Ping Luo

Bioinformatics Specialist at Princess Margaret Cancer Centre with experience in deep learning

Toronto, Ontario, Canada

Research Expertise

single-cell genomics
deep learning
complex network analysis
Genetics (clinical)
Genetics
Molecular Medicine
Computational Mathematics
Computational Theory and Mathematics
Computer Science Applications
Molecular Biology
Biochemistry
Statistics and Probability
Applied Mathematics
Biotechnology
Artificial Intelligence
Cognitive Neuroscience
Structural Biology
Cell Biology
Hematology
Immunology
Information Systems
Biophysics

About

8 years of science and engineering experience integrating multi-omics data to identify biomarkers for cancer studies. Seeking to apply data analytics expertise to develop new diagnosis and treatment strategies.

Publications

deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks

Frontiers in Genetics / Jan 29, 2019

Luo, P., Ding, Y., Lei, X., & Wu, F.-X. (2019). deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks. Frontiers in Genetics, 10. https://doi.org/10.3389/fgene.2019.00013

Enhancing the prediction of disease–gene associations with multimodal deep learning

Bioinformatics / Mar 02, 2019

Luo, P., Li, Y., Tian, L.-P., & Wu, F.-X. (2019). Enhancing the prediction of disease–gene associations with multimodal deep learning. Bioinformatics, 35(19), 3735–3742. https://doi.org/10.1093/bioinformatics/btz155

Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data

IEEE/ACM Transactions on Computational Biology and Bioinformatics / Jan 01, 2019

Luo, P., Tian, L.-P., Ruan, J., & Wu, F.-X. (2019). Disease Gene Prediction by Integrating PPI Networks, Clinical RNA-Seq Data and OMIM Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(1), 222–232. https://doi.org/10.1109/tcbb.2017.2770120

Identifying Disease-Gene Associations With Graph-Regularized Manifold Learning

Frontiers in Genetics / Apr 02, 2019

Luo, P., Xiao, Q., Wei, P.-J., Liao, B., & Wu, F.-X. (2019). Identifying Disease-Gene Associations With Graph-Regularized Manifold Learning. Frontiers in Genetics, 10. https://doi.org/10.3389/fgene.2019.00270

CReSCENT: CanceR Single Cell ExpressioN Toolkit

Nucleic Acids Research / Jun 01, 2020

Mohanraj, S., Díaz-Mejía, J. J., Pham, M. D., Elrick, H., Husić, M., Rashid, S., Luo, P., Bal, P., Lu, K., Patel, S., Mahalanabis, A., Naidas, A., Christensen, E., Croucher, D., Richards, L. M., Shooshtari, P., Brudno, M., Ramani, A. K., & Pugh, T. J. (2020). CReSCENT: CanceR Single Cell ExpressioN Toolkit. Nucleic Acids Research, 48(W1), W372–W379. https://doi.org/10.1093/nar/gkaa437

CASNMF: A Converged Algorithm for symmetrical nonnegative matrix factorization

Neurocomputing / Jan 01, 2018

Tian, L.-P., Luo, P., Wang, H., Zheng, H., & Wu, F.-X. (2018). CASNMF: A Converged Algorithm for symmetrical nonnegative matrix factorization. Neurocomputing, 275, 2031–2040. https://doi.org/10.1016/j.neucom.2017.10.039

Identifying disease genes from PPI networks weighted by gene expression under different conditions

2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) / Dec 01, 2016

Ping Luo, Li-Ping Tian, Jishou Ruan, & Wu, F.-X. (2016). Identifying disease genes from PPI networks weighted by gene expression under different conditions. 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). https://doi.org/10.1109/bibm.2016.7822699

Identifying cell types from single-cell data based on similarities and dissimilarities between cells

BMC Bioinformatics / May 01, 2021

Li, Y., Luo, P., Lu, Y., & Wu, F.-X. (2021). Identifying cell types from single-cell data based on similarities and dissimilarities between cells. BMC Bioinformatics, 22(S3). https://doi.org/10.1186/s12859-020-03873-z

Predicting Gene-Disease Associations with Manifold Learning

Bioinformatics Research and Applications / Jan 01, 2018

Luo, P., Tian, L.-P., Chen, B., Xiao, Q., & Wu, F.-X. (2018). Predicting Gene-Disease Associations with Manifold Learning. Lecture Notes in Computer Science, 265–271. https://doi.org/10.1007/978-3-319-94968-0_26

