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Que-Tran Bui Nguyen

dblp:370/5809 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2023
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Medical and health informatics · 50% Bioinformatics and computational biology · 50%

Topics — the 2 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Medical and health informatics
immunotherapy
0.712023
epiTCR: a highly sensitive predictor for TCR-peptide binding · Bioinform. 2023
Bioinformatics and computational biology › immunoinformatics
TCR-epitope binding prediction
0.712023
epiTCR: a highly sensitive predictor for TCR-peptide binding · Bioinform. 2023

Methods — techniques the papers use, named apart from their topics

random forest · 0.7BLOSUM62 encoding · 0.7
YearPublicationVenuePosition
2023 epiTCR: a highly sensitive predictor for TCR-peptide binding
abstract
MOTIVATION: Predicting the binding between T-cell receptor (TCR) and peptide presented by human leucocyte antigen molecule is a highly challenging task and a key bottleneck in the development of immunotherapy. Existing prediction tools, despite exhibiting good performance on the datasets they were built with, suffer from low true positive rates when used to predict epitopes capable of eliciting T-cell responses in patients. Therefore, an improved tool for TCR-peptide prediction built upon a large dataset combining existing publicly available data is still needed. RESULTS: We collected data from five public databases (IEDB, TBAdb, VDJdb, McPAS-TCR, and 10X) to form a dataset of >3 million TCR-peptide pairs, 3.27% of which were binding interactions. We proposed epiTCR, a Random Forest-based method dedicated to predicting the TCR-peptide interactions. epiTCR used simple input of TCR CDR3β sequences and antigen sequences, which are encoded by flattened BLOSUM62. epiTCR performed with area under the curve (0.98) and higher sensitivity (0.94) than other existing tools (NetTCR, Imrex, ATM-TCR, and pMTnet), while maintaining comparable prediction specificity (0.9). We identified seven epitopes that contributed to 98.67% of false positives predicted by epiTCR and exerted similar effects on other tools. We also demonstrated a considerable influence of peptide sequences on prediction, highlighting the need for more diverse peptides in a more balanced dataset. In conclusion, epiTCR is among the most well-performing tools, thanks to the use of combined data from public sources and its use will contribute to the quest in identifying neoantigens for precision cancer immunotherapy. AVAILABILITY AND IMPLEMENTATION: epiTCR is available on GitHub (https://github.com/ddiem-ri-4D/epiTCR).
My-Diem Nguyen Pham, Le Son Tran, Que-Tran Bui Nguyen, Thien-Phuc Hoang Nguyen, Thi Mong Quynh Pham, Hoai-Nghia Nguyen, Hoa Giang, Minh-Duy Phan, Vy Nguyen
Bioinform.4