• 6682 Citations
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20052020

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Article
2020
Open Access
1 Scopus citations

Integrating germline and somatic genetics to identify genes associated with lung cancer

Pattee, J., Zhan, X., Xiao, G. & Pan, W., Apr 1 2020, In : Genetic Epidemiology. 44, 3, p. 233-247 15 p.

Research output: Contribution to journalArticle

Interaction between the autophagy protein Beclin 1 and Na+,K+-ATPase during starvation, exercise, and ischemia

Fernández, Á. F., Liu, Y., Ginet, V., Shi, M., Nah, J., Zou, Z., Zhou, A., Posner, B. A., Xiao, G., Tanguy, M., Paradis, V., Sadoshima, J., Rautou, P. E., Puyal, J., Hu, M. C. & Levine, B., Jan 16 2020, In : JCI Insight. 5, 1, e133282.

Research output: Contribution to journalArticle

Open Access

Large-scale profiling of RBP-circRNA interactions from public CLIP-seq datasets

Zhang, M., Wang, T., Xiao, G. & Xie, Y., Jan 2020, In : Genes. 11, 1, 54.

Research output: Contribution to journalArticle

Open Access

TLR9 and beclin 1 crosstalk regulates muscle AMPK activation in exercise

Liu, Y., Nguyen, P. T., Wang, X., Zhao, Y., Meacham, C. E., Zou, Z., Bordieanu, B., Johanns, M., Vertommen, D., Wijshake, T., May, H., Xiao, G., Shoji-Kawata, S., Rider, M. H., Morrison, S. J., Mishra, P. & Levine, B., Feb 27 2020, In : Nature. 578, 7796, p. 605-609 5 p.

Research output: Contribution to journalArticle

2 Scopus citations

VaMPR: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning

Kim, J., Greenberg, D. E., Pifer, R., Jiang, S., Xiao, G., Shelburne, S. A., Koh, A., Xie, Y. & Zhan, X., Jan 1 2020, In : PLoS Computational Biology. 16, 1, e1007511.

Research output: Contribution to journalArticle

Open Access
2019

A Bayesian hidden Potts mixture model for analyzing lung cancer pathology images

Li, Q., Wang, X., Liang, F., Yi, F., Xie, Y., Gazdar, A. & Xiao, G., Oct 1 2019, In : Biostatistics (Oxford, England). 20, 4, p. 565-581 17 p.

Research output: Contribution to journalArticle

1 Scopus citations

A bayesian mark interaction model for analysis of tumor pathology images

Li, B. Q., Wang, X., Liang, F. & Xiao, G., Sep 2019, In : Annals of Applied Statistics. 13, 3, p. 1708-1732 25 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

A comparative study of rank aggregation methods for partial and top ranked lists in genomic applications

Li, X., Wang, X. & Xiao, G., Jan 18 2019, In : Briefings in Bioinformatics. 20, 1, p. 178-189 12 p.

Research output: Contribution to journalArticle

8 Scopus citations

ConvPath: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network

Wang, S., Wang, T., Yang, L., Yang, D. M., Fujimoto, J., Yi, F., Luo, X., Yang, Y., Yao, B., Lin, S. Y., Moran, C., Kalhor, N., Weissferdt, A., Minna, J., Xie, Y., Wistuba, I. I., Mao, Y. & Xiao, G., Dec 2019, In : EBioMedicine. 50, p. 103-110 8 p.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Development and Validation of a Nomogram Prognostic Model for Patients With Advanced Non-Small-Cell Lung Cancer

Wang, T., Lu, R., Lai, S., Schiller, J. H., Zhou, F. L., Ci, B., Wang, S., Gao, X., Yao, B., Gerber, D. E., Johnson, D. H., Xiao, G. & Xie, Y., Apr 1 2019, In : Cancer Informatics. 18

Research output: Contribution to journalArticle

Open Access

Development and Validation of a Pathology Image Analysis-based Predictive Model for Lung Adenocarcinoma Prognosis - A Multi-cohort Study

Luo, X., Yin, S., Yang, L., Fujimoto, J., Yang, Y., Moran, C., Kalhor, N., Weissferdt, A., Xie, Y., Gazdar, A., Minna, J., Wistuba, I. I., Mao, Y. & Xiao, G., Dec 1 2019, In : Scientific reports. 9, 1, 6886.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

DIGREM: An integrated web-based platform for detecting effective multi-drug combinations

Zhang, M., Lee, S., Yao, B., Xiao, G., Xu, L. & Xie, Y., May 15 2019, In : Bioinformatics. 35, 10, p. 1792-1794 3 p.

