Clinical Sciences - QBRC – Research output — University of Texas Southwestern Medical Center

2021

Automatic extraction of cell nuclei using dilated convolutional network

Khatri, R. K. C., Caseria, B. J., Lou, Y., Xiao, G. & Cao, Y., 2021, In: Inverse Problems and Imaging. 15, 1, p. 27-40 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2019

Immune dysregulation in cancer patients developing immune-related adverse events

Khan, S., Khan, S., Luo, X., Fattah, F. J., Saltarski, J., Gloria-McCutchen, Y., Lu, R., Xie, Y., Li, Q., Wakeland, E. K. & Gerber, D. E., Jan 8 2019, In: British journal of cancer. 120, 1, p. 63-68 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

123 Scopus citations

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 journal › Article › peer-review

Open Access

64 Scopus citations

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 journal › Article › peer-review

Open Access

12 Scopus citations

2018

A Bayesian hierarchical model for analyzing methylated RNA immunoprecipitation sequencing data

Zhang, M., Li, Q. & Xie, Y., Sep 1 2018, In: Quantitative Biology. 6, 3, p. 275-286 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

An empirical approach leveraging tumorgrafts to dissect the tumor microenvironment in renal cell carcinoma identifies missing link to prognostic inflammatory factors

Wang, T., Lu, R., Kapur, P., Jaiswal, B. S., Hannan, R., Zhang, Z., Pedrosa, I., Luke, J. J., Zhang, H., Goldstein, L. D., Yousuf, Q., Gu, Y. F., McKenzie, T., Joyce, A., Kim, M. S., Wang, X., Luo, D., Onabolu, O., Stevens, C., Xie, Z., & 11 othersChen, M., Filatenkov, A., Torrealba, J., Luo, X., Guo, W., He, J., Stawiski, E., Modrusan, Z., Durinck, S., Seshagiri, S. & Brugarolas, J., Sep 2018, In: Cancer discovery. 8, 9, p. 1142-1155 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

113 Scopus citations

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 journal › Article › peer-review

Open Access

4 Scopus citations

Beclin-1-Dependent Autophagy Protects the Heart during Sepsis

Sun, Y., Yao, X., Zhang, Q. J., Zhu, M., Liu, Z-P., Ci, B., Xie, Y., Carlson, D. L., Rothermel, B. A., Sun, Y., Levine, B., Hill, J. A., Wolf, S. E., Minei, J. P. & Zang, Q., Nov 13 2018, In: Circulation. 138, 20, p. 2247-2262 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

256 Scopus citations

Chemistry-First Approach for Nomination of Personalized Treatment in Lung Cancer

McMillan, E. A., Ryu, M. J., Diep, C. H., Mendiratta, S., Clemenceau, J. R., Vaden, R. M., Kim, J. H., Motoyaji, T., Covington, K. R., Peyton, M., Huffman, K., Wu, X., Girard, L., Sung, Y., Chen, P. H., Mallipeddi, P. L., Lee, J. Y., Hanson, J., Voruganti, S., Yu, Y., & 20 othersPark, S., Sudderth, J., DeSevo, C., Muzny, D. M., Doddapaneni, H. V., Gazdar, A., Gibbs, R. A., Hwang, T. H., Heymach, J. V., Wistuba, I., Coombes, K. R., Williams, N. S., Wheeler, D. A., MacMillan, J. B., Deberardinis, R. J., Roth, M. G., Posner, B. A., Minna, J. D., Kim, H. S. & White, M. A., May 3 2018, In: Cell. 173, 4, p. 864-878.e29

Research output: Contribution to journal › Article › peer-review

Open Access

86 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 journal › Article › peer-review

Open Access

84 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 2018, In: Journal of Thoracic Oncology. 13, 9, p. 1338-1348 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

132 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., Oct 2018, In: Statistical Analysis and Data Mining. 11, 5, p. 203-226 24 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 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., Jul 1 2018, In: Journal of neuropathology and experimental neurology. 77, 7, p. 542-548 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

31 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 journal › Article › peer-review

Open Access

93 Scopus citations

Kub5-Hera ^RPRD1B Deficiency Promotes "BRCAness" and Vulnerability to PARP Inhibition in BRCA-proficient Breast Cancers