Ensemble disease gene prediction by clinical sample-based networks

BMC Bioinformatics / Mar 01, 2020

Luo, P., Tian, L.-P., Chen, B., Xiao, Q., & Wu, F.-X. (2020). Ensemble disease gene prediction by clinical sample-based networks. BMC Bioinformatics, 21(S2). https://doi.org/10.1186/s12859-020-3346-8

A Novel Core-Attachment-Based Method to Identify Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks

PROTEOMICS / Feb 20, 2019

Xiao, Q., Luo, P., Li, M., Wang, J., & Wu, F.-X. (2019). A Novel Core-Attachment-Based Method to Identify Dynamic Protein Complexes Based on Gene Expression Profiles and PPI Networks. PROTEOMICS, 19(5), 1800129. Portico. https://doi.org/10.1002/pmic.201800129

Predicting disease‐associated genes: Computational methods, databases, and evaluations

WIREs Data Mining and Knowledge Discovery / Jul 28, 2020

Luo, P., Chen, B., Liao, B., & Wu, F. (2020). Predicting disease‐associated genes: Computational methods, databases, and evaluations. WIREs Data Mining and Knowledge Discovery, 11(2). Portico. https://doi.org/10.1002/widm.1383

Normalization of the Immune Microenvironment during Lenalidomide Maintenance Is Associated with Sustained MRD Negativity in Patients with Multiple Myeloma

Blood / Nov 05, 2021

Coffey, D. G., Maura, F., Gonzalez-Kozlova, E., Diaz-Mejia3, J., Luo, P., Zhang, Y., Xu, Y., Warren, E. H., Smith, E. L., Cho, H. J., Lesokhin, A., Diamond, B., Kazandjian, D., Pugh, T. J., Green, D. J., Gnjatic, S., & Landgren, O. (2021). Normalization of the Immune Microenvironment during Lenalidomide Maintenance Is Associated with Sustained MRD Negativity in Patients with Multiple Myeloma. Blood, 138(Supplement 1), 329–329. https://doi.org/10.1182/blood-2021-154506

Network Learning for Biomarker Discovery

International Journal of Network Dynamics and Intelligence / Feb 23, 2023

Ding, Y., Fu, M., Luo, P., & Wu, F.-X. (2023). Network Learning for Biomarker Discovery. International Journal of Network Dynamics and Intelligence. https://doi.org/10.53941/ijndi0201004

Predicting Disease Genes from Clinical Single Sample-Based PPI Networks

Bioinformatics and Biomedical Engineering / Jan 01, 2018

Luo, P., Tian, L.-P., Chen, B., Xiao, Q., & Wu, F.-X. (2018). Predicting Disease Genes from Clinical Single Sample-Based PPI Networks. Lecture Notes in Computer Science, 247–258. https://doi.org/10.1007/978-3-319-78723-7_21

Integrated, Longitudinal Analysis of Cell-free DNA in Uveal Melanoma

Cancer Research Communications / Feb 15, 2023

Wong, D., Luo, P., Znassi, N., Arteaga, D. P., Gray, D., Danesh, A., Han, M., Zhao, E. Y., Pedersen, S., Prokopec, S., Sundaravadanam, Y., Torti, D., Marsh, K., Keshavarzi, S., Xu, W., Krema, H., Joshua, A. M., Butler, M. O., & Pugh, T. J. (2023). Integrated, Longitudinal Analysis of Cell-free DNA in Uveal Melanoma. Cancer Research Communications, 3(2), 267–280. https://doi.org/10.1158/2767-9764.crc-22-0456

Evaluation of single-cell RNAseq labelling algorithms using cancer datasets

Briefings in Bioinformatics / Dec 30, 2022

Christensen, E., Luo, P., Turinsky, A., Husić, M., Mahalanabis, A., Naidas, A., Diaz-Mejia, J. J., Brudno, M., Pugh, T., Ramani, A., & Shooshtari, P. (2022). Evaluation of single-cell RNAseq labelling algorithms using cancer datasets. Briefings in Bioinformatics, 24(1). https://doi.org/10.1093/bib/bbac561

Integrated analysis of cell-free DNA for the early detection of cancer in people with Li-Fraumeni Syndrome

