Clinical Sciences - QBRC

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2020

Bayesian modeling identifies PLAG1 as a key regulator of proliferation and survival in rhabdomyosarcoma cells

Zheng, Y., Xu, L., Hassan, M., Zhou, X., Zhou, Q., Rakheja, D. & Skapek, S. X., Jan 1 2020, In : Molecular Cancer Research. 18, 3, p. 364-374 11 p.

Research output: Contribution to journalArticle

Closing the gap: Contribution of surgical best practices to outcome differences between high- and low-volume centers for lung cancer resection

von Itzstein, M. S., Lu, R., Kernstine, K. H., Halm, E. A., Wang, S., Xie, Y. & Gerber, D. E., Jan 1 2020, (Accepted/In press) In : Cancer Medicine.

Research output: Contribution to journalArticle

Open Access

Diverse AR gene rearrangements mediate resistance to androgen receptor inhibitors in metastatic prostate cancer

Li, Y., Yang, R., Henzler, C. M., Ho, Y., Passow, C., Auch, B., Carreira, S., Rodrigues, D. N., Bertan, C., Hwang, T. H., Quigley, D. A., Dang, H. X., Morrissey, C., Fraser, M., Plymate, S. R., PlymateMaher, C. A., Feng, F. Y., De Bono, J. S. & Dehm, S. M., Apr 15 2020, In : Clinical Cancer Research. 26, 8, p. 1965-1976 12 p.

Research output: Contribution to journalArticle

Open Access

DNA Methylation Regulates Alternative Polyadenylation via CTCF and the Cohesin Complex

Nanavaty, V., Abrash, E. W., Hong, C., Park, S., Fink, E. E., Li, Z., Sweet, T. J., Bhasin, J. M., Singuri, S., Lee, B. H., Hwang, T. H. & Ting, A. H., May 21 2020, In : Molecular cell. 78, 4, p. 752-764.e6

Research output: Contribution to journalArticle

Does Tumor FDG-PET Avidity Represent Enhanced Glycolytic Metabolism in Non-Small Cell Lung Cancer?

Kernstine, K. H., Faubert, B., Do, Q. N., Rogers, T. J., Hensley, C. T., Cai, L., Torrealba, J., Oliver, D., Wachsmann, J. W., Lenkinski, R. E., Malloy, C. R. & Deberardinis, R. J., Apr 2020, In : Annals of Thoracic Surgery. 109, 4, p. 1019-1025 7 p.

Research output: Contribution to journalArticle

Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing

Cui, M., Wang, Z., Chen, K., Shah, A. M., Tan, W., Duan, L., Sanchez-Ortiz, E., Li, H., Xu, L., Liu, N., Bassel-Duby, R. & Olson, E. N., Apr 6 2020, In : Developmental cell. 53, 1, p. 102-116.e8

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

GCNA Preserves Genome Integrity and Fertility Across Species

Bhargava, V., Goldstein, C. D., Russell, L., Xu, L., Ahmed, M., Li, W., Casey, A., Servage, K., Kollipara, R., Picciarelli, Z., Kittler, R., Yatsenko, A., Carmell, M., Orth, K., Amatruda, J. F., Yanowitz, J. L. & Buszczak, M., Jan 6 2020, In : Developmental cell. 52, 1, p. 38-52.e10

Research output: Contribution to journalArticle

3 Scopus citations

Identification of scavenger receptor B1 as the airway microfold cell receptor for mycobacterium tuberculosis

Khan, H. S., Nair, V. R., Ruhl, C. R., Alvarez-Arguedas, S., Rendiz, J. L. G., Franco, L. H., Huang, L., Shaul, P. W., Kim, J., Xie, Y., Mitchell, R. B. & Shiloh, M. U., Mar 2020, In : eLife. 9, e52551.

Research output: Contribution to journalArticle

Open Access

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

Lack of Association Between Radiographic Tumor Burden and Efficacy of Immune Checkpoint Inhibitors in Advanced Lung Cancer

Popat, V., Lu, R., Ahmed, M., Park, J. Y., Xie, Y. & Gerber, D. E., Jan 1 2020, (Accepted/In press) In : Oncologist.

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

Late-Onset Immunotherapy Toxicity and Delayed Autoantibody Changes: Checkpoint Inhibitor–Induced Raynaud's-Like Phenomenon

Khan, S., von Itzstein, M. S., Lu, R., Bermas, B. L., Karp, D. R., Khan, S. A., Fattah, F. J., Park, J. Y., Saltarski, J. M., Gloria-McCutchen, Y., Xie, Y., Li, Q. Z., Wakeland, E. K. & Gerber, D. E., May 1 2020, In : Oncologist. 25, 5, p. e753-e757

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

Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes

Lu, T., Wang, S., Xu, L., Zhou, Q., Singla, N., Gao, J., Manna, S., Pop, L., Xie, Z., Chen, M., Luke, J. J., Brugarolas, J., Hannan, R. & Wang, T., Feb 21 2020, In : Science Immunology. 5, 44

Research output: Contribution to journalArticle

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

Aryl Sulfonamides Degrade RBM39 and RBM23 by Recruitment to CRL4-DCAF15

Ting, T. C., Goralski, M., Klein, K., Wang, B., Kim, J., Xie, Y. & Nijhawan, D., Nov 5 2019, In : Cell Reports. 29, 6, p. 1499-1510.e6

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

Assessment of circularized E7 RNA, GLUT1, and PD-L1 in anal squamous cell carcinoma

Chamseddin, B. H., Lee, E. E., Kim, J., Zhan, X., Yang, R., Murphy, K. M., Lewis, C., Hosler, G. A., Hammer, S. T. & Wang, R. C., Oct 1 2019, In : Oncotarget. 10, 57, p. 5958-5969 12 p.

Research output: Contribution to journalArticle

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

AstraZeneca-Sanger Drug Combination DREAM Consortium, Dec 1 2019, In : Nature communications. 10, 1, 2674.

Research output: Contribution to journalArticle

Open Access
18 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

DEFOR: Depth- and frequency-based somatic copy number alteration detector

Zhang, H., Zhan, X., Brugarolas, J. & Xie, Y., Oct 1 2019, In : Bioinformatics. 35, 19, p. 3824-3825 2 p.

Research output: Contribution to journalArticle

Open Access

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

Engineering Forward Genetics into Cultured Cancer Cells for Chemical Target Identification

Povedano, J. M., Liou, J., Wei, D., Srivatsav, A., Kim, J., Xie, Y., Nijhawan, D. & McFadden, D. G., Sep 19 2019, In : Cell Chemical Biology. 26, 9, p. 1315-1321.e3

Research output: Contribution to journalArticle

1 Scopus citations

Exome Chip Meta-analysis Fine Maps Causal Variants and Elucidates the Genetic Architecture of Rare Coding Variants in Smoking and Alcohol Use

CHD Exome+ Consortium & Consortium for Genetics of Smoking Behaviour, Jun 1 2019, In : Biological Psychiatry. 85, 11, p. 946-955 10 p.

Research output: Contribution to journalArticle

8 Scopus citations

Functional Assessment of Lipoyltransferase-1 Deficiency in Cells, Mice, and Humans

Ni, M., Solmonson, A., Pan, C., Yang, C., Li, D., Notzon, A., Cai, L., Guevara, G., Zacharias, L. G., Faubert, B., Vu, H. S., Jiang, L., Ko, B., Morales, N. M., Pei, J., Vale, G., Rakheja, D., Grishin, N. V., McDonald, J. G., Gotway, G. K. & 3 others, McNutt, M. C., Pascual, J. M. & DeBerardinis, R. J., Apr 30 2019, In : Cell Reports. 27, 5, p. 1376-1386.e6

Research output: Contribution to journalArticle

Open Access
2 Scopus citations

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

Identification of De Novo Enhancers Activated by TGFβ to Drive Expression of CDKN2A and B in HeLa Cells

Liu, Y. T., Xu, L., Bennett, L., Hooks, J. C., Liu, J., Zhou, Q., Liem, P., Zheng, Y. & Skapek, S. X., Sep 1 2019, In : Molecular cancer research : MCR. 17, 9, p. 1854-1866 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

Identification of testicular cancer driver genes by a cross-species comparative oncology approach

Sanchez, A., Xu, L., Pierce, J. L., Lafin, J. T., Abe, D., Bagrodia, A., Frazier, A. L. & Amatruda, J. F., Jan 1 2019, In : Andrology.

Research output: Contribution to journalArticle

Identifying genes with tri-modal association with survival and tumor grade in cancer patients

Zhang, M., Wang, T., Sirianni, R., Shaul, P. W. & Xie, Y., Jan 8 2019, In : BMC Bioinformatics. 20, 1, 13.