Motea, E. A., Fattah, F. J., Xiao, L., Girard, L., Rommel, A., Morales, J. C., Patidar, P., Zhou, Y., Porter, A., Xie, Y., Minna, J. D. & Boothman, D. A., Dec 15 2018, In: Clinical Cancer Research. 24, 24, p. 6459-6470 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Large-scale forward genetics screening identifies Trpa1 as a chemosensor for predator odor-evoked innate fear behaviors

Wang, Y., Cao, L., Lee, C. Y., Matsuo, T., Wu, K., Asher, G., Tang, L., Saitoh, T., Russell, J. L., Klewe-Nebenius, D., Wang, L., Soya, S., Hasegawa, E., Chérasse, Y., Zhou, J., Li, Y., Wang, T., Zhan, X., Miyoshi, C., Irukayama, Y., & 13 othersCao, J., Meeks, J., Gautron, L., Wang, Z., Sakurai, K., Funato, H., Sakurai, T., Yanagisawa, M., Nagase, H., Kobayakawa, R., Kobayakawa, K., Beutler, B. A. & Liu, Q., Dec 1 2018, In: Nature communications. 9, 1, 2041.

Research output: Contribution to journal › Article › peer-review

Open Access

43 Scopus citations

Loss of Dis3l2 partially phenocopies perlman syndrome in mice and results in upregulation of Igf2 in nephron progenitor cells

Hunter, R. W., Liu, Y., Manjunath, H., Acharya, A., Jones, B. T., Zhang, H., Chen, B., Ramalingam, H., Hammer, R. E., Xie, Y., Richardson, J. A., Rakheja, D., Carroll, T. J. & Mendell, J. T., Jul 1 2018, In: Genes and Development. 32, 13-14, p. 903-908 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

30 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 2018, In: Lung Cancer. 120, p. 22-26 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

18 Scopus citations

Meta-analysis approaches to combine multiple gene set enrichment studies

Lu, W., Wang, X., Zhan, X. & Gazdar, A. F., Feb 20 2018, In: Statistics in Medicine. 37, 4, p. 659-672 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 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 journal › Article › peer-review

Open Access

33 Scopus citations

Phase 1 study of ARQ 761, a β-lapachone analogue that promotes NQO1-mediated programmed cancer cell necrosis

Gerber, D. E., Beg, M. S., Fattah, F., Frankel, A. E., Fatunde, O., Arriaga, Y., Dowell, J. E., Bisen, A., Leff, R. D., Meek, C. C., Putnam, W. C., Kallem, R. R., Subramaniyan, I., Dong, Y., Bolluyt, J., Sarode, V., Luo, X., Xie, Y., Schwartz, B. & Boothman, D. A., Oct 16 2018, In: British journal of cancer. 119, 8, p. 928-936 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

57 Scopus citations

Probability of phenotypically detectable protein damage by ENU-induced mutations in the Mutagenetix database

Wang, T., Bu, C. H., Hildebrand, S., Jia, G., Siggs, O. M., Lyon, S., Pratt, D., Scott, L., Russell, J., Ludwig, S., Murray, A. R., Moresco, E. M. Y. & Beutler, B., Dec 1 2018, In: Nature communications. 9, 1, 441.

Research output: Contribution to journal › Article › peer-review

Open Access

35 Scopus citations

Proper conditional analysis in the presence of missing data: Application to large scale meta-analysis of tobacco use phenotypes

Jiang, Y., Chen, S., McGuire, D., Chen, F., Liu, M., Iacono, W. G., Hewitt, J. K., Hokanson, J. E., Krauter, K., Laakso, M., Li, K. W., Lutz, S. M., McGue, M., Pandit, A., Zajac, G. J. M., Boehnke, M., Abecasis, G. R., Vrieze, S. I., Zhan, X., Jiang, B., & 1 othersLiu, D. J., Jul 2018, In: PLoS genetics. 14, 7, e1007452.

Research output: Contribution to journal › Article › peer-review

Open Access

14 Scopus citations

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity

Turcot, V., Lu, Y., Highland, H. M., Schurmann, C., Justice, A. E., Fine, R. S., Bradfield, J. P., Esko, T., Giri, A., Graff, M., Guo, X., Hendricks, A. E., Karaderi, T., Lempradl, A., Locke, A. E., Mahajan, A., Marouli, E., Sivapalaratnam, S., Young, K. L., Alfred, T., & 380 othersFeitosa, M. F., Masca, N. G. D., Manning, A. K., Medina-Gomez, C., Mudgal, P., Ng, M. C. Y., Reiner, A. P., Vedantam, S., Willems, S. M., Winkler, T. W., Abecasis, G., Aben, K. K., Alam, D. S., Alharthi, S. E., Allison, M., Amouyel, P., Asselbergs, F. W., Auer, P. L., Balkau, B., Bang, L. E., Barroso, I., Bastarache, L., Benn, M., Bergmann, S., Bielak, L. F., Blüher, M., Boehnke, M., Boeing, H., Boerwinkle, E., Böger, C. A., Bork-Jensen, J., Bots, M. L., Bottinger, E. P., Bowden, D. W., Brandslund, I., Breen, G., Brilliant, M. H., Broer, L., Brumat, M., Burt, A. A., Butterworth, A. S., Campbell, P. T., Cappellani, S., Carey, D. J., Catamo, E., Caulfield, M. J., Chambers, J. C., Chasman, D. I., Chen, Y. D. I., Chowdhury, R., Christensen, C., Chu, A. Y., Cocca, M., Collins, F. S., Cook, J. P., Corley, J., Corominas Galbany, J., Cox, A. J., Crosslin, D. S., Cuellar-Partida, G., D'Eustacchio, A., Danesh, J., Davies, G., Bakker, P. I. W., Groot, M. C. H., Mutsert, R., Deary, I. J., Dedoussis, G., Demerath, E. W., Heijer, M., Hollander, A. I., Ruijter, H. M., Dennis, J. G., Denny, J. C., Angelantonio, E., Drenos, F., Du, M., Dubé, M. P., Dunning, A. M., Easton, D. F., Edwards, T. L., Ellinghaus, D., Ellinor, P. T., Elliott, P., Evangelou, E., Farmaki, A. E., Farooqi, I. S., Faul, J. D., Fauser, S., Feng, S., Ferrannini, E., Ferrieres, J., Florez, J. C., Ford, I., Fornage, M., Franco, O. H., Franke, A., Franks, P. W., Friedrich, N., Frikke-Schmidt, R., Galesloot, T. E., Gan, W., Gandin, I., Gasparini, P., Gibson, J., Giedraitis, V., Gjesing, A. P., Gordon-Larsen, P., Gorski, M., Grabe, H. J., Grant, S. F. A., Grarup, N., Griffiths, H. L., Grove, M. L., Gudnason, V., Gustafsson, S., Haessler, J., Hakonarson, H., Hammerschlag, A. R., Hansen, T., Harris, K. M., Harris, T. B., Hattersley, A. T., Have, C. T., Hayward, C., He, L., Heard-Costa, N. L., Heath, A. C., Heid, I. M., Helgeland, Ø., Hernesniemi, J., Hewitt, A. W., Holmen, O. L., Hovingh, G. K., Howson, J. M. M., Hu, Y., Huang, P. L., Huffman, J. E., Ikram, M. A., Ingelsson, E., Jackson, A. U., Jansson, J. H., Jarvik, G. P., Jensen, G. B., Jia, Y., Johansson, S., Jørgensen, M. E., Jørgensen, T., Jukema, J. W., Kahali, B., Kahn, R. S., Kähönen, M., Kamstrup, P. R., Kanoni, S., Kaprio, J., Karaleftheri, M., Kardia, S. L. R., Karpe, F., Kathiresan, S., Kee, F., Kiemeney, L. A., Kim, E., Kitajima, H., Komulainen, P., Kooner, J. S., Kooperberg, C., Korhonen, T., Kovacs, P., Kuivaniemi, H., Kutalik, Z., Kuulasmaa, K., Kuusisto, J., Laakso, M., Lakka, T. A., Lamparter, D., Lange, E. M., Lange, L. A., Langenberg, C., Larson, E. B., Lee, N. R., Lehtimäki, T., Lewis, C. E., Li, H., Li, J., Li-Gao, R., Lin, H., Lin, K. H., Lin, L. A., Lin, X., Lind, L., Lindström, J., Linneberg, A., Liu, C. T., Liu, D. J., Liu, Y., Lo, K. S., Lophatananon, A., Lotery, A. J., Loukola, A., Luan, JA., Lubitz, S. A., Lyytikäinen, L. P., Männistö, S., Marenne, G., Mazul, A. L., McCarthy, M. I., McKean-Cowdin, R., Medland, S. E., Meidtner, K., Milani, L., Mistry, V., Mitchell, P., Mohlke, K. L., Moilanen, L., Moitry, M., Montgomery, G. W., Mook-Kanamori, D. O., Moore, C., Mori, T. A., Morris, A. D., Morris, A. P., Müller-Nurasyid, M., Munroe, P. B., Nalls, M. A., Narisu, N., Nelson, C. P., Neville, M., Nielsen, S. F., Nikus, K., Njølstad, P. R., Nordestgaard, B. G., Nyholt, D. R., O'Connel, J. R., O'Donoghue, M. L., Olde Loohuis, L. M., Ophoff, R. A., Owen, K. R., Packard, C. J., Padmanabhan, S., Palmer, C. N. A., Palmer, N. D., Pasterkamp, G., Patel, A. P., Pattie, A., Pedersen, O., Peissig, P. L., Peloso, G. M., Pennell, C. E., Perola, M., Perry, J. A., Perry, J. R. B., Pers, T. H., Person, T. N., Peters, A., Petersen, E. R. B., Peyser, P. A., Pirie, A., Polasek, O., Polderman, T. J., Puolijoki, H., Raitakari, O. T., Rasheed, A., Rauramaa, R., Reilly, D. F., Renström, F., Rheinberger, M., Ridker, P. M., Rioux, J. D., Rivas, M. A., Roberts, D. J., Robertson, N. R., Robino, A., Rolandsson, O., Rudan, I., Ruth, K. S., Saleheen, D., Salomaa, V., Samani, N. J., Sapkota, Y., Sattar, N., Schoen, R. E., Schreiner, P. J., Schulze, M. B., Scott, R. A., Segura-Lepe, M. P., Shah, S. H., Sheu, W. H. H., Sim, X., Slater, A. J., Small, K. S., Smith, A. V., Southam, L., Spector, T. D., Speliotes, E. K., Starr, J. M., Stefansson, K., Steinthorsdottir, V., Stirrups, K. E., Strauch, K., Stringham, H. M., Stumvoll, M., Sun, L., Surendran, P., Swift, A. J., Tada, H., Tansey, K. E., Tardif, J. C., Taylor, K. D., Teumer, A., Thompson, D. J., Thorleifsson, G., Thorsteinsdottir, U., Thuesen, B. H., Tönjes, A., Tromp, G., Trompet, S., Tsafantakis, E., Tuomilehto, J., Tybjaerg-Hansen, A., Tyrer, J. P., Uher, R., Uitterlinden, A. G., Uusitupa, M., Laan, S. W., Duijn, C. M., Leeuwen, N., Van Setten, J., Vanhala, M., Varbo, A., Varga, T. V., Varma, R., Velez Edwards, D. R., Vermeulen, S. H., Veronesi, G., Vestergaard, H., Vitart, V., Vogt, T. F., Völker, U., Vuckovic, D., Wagenknecht, L. E., Walker, M., Wallentin, L., Wang, F., Wang, C. A., Wang, S., Wang, Y., Ware, E. B., Wareham, N. J., Warren, H. R., Waterworth, D. M., Wessel, J., White, H. D., Willer, C. J., Wilson, J. G., Witte, D. R., Wood, A. R., Wu, Y., Yaghootkar, H., Yao, J., Yao, P., Yerges-Armstrong, L. M., Young, R., Zhan, X., Zhan, X., Zhang, W., Zhao, J. H., Zhao, W., Zhou, W., Zondervan, K. T., Rotter, J. I., Pospisilik, J. A., Rivadeneira, F., Borecki, I. B., Deloukas, P., Frayling, T. M., Lettre, G., North, K. E., Lindgren, C. M., Hirschhorn, J. N. & Loos, R. J. F., Jan 1 2018, In: Nature genetics. 50, 1, p. 26-35 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

236 Scopus citations

The class i myosin MYO1D binds to lipid and protects against colitis

McAlpine, W., Wang, K. W., Choi, J. H., Miguel, M. S., McAlpine, S. G., Russell, J., Ludwig, S., Li, X., Tang, M., Zhan, X., Choi, M., Wang, T., Bu, C. H., Murray, A. R., Moresco, E. M. Y., Turer, E. E. & Beutler, B., Sep 2018, In: DMM Disease Models and Mechanisms. 11, 9, dmm035923.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

The Hormone FGF21 Stimulates Water Drinking in Response to Ketogenic Diet and Alcohol

Song, P., Zechner, C. P. G., Hernandez, G., Cánovas, J., Xie, Y., Sondhi, V., Wagner, M., Stadlbauer, V., Horvath, A., Leber, B., Hu, M. C., Moe, O. W., Mangelsdorf, D. J. & Kliewer, S. A., Jun 5 2018, In: Cell Metabolism. 27, 6, p. 1338-1347.e4

Research output: Contribution to journal › Article › peer-review

Open Access

67 Scopus citations

TNF-driven adaptive response mediates resistance to EGFR inhibition in lung cancer

Gong, K., Guo, G., Gerber, D. E., Gao, B., Peyton, M., Huang, C., Minna, J. D., Hatanpaa, K. J., Kernstine, K., Cai, L., Xie, Y., Zhu, H., Fattah, F. J., Zhang, S., Takahashi, M., Mukherjee, B., Burma, S., Dowell, J., Dao, K., Papadimitrakopoulou, V. A., & 4 othersOlivas, V., Bivona, T. G., Zhao, D. & Habib, A. A., Jun 1 2018, In: Journal of Clinical Investigation. 128, 6, p. 2500-2518 19 p.

Research output: Contribution to journal › Article › peer-review

Open Access

71 Scopus citations

Usage and survival implications of surgical staging of inguinal lymph nodes in intermediate- to high-risk, clinical localized penile cancer: A propensity-score matched analysis

Woldu, S. L., Ci, B., Hutchinson, R. C., Krabbe, L. M., Singla, N., Passoni, N. M., Clinton, T. N., Raj, G., Miller, D. S., Sagalowsky, A. I., Lotan, Y., Xie, Y., Margulis, V. & Bagrodia, A., Apr 2018, In: Urologic Oncology: Seminars and Original Investigations. 36, 4, p. 159.e7-159.e17

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

Usefulness of a Simple Algorithm to Identify Hypertensive Patients Who Benefit from Intensive Blood Pressure Lowering

Wang, S., Khera, R., Das, S. R., Vigen, R., Wang, T., Luo, X., Lu, R., Zhan, X., Xiao, G., Vongpatanasin, W. & Xie, Y., Jul 15 2018, In: American Journal of Cardiology. 122, 2, p. 248-254 7 p.

Research output: Contribution to journal › Article › peer-review

4 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 othersEllrott, 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., Jan 1 2017, In: Cell Systems. 5, 5, p. 485-497.e3

Research output: Contribution to journal › Article › peer-review

Open Access

15 Scopus citations

A mixed-effects model approach for the statistical analysis of vocal fold viscoelastic shear properties

Xu, C., Chan, R. W., Sun, H. & Zhan, X., Nov 2017, In: Journal of the Mechanical Behavior of Biomedical Materials. 75, p. 477-485 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

An Argonaute phosphorylation cycle promotes microRNA-mediated silencing

Golden, R. J., Chen, B., Li, T., Braun, J., Manjunath, H., Chen, X., Wu, J., Schmid, V., Chang, T. C., Kopp, F., Ramirez-Martinez, A., Tagliabracci, V. S., Chen, Z. J., Xie, Y. & Mendell, J. T., Feb 9 2017, In: Nature. 542, 7640, p. 197-202 6 p.

Research output: Contribution to journal › Article › peer-review

Open Access

180 Scopus citations

Antibiotic-Induced Depletion of Anti-inflammatory Clostridia Is Associated with the Development of Graft-versus-Host Disease in Pediatric Stem Cell Transplantation Patients

Simms-Waldrip, T. R., Sunkersett, G., Coughlin, L. A., Savani, M. R., Arana, C., Kim, J., Kim, M., Zhan, X., Greenberg, D. E., Xie, Y., Davies, S. M. & Koh, A., May 1 2017, In: Biology of Blood and Marrow Transplantation. 23, 5, p. 820-829 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

113 Scopus citations

Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15

Han, T., Goralski, M., Gaskill, N., Capota, E., Kim, J., Ting, T. C., Xie, Y., Williams, N. S. & Nijhawan, D., Apr 28 2017, In: Science. 356, 6336, eaal3755.

Research output: Contribution to journal › Article › peer-review

392 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 journal › Article › peer-review

Open Access

20 Scopus citations

A Phase I/II Study of Nab-Paclitaxel, Cisplatin, and Cetuximab With Concurrent Radiation Therapy for Locally Advanced Squamous Cell Cancer of the Head and Neck

Chun, S. G., Hughes, R., Sumer, B. D., Myers, L. L., Truelson, J. M., Khan, S. A., Ma, T. W., Xie, Y., Yordy, J. S., Cooley, S., Wu, J., Choy, H. & Nedzi, L. A., Jan 2 2017, In: Cancer Investigation. 35, 1, p. 23-31 9 p.

Research output: Contribution to journal › Article › peer-review

9 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 journal › Article › peer-review

Open Access

36 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 journal › Article › peer-review

Open Access

124 Scopus citations

Creatine maintains intestinal homeostasis and protects against colitis

Turer, E. E., McAlpine, W., Wang, K. W., Lu, T., Li, X., Tang, M., Zhan, X., Wang, T., Zhan, X., Bu, C. H., Murray, A. R. & Beutler, B. A., Feb 14 2017, In: Proceedings of the National Academy of Sciences of the United States of America. 114, 7, p. E1273-E1281

Research output: Contribution to journal › Article › peer-review

Open Access

48 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 journal › Article › peer-review

Open Access

70 Scopus citations

Genetic pleiotropy between age-related macular degeneration and 16 complex diseases and traits

International AMD Genomics Consortium (IAMDGC), Mar 27 2017, In: Genome Medicine. 9, 1, 29.

Research output: Contribution to journal › Article › peer-review

Open Access

48 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 journal › Article › peer-review

Open Access

16 Scopus citations

IgD class switching is initiated by microbiota and limited to mucosa-associated lymphoid tissue in mice

Choi, J. H., Wang, K. W., Zhang Ph.D., D-W., Zhan, X., Wang, T., Bu, C. H., Behrendt, C. L., Zeng, M., Wang, Y., Misawa, T., Li, X., Tang, M., Zhan, X., Scott, L., Hildebrand, S., Murray, A. R., Moresco, E. M. Y., Hooper, L. V. & Beutler, B. A., Feb 14 2017, In: Proceedings of the National Academy of Sciences of the United States of America. 114, 7, p. E1196-E1204

Research output: Contribution to journal › Article › peer-review

Open Access

43 Scopus citations

Inhibition of discoidin domain receptor 1 reduces collagen-mediated tumorigenicity in pancreatic ductal adenocarcinoma

Aguilera, K. Y., Huang, H., Du, W., Hagopian, M. M., Wang, Z., Hinz, S., Hwang, T. H., Wang, H., Fleming, J. B., Castrillon, D. H., Ren, X., Ding, K. & Brekken, R. A., Nov 2017, In: Molecular Cancer Therapeutics. 16, 11, p. 2473-2485 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

76 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 journal › Article › peer-review

Open Access

1 Scopus citations

Integrative gene set enrichment analysis utilizing isoform-specific expression

Li, L., Wang, X., Xiao, G. & Gazdar, A., Sep 2017, In: Genetic Epidemiology. 41, 6, p. 498-510 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Learning gene regulatory networks from next generation sequencing data

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

Research output: Contribution to journal › Article › peer-review

Open Access

19 Scopus citations

Lung cancer pathological image analysis using a hidden potts model

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

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients

Frankel, A. E., Coughlin, L. A., Kim, J., Froehlich, T. W., Xie, Y., Frenkel, E. P. & Koh, A. Y., Oct 2017, In: Neoplasia (United States). 19, 10, p. 848-855 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

447 Scopus citations

Modeling renal cell carcinoma in mice: Bap1 and Pbrm1 inactivation drive tumor grade

Gu, Y. F., Cohn, S., Christie, A., McKenzie, T., Wolff, N., Do, Q. N., Madhuranthakam, A. J., Pedrosa, I., Wang, T., Dey, A., Busslinger, M., Xie, X-J., Hammer, R. E., McKay, R. M., Kapur, P. & Brugarolas, J. B., 2017, In: Cancer discovery. 7, 8, p. 900-917 18 p.

Research output: Contribution to journal › Article › peer-review

Open Access

109 Scopus citations

Clinical Sciences - QBRC

Research output

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