UT Southwestern Medical Center

Research Projects

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    Methodology development for tumor pathology image and brain image analysis

    Since 2014, my lab starts to work on developing methodology for pathology image analysis. We have collected a large amount of high-quality digital pathological data and genomic data in lung cancer. We have developed pathological image analysis pipelines for lung cancer, kidney cancer and head and neck cancer. In addition working together with investigators in Advanced Imaging Center at UTSW, my lab is actively developing statistical methods and analysis pipelines for brain imaging data, such as functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (TDI) data.

    • Yi F, Yang L, Wang S, Lei G, Huang C; Xie Y, Xiao G, Micro-vessel Prediction in H&E Stained Pathology Images using Fully Convolutional Neural Networks, BMC Bioinformatics, 2018 (Accepted)
    • Luo X, Zang X, Yang L, Huang J, Liang F, Rodriguez Canales J, Wistuba, II, Gazdar A, Xie Y, Xiao G. Comprehensive Computational Pathological Image Analysis Predicts Lung Cancer Prognosis. Journal of Thoracic Oncology. 2017, 12:3, Pages 501–509
    • Huang C, Zhang A, Xiao G. Deep Integrative Analysis for Survival Prediction. Pac Symp Biocomput. 2018;23:343-352. PMID: 29218895
    • Yi F, Huang J, Yang L, Xie Y, Xiao G. Automatic extraction of cell nuclei from H&E-stained histopathological images. J Med Imaging. 2017 Apr;4(2):027502. doi: 10.1117/1.JMI.4.2.027502. Epub 2017 Jun 21. PMID: 28653017
    • Li Q, Yi F, Wang T, Xiao G Liang F. Lung Cancer Pathological Image Analysis Using a Hidden Potts Model. Cancer Inform. 2017 Jun 5;16, PMID: 28615918
    • Tung KC, Uh J, Mao D, Xu F, Xiao G, Lu H. Alterations in resting functional connectivity due to recent motor task. NeuroImage. 2013;78:316-24. PMCID: 3672369.
    • Aslan S, Huang H, Uh J, Mishra V, Xiao G, van Osch MJ, Lu H. White matter cerebral blood flow is inversely correlated with structural and functional connectivity in the human brain. NeuroImage. 2011;56(3):1145-53. PMCID: 3085605.
    • Lu H, Yezhuvath US, Xiao G. Improving fMRI sensitivity by normalization of basal physiologic state. Human brain mapping. 2010;31(1):80-7. PMCID: 2797559.
    • Yezhuvath US, Lewis-Amezcua K, Varghese R, Xiao G, Lu H. On the assessment of cerebrovascular reactivity using hypercapnia BOLD MRI. NMR in biomedicine. 2009;22(7):779-86. PMCID: 2726998.
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    Develop statistical methods for high-dimensional data and spatial modeling

    We are developing statistical methodologies for Bayesian analysis, spatial modeling and integrative analysis of different molecular profiling datasets.

    • Lee S, Liang F, Cai L, Xiao G. A two-stage approach of gene network analysis for high-dimensional heterogeneous data. Biostatistics. 2017 Jul 18. PMID: 29036516
    • Jia B, Xu S, Xiao G, Lamba V, Liang F., Learning gene regulatory networks from next generation sequencing data. Biometrics. 2017 Mar 10. doi: 10.1111/biom.12682. [Epub ahead of print] PMID: 28294287
    • Yu D, Won S, Lim J, Xiao G, Statistical completion of a partially identified graph with applications for the estimation of gene regulatory networks, Biostatistics, 2015, First published online April 1, 2015 doi:10.1093/biostatistics/kxv013
    • Yun J, Wang T, Xiao G. Bayesian hidden Markov models to identify RNA–protein interaction sites in PAR-CLIP. Biometrics (2014) 70(2):430-440. PMCID: PMC4061157.
    • Yang J, Wang X, Kim M, Xie Y,Xiao G. Detection of candidate tumor driver genes using a fully integrated Bayesian approach. Statistics in Medicine (2013) 33(10):1784-1800. PMCID: PMC3981913.
    • Wang X, Zang M, Xiao G, Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models, Statistics in Medicine. (2012) 32(13):2292-2307. PMCID: PMC4009397.
    • Xiao G, Wang, X, and Khodursky AB. Modelling three-dimensional chromosome structure using gene expression data. Journal of American Statistician Association (2011) 106(493):61-72.
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    Develop computational algorithms and bioinformatics tools

    We are actively developing new bioinformatics tools and computational algorithms for big data, such as genome-wide RNAi screening data and next-generation sequencing data.