Research output: Contribution to journalArticle

GeNeCK: A web server for gene network construction and visualization

Zhang, M., Li, Q., Yu, D., Yao, B., Guo, W., Xie, Y. & Xiao, G., Jan 7 2019, In : BMC Bioinformatics. 20, 1, 12.

Research output: Contribution to journalArticle

3 Scopus citations

Histone lysine demethylase KDM4B regulates the alternative splicing of the androgen receptor in response to androgen deprivation

Duan, L., Chen, Z., Lu, J., Liang, Y., Wang, M., Roggero, C. M., Zhang, Q. J., Gao, J., Fang, Y., Cao, J., Lu, J., Zhao, H., Dang, A., Pong, R. C., Hernandez, E., Chang, C. M., Hoang, D. T., Ahn, J. M., Xiao, G., Wang, R. T. & 6 others, Yu, K. J., Kapur, P., Rizo, J., Hsieh, J. T., Luo, J. & Liu, Z. P., Dec 16 2019, In : Nucleic acids research. 47, 22, p. 11623-11636 14 p.

Research output: Contribution to journalArticle

Open Access

LCE: an open web portal to explore gene expression and clinical associations in lung cancer

Cai, L., Lin, S. Y., Girard, L., Zhou, Y., Yang, L., Ci, B., Zhou, Q., Luo, D., Yao, B., Tang, H., Allen, J., Huffman, K., Gazdar, A. F., Heymach, J., Wistuba, I., Xiao, G., Minna, J. D. & Xie, Y., Apr 4 2019, In : Oncogene. 38, 14, p. 2551-2564 14 p.

Research output: Contribution to journalArticle

5 Scopus citations

Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells

Chen, P. H., Cai, L., Huffman, K., Yang, C., Kim, J., Faubert, B., Boroughs, L., Ko, B., Sudderth, J., McMillan, E. A., Girard, L., Chen, D., Peyton, M., Shields, M. D., Yao, B., Shames, D. S., Kim, H. S., Timmons, B., Sekine, I., Britt, R. & 8 others, Weber, S., Byers, L. A., Heymach, J. V., Chen, J., White, M. A., Minna, J. D., Xiao, G. & DeBerardinis, R. J., Dec 5 2019, In : Molecular cell. 76, 5, p. 838-851.e5

Research output: Contribution to journalArticle

5 Scopus citations

Systematic analysis of gene expression in lung adenocarcinoma and squamous cell carcinoma with a case study of FAM83A and FAM83B

Cai, L., Luo, D., Yao, B., Yang, D. M., Lin, S., Girard, L., Deberardinis, R. J., Minna, J. D., Xie, Y. & Xiao, G., Jun 1 2019, In : Cancers. 11, 6, 886.

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Type and case volume of health care facility influences survival and surgery selection in cases with early-stage non–small cell lung cancer

Wang, S., Lai, S., von Itzstein, M. S., Yang, L., Yang, D. M., Zhan, X., Xiao, G., Halm, E. A., Gerber, D. E. & Xie, Y., Jan 1 2019, (Accepted/In press) In : Cancer.

Research output: Contribution to journalArticle

Validation of the 12-gene predictive signature for adjuvant chemotherapy response in lung cancer

Xie, Y., Lu, W., Wang, S., Tang, X., Tang, H., Zhou, Y., Moran, C., Behrens, C., Roth, J. A., Zhou, Q., Johnson, D. H., Swisher, S. G., Heymach, J. V., Papadimitrakopoulou, V. A., Xiao, G., Minna, J. D. & Wistuba, I. I., Jan 1 2019, In : Clinical Cancer Research. 25, 1, p. 150-157 8 p.

Research output: Contribution to journalArticle

2018

A two-stage approach of gene network analysis for high-dimensional heterogeneous data

Lee, S., Liang, F., Cai, L. & Xiao, G., Apr 1 2018, In : Biostatistics. 19, 2, p. 216-232 17 p.

Research output: Contribution to journalArticle

1 Scopus citations

Comprehensive analysis of lung cancer pathology images to discover tumor shape and boundary features that predict survival outcome

Wang, S., Chen, A., Yang, L., Cai, L., Xie, Y., Fujimoto, J., Gazdar, A. & Xiao, G., Dec 1 2018, In : Scientific Reports. 8, 1, 10393.

Research output: Contribution to journalArticle

10 Scopus citations

Development and Validation of a Nomogram Prognostic Model for SCLC Patients

Wang, S., Yang, L., Ci, B., Maclean, M., Gerber, D. E., Xiao, G. & Xie, Y., Sep 1 2018, In : Journal of Thoracic Oncology. 13, 9, p. 1338-1348 11 p.

