Author details

Full Name

Xinghua Lu

Affiliation

ORCID

Career Start Year

1999

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
36608132	Proteolytic regulation of CD73 by TRIM21 orchestrates tumor immunogenicity.	Sci Adv	2023
37686554	scGEM: Unveiling the Nested Tree-Structured Gene Co-Expressing Modules in Single Cell Transcriptome Data.		2023
37611111	Amphiregulin couples IL1RL1 regulatory T cells and cancer-associated fibroblasts to impede antitumor immunity.		2023
37568673	Revealing the Impact of Genomic Alterations on Cancer Cell Signaling with an Interpretable Deep Learning Model.		2023
37503199	An interpretable deep learning framework for genome-informed precision oncology.	bioRxiv	2023
36993280	Accurate estimation of rare cell type fractions from tissue omics data via hierarchical deconvolution.		2023
36778401	FAK loss reduces BRAFV600E-induced ERK phosphorylation to promote intestinal stemness and cecal tumor formation.		2023
36230748	A Novel Bayesian Framework Infers Driver Activation States and Reveals Pathway-Oriented Molecular Subtypes in Head and Neck Cancer.	Cancers (Basel)	2022
35954396	CDC20-Mediated hnRNPU Ubiquitination Regulates Chromatin Condensation and Anti-Cancer Drug Response.	Cancers (Basel)	2022
35581469	Machine learning based algorithms to impute PaO<sub>2</sub> from SpO<sub>2</sub> values and development of an online calculator.	Sci Rep	2022
35307764	Targeting Myc-driven stress vulnerability in mutant KRAS colorectal cancer.	Molecular Biomedicine	2022
34890156	De novo Prediction of Cell-Drug Sensitivities Using Deep Learning-based Graph Regularized Matrix Factorization.	Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing	2022
36548438	An individualized causal framework for learning intercellular communication networks that define microenvironments of individual tumors.	PLoS Comput Biol	2022
36243974	Interpretable deep learning for chromatin-informed inference of transcriptional programs driven by somatic alterations across cancers.	Nucleic Acids Research	2022
34228644	Chitinase-3-like 1 protein complexes modulate macrophage-mediated immune suppression in glioblastoma.	J Clin Invest	2021
34933446	GRWD1-WDR5-MLL2 Epigenetic Complex Mediates H3K4me3 Mark and Is Essential for Kaposi's Sarcoma-Associated Herpesvirus-Induced Cellular Transformation.	mBio	2021
34921143	Investigating immune and non-immune cell interactions in head and neck tumors by single-cell RNA sequencing.	Nat Commun	2021
34613772	Interferon b drives intestinal regeneration after radiation.	Science advances	2021
31797588	From genome to phenome: Predicting multiple cancer phenotypes based on somatic genomic alterations via the genomic impact transformer.	Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing	2020
33159077	Learning to encode cellular responses to systematic perturbations with deep generative models.	npj Systems Biology and Applications	2020
33135632	eIF4E S209 phosphorylation licenses myc- and stress-driven oncogenesis.	Elife	2020
32938586	Pharmacologic Suppression of B7-H4 Glycosylation Restores Antitumor Immunity in Immune-Cold Breast Cancers.	Cancer Discov	2020
32938361	Explicit representation of protein activity states significantly improves causal discovery of protein phosphorylation networks.	BMC Bioinformatics	2020
31519988	Tumour-specific Causal Inference Discovers Distinct Disease Mechanisms Underlying Cancer Subtypes.	Sci Rep	2019
31276486	Systematic discovery of the functional impact of somatic genome alterations in individual tumors through tumor-specific causal inference.	PLoS Comput Biol	2019
31046665	Integrating data and knowledge to identify functional modules of genes: a multilayer approach.	BMC Bioinformatics	2019
30759398	Phenotypic Plasticity of Invasive Edge Glioma Stem-like Cells in Response to Ionizing Radiation.	Cell Rep	2019
31669221	A novel strategy to block mitotic progression for targeted therapy.	EBioMedicine	2019
29133589	Precision Oncology beyond Targeted Therapy: Combining Omics Data with Machine Learning Matches the Majority of Cancer Cells to Effective Therapeutics.	Mol Cancer Res	2018
30598118	Discovering functional impacts of miRNAs in cancers using a causal deep learning model.	BMC Medical Genomics	2018
30208101	A novel method of using Deep Belief Networks and genetic perturbation data to search for yeast signaling pathways.	PLoS ONE	2018
29927689	Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma.	Epigenetics	2018
29531161	Activation of the Receptor Tyrosine Kinase AXL Regulates the Immune Microenvironment in Glioblastoma.	Cancer Research	2018
28984190	Unsupervised deep learning reveals prognostically relevant subtypes of glioblastoma.	BMC Bioinformatics	2017
28855549	A signal-based method for finding driver modules of breast cancer metastasis to the lung.	Scientific Reports	2017
28361690	Revealing common disease mechanisms shared by tumors of different tissues of origin through semantic representation of genomic alterations and topic modeling.	BMC Genomics	2017
29232556	MST4 Phosphorylation of ATG4B Regulates Autophagic Activity, Tumorigenicity, and Radioresistance in Glioblastoma.	Cancer Cell	2017
26818848	Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model.	BMC Bioinformatics	2016
27758891	Signal-Oriented Pathway Analyses Reveal a Signaling Complex as a Synthetic Lethal Target for p53 Mutations.	Cancer Res	2016
27698350	A regulatory circuit of miR-125b/miR-20b and Wnt signalling controls glioblastoma phenotypes through FZD6-modulated pathways.	Nat Commun	2016
27148394	An exact algorithm for finding cancer driver somatic genome alterations: the weighted mutually exclusive maximum set cover problem.	Algorithms for Molecular Biology	2016
25995230	Trans-species learning of cellular signaling systems with bimodal deep belief networks.		2015
26317392	Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets.	PLoS Comput Biol	2015
26202217	Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data.	BMC Bioinformatics	2015
26138794	The center for causal discovery of biomedical knowledge from big data.	J Am Med Inform Assoc	2015
24737607	A comparative analysis of methods for predicting clinical outcomes using high-dimensional genomic datasets.	J Am Med Inform Assoc	2014
25392684	Modeling signal transduction from protein phosphorylation to gene expression.	Cancer Informatics	2014
24170935	Distinct signaling roles of ceramide species in yeast revealed through systematic perturbation and systems biology analyses.	Sci Signal	2013
23821662	Estrogen represses gene expression through reconfiguring chromatin structures.	Nucleic Acids Res	2013
23637789	From data towards knowledge: revealing the architecture of signaling systems by unifying knowledge mining and data mining of systematic perturbation data.	PLoS ONE	2013