Luo Lab

Research

Highlighted

Predicting T Cell Receptor Specificity with Graph Attention Networks
Predicting T Cell Receptor Specificity with Graph Attention Networks
Aiwu Xu, Dhritiben Patel, Wenjun Lin, Ping Luo
12th International Work-Conference on Bioinformatics and Biomedical Engineering  ·  [no date info]  ·  xu2025iwbbio-tcr
Early Cancer Detection in Li Fraumeni Syndrome with Cell-Free DNA
Early Cancer Detection in Li–Fraumeni Syndrome with Cell-Free DNA
Derek Wong, Ping Luo, Leslie E. Oldfield, Haifan Gong, Ledia Brunga, …, Patrick Veit-Haibach, Andrea S. Doria, David Malkin, Raymond H. Kim, Trevor J. Pugh
Cancer Discovery  ·  16 Oct 2023  ·  doi:10.1158/2159-8290.CD-23-0456

All

2025

Cholinergic regulation of thymocyte negative selection
Cholinergic regulation of thymocyte negative selection
Shaofeng Liu, Chunxing Zheng, Robert Nechanitzky, Ping Luo, Parameswaran Ramachandran, …, Mahmood Mohtashami, Hai Qi, Pamela S. Ohashi, Juan Carlos Zúñiga-Pflücker, Tak W. Mak
Nature Immunology  ·  21 May 2025  ·  doi:10.1038/s41590-025-02152-4
B cell-derived acetylcholine promotes liver regeneration by regulating Kupffer cell and hepatic CD8 T cell function
B cell-derived acetylcholine promotes liver regeneration by regulating Kupffer cell and hepatic CD8+ T cell function
Nastaran Fazel Modares, Liam D. Hendrikse, Logan K. Smith, Michael St. Paul, Jillian Haight, …, Bruna Araujo David, Tashi Rastogi, Woo-Yong Lee, Paul Kubes, Tak W. Mak
Immunity  ·  01 May 2025  ·  doi:10.1016/j.immuni.2025.04.002

2024

Cell-free DNA from germline TP53 mutation carriers reflect cancer-like fragmentation patterns
Cell-free DNA from germline TP53 mutation carriers reflect cancer-like fragmentation patterns
Derek Wong, Maha Tageldein, Ping Luo, Erik Ensminger, Jeffrey Bruce, …, Anita Villani, Adam Shlien, Raymond H. Kim, David Malkin, Trevor J. Pugh
Nature Communications  ·  27 Aug 2024  ·  doi:10.1038/s41467-024-51529-w
Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors
Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors
Eric Y. Stutheit-Zhao, Enrique Sanz-Garcia, Zhihui (Amy) Liu, Derek Wong, Kayla Marsh, …, Philip Awadalla, Scott V. Bratman, Pamela S. Ohashi, Trevor J. Pugh, Lillian L. Siu
Cancer Discovery  ·  22 Feb 2024  ·  doi:10.1158/2159-8290.CD-23-1060

2023

Early Cancer Detection in Li Fraumeni Syndrome with Cell-Free DNA
Early Cancer Detection in Li–Fraumeni Syndrome with Cell-Free DNA
Derek Wong, Ping Luo, Leslie E. Oldfield, Haifan Gong, Ledia Brunga, …, Patrick Veit-Haibach, Andrea S. Doria, David Malkin, Raymond H. Kim, Trevor J. Pugh
Cancer Discovery  ·  16 Oct 2023  ·  doi:10.1158/2159-8290.CD-23-0456
Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma
Immunophenotypic correlates of sustained MRD negativity in patients with multiple myeloma
David G. Coffey, Francesco Maura, Edgar Gonzalez-Kozlova, J. Javier Diaz-Mejia, Ping Luo, …, Dickran Kazandjian, Trevor J. Pugh, Damian J. Green, Sacha Gnjatic, Ola Landgren
Nature Communications  ·  02 Sep 2023  ·  doi:10.1038/s41467-023-40966-8
Multiple Germline Events Contribute to Cancer Development in Patients with Li-Fraumeni Syndrome
Multiple Germline Events Contribute to Cancer Development in Patients with Li-Fraumeni Syndrome
Vallijah Subasri, Nicholas Light, Nisha Kanwar, Jack Brzezinski, Ping Luo, …, Trevor J. Pugh, Anita Villani, Adam Shlien, Anna Goldenberg, David Malkin
Cancer Research Communications  ·  01 May 2023  ·  doi:10.1158/2767-9764.CRC-22-0402
Network Learning for Biomarker Discovery
Network Learning for Biomarker Discovery
Yulian Ding, Minghan Fu, Ping Luo, Fang-Xiang Wu
International Journal of Network Dynamics and Intelligence  ·  27 Mar 2023  ·  doi:10.53941/ijndi0201004
Integrated, Longitudinal Analysis of Cell-free DNA in Uveal Melanoma
Integrated, Longitudinal Analysis of Cell-free DNA in Uveal Melanoma
Derek Wong, Ping Luo, Nadia Znassi, Diana P. Arteaga, Diana Gray, …, Wei Xu, Hatem Krema, Anthony M. Joshua, Marcus O. Butler, Trevor J. Pugh
Cancer Research Communications  ·  15 Feb 2023  ·  doi:10.1158/2767-9764.CRC-22-0456