Research output: Contribution to journalArticle

4 Scopus citations

Fused lasso regression for identifying differential correlations in brain connectome graphs

Yu, D., Lee, S. H., Lim, J., Xiao, G., Craddock, R. C. & Biswal, B. B., Jan 1 2018, (Accepted/In press) In : Statistical Analysis and Data Mining.

Research output: Contribution to journalArticle

1 Scopus citations

Genetic and epigenetic features of rapidly progressing IDH-mutant astrocytomas

Richardson, T. E., Sathe, A. A., Kanchwala, M., Jia, G., Habib, A. A., Xiao, G., Snuderl, M., Xing, C. & Hatanpaa, K. J., Jan 1 2018, In : Journal of Neuropathology and Experimental Neurology. 77, 7, p. 542-548 7 p.

Research output: Contribution to journalArticle

6 Scopus citations

Increased autophagy blocks HER2-mediated breast tumorigenesis

Vega-Rubín-De-Celis, S., Zou, Z., Fernández, Á. F., Ci, B., Kim, M., Xiao, G., Xie, Y. & Levine, B., Apr 17 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 16, p. 4176-4181 6 p.

Research output: Contribution to journalArticle

25 Scopus citations

Main bronchus location is a predictor for metastasis and prognosis in lung adenocarcinoma: A large cohort analysis

Yang, L., Wang, S., Gerber, D. E., Zhou, Y., Xu, F., Liu, J., Liang, H., Xiao, G., Zhou, Q., Gazdar, A. & Xie, Y., Jun 1 2018, In : Lung Cancer. 120, p. 22-26 5 p.

Research output: Contribution to journalArticle

3 Scopus citations

Microvessel prediction in H&E Stained Pathology Images using fully convolutional neural networks

Yi, F., Yang, L., Wang, S., Guo, L., Huang, C., Xie, Y. & Xiao, G., Feb 27 2018, In : BMC Bioinformatics. 19, 1, 64.

Research output: Contribution to journalArticle

7 Scopus citations
1 Scopus citations
2017

A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines

Gönen, M., Weir, B. A., Cowley, G. S., Vazquez, F., Guan, Y., Jaiswal, A., Karasuyama, M., Uzunangelov, V., Wang, T., Tsherniak, A., Howell, S., Marbach, D., Hoff, B., Norman, T. C., Airola, A., Bivol, A., Bunte, K., Carlin, D., Chopra, S., Deran, A. & 105 others, Ellrott, K., Gopalacharyulu, P., Graim, K., Kaski, S., Khan, S. A., Newton, Y., Ng, S., Pahikkala, T., Paull, E., Sokolov, A., Tang, H., Tang, J., Wennerberg, K., Xie, Y., Zhan, X., Zhu, F., Afsari, B., Airola, A., Aittokallio, T., Bivol, A., Boehm, J. S., Bunte, K., Carlin, D., Chang, Y. C., Chen, T., Chong, Z., Chopra, S., Cowley, G. S., Deran, A., Ellrott, K., Elmarakeby, H., Fertig, E. J., Gonçalves, E., Gönen, M., Gong, P., Gopalacharyulu, P., Graim, K., Guan, Y., Hafemeister, C., Hahn, W. C., Heath, L., Hoff, B., Howell, S., Jaiswal, A., Karasuyama, M., Kaski, S., Kędziorski, Ł., Khan, S. A., Khemka, N., King, E. K., Lauria, M., Liu, M., Machado, D., Mamitsuka, H., Marbach, D., Margolin, A. A., Xiao, G., Menden, M. P., Migacz, S., Newton, Y., Ng, S., Nie, Z., Norman, T. C., Pahikkala, T., Paull, E., Praveen, P., Priami, C., Rizzetto, S., Rocha, M., Root, D. E., Rudd, C., Rudnicki, W. R., Saez-Rodriguez, J., Sokolov, A., Song, L., Stolovitzky, G., Stuart, J. M., Sun, D., Szalai, B., Tang, H., Tang, J., Tsherniak, A., Uzunangelov, V., Vazquez, F., Wang, T., Wang, D., Weir, B. A., Wennerberg, K., Wu, L. Y., Xiao, G., Xie, Y., Ye, J., Ye, Y., Zhan, X., Zhou, W., Zhu, F., Aittokallio, T., Mamitsuka, H., Stuart, J. M., Boehm, J. S., Root, D. E., Xiao, G., Stolovitzky, G., Hahn, W. C. & Margolin, A. A., Nov 22 2017, In : Cell Systems. 5, 5, p. 485-497.e3

Research output: Contribution to journalArticle

7 Scopus citations

A permutation-based non-parametric analysis of CRISPR screen data

Jia, G., Wang, X. & Xiao, G., Jul 19 2017, In : BMC Genomics. 18, 1, 545.

