| 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 | 186 | 2016 |
| 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 | 180 | 2016 |
| 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 | 137 | 2015 |
| 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 | 116 | 2017 |
| 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), 6, 2018 | 99 | 2018 |
| 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 | 96 | 2017 |
| Predicting DNA structure using a deep learning method J Li, TP Chiu, R Rohs Nature communications 15 (1), 1243, 2024 | 70 | 2024 |
| 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 | 68 | 2015 |
| 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 | 54 | 2024 |
| 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 | 47 | 2020 |
| 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 | 45 | 2022 |
| 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 | 35 | 2020 |
| 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 | 30 | 2013 |
| 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 | 28 | 2018 |
| 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 | 25 | 2023 |
| 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 | 20 | 2022 |
| 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 | 16 | 2024 |
| 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 | 9 | 2024 |
| 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 | 5 | 2022 |
| 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 | 3 | 2023 |
Remo RohsProfessor and Chair of Quantitative and Computational Biology, University of Southern CaliforniaVerified email at usc.edu
