Songjian Lu, PhD

Lifan Liang, Kunju Zhu, Songjian Lu. BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization.

Bioinformatics 2020 Jan 8. pii: btz977. doi: 10.1093/bioinformatics/btz977

Y. Xue, G. Cooper, C. Cai, S. Lu, B. Hu, X. Ma, and X. Lu. Tumour-specific Causal Inference Discovers Distinct Disease Mechanisms Underlying Cancer Subtypes. Scientific Reports; 2019 Sep 13;9(1):13225. doi: 10.1038/s41598-019-48318-7; PMID: 31519988​

Cai C, Cooper GF, Lu KN, Ma X, Xu S, Zhao Z, Chen X, Xue Y, Lee AV, Clark N, Chen V, Lu S, Chen L, Yu L, Hochheiser HS, Jiang X, Wang JQ, Lu X. Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference. PLOS Comput Biol, 2019 Jul 15(7):e1007088. doi: 10.1371/journal.pcbi.1007088. [Epub ahead of print] PMID: 31276486; PMCID: PMC6650088.

Liang L, Chen V, Zhu K, Fan X, Lu X, Lu S. Integrating data and knowledge to identify functional modules of genes: a multilayer approach. BMC Bioinformatics. 2019 May 2;20(1):225. doi: 10.1186/s12859-019-2800-y. PubMed PMID: 31046665

M. Minata, A. Audia, J. Shi, S. Lu, J. Bernstock, M. Pavlyukov, A. Das, S.Kim, Y. Shin, Y. Lee, H. Koo, K. Snigdha, I. Waghmare, X. Guo, A. Mohyeldin, D. Gallego-Perez, J. Wang, D. Chen, P. Cheng, F. Mukheef, M. Contreras, J.Reyes, B. Vaillant, E.Sulman, S. Cheng, J. Markert, B.Tannous, X. Lu, M. Kango-Singh, L J. Lee, D. Nam, I. Nakano, K.Bhat. Phenotypic Plasticity of Invasive Edge Glioma Stem-like Cells in Response to Ionizing Radiation. Cell Reports; 2019; 26(7); PMID:30759398.​

X. Fan, S. Zhang *, S. Zhang, K. Zhu, S. Lu*. Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information. BMC Bioinformatics; 2019; 20(87); PMID: 30782113.​

X. Wang, M. O'Brien, J. Yu, L. Liang, Q. Zhang, S. Lu, X. An, J. McDyer, R. Mallampalli. Prolonged cold-ischemia induces necroptotic cell death after experimental  lung transplantation. American Journal of Respiratory Cell and Molecular Biology; 2019; PMID: 30742487.​

Lu S, Fan X, Chen L, Lu X. A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways. Plos One. September 2018; 13(9). https://doi.org/10.1371/journal.pone.0203871. 

Pangeni RP, Zhang Z, Alvarez AA, Wan X, Sastry N, Lu S, Shi T, Huang T, Lei CX, James CD, Kessler JA, Brennan CW, Nakano I, Lu X, Hu B, Zhang W, Cheng SY. Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma. Epigenetics. 2018;13(4):432-448. doi: 10.1080/15592294.2018.1469892. Epub 2018 Aug 6. PMID: 29927689.

Sadahiro H, Kang K, Gibson J, Minata M, Yu H, Shi J, Chhipa R, Chen Z, Lu S, Simoni Y, Furuta T, Sabit H, Zhang S, Bastola S, Yamaguchi S, Alsheikh H, Komarova S, Wang J, Kim S, Hambardzumyan D, Lu X, Newell E, Dasgupta B, Nakada M, Lee L, Nabors B, Norian L, Nakano I. Activation of the receptor tyrosine kinase AXL mediates the immune microenvironment in glioblastoma.  2018 Jun 1;78(11):3002-3013. doi: 10.1158/0008-5472.CAN-17-2433. Epub 2018 Mar 12. PMID: 29531161.

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