Research output: Contribution to journalArticle

6 Scopus citations

Automatic extraction of cell nuclei from H&E-stained histopathological images

Yi, F., Huang, J., Yang, L., Xie, Y. & Xiao, G., Apr 1 2017, In : Journal of Medical Imaging. 4, 2, 027502.

Research output: Contribution to journalArticle

5 Scopus citations

Comprehensive Computational Pathological Image Analysis Predicts Lung Cancer Prognosis

Luo, X., Zang, X., Yang, L., Huang, J., Liang, F., Rodriguez-Canales, J., Wistuba, I. I., Gazdar, A., Xie, Y. & Xiao, G., Mar 1 2017, In : Journal of Thoracic Oncology. 12, 3, p. 501-509 9 p.

Research output: Contribution to journalArticle

30 Scopus citations

Enhanced construction of gene regulatory networks using hub gene information

Yu, D., Lim, J., Wang, X., Liang, F. & Xiao, G., Mar 23 2017, In : BMC Bioinformatics. 18, 1, 186.

Research output: Contribution to journalArticle

11 Scopus citations

Genomic regression analysis of coordinated expression

Cai, L., Li, Q., Du, Y., Yun, J., Xie, Y., Deberardinis, R. J. & Xiao, G., Dec 1 2017, In : Nature Communications. 8, 1, 2187.

Research output: Contribution to journalArticle

3 Scopus citations

Integrative analysis of gene networks and their application to lung adenocarcinoma studies

Lee, S., Liang, F., Cai, L. & Xiao, G., Feb 23 2017, In : Cancer Informatics. 16, 1176935117690778.

Research output: Contribution to journalArticle

Integrative gene set enrichment analysis utilizing isoform-specific expression

Li, L., Wang, X., Xiao, G. & Gazdar, A., 2017, (Accepted/In press) In : Genetic Epidemiology.

Research output: Contribution to journalArticle

2 Scopus citations

Learning gene regulatory networks from next generation sequencing data

Jia, B., Xu, S., Xiao, G., Lamba, V. & Liang, F., Jan 1 2017, In : Biometrics. 73, 4, p. 1221-1230 10 p.

Research output: Contribution to journalArticle

7 Scopus citations

Lung cancer pathological image analysis using a hidden potts model

Li, Q., Yi, F., Wang, T., Xiao, G. & Liang, F., Jan 1 2017, In : Cancer Informatics. 16

Research output: Contribution to journalArticle

3 Scopus citations
2016

Comparison of Ambulatory Blood Pressure Patterns in Patients With Intradialytic Hypertension and Hemodialysis Controls

Hompesch, C., Ma, T. W., Neyra, J. A., Ripley, L., Xiao, G., Inrig, J., Toto, R. & Van Buren, P. N., Apr 22 2016, (Accepted/In press) In : Kidney and Blood Pressure Research. p. 240-249 10 p.

Research output: Contribution to journalArticle

8 Scopus citations

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

The Rheumatoid Arthritis Challenge Consortium & Tang, H., Aug 23 2016, In : Nature communications. 7, 12460.

Research output: Contribution to journalArticle

41 Scopus citations

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease

Allen, G. I., Amoroso, N., Anghel, C., Balagurusamy, V., Bare, C. J., Beaton, D., Bellotti, R., Bennett, D. A., Boehme, K. L., Boutros, P. C., Caberlotto, L., Caloian, C., Campbell, F., Chaibub Neto, E., Chang, Y. C., Chen, B., Chen, C. Y., Chien, T. Y., Clark, T., Das, S. & 81 others, Davatzikos, C., Deng, J., Dillenberger, D., Dobson, R. J. B., Dong, Q., Doshi, J., Duma, D., Errico, R., Erus, G., Everett, E., Fardo, D. W., Friend, S. H., Fröhlich, H., Gan, J., St George-Hyslop, P., Ghosh, S. S., Glaab, E., Green, R. C., Guan, Y., Hong, M. Y., Huang, C., Hwang, J., Ibrahim, J., Inglese, P., Iyappan, A., Jiang, Q., Katsumata, Y., Kauwe, J. S. K., Klein, A., Kong, D., Krause, R., Lalonde, E., Lauria, M., Lee, E., Lin, X., Liu, Z., Livingstone, J., Logsdon, B. A., Lovestone, S., Ma, T. W., Malhotra, A., Mangravite, L. M., Maxwell, T. J., Merrill, E., Nagorski, J., Namasivayam, A., Narayan, M., Naz, M., Newhouse, S. J., Norman, T. C., Nurtdinov, R. N., Oyang, Y. J., Pawitan, Y., Peng, S., Peters, M. A., Piccolo, S. R., Praveen, P., Priami, C., Sabelnykova, V. Y., Senger, P., Shen, X., Simmons, A., Sotiras, A., Stolovitzky, G., Tangaro, S., Tateo, A., Tung, Y. A., Tustison, N. J., Varol, E., Vradenburg, G., Weiner, M. W., Xiao, G., Xie, L., Xie, Y., Xu, J., Yang, H., Zhan, X., Zhou, Y., Zhu, F., Zhu, H. & Zhu, S., Jun 1 2016, In : Alzheimer's and Dementia. 12, 6, p. 645-653 9 p.

