Publications for Xinghua Lu, MD, PhD, MS
2020

Yifeng Tao, Shuangxia Ren, Michael Q. Ding, Russell Schwartz, Xinghua Lu. Predicting Drug Sensitivity of Cancer Cells Lines via Collaborative Filtering with Contextual Attention. Proceedings of Machine Learning Research. 2020. 1-A7

Ruan H, Li X, Xu X, Leibowitz BJ, Tong J, Chen L, Ao l, Xing W, Luo J, Yu Y, Schoen RE, Sonenberg N, Lu X, Zhang L, Yu J. elF4E S209 phosphorylation licenses Myc- and stress-driven oncogenesis. Elife. 2020 Nov 2;e60151. Doi: 10.7554/eLife.60151. PMID: 33135632

Song X, Zhou Z, Li H, Xue Y, Lu X, Bahar I, Kepp O, Hung M-C, Kromer G, Wan Y. Pharmacologic Suppression of B7-H4 Glycosylation Restores Antitumor Immunity in Immune-Cold Breast Cancers. Cancer Discovery December 2020. doi:10.1158/2159-8290.CD-20-0402

2019
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.

2018
Ding MQ, Chen L, Cooper GF, Young JD, Lu X. Precision Oncology Beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics. Mol Cancer Res. 2018 Feb;16(2):269-278. doi: 10.1158/1541-7786.MCR-17-0378. Epub 2017 Nov 13. PMID: 29133589. PMCID: PMC5821274.

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. Cancer Res. 2018 Jun 1;78(11):3002-3013. doi: 10.1158/0008-5472.CAN-17-2433. Epub 2018 Mar 12. PMID: 29531161.
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.
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.

Jin Q, Dhingra B, Cohen WW, Lu X. Attention MeSH: Simple, Effective and Interpretable Automatic MeSH Indexer.

2017
Yan G, Chen V, Lu X, Lu S. A signal-based method for finding driver modules of breast cancer metastasis to the lung. Sci Rep. 2017 Aug 30; 7(1):10023. doi: 10.1038/s41598-09951-2. PMID: 28855549. PMC ID: PMC5577160.

Huang T, Kim CK, Alvarez AA, Pangeni RP, Wan X, Song X, Shi T, Yang Y, Sastry N, Horbinski CM, Lu S, Stupp R, Kessler JA, Nishikawa R, Nakano I, Sulman EP, Lu X, James CD, Yin XM, Hu B, Cheng SY. MST4 Phosphorylation of ATG4B Regulates Autophagic Activity, Tumorigenicity, and Radioresistance in Glioblastoma. Cancer Cell. 2017 Dec 11; 32(6):840-855.e8. doi: 10.1016/j.ccell.2017.11.005. PMID: 29232556.

Young JD, Cai C, Lu X. Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma. BMC Bioinformatics. 2017 Oct 3;18(Suppl 11): 381. doi: 10.1186/s12859-017-1798-2. PMID: 28984190. PMCID: PMC5629551.

Chen V, Paisley J, Lu X. Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling. BMC Genomics. 2017 Mar 14;18 (Suppl 2):105. doi: 10.1186/s12864-017-3494-z. PMID: 28361690. PMC ID: PMC5374647.

Cooper G, Cai C, Lu X. Tumor-specific Causal Inference (TCI): A Bayesian Method for Identifying Causative Genome Alterations within Individual Tumors. bioRxiv (2017). Doi: https://doi.org/10.1101/225631.

2016
Lu S, Mandava G, Yan G, and Lu X. An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem. Algorithms Mol Biol. 2016 May 4;11:11. doi: 10.1186/s13015-016-0073-9. PMID: 27148394. PMCID: PMC4855522.

Chen, L., Cai, C., Chen, V., and Lu, X (2015) Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model. BMC Bioinformatics Suppl 1:9. doi: 10.1186/s12859-015-0852-1. PMID: 26818848 PMCID: PMC4895523
Lu S, Cai C, Yan G, Zhou Z, Wan Y, Chen V, Chen L, Cooper GF, Obeid LM, Hannun YA, Lee AV, Lu X. Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations. Cancer Res. 206 Dec 1:76(23):6785-6794. doi: 10.1158/0008-5472.CAN-16-1740. Epub 2016 Oct 10. PMID: 27758891. PMCID: PMC5165695.

Huang T, Alvarez AA, Pangeni RP, Horbinski CM, Lu S, Kim SH, James CD, J Raizer J, A Kessler J, Brenann CW, Sulman EP, Finocchiaro G, Tan M, Nishikawa R, Lu X, Nakano I, Hu B, Cheng SY. A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways. Nat Commun. 2016 Oct 4;7:12885. doi: 10.1038/ncomms12885. PMID: 27698350. PMCID: PMC5059456.

2015
Cooper GF, Bahar I, Becich MJ, Benos PV, Berg J, Espino JU, Jacobson RC, Kienholz M, Lee AV, Lu X, Scheines R, Center for Causal Discovery team. The Center for causal discovery of biomedical knowledge from Big Data. J Am Med Inform Assoc. 2015 Nov;22(6): 1132-6. doi: 10.1093/jamia/ocv059. Epub 2015 Jul 2. PMID: 26138794. PMCID: PMC5009908.