Oct 11, 2022

Wong, D., Luo, P., Oldfield, L., Gong, H., Brunga, L., Rabinowicz, R., Subasri, V., Chan, C., Downs, T., Farncombe, K. M., Luu, B., Norman, M., Eagles, J., Pederson, S., Wellum, J., Danesh, A., Prokopec, S., Zhao, E., Znassi, N., … Pugh, T. J. (2022). Integrated analysis of cell-free DNA for the early detection of cancer in people with Li-Fraumeni Syndrome. https://doi.org/10.1101/2022.10.07.22280848

Improved Spectral Clustering Method for Identifying Cell Types from Single-Cell Data

Intelligent Computing Theories and Application / Jan 01, 2019

Li, Y., Luo, P., Lu, Y., & Wu, F.-X. (2019). Improved Spectral Clustering Method for Identifying Cell Types from Single-Cell Data. Lecture Notes in Computer Science, 177–189. https://doi.org/10.1007/978-3-030-26969-2_17

Multiple Germline Events Contribute to Cancer Development in Patients with Li-Fraumeni Syndrome

Cancer Research Communications / May 01, 2023

Subasri, V., Light, N., Kanwar, N., Brzezinski, J., Luo, P., Hansford, J. R., Cairney, E., Portwine, C., Elser, C., Finlay, J. L., Nichols, K. E., Alon, N., Brunga, L., Anson, J., Kohlmann, W., de Andrade, K. C., Khincha, P. P., Savage, S. A., Schiffman, J. D., … Malkin, D. (2023). Multiple Germline Events Contribute to Cancer Development in Patients with Li-Fraumeni Syndrome. Cancer Research Communications, 3(5), 738–754. https://doi.org/10.1158/2767-9764.crc-22-0402

P087: Integrated analysis of cell-free DNA for the detection of malignant peripheral nerve sheath tumors in patients with neurofibromatosis type 1

Genetics in Medicine Open / Jan 01, 2023

Wong, D., Luo, P., Pederson, S., Chan, C., Farncombe, K., Norman, M., Oldfield, L. E., Kim, R., & Pugh, T. (2023). P087: Integrated analysis of cell-free DNA for the detection of malignant peripheral nerve sheath tumors in patients with neurofibromatosis type 1. Genetics in Medicine Open, 1(1), 100106. https://doi.org/10.1016/j.gimo.2023.100106

OP015: Multi-omic analysis of circulating tumour DNA for the early detection of cancer in patients with Li-Fraumeni syndrome

Genetics in Medicine / Mar 01, 2022

Wong, D., Znassi, N., Luo, P., Oldfield, L. E., Bruce, J., Danesh, A., Prokopec, S., Basra, P., Pederson, S., Wellum, J., Chan, C., Farncombe, K., Norman, M., Brunga, L., Light, N., Shien, A., Subasri, V., Malkin, D., Kim, R., & Pugh, T. (2022). OP015: Multi-omic analysis of circulating tumour DNA for the early detection of cancer in patients with Li-Fraumeni syndrome. Genetics in Medicine, 24(3), S346–S347. https://doi.org/10.1016/j.gim.2022.01.609

Evaluation of single-cell RNA-seq clustering algorithms on cancer tumor datasets

Computational and Structural Biotechnology Journal / Jan 01, 2022

Mahalanabis, A., Turinsky, A. L., Husić, M., Christensen, E., Luo, P., Naidas, A., Brudno, M., Pugh, T., Ramani, A. K., & Shooshtari, P. (2022). Evaluation of single-cell RNA-seq clustering algorithms on cancer tumor datasets. Computational and Structural Biotechnology Journal, 20, 6375–6387. https://doi.org/10.1016/j.csbj.2022.10.029

Education

University of Saskatchewan

Ph.D., Biomedical Engineering / September, 2019

Saskatoon, Saskatchewan, Canada

Beijing Institute of Technology

M.Eng., Biomedical Engineering / June, 2015

Beijing

Hunan University

B.Eng., Computer Science / June, 2010

Changsha

Experience

Princess Margaret Cancer Centre

Postdoctoral Researcher / November, 2019Present

I work in Dr. Trevor Pugh's lab and design cancer diagnosis and treatment strategies by analyze cell-free DNA and single cell sequencing data

Princess Margaret Cancer Centre

Bioinformatics Specialist / September, 2023Present

I work in Dr. Tak Mak's lab and study tumor immunology using single cell and TCR sequencing data.

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