Publications

2021

  1. Li Q, Bedi T, Lehmann CU, Xiao G, Xie Y. (2020) Evaluating short-term forecasting of COVID-19 cases among different epidemiological models under a Bayesian framework. Gigascience 10(2)

  2. Zhang L, Rong R, Li Q, Yang DM, Yao B, Luo D, Zhang X, Zhu X, Luo J, Liu Y, Yang X, Ji X, Liu Z, Xie Y, Sha Y, Li Z, Xiao G. (2020) A deep learning-based model for screening and staging pneumoconiosis. Sci Rep 11(1):2201

  3. Wijshake T, Zou Z, Chen B, Zhong L, Xiao G, Xie Y, Doench JG, Bennett L, Levine B. (2020) Tumor-suppressor function of Beclin 1 in breast cancer cells requires E-cadherin. Proc Natl Acad Sci U S A 118(5):e2020478118

  4. Dong X, Yang Y, Zou Z, Zhao Y, Ci B, Zhong L, Bhave M, Wang L, Kuo YC, Zang X, Zhong R, Aguilera ER, Richardson RB, Simonetti B, Schoggins JW, Pfeiffer JK, Yu L, Zhang X, Xie Y, Schmid SL, Xiao G, Gleeson PA, Ktistakis NT, Cullen PJ, Xavier RJ, Levine B. (2020) Sorting nexin 5 mediates virus-induced autophagy and immunity. Nature 589(7842):456-461

  5. Zhang L, Rong R, Li Q, Yang DM, Yao B, Luo D, Zhang X, Zhu X, Luo J, Liu Y, Yang X, Ji X, Liu Z, Xie Y, Sha Y, Li Z, Xiao G* (2020) 3A deep learning-based model for screening and staging pneumoconiosis. Sci Rep 11(1):2201

  6. Lu, C., Guan, J., Lu, S., Jin, Q., Rousseau, B., Lu, T., Stephens, D., Zhang, H., Zhu, J., Yang, M., et al. (2021) DNA sensing in mismatch repair-deficient tumor cells is essential for anti-tumor immunity. Cancer Cell 39 (1), 96-108

  7. Lu, T., Park, S., Zhu, J., Wang, Y., Zhan, X., Wang, X., Wang, L., Zhu, H., Wang, T. (2021) Overcoming Expressional Drop-outs in Lineage Reconstruction from Single-Cell RNA-Sequencing Data. Cell Reports 34 (1), 108589

  8. Zhang, Z., Xiong, D., Wang, X., Liu, H., Wang, T. (2021) Mapping the functional landscape of T cell receptor repertoires by single-T cell transcriptomics. Nature Methods 18 (1), 92-99

  9. Wei, Y., Wang, Y. G., Jia, Y., Li, L., Yoon, J., Zhang, S., ... & Zhu, H. (2021). Liver homeostasis is maintained by midlobular zone 2 hepatocytes. Science, 371(6532).

  10. Zhang, C., Wang, X., Chen, M., & Wang, T. (2021) A Comparison of Hypothesis Tests for Homogeneity in Meta-analysis with Focus on Rare Binary Events. Research Synthesis Methods

  11. Cai, L., Liu, H., Huang, F., Fujimoto, J., Girard, L., Chen, J., ... & Gazdar, A. F. (2021) Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. Communications Biology, 4(1), 1-13.

  12. Rong, R., Jiang, S., Xu, L., Xiao, G., Xie, Y., Liu, D.J., Li, Q., Zhan, X. (2021) MB-GAN: microbiome simulation via generative adversarial network. GigaScience 10 (2), giab005

  13. Badia, R.R., Abe, D., Wong, D., Singla, N., Savelyeva, A., Chertack, N., Woldu, S.L., Lotan, Y., Mauck, R., Ouyang, D., et al. (2021) Real-World Application of Pre-Orchiectomy miR-371a-3p Test in Testicular Germ Cell Tumor Management. The Journal of Urology 205 (1), 137-144

  14. Shaik, S., Maegawa, S., Haltom, A.R., Wang, F., Xiao, X., Dobson, T., Sharma, A., Yang, Y., Swaminathan, J., Kundra, V., et al. (2021) REST promotes ETS1-dependent vascular growth in medulloblastoma. Molecular Oncology

