Welcome to the Dr. Lin Xu Lab.
The lab focuses on developing bioinformatics algorithms and deep learning models to identify new disease genes and therapeutic targets for human diseases, as well as development and maintenance of data management system for genomic and clinical databases. The lab’s research works have been published in a series of high-impact journals, including Nature, Elife, PNAS, Genes & Development, Cell Reports, Nature Communications, Science Immunology, Cancer Research, Nature Machine Intelligence, Circulation Research, Clinical Cancer Research and Developmental Cell, and has received grant supports from a variety of funding resources, including the National Cancer Institute (NCI), National Heart, Lung, and Blood Institute (NHLBI), National Human Genome Research Institute (NHGRI), Cancer Prevention and Research Institute of Texas (CPRIT), Hyundai Pediatric Cancer Foundation, Children’s Cancer Fund, Rally Foundation, Dysimmune Diseases Foundation and Andrew McDonough B+ Foundation.
Develop NGS-based analysis algorithms and conduct integrated genomics analysis to uncover the molecular mechanisms of human diseases
Develop statistics and deep learning algorithms to build novel predictive models on drug response, clinical outcomes and other biological features for various human diseases
Develop statistical algorithms and conduct integrated genomics analysis to identify new biomarkers and therapeutic targets for human cancer
Develop statistical algorithms and conduct integrated genomics analysis to identify new biomarkers and therapeutic targets in a variety of non-cancer human diseases
Lu Z, Xiao X, Zheng Q, Wang X*, Lin Xu* (Corresponding Author). (2024) Assessing next-generation sequencing-based computational methods for predicting transcriptional regulators with query gene sets. Briefings in Bioinformatics. 2024 Jul 25;25(5):bbae366. (impact factor 13.9)
Jiang X. …Lin Xu*, Guanghua Xiao*, Qiwei Li* (Corresponding Author). (2024) iIMPACT: integrating image and molecular profiles for spatial transcriptomics analysis. Genome Biology 25 (1), 1-25 (impact factor 12.3)
Venkateswaran N, et al. (2024) Tryptophan fuels MYC-dependent liver tumorigenesis through indole 3-pyruvate synthesis. Nature Communications. 15(1):4266. doi: 10.1038/s41467-024-47868-3.
Lin CC. et al. (2024) PRMT5 is an actionable therapeutic target in CDK4/6 inhibitor-resistant ER+/RB-deficient breast cancer. Nature Communications 15 (1), 2287
Eglenen-Polat B. et al. (2024) A telomere-targeting drug depletes cancer initiating cells and promotes anti-tumor immunity in small cell lung cancer. Nature Communications 15 (1), 672
Tiburcio PDB, …Lin Xu*, Chen KS * (Corresponding Author). (2024) DROSHA Regulates Mesenchymal Gene Expression in Wilms Tumor. Xu L, Chen KS. Molecular Cancer Research 2024 Aug 2;22(8):711-720. (impact factor 6.3)
Vishlaghi N, et al. (2024) Vegfc-expressing cells form heterotopic bone after musculoskeletal injury. Cell Reports. 43(4):114049.
Gan P. et al (2024) Coactivator condensation drives cardiovascular cell lineage specification. Science Advances 10(11):eadk7160.