Research output: Contribution to journalArticle

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

LMBR1L regulates lymphopoiesis through Wnt/β-catenin signaling

Choi, J. H., Zhong, X., McAlpine, W., Liao, T. C., Zhang, D., Fang, B., Russell, J., Ludwig, S., Nair-Gill, E., Zhang, Z., Wang, K. W., Misawa, T., Zhan, X., Choi, M., Wang, T., Li, X., Tang, M., Sun, Q., Yu, L., Murray, A. R. & 2 others, Moresco, E. Y. & Beutler, B., Jan 1 2019, In : Science. 364, 6440, eaau0812.

Research output: Contribution to journalArticle

3 Scopus citations

Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci

Understanding Society Scientific Group, EPIC-CVD, GSCAN, Consortium for Genetics of Smoking Behaviour, CHD Exome+ consortium, Jan 1 2019, (Accepted/In press) In : Molecular psychiatry.

Research output: Contribution to journalArticle

6 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

Mobile Device Applications for Electronic Patient Portals in Oncology

Pho, K. K., Lu, R., Gates, S., Cai, J., Xie, D., Xie, Y., Lee, S. C. & Gerber, D. E., Feb 1 2019, In : JCO clinical cancer informatics. 3, p. 1-8 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution

T2D-Genes Consortium, The MAGIC Investigators, CHD Exome+ Consortium, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, EPIC-CVD Consortium, ExomeBP Consortium, Global Lipids Genetic Consortium, GoT2D Genes Consortium, InterAct & ReproGen Consortium, Mar 1 2019, In : Nature genetics. 51, 3, p. 452-469 18 p.

Research output: Contribution to journalArticle

13 Scopus citations

PUMILIO hyperactivity drives premature aging of norad-deficient mice

Kopp, F., Elguindy, M. M., Yalvac, M. E., Zhang, H., Chen, B., Gillett, F. A., Lee, S., Sivakumar, S., Yu, H., Xie, Y., Mishra, P., Sahenk, Z. & Mendell, J. T., Feb 2019, In : eLife. 8, e42650.

Research output: Contribution to journalArticle

Open Access
10 Scopus citations

Rcrnorm: An integrated system of random-coefficient hierarchical regression models for normalizing nanostring ncounter data

Jia, G., Wang, X., Li, Q., Lu, W. E. I., Tang, X., Wistuba, I. & Xie, Y., Sep 2019, In : Annals of Applied Statistics. 13, 3, p. 1617-1647 31 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Scina: Semi-supervised analysis of single cells in silico

Zhang, Z., Luo, D., Zhong, X., Choi, J. H., Ma, Y., Wang, S., Mahrt, E., Guo, W., Stawiski, E. W., Modrusan, Z., Seshagiri, S., Kapur, P., Hon, G. C., Brugarolas, J. & Wang, T., Jul 1 2019, In : Genes. 10, 7, 531.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Somatic Mutations Increase Hepatic Clonal Fitness and Regeneration in Chronic Liver Disease

Zhu, M., Lu, T., Jia, Y., Luo, X., Gopal, P., Li, L., Odewole, M., Renteria, V., Singal, A. G., Jang, Y., Ge, K., Wang, S. C., Sorouri, M., Parekh, J. R., MacConmara, M. P., Yopp, A. C., Wang, T. & Zhu, H., Apr 18 2019, In : Cell. 177, 3, p. 608-621.e12

Research output: Contribution to journalArticle

20 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

Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus

Zhao, J., Lee, E. E., Kim, J., Yang, R., Chamseddin, B., Ni, C., Gusho, E., Xie, Y., Chiang, C. M., Buszczak, M., Zhan, X., Laimins, L. & Wang, R. C., Dec 1 2019, In : Nature communications. 10, 1, 2300.

Research output: Contribution to journalArticle

Open Access
11 Scopus citations

Twist2 amplification in rhabdomyosarcoma represses myogenesis and promotes oncogenesis by redirecting MyoD DNA binding

Li, S., Chen, K., Zhang, Y., Barnes, S. D., Jaichander, P., Zheng, Y., Hassan, M., Malladi, V. S., Skapek, S. X., Xu, L., Bassel-Duby, R., Olson, E. N. & Liu, N., Jun 1 2019, In : Genes & development. 33, 11-12, p. 626-640 15 p.

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