Lujia Chen

Precision Medicine Research Lab

University of Pittsburgh

Department of Biomedical Informatics

Publications

  1. Zhang, H., Lu, B., Lu, X., Saeed, A., Chen, L. (2024) Current transcriptome database and biomarker discovery for immunotherapy by immune checkpoint blockade, bioRxiv.

  2. Kim, J., Yuan, Y., Agaronyan, K., Zhao, A., Wang, V.D., Gupta, G., Essayas, H., ... Chen, L. (2024) Damage sensing through TLR9 Regulates Inflammatory and Antiviral Responses During Influenza Infection, bioRxiv.

  3. Ren, S., Cooper, G.F., Chen, L., Lu, X. (2024) An interpretable deep learning framework for genome-informed precision oncology, Nature Machine Intelligence, 6(8), 864-875.

  4. Chen, L., Wang, Y., Cai, C., Ding, Y., Kim, R.S., Lipchik, C., Gavin, P.G., ... Lu, X. (2024) Machine Learning Predicts Oxaliplatin Benefit in Early Colon Cancer, Journal of Clinical Oncology, 42(13), 1520-1530.

  5. Al-Bzour, N.N., Al-Bzour, A.N., Qasaymeh, A., Saeed, A., Chen, L., Saeed, A. (2024) Identification of survival-associated epithelial cell markers linked to TROP2 through single-cell and bulk sequencing analysis, Cancer Research, 84(6_Supplement), 866-866.

  6. Zhang, H., Lu, X., Lu, B., Gullo, G., Chen, L. (2024) Measuring the composition of the tumor microenvironment with transcriptome analysis: past, present and future, Future Oncology.

  7. Zhang, H., Lu, X., Lu, B., Chen, L. (2023) scGEM: Unveiling the Nested Tree-Structured Gene Co-Expressing Modules in Single Cell Transcriptome Data, Cancers, 15(17), 4277.

  8. Sun, R., Zhao, H., Gao, D.S., Ni, A., Li, H., Chen, L., Lu, X., Chen, K., Lu, B. (2023) Amphiregulin couples IL1RL1+ regulatory T cells and cancer-associated fibroblasts to impede antitumor immunity, Science Advances, 9(34), eadd7399.

  9. Young, J.D., Ren, S., Chen, L., Lu, X. (2023) Revealing the Impact of Genomic Alterations on Cancer Cell Signaling with an Interpretable Deep Learning Model, Cancers, 15(15), 3857.

  10. Zhang, H., Lu, X., Chen, L. (2023) IOhub: a web server that tracks integrative transcriptomic data for immune-oncology, Proceedings of The 22nd International Conference on Bio.

  11. Zhang, H., Lu, X., Lu, B., Chen, L. (2023) Measuring the composition of tumor microenvironment from transcriptome analysis: past, now and future, Preprint.

  12. Chen, X., Chen, L., Kürten, C.H.L., Jabbari, F., Vujanovic, L., Ding, Y., Lu, B., Lu, K., ... Lu, X. (2022) An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors, PLOS Computational Biology, 18(12), e1010761.

  13. Liu, Z., Cai, C., Ma, X., Liu, J., Chen, L., Lui, V.W.Y., Cooper, G.F., Lu, X. (2022) A Novel Bayesian Framework Infers Driver Activation States and Reveals Pathway-Oriented Molecular Subtypes in Head and Neck Cancer, Cancers, 14(19), 4825.

  14. Ruan, H., Leibowitz, B.J., Peng, Y., Shen, L., Chen, L., Kuang, C., Schoen, R.E., ... Zhang, L. (2022) Targeting Myc-driven stress vulnerability in mutant KRAS colorectal cancer, Molecular Biomedicine, 3(1), 10.

  15. Leibowitz, B.J., Zhao, G., Wei, L., Ruan, H., Epperly, M., Chen, L., Lu, X., ... Zhang, L. (2021) Interferon β drives intestinal regeneration after radiation, Science Advances, 7(41), eabi5253.

  16. Ruan, H., Li, X., Xu, X., Leibowitz, B.J., Tong, J., Chen, L., Ao, L., Xing, W., Luo, J., Zhang, L. (2020) eIF4E S209 phosphorylation licenses myc-and stress-driven oncogenesis, eLife, 9, e60151.

  17. Chen, X., Chen, L., Kurten, C., Vujanovic, L., Kulkarni, A., Ferris, R., Lu, X. (2020) Abstract B33: Discovering distinct immune environments defined by the states of single cells within tumor microenvironment, Clinical Cancer Research, 26(12_Supplement_2), B33-B33.

  18. Chen, X., Chen, L., Kurten, C., Vujanovic, L., Kulkarni, A., Ferris, R., Lu, X. (2020) Discovering distinct immune environments defined by the states of single cells within tumor microenvironment, Clinical Cancer Research, 26(12), 68-68.

  19. Cai, C., Cooper, G.F., Lu, K.N., Ma, X., Xu, S., Zhao, Z., Chen, X., Xue, Y., Lee, A.V., Chen, L., Lu, X. (2019) Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference, PLoS Computational Biology, 15(7), e1007088.

  20. Chen, L., Lu, X. (2018) Discovering functional impacts of miRNAs in cancers using a causal deep learning model, BMC Medical Genomics, 11, 53-63.

  21. Lu, S., Fan, X., Chen, L., Lu, X. (2018) A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways, PLoS ONE, 13(9), e0203871.

  22. Chen, L., Lu, X. (2018) Making deep learning models transparent, J Med Artif Intell, 1(5).

  23. Ding, M.Q., Chen, L., Cooper, G.F., Young, J.D., Lu, X. (2018) Precision oncology beyond targeted therapy: combining omics data with machine learning matches the majority of cancer cells to effective therapeutics, Molecular Cancer Research, 16(2), 269-278.

  24. Chen, L. (2017) Deep Learning Models for modeling cellular transcription systems, University of Pittsburgh (Dissertation).

  25. Lu, S., Cai, C., Yan, G., Zhou, Z., Wan, Y., Chen, V., Chen, L., Cooper, G.F., ... Lu, X. (2016) Signal-oriented pathway analyses reveal a signaling complex as a synthetic lethal target for p53 mutations, Cancer Research, 76(23), 6785-6794.

  26. Chen, L., Cai, C., Chen, V., Lu, X. (2016) Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model, BMC Bioinformatics, 17(Suppl 1), 9.

  27. Hill, S., Heiser, L.M., Cokelaer, T., Unger, M., Nesser, N.K., Carlin, D.E., Zhang, Y., ... Mukherjee, S. (2016) Inferring causal molecular networks: empirical assessment through a community-based effort, Nature Methods, 13(4), 310–318.

  28. Chen, L., Cai, C., Chen, V., Lu, X. (2015) Trans-species learning of cellular signaling systems with bimodal deep belief networks, Bioinformatics, 31(18), 3008-3015.

  29. Cai, C., Chen, L., Jiang, X., Lu, X. (2014) Modeling signal transduction from protein phosphorylation to gene expression, Cancer Informatics, 13, CIN.S13883.

  30. Montefusco, D.J.*, Chen, L.*, Matmati, N., Lu, S., Newcomb, B., Cooper, G.F., Hannun, Y.A., Lu, X. (2013) Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses, Science Signaling, 6(299), rs14. (* indicates co-first author)

  31. Jin, B., Chen, V., Chen, L., Lu, X. (2011) Mapping annotations with textual evidence using an scLDA model, AMIA Annual Symposium Proceedings, 2011, 834.