Hu L. et al. (2024) Kinome-wide siRNA screen identifies a DCLK2-TBK1 oncogenic signaling axis in clear cell renal cell carcinoma. Molecular Cell 84 (4), 776-790. e5
Hernandez KC. et al. (2024) CD73 contributes to the pathogenesis of fusion-negative rhabdomyosarcoma through the purinergic signaling pathway. Proceedings of the National Academy of Sciences USA 121 (4), e2315925121
Lebek S. et al. (2024) CRISPR-Cas9 base editing of pathogenic CaMKIIδ improves cardiac function in a humanized mouse model. The Journal of Clinical Investigation 134 (1)
Wei Y. et al. (2023) Dissecting embryonic and extraembryonic lineage crosstalk with stem cell co-culture. Cell 186 (26), 5859-5875. e24
He F. et al. (2023) Genomic profiling of subcutaneous patient-derived xenografts reveals immune constraints on tumor evolution in childhood solid cancer. Nature Communications 14 (1), 7600
Lin Xu* (Corresponding Author). et al. (2023) Integrated genomic analysis reveals aberrations in WNT signaling in germ cell tumors of childhood and adolescence. Nature Communications 14 (1), 2636
Rogojina A. …Peter J Houghton*, Lin Xu* (Corresponding Author). (2023) Comprehensive characterization of patient-derived xenograft models of pediatric leukemia. IScience 26 (11)
Zhu M. et al. (2023) Loss of p53 and mutational heterogeneity drives immune resistance in an autochthonous mouse lung cancer model with high tumor mutational burden. Cancer Cell 41 (10), 1731-1748. e8
Yu L. et al. (2023) Macrophage-to-endothelial cell crosstalk by the cholesterol metabolite 27HC promotes atherosclerosis in male mice. Nature Communications 14 (1), 4101
Dos Santos et al. (2023) Opposing gene regulatory programs governing myofiber development and maturation revealed at single nucleus resolution. Nature Communications 14 (1), 4333
Li Y, et al. (2023) Neutrophil metabolomics in severe COVID-19 reveal GAPDH as a suppressor of neutrophil extracellular trap formation. Nature Communications 14 (1), 2610
Lee S. et al. (2023) Genetic or therapeutic neutralization of ALK1 reduces LDL transcytosis and atherosclerosis in mice. Nature Cardiovascular Research 2 (5), 438-448.
Shah AM. et al. (2023) TWIST2-mediated chromatin remodeling promotes fusion-negative rhabdomyosarcoma. Science Advances 9 (17), eade8184
Chai AC. et al. (2023) Base editing correction of hypertrophic cardiomyopathy in human cardiomyocytes and humanized mice. Nature Medicine 29 (2), 401-411
Watson S. et al. (2023) VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis. Cell Reports 42 (1)
Lebek S. et al. (2023) Ablation of CaMKIIδ oxidation by CRISPR-Cas9 base editing as a therapy for cardiac disease. Science 379 (6628), 179-185
Nishiyama T. et al. (2022) Precise genomic editing of pathogenic mutations in RBM20 rescues dilated cardiomyopathy. Science Translational Medicine 14 (672), eade1633
Shi DD, et al. De novo pyrimidine synthesis is a targetable vulnerability in IDH mutant glioma. Cancer Cell. 2022 Aug 12; doi: 10.1016/j.ccell.2022.07.011.
Zhang Q, et al. Distinct functional properties of murine perinatal and adult adipose progenitor subpopulations. Nature Metabolism 2022 Aug 18; doi: 10.1038/s42255-022-00613-w.
Chu H, et al. (2021) Protein Phosphatase 2A Activation via ApoER2 in Trophoblasts Drives Preeclampsia in a Mouse Model of the Antiphospholipid Syndrome. Circulation Research 129 (7), 735-750.
Cui M, et al. (2021) Nrf1 promotes heart regeneration and repair by regulating proteostasis and redox balance. Nature Communications 12 (1), 1-15.
Ramirez-Martinez A, et al. (2021) Essentiality of the nuclear envelope protein Net39 for nuclear integrity, chromatin organization, and muscle growth. Nature Communications 12 (1), 1-12.
Cannavino J, et al. (2021) Regulation of cold-induced thermogenesis by the RNA binding protein FAM195A. Proceedings of the National Academy of Sciences USA 118 (23) e2104650118.
Bhargava V et al. (2020) GCNA Preserves Genome Integrity and Fertility Across Species. Developmental Cell 52 (1), 38-52. e10.
Huang L, et al. (2019) SR-B1 drives endothelial cell LDL transcytosis via DOCK4 to promote atherosclerosis. Nature 569(7757):565-569.
Li S, et al. (2019) Twist2 amplification in rhabdomyosarcoma represses myogenesis and promotes oncogenesis by redirecting MyoD DNA binding. Genes & Development 33(11-12):626-640.
Xu L, et al. (2018) Integrative Bayesian analysis identifies rhabdomyosarcoma disease genes. Cell Reports 24, 238–251.
Kendall GC, et al. (2018) PAX3-FOXO1 transgenic zebrafish models identify HES3 as a mediator of tumorigenesis. Elife 5;7. e.33800.
Xu L, et al. (2013) Dynamic epistasis for different alleles of the same gene. Proceedings of the National Academy of Sciences USA 109:10420-10425.