🏆 Finalist — NIH Data Sharing Index (“S-Index”) Challenge

Tsu-Pei Chiu

University of Southern California

ORCID: 0000-0002-2472-6557
Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile
0Author DataRank

Indexed papers

0in pilot corpus
datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 13 papers. Top paper: “DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum”.

DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum

Nucleic Acids Research(2024)10.1093/nar/gkae585
N/A
0.467DataRank · unranked
16 citations

Yuning Zhang, Alan S. Brown, J.R. Horton, Gabrielle A. Josling, Tsu-Pei Chiu +5 more

It is in the flanks: Conformational flexibility of transcription factor binding sites

Biophysical Journal(2022)10.1016/j.bpj.2022.09.020
N/A
0DataRank · unranked
31 citations

Jinsen Li, Yibei Jiang, Remo Rohs, Tsu-Pei Chiu

Top-Down Crawl: a method for the ultra-rapid and motif-free alignment of sequences with associated binding metrics

Bioinformatics(2022)10.1093/bioinformatics/btac653
N/A
0DataRank · unranked
6 citations

Tsu-Pei Chiu, Remo Rohs, Brendon H Cooper

Physicochemical models of protein–DNA binding with standard and modified base pairs

Proceedings of the National Academy of Sciences(2023)10.1073/pnas.2205796120
N/A
0DataRank · unranked
27 citations

Satyanarayan Rao, Remo Rohs, Tsu-Pei Chiu

Probing the role of the protonation state of a minor groove-linker histidine in Exd-Hox–DNA binding

Biophysical Journal(2023)10.1016/j.bpj.2023.12.013
N/A
0DataRank · unranked
9 citations

Tsu-Pei Chiu, Raktim Mitra, Remo Rohs, Yibei Jiang

DeepPBS: Geometric deep learning for interpretable prediction of protein–DNA binding specificity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.12.15.571942
N/A
0DataRank · unranked
3 citations

Jinsen Li, Jared M. Sagendorf, Yibei Jiang, Tsu-Pei Chiu, Remo Rohs +1 more

Deep DNAshape: Predicting DNA shape considering extended flanking regions using a deep learning method

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.22.563383
N/A
0DataRank · unranked
2 citations

Tsu-Pei Chiu, Remo Rohs, Jinsen Li

Predicting DNA structure using a deep learning method

Nature Communications(2024)10.1038/s41467-024-45191-5
N/A
0DataRank · unranked
76 citations

Tsu-Pei Chiu, Remo Rohs, Jinsen Li

Geometric deep learning of protein–DNA binding specificity

Nature Methods(2024)10.1038/s41592-024-02372-w
N/A
0DataRank · unranked
67 citations

Jinsen Li, Jared M. Sagendorf, Yibei Jiang, Ari S Cohen, Tsu-Pei Chiu +3 more

Targeting circadian transcriptional programs through a cis-regulatory mechanism in triple negative breast cancer

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.26.590360
N/A
0DataRank · unranked
1 citations

Tsu-Pei Chiu, Lili Zhou, Priscilla Chan, Tia Tyrsett Kuo, Francesca Battaglin +9 more

DNAdesign: feature-aware in silico design of synthetic DNA through mutation

Bioinformatics(2025)10.1093/bioinformatics/btaf052
N/A
0DataRank · unranked
1 citations

Jinsen Li, Tsu-Pei Chiu, Nicolas Gompel, Remo Rohs, Yingfei Wang

Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2002933117
N/A
0DataRank · unranked
34 citations

Bo Cao, Patricia Aquino, Tsu-Pei Chiu, Chao Chen, Susu Jiang +7 more

Contribution of DNA breathing to physical interactions with transcription factors

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.20.633840
N/A
0DataRank · unranked
0 citations

Ben Lai, Tsu-Pei Chiu, Manish Bhattarai, Sheng Qian, A. R. Bishop +5 more