2022

Evaluation of single-cell RNAseq labelling algorithms using cancer datasets
Evaluation of single-cell RNAseq labelling algorithms using cancer datasets
Erik Christensen, Ping Luo, Andrei Turinsky, Mia Husić, Alaina Mahalanabis, …, Juan Javier Diaz-Mejia, Michael Brudno, Trevor Pugh, Arun Ramani, Parisa Shooshtari
Briefings in Bioinformatics  ·  30 Dec 2022  ·  doi:10.1093/bib/bbac561
Integrated analysis of cell-free DNA for the early detection of cancer in people with Li-Fraumeni Syndrome
Integrated analysis of cell-free DNA for the early detection of cancer in people with Li-Fraumeni Syndrome
Derek Wong, Ping Luo, Leslie Oldfield, Haifan Gong, Ledia Brunga, …, Yogi Sundaravadanam, Dax Torti, David Malkin, Raymond H Kim, Trevor J Pugh
Cold Spring Harbor Laboratory  ·  11 Oct 2022  ·  doi:10.1101/2022.10.07.22280848
Evaluation of single-cell RNA-seq clustering algorithms on cancer tumor datasets
Evaluation of single-cell RNA-seq clustering algorithms on cancer tumor datasets
Alaina Mahalanabis, Andrei L. Turinsky, Mia Husić, Erik Christensen, Ping Luo, Alaine Naidas, Michael Brudno, Trevor Pugh, Arun K. Ramani, Parisa Shooshtari
Computational and Structural Biotechnology Journal  ·  01 Jan 2022  ·  doi:10.1016/j.csbj.2022.10.029

2021

Identifying cell types from single-cell data based on similarities and dissimilarities between cells
Identifying cell types from single-cell data based on similarities and dissimilarities between cells
Yuanyuan Li, Ping Luo, Yi Lu, Fang-Xiang Wu
BMC Bioinformatics  ·  01 May 2021  ·  doi:10.1186/s12859-020-03873-z

2020

Predicting disease associated genes: Computational methods, databases, and evaluations
Predicting disease‐associated genes: Computational methods, databases, and evaluations
Ping Luo, Bolin Chen, Bo Liao, Fang‐Xiang Wu
WIREs Data Mining and Knowledge Discovery  ·  28 Jul 2020  ·  doi:10.1002/widm.1383
CReSCENT: CanceR Single Cell ExpressioN Toolkit
CReSCENT: CanceR Single Cell ExpressioN Toolkit
Suluxan Mohanraj, J Javier Díaz-Mejía, Martin D Pham, Hillary Elrick, Mia Husić, …, Laura M Richards, Parisa Shooshtari, Michael Brudno, Arun K Ramani, Trevor J Pugh
Nucleic Acids Research  ·  01 Jun 2020  ·  doi:10.1093/nar/gkaa437
Ensemble disease gene prediction by clinical sample-based networks
Ensemble disease gene prediction by clinical sample-based networks
Ping Luo, Li-Ping Tian, Bolin Chen, Qianghua Xiao, Fang-Xiang Wu
BMC Bioinformatics  ·  01 Mar 2020  ·  doi:10.1186/s12859-020-3346-8