Lu S, Lu KN, Cheng SY, Hu B, Ma X, Nystrom N, Lu X. Identifying driver genomic alterations in cancers by searching minimum-weight, mutually exclusive sets. PLoS Comput Biol. 2015 Aug 28; 11(8):e1004257. doi: 10.1371/journal.pcbi.1004257. eCollection 2015 Aug. PMID:26317392. PMCID: PMC4552843.

Ogoe, HA, Visweswaran, S, Lu, X, Gopalakrishnan, V. (2015) Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. BMC Bioinformatics 16:226 (designated as a Highly Accessed paper) PMID: 26202217 PMCID: PMC4512094
2014
Cai C, Chen L, Jiang X, Lu X. Modeling Signal Transduction from Protein Phosphorylation to Gene Expression. Cancer Inform. 2014 Oct 13; 13(Suppl 1): 59-67. doi: 10.4137/CIN.S13883. eCollection 2014. PMID: 25392684. PMCID: PMC4216050.

Jiang X, Cai B, Xue D, Lu X, Cooper GF, Neapolitan RE. A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets. J Am Med Inform Assoc. 2014 Oct;21(e2):e312-9. doi: 10.1136/amiajnl-2013-002358. Epub 2014 Apr 15. PMID: 24737607. PMCID: PMC4173174.

2013
Montefusco DJ, Chen L, Matmati N, Lu S, Newcomb B, Cooper GF, Hannun YA, Lu X. Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses. Sci Signal. 2013 Oct 29;6(299): rs14. doi: 10.1126/scisignal.2004515. PMID: 24170935. PMC3974757.

Osmanbeyoglu HU, Lu KN, Oesterreich S, Day RS, Benos PV, Coronnello C, Lu X. Estrogen represses gene expression through reconfiguring chromatin structures. Nucleic Acids Res. 2013 Sep;41(17):8061-71. doi: 10.1093/nar/gkt586. Epub 2013 Jul 1. PubMed PMID: 23821662. PMCID: PMC3783169.

Lu S, Jin B, Cowart LA. Lu X. From data towards knowledge: Revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data. PLoS One. 2013 Apr 23;8(4):e61134. doi: 10.1371/journal.pone.0061134. Print 2013. PMID: 23637789. PMCID: PMC3634064.

Lu S, Lu X. Using graph models to find transcription factor modules: the hitting set problem and an exact algorithm. Algorithms Mol Biol. 2013 Jan 16;8(1):2. doi: 10.1186/1748-7188-8-2. PMID: 23324335. PMCID: PMC3622577.

2012
Lu S, Lu, X. Integrating genome and functional genomics data to reveal perturbed signaling pathways in ovarian cancers. 2012 AMIA Jt Summits Transl Sci Proc. 2012;2012:72-8. Epub 2012 Mar 19. PMID: 22779056. PMCID: PMC3392049.

Osmanbeyoglu HU, Hartmaier RJ, Oesterreich S, Lu X. Improving ChIP-seq peak-calling for functional indirect co-regulator binding by integrating multiple sources of biological information. BMC Genomics. 2012;13 Suppl 1:S1. doi: 10.1186/1471-2164-13-S1-S1. Epub 2012 Jan 17. PubMed PMID: 22369349. PMCID: PMC3439677.

2011
Feng H, Hu B, Liu KW, Li Y, Lu X, Cheng T, Yiin JJ, Lu S, Keezer S, Fenton T, Furnari FB, Hamilton RL, Vuori K, Sarkaria JN, Nagane M, Nishikawa R, Cavenee WK, Cheng SY. Activation of Rac1 by Src-dependent phosphorylation of Dock180(Y1811) mediates PDGFRα-stimulated glioma tumorigenesis in mice and humans. J Clin Invest. 2011 Dec;121(12):4670-84. doi: 10.1172/JCI58559. Epub 2011 Nov 14. PMID: 22080864. PMCID: PMC3223070.