Research output: Contribution to journalArticle

44 Scopus citations

Extracellular Volume Overload and Increased Vasoconstriction in Patients With Recurrent Intradialytic Hypertension

Van Buren, P. N., Zhou, Y., Neyra, J. A., Xiao, G., Vongpatanasin, W., Inrig, J. & Toto, R., Nov 11 2016, (Accepted/In press) In : Kidney and Blood Pressure Research. p. 802-814 13 p.

Research output: Contribution to journalArticle

9 Scopus citations

Loss of DAB2IP in RCC cells enhances their growth and resistance to mTOR-targeted therapies

Zhou, J., Luo, J., Wu, K., Yun, E. J., Kapur, P., Pong, R. C., Du, Y., Wang, B., Authement, C., Hernandez, E., Yang, J., Xiao, G., Cha, T. L., Wu, H. C., Wu, D., Margulis, V., Lotan, Y., Brugarolas, J. B., He, D. & Hsieh, J-T., Feb 15 2016, (Accepted/In press) In : Oncogene.

Research output: Contribution to journalArticle

13 Scopus citations

Multisite evaluations of a T2-relaxation-under-spin-tagging (TRUST) MRI technique to measure brain oxygenation

Liu, P., Dimitrov, I., Andrews, T., Crane, D. E., Dariotis, J. K., Desmond, J., Dumas, J., Gilbert, G., Kumar, A., Maclntosh, B. J., Tucholka, A., Yang, S., Xiao, G. & Lu, H., Feb 1 2016, In : Magnetic resonance in medicine. 75, 2, p. 680-687 8 p.

Research output: Contribution to journalArticle

19 Scopus citations

SHOX2 is a Potent Independent Biomarker to Predict Survival of WHO Grade II–III Diffuse Gliomas

Zhang, Y. A., Zhou, Y., Luo, X., Song, K., Ma, X., Sathe, A., Girard, L., Xiao, G. & Gazdar, A. F., Nov 1 2016, In : EBioMedicine. 13, p. 80-89 10 p.

Research output: Contribution to journalArticle

6 Scopus citations
2015

Acute effect of glucose on cerebral blood flow, blood oxygenation, and oxidative metabolism

Xu, F., Liu, P., Pascual, J. M., Xiao, G., Huang, H. & Lu, H., Feb 1 2015, In : Human Brain Mapping. 36, 2, p. 707-716 10 p.

Research output: Contribution to journalArticle

14 Scopus citations

Decreased BECN1 mRNA Expression in Human Breast Cancer is Associated With Estrogen Receptor-Negative Subtypes and Poor Prognosis

Tang, H., Sebti, S., Titone, R., Zhou, Y., Isidoro, C., Ross, T. S., Hibshoosh, H., Xiao, G., Packer, M., Xie, Y. & Levine, B., Mar 1 2015, In : EBioMedicine. 2, 3, p. 255-263 9 p.

Research output: Contribution to journalArticle

51 Scopus citations

Design and bioinformatics analysis of genome-wide CLIP experiments

Wang, T., Xiao, G., Chu, Y., Zhang, M. Q., Corey, D. R. & Xie, Y., Apr 23 2015, In : Nucleic Acids Research. 43, 11, p. 5263-5274 12 p.

Research output: Contribution to journalArticle

33 Scopus citations

DIGRE: Drug-induced genomic residual effect model for successful prediction of multidrug effects

Yang, J., Tang, H., Li, Y., Zhong, R., Wang, T., Wong, S. T. C., Xiao, G. & Xie, Y., Feb 1 2015, In : CPT: Pharmacometrics and Systems Pharmacology. 4, 2, p. 91-97 7 p.

Research output: Contribution to journalArticle

19 Scopus citations