2019

Identifying Disease-Gene Associations With Graph-Regularized Manifold Learning
Identifying Disease-Gene Associations With Graph-Regularized Manifold Learning
Ping Luo, Qianghua Xiao, Pi-Jing Wei, Bo Liao, Fang-Xiang Wu
Frontiers in Genetics  ·  02 Apr 2019  ·  doi:10.3389/fgene.2019.00270
Enhancing the prediction of disease gene associations with multimodal deep learning
Enhancing the prediction of disease–gene associations with multimodal deep learning
Ping Luo, Yuanyuan Li, Li-Ping Tian, Fang-Xiang Wu
Bioinformatics  ·  02 Mar 2019  ·  doi:10.1093/bioinformatics/btz155
A Novel Core Attachment Based Method to Identify Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks
A Novel Core‐Attachment–Based Method to Identify Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks
Qianghua Xiao, Ping Luo, Min Li, Jianxin Wang, Fang‐Xiang Wu
PROTEOMICS  ·  20 Feb 2019  ·  doi:10.1002/pmic.201800129
deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks
deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks
Ping Luo, Yulian Ding, Xiujuan Lei, Fang-Xiang Wu
Frontiers in Genetics  ·  29 Jan 2019  ·  doi:10.3389/fgene.2019.00013
Improved Spectral Clustering Method for Identifying Cell Types from Single-Cell Data
Improved Spectral Clustering Method for Identifying Cell Types from Single-Cell Data
Yuanyuan Li, Ping Luo, Yi Lu, Fang-Xiang Wu
Lecture Notes in Computer Science  ·  01 Jan 2019  ·  doi:10.1007/978-3-030-26969-2_17
Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data
Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data
Ping Luo, Li-Ping Tian, Jishou Ruan, Fang-Xiang Wu
IEEE/ACM Transactions on Computational Biology and Bioinformatics  ·  01 Jan 2019  ·  doi:10.1109/TCBB.2017.2770120

2018

Predicting Disease Genes from Clinical Single Sample-Based PPI Networks
Predicting Disease Genes from Clinical Single Sample-Based PPI Networks
Ping Luo, Li-Ping Tian, Bolin Chen, Qianghua Xiao, Fang-Xiang Wu
Lecture Notes in Computer Science  ·  01 Jan 2018  ·  doi:10.1007/978-3-319-78723-7_21
Predicting Gene-Disease Associations with Manifold Learning
Predicting Gene-Disease Associations with Manifold Learning
Ping Luo, Li-Ping Tian, Bolin Chen, Qianghua Xiao, Fang-Xiang Wu
Lecture Notes in Computer Science  ·  01 Jan 2018  ·  doi:10.1007/978-3-319-94968-0_26
CASNMF: A Converged Algorithm for symmetrical nonnegative matrix factorization
CASNMF: A Converged Algorithm for symmetrical nonnegative matrix factorization
Li-Ping Tian, Ping Luo, Haiying Wang, Huiru Zheng, Fang-Xiang Wu
Neurocomputing  ·  01 Jan 2018  ·  doi:10.1016/j.neucom.2017.10.039

2016

Identifying disease genes from PPI networks weighted by gene expression under different conditions
Identifying disease genes from PPI networks weighted by gene expression under different conditions
Ping Luo, Li-Ping Tian, Jishou Ruan, Fang-Xiang Wu
2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  ·  01 Dec 2016  ·  doi:10.1109/BIBM.2016.7822699

Creation of Visualizations with a Multi-Agent LLM Approach
Creation of Visualizations with a Multi-Agent LLM Approach
Ping Luo, Kyle Gauthier, Bo Huang, Wenjun Lin
10th International Congress on Information and Communication Technology  ·  [no date info]  ·  luo2025icict-viz
Predicting T Cell Receptor Specificity with Graph Attention Networks
Predicting T Cell Receptor Specificity with Graph Attention Networks
Aiwu Xu, Dhritiben Patel, Wenjun Lin, Ping Luo
12th International Work-Conference on Bioinformatics and Biomedical Engineering  ·  [no date info]  ·  xu2025iwbbio-tcr