2010
Cowart, LA., Shotwell, M., Worley, ML., Richards, AJ, Montefusco, DJ, Hannun YA, and Lu, X. (2010) Revealing a signaling role of PHS1P in yeast using integrative systems approaches. Molecular Systems Biology 6:349 PMID: 20160710(Selected for presentation at the Highlight Track of ISMB 2010 as a major advance in the field)
Richards*, AJ, Muller, B., Shotwell, M, Cowart, LA, Rohrer, B, and Lu, X (2010) Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph. Bioinformatics, supplement issue for the Proceedings for the Intelligent Systems in Molecular Biology (ISMB) 2010 (19% acceptance) PMID: 20529941
2009
Muller*, B., Richards, AJ., Jin, B., Lu, X. (2009) GOGrapher; A Python library for GO graph representation and analysis. BMC Research Notes 2:122 PMID:19583843
Kozel, FA., Johnson, KA., Grenesko,EL., Laken, SJ., Kose, S, Lu, X., Pollina, D., Ryan, A and George, MS (2009) Functional MRI detection of deception after committing a mock sabotage crime. J. Forensic Sciences, 54(1):220-31. PMID: 19067772
Jin*, B., Strasburger, A., Laken, SJ., Kozel, FA., Johnson, KA., George, MS., and Lu, X. (2009) Feature selection for fMRI-based deception detection. BMC Bioinformatics 10 (Suppl 9):S15 (Outstanding Paper Award at the AMIA Summit on Translational Bioinformatics) PMID: 19761569
2008
Jin, B*., Muller*, B., Zhai, CX, and Lu, X (2008) Multi-label literature classification based on the Gene Ontology graph. BMC Bioinformatics 9:525. PMID: 19063730
2007
Chen, Y., Zheng*, B., Robbins, DH., Lewin, DN., Mikhitarian, K, Graham, A., Rumpp, L, Glenn, T, Gillanders, WE, Cole, DJ, Lu, X, Hoffman, BJ. and Michael Mitas (2007) Accurate discrimination of pancreatic ductal adenocarcinoma and chronic focal pancreatitis using multi-marker expression data and samples obtained by minimally invasive fine needle aspiration. International Journal of Cancer, 120(7):1511. PMID: 17192896
Zheng*, B., and Lu, X. (2007) Novel metrics for evaluating the functional coherence of protein groups via protein-semantic-network. Genome Biology 8:R153 [doi:10.1186/gb-2007-8-7-r153] PMID: 17672896
2006
Cowart, L.A., Okamoto, Y., Lu, X. and Hannun, Y.A. (2006) Distinct roles for de novo versus hydrolytic pathways of sphingolipid biosynthesis in Saccharomyces cerevisiae. Biochemical J. 393(3):733. PMID: 16201964
Zheng*, B., McLean*, DC., and Lu, X. (2006) Identifying biological concepts from a protein-related corpus with a probabilistic topic model. BMC Bioinformatics 7:58. PMID: 16466569
Chen*, Y.A., Chou, C.C., Lu, X., Slate, E.H., Peck, K., Xu, W., Voit, E.O., and Almeida, J.S. A (2006) Multivariate prediction model for microarray cross-hybridization. BMC Bioinformatics 7:101 (Designated as highly accessed paper) PMID: 16509965
Lu, X., Zheng*, B., Velivelli, A. and Zhai, C (2006) Enhancing text categorization with semantic-enriched representation and training data augmentation. J Am Med Inform Assoc, 13(5):526-35. PMID: 16799127
2004
Lu, X., Zhai, C., Gopalakrishnan, V., and Buchanan, B.G. (2004) Automatic annotation of protein motif function with Gene Ontology terms. BMC Bioinformatics 5:122. PMID: 15345032
Tao, T., Zhai, C., Lu, X. and Fang, H. (2004) A study of statistical methods for predicting function of protein motifs. Applied Bioinformatics, 3:115-124. PMID: 15693737
2003
Lu, X., Ellis-Davies, G.C.R., and Levitan E.S.(2003) Calcium requirements do not delimit the releasable neuropeptide pool. Cell Calcium 33(4):267-271. PMID: 12618147
2002
Ng K, Lu X, Levitan ES. (2002) Physical mobilization of secretory vesicles facilitates neuropeptide release by nerve growth factor-differentiated PC12 cells. J Physiol (London) 542 (Pt2) 395-402. PMID: 12122140
Ng YK, Lu X, Walkins SC, Ellis-Davies GC, Levitan ES. (2002) Nerve growth factor-induced differentiation changes the cellular organization of regulated peptide release by PC12 cells. J. Neurosci. 22(10):3890-7. PMID: 12019308
2000
Laplante JM, O'rourke F, Lu, X, Fein A, Olsen A, Feinstein MB (2000) Cloning of human Ca2+ homoeostasis endoplasmic reticulum protein (CHERP): regulated expression of antisense cDNA depletes CHERP, inhibits intracellular Ca2+ mobilization and decreases cell proliferation. Biochem. J. 348:189-99. PMID: 10794731
Zhang T, Gealy R, Lu X, Takimoto K, Levitan ES. (2000) TRH regulates Kv1.5 gene expression though a Galphaq-mediated PLC-independent pathway. Mol. Cell Endocrinol. 25;165(1-2):33-39. PMID: 10940481
1999
Signore A, O’Rourke F, Lu X, Feinstein, Yeh H. (1999) Immunohistochemical localization of the InsP4 Receptor GTPase-Activating Protein GAP1IP4BP in the rat Brain. J. Neurosci. Res. 55:321-328. PMID: 10348663
1998
Lu X, Fein A, Feinstein MB, O’Rourke FA. (1999) Antisense knock out of the Inositol 1,3,4,5-tetrakisphosphate receptor GAP1IP4BP in the human erythroleukemia cell line leads to the appearance of intermediate conductance K(Ca) channels that hyperpolarize the membrane and enhance calcium influx. J. Gen. Physiol. 113:81-9