  15. Ramirez-Martinez, A., Zhang, Y., Chen, K., Kim, J., Cenik, B.K., McAnally, J.R., Cai, C., Shelton, J.M., Huang, J., Brennan, A., et al. (2021) The nuclear envelope protein Net39 is essential for muscle nuclear integrity and chromatin organization. Nature communications 12 (1), 1-12

  16. Pham, T.Q., Robinson, K., Xu, L., Pavlova, M.N., Skapek, S.X., Chen, E.Y. (2021) HDAC6 promotes growth, migration/invasion, and self-renewal of rhabdomyosarcoma. Oncogene 40 (3), 578-591

  17. Yin, S., Zhan, X., Yao, B., Xiao, G., Wang, X., Xie, Y. (2021) SMIXnorm: Fast and Accurate RNA-seq Data Normalization for Formalin-Fixed Paraffin-Embedded Samples. Frontiers in Genetics 12, 395

  18. Kim, J., Jiang, S., Wang, Y., Xiao, G., Xie, Y., Liu, D.J., Li, Q., Koh, A., Zhan, X. (2021) MetaPrism: A Versatile Toolkit for Joint Taxa/Gene Analysis of Metagenomic Sequencing Data. G3 Genes| Genomes| Genetics

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2020

  1. Wang S, Wang T, Yang L, Yang DM, Fujimoto J, Yi F, Luo X, Yang Y, Yao B, Lin S, Moran C, Kalhor N, Weissferdt A, Minna J, Xie Y, Wistuba II, Mao Y, Xiao G. (2020) ConvPath: A software tool for lung adenocarcinoma digital pathological image analysis aided by a convolutional neural network. EBioMedicine 50:103-110

  2. Ting TC, Goralski M, Klein K, Wang B, Kim J, Xie Y, Nijhawan D. (2020) Aryl Sulfonamides Degrade RBM39 and RBM23 by Recruitment to CRL4-DCAF15. Cell Rep 29(6):1499-1510

  3. Wang S, Yang DM, Rong R, Zhan X, Fujimoto J, Liu H, Minna J, Wistuba II, Xie Y, Xiao G. (2020) Artificial Intelligence in Lung Cancer Pathology Image Analysis. Cancers 11(11)

  4. Cai L, Luo D, Yao B, Yang DM, Lin S, Girard L, DeBerardinis RJ, Minna JD, Xie Y, Xiao G. (2020) Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of FAM83A and FAM83B. Cancers 11(6)

  5. Ci B, Yang DM, Krailo M, Xia C, Yao B, Luo D, Zhou Q, Xiao G, Xu L, Skapek SX, Murray MM, Amatruda JF, Klosterkemper L, Shaikh F, Faure-Conter C, Fresneau B, Volchenboum SL, Stoneham S, Lopes LF, Nicholson J, Frazier AL, Xie Y*. (2020) Development of a Data Model and Data Commons for Germ Cell Tumors. JCO Clin Cancer Inform 4:555-566

  6. Yin S, Wang X, Jia G, Xie Y. (2020) MIXnorm: normalizing RNA-seq data from formalin-fixed paraffin-embedded samples. Bioinformatics 36(11):3401-8

  7. Ci B, Yang DM, Cai L, Yang L, Girard L, Fujimoto J, Wistuba, II, Xie Y, Minna JD, Travis W, Xiao G. (2020) Molecular differences across invasive lung adenocarcinoma morphological subgroups. Transl Lung Cancer Res 9(4):1029-40

  8. Gerber DE, Sheffield TY, Beg MS, Williams EL, Clark VL, Xie Y, Holbein MEB, Skinner CS, Lee SJC. (2020) Experience, Perceptions, and Recommendations Concerning COVID-19-Related Clinical Research Adjustments. J Natl Compr Canc Netw 1-8

  9. Hsiehchen D, Goralski M, Kim J, Xie Y, Nijhawan D. (2020) Biomarkers for RBM39 degradation in acute myeloid leukemia. Leukemia 34(7):1924-8

  10. Khan HS, Nair VR, Ruhl CR, Alvarez-Arguedas S, Galvan Rendiz JL, Franco LH, Huang L, Shaul PW, Kim J, Xie Y, Mitchell RB, Shiloh MU. (2020) Identification of scavenger receptor B1 as the airway microfold cell receptor for Mycobacterium tuberculosis. Elife 9