    • Cai L, Li Q, Du Y, Yun J, Xie Y, DeBerardinis R, Xiao G, Genomic Regression Analysis of Coordinated Expression, Nature Communications, 2017 Dec 19;8(1):2187. doi: 10.1038/s41467-017-02181-0. PMID:29259170.
    • Yu D, Lim J, Wang X, Liang F, Xiao G. Enhanced construction of gene regulatory networks using hub gene information. BMC Bioinformatics. 2017 Mar 23;18(1):186. doi: 10.1186/s12859-017-1576-1. PMID: 28335719
    • Jia G, Wang X, Xiao G. A permutation-based non-parametric analysis of CRISPR screen data. BMC Genomics. 2017 Jul 19;18(1):545. doi: 10.1186/s12864-017-3938-5. PMID: 28724352
    • Li X, Wang X, Xiao G. A comparative study of rank aggregation methods for partial and top ranked lists in genomic applications. Briefings in Bioinformatics, (In Press)
    • Wang T, Yun J, Xie Y, Xiao G. Finding RNA-Protein Interaction Sites Using HMMs. Methods Mol Biol. 2017;1552:177-184. PMID: 28224499
    • Yu D, Lim J, Wang X, Liang F, Xiao G. Enhanced construction of gene regulatory networks using hub gene information. BMC Bioinformatics. 2017 Mar 23;18(1):186. doi: 10.1186/s12859-017-1576-1. PMID: 28335719
    • Lee S, Liang F, Cai Ling, Xiao G, Integrative analysis of gene networks and their application to lung adenocarcinoma studies, Cancer Informatics, 2016 (In press).
    • Wang T, Xie Y and Xiao G. dCLIP: a computational approach for comparative CLIP-seq analyses, Genome Biology (2014) 15:R11. PMCID: PMC405496.
    • Wang T, Chen B, Kim M, Xie Y, Xiao G. A model-based approach to identify binding sites in CLIP-Seq data. PLoS One. 2014;9(4):e93248.. PMID:24714572 | PMCID:PMC3979666
    • Zhong R, Dong X, Levine B, Xie Y, Xiao G. iScreen: Image-Based High-Content RNAi Screening Analysis Tools. J Biomol Screen. 2014 Dec 29. PMID: 25548139
    • Zhong R, Kim M, White M, Yang X, Xiao G. Spatial background noise correction for high-throughput RNAi screening. Bioinformatics (2013) 29(17):2218-20. PMCID: PMC3740628.
    • Chen M, Miao Z, Wang X, Xiao G, A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies, Bioinformatics, 2013 Apr 1;29(7):862-9. Epub 2013 Feb 15. PMCID: PMC3605602
    • Allen JD, Xie Y, Chen M, Girard L, Xiao G. Comparing statistical methods for constructing large scale gene networks. PLoS One. 2012;7(1):e29348. doi: 10.1371/journal.pone.0029348. Epub 2012 Jan 17. PMID:22272232 | PMCID:PMC3260142
    • Allen JD, Wang S, Chen M, Girard L, Minna J, Xie Y, Xiao G. Probe mapping across multiple microarray platforms. Briefings in Bioinformatics (2011) Dec 23. PMCID: PMC3431719.
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    Cancer biomarkers

    Computational models can be used to predict patient outcomes.

    I am interested in developing computational models to predict patient outcomes, which will allow clinicians to tailor treatment plans for individual patients. We have developed gene expression signatures to predict patient prognosis and response to chemotherapy. Using an innovative computational and systems biology approach, we previously identified a set of 12 genes that predicts which patients are most likely to benefit from post-surgery chemotherapy (Patent #UTSD2627). Working together with investigators at both UT Southwestern Medical Center and MD Anderson Cancer Center, we are developing a Clinical Laboratory Improvement Amendments (CLIA) -certifiable medical device and designing a prospective clinical study to translate our 12-gene predictive signature to clinical use. Relative publications:

    • Tang, H., Xiao G, Behrens, C., Schiller, J., Allen, J., Chow, C. W., Suraokar, M., Corvalan, A., Mao, J., White, M. A., Wistuba, II, Minna, J. D., and Xie, Y. (2013) A 12-gene set predicts survival benefits from adjuvant chemotherapy in non-small cell lung cancer patients, Clinical Cancer Research 19, 1577-1586.
    • Xie, Y., Xiao G, Coombes, K. R., Behrens, C., Solis, L. M., Raso, G., Girard, L., Erickson, H. S., Roth, J., Heymach, J. V., Moran, C., Danenberg, K., Minna, J. D., and Wistuba, II. (2011) Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients, Clinical Cancer Research 17, 5705-5714.
    • Xiao G, Ma S, Minna J, Xie Y, Adaptive prediction model in prospective molecular-signature-based clinical studies, Clinical Cancer Research, 2014 Feb 1;20(3):531-9. PMID:24323903.
    • Luo X, Zang X, Yang L, Huang J, Liang F, Rodriguez Canales J, Wistuba II, Gazdar A, Xie Y, Xiao G, Comprehensive Computational Pathological Image Analysis Predicts Lung Cancer Prognosis, Journal of Thoracic Oncology 2017 Mar;12(3):501-509. doi: 10.1016/j.jtho.2016.10.017. Epub 2016 Nov 4.
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    Statistical application in biomedical research

    I am devoted to apply the state-of-art statistical methods in biomedical research

    Besides my research in developing statistical methodology, I am also devoted to apply the state-of-art statistical methods in biomedical research. Collaborating with top scientists at UT Southwestern Medical Center, I have co-authored more than sixty biomedical research publications, including seven publications in Nature, Science and Cell.

    • Han T, Kato M, Xie S, Wu L, Mirzaei H, Pei J, Chen M; Xie Y, Allen J; Xiao G, McKnight SL. Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies. Cell (2013) 149(4): 768-779. PMID: 22579282.
    • He C, Bassik MC, Moresi V, Sun K, Wei Y, Zou Z, Loh J, Fisher J, Sun Q, Korsmeyer S, Packer M, May H, Hill JA, Virgin HW, Gilpin C, Xiao G, Bassel-Duby, Scherer PE, Levine B, Exercise-induced Bcl-2-regulated autophagy is required for muscle glucose homeostasis, Nature (2012) 481:511-515. PMCID: 3518436.
    • Orvddahl A, Sumpter R, Xiao G, Ng A, Zou Z, Tang Y, Narimatsu M, Gilpin C, Sun Q, Roth M, Forst C, Wrana J, Zhang Y, Luby-Phelps K, Xavier R, Xie Y, Levine B. Image-Based Genome-Wide siRNA Screen Identifies Host Factors Involved in Selective Autophagy. Nature. 2011 Dec 1;480(7375):113-7. PMID: 22020285; PMCID: PMC3229641
    • He C, Wei Y, Sun K, Li B, Dong X, Zou Z, Liu Y, Kinch LN, Khan S, Sinha S, Xavier RJ, Grishin NV, Xiao G, Eskelinen EL, Scherer PE, Whistler JL, Levine B. Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism. Cell. 2013 Aug 29;154(5):1085-99. doi: 10.1016/j.cell.2013.07.035. Epub 2013 Aug 15. PMID:23954414 | PMCID:PMC4231430
    • Wei Y, Zou Z, Becker N, Anderson M, Sumpter R, Xiao G, Kinch L, Koduru P, Christudass CS, Veltri RW, Grishin NV, Peyton M, Minna J, Bhagat G, Levine B. EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance. Cell. 2013 Sep 12;154(6):1269-84. PMID:24034250 | PMCID:PMC3917713
    • Wang R, Wei Y, An Z, Zou Z, Xiao G, Bhagat G, White M, Reichelt J, Levine B, Akt-Mediated regulation of autophagy and tumorigenesis through beclin 1 phosphorylation. Science (2012) 338(6109):956-959; PMCID: PMC3507442.
    • Xue Z, Ye Q, Anson SR, Yang J, Xiao G, Kowbel D, Glass NL, Crosthwaite SK, Liu Y., Transcriptional interference by antisense RNA is required for circadian clock function. Nature. 2014 Oct 30;514(7524):650-3.