu, Tsu-Pei, Saito, Takeshi, Wang, Sean, Ann, David K, Ou, Jing-Hsiung James
Published in Cell reports (Cambridge) (05.07.2022)
Published in Cell reports (Cambridge) (05.07.2022)
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Journal Article
Feruloyl-l-arabinose attenuates migration, invasion and production of reactive oxygen species in H1299 lung cancer cells
Fang, Hsin-Yu, Wang, Hui-Min, Chang, Kuo-Feng, Hu, Huei-Ting, Hwang, Lian-Je, Fu, Tzu-Fun, Lin, Yin-Chieh, Chang, Wei-Chiao, Chiu, Tsu-Pei, Wen, Zhi-Hong, Fong, Yao, Chiu, Chien-Chih, Chen, Bing-Hung
Published in Food and chemical toxicology (01.08.2013)
Published in Food and chemical toxicology (01.08.2013)
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Journal Article
DeepPBS: Geometric deep learning for interpretable prediction of protein-DNA binding specificity
Mitra, Raktim, Li, Jinsen, Sagendorf, Jared M, Jiang, Yibei, Chiu, Tsu-Pei, Rohs, Remo
Published in bioRxiv (16.12.2023)
Published in bioRxiv (16.12.2023)
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Journal Article
GBshape: a genome browser database for DNA shape annotations
Chiu, Tsu-Pei, Yang, Lin, Zhou, Tianyin, Main, Bradley J., Parker, Stephen C.J., Nuzhdin, Sergey V., Tullius, Thomas D., Rohs, Remo
Published in Nucleic acids research (28.01.2015)
Published in Nucleic acids research (28.01.2015)
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Journal Article
Geometric deep learning of protein–DNA binding specificity
Mitra, Raktim, Li, Jinsen, Sagendorf, Jared M., Jiang, Yibei, Cohen, Ari S., Chiu, Tsu-Pei, Glasscock, Cameron J., Rohs, Remo
Published in Nature methods (01.09.2024)
Published in Nature methods (01.09.2024)
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Journal Article