  11. Khan S, von Itzstein MS, Lu R, Bermas BL, Karp DR, Khan SA, Fattah FJ, Park JY, Saltarski JM, Gloria-McCutchen Y, Xie Y, Li QZ, Wakeland EK, Gerber DE. (2020) Late-Onset Immunotherapy Toxicity and Delayed Autoantibody Changes: Checkpoint Inhibitor-Induced Raynaud's-Like Phenomenon. Oncologist 25(5):e753-e7

  12. Popat V, Lu R, Ahmed M, Park JY, Xie Y, Gerber DE. (2020) Lack of Association Between Radiographic Tumor Burden and Efficacy of Immune Checkpoint Inhibitors in Advanced Lung Cancer. Oncologist 25(6):515-22

  13. Povedano JM, Rallabandi R, Bai X, Ye X, Liou J, Chen H, Kim J, Xie Y, Posner B, Rice L, De Brabander JK, McFadden DG. (2020) A Multipronged Approach Establishes Covalent Modification of β-Tubulin as the Mode of Action of Benzamide Anti-cancer Toxins. J Med Chem 63(22):14054-66

  14. Suresh S, Chen B, Zhu J, Golden RJ, Lu C, Evers BM, Novaresi N, Smith B, Zhan X, Schmid V, Jun S, Karacz CM, Peyton M, Zhong L, Wen Z, Sathe AA, Xing C, Behrens C, Wistuba, II, Xiao G, Xie Y, Fu YX, Minna JD, Mendell JT, O'Donnell KA. (2020) eIF5B drives integrated stress response-dependent translation of PD-L1 in lung cancer. Nat Cancer 1(5):533-45

  15. von Itzstein MS, Khan S, Popat V, Lu R, Khan SA, Fattah FJ, Park JY, Bermas BL, Karp DR, Ahmed M, Saltarski JM, Gloria-McCutchen Y, Xie Y, Li QZ, Wakeland EK, Gerber DE. (2020) Statin Intolerance, Anti-HMGCR Antibodies, and Immune Checkpoint Inhibitor-Associated Myositis: A "Two-Hit" Autoimmune Toxicity or Clinical Predisposition? Oncologist 25(8):e1242-e5

  16. von Itzstein MS, Lu R, Kernstine KH, Halm EA, Wang S, Xie Y, Gerber DE. (2020) Closing the gap: Contribution of surgical best practices to outcome differences between high- and low-volume centers for lung cancer resection. Cancer Med. 2020;9(12):4137-47

  17. Fernández ÁF, Liu Y, Ginet V, Shi M, Nah J, Zou Z, Zhou A, Posner BA, Xiao G, Tanguy M, Paradis V, Sadoshima J, Rautou PE, Puyal J, Hu MC, Levine B. (2020) Interaction between the autophagy protein Beclin 1 and Na+,K+-ATPase during starvation, exercise, and ischemia. JCI Insight 16;5(1)

  18. Courtney, K.D., Ma, Y., de Leon, A.D., Christie, A., Xie, Z., Woolford, L., Singla, N., Joyce, A., Hill, H., Madhuranthakam, A.J., et al. (2020) HIF-2 complex dissociation, target inhibition, and acquired resistance with PT2385, a first-in-class HIF-2 inhibitor, in patients with clear cell renal cell carcinoma. Clinical Cancer Research 26 (4), 793-803

  19. Zhang, M., Wang, T., Xiao, G., Xie, Y. (2020) Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Genes 11 (1), 54

  20. Wang, S., Rong, R., Yang, D.M., Fujimoto, J., Yan, S., Cai, L., Yang, L., Luo, D., Behrens, C., Parra, E.R., et al. (2020) Computational staining of pathology images to study the tumor microenvironment in lung cancer. Cancer research 80 (10), 2056-2066

  21. Zhu, M., Li, L., Lu, T., Yoo, H., Zhu, J., Gopal, P., Wang, S.C., Porembka, M.R., Rich, N.E., Kagan, S., et al. (2020) Uncovering Biological Factors That Regulate Hepatocellular Carcinoma Growth Using Patient-Derived Xenograft Assays. Hepatology 72 (3), 1085-1101

  22. Lu, T., Wang, S., Xu, L., Zhou, Q., Singla, N., Gao, J., Manna, S., Pop, L., Xie, Z., Chen, M., et al. (2020) Tumor neoantigenicity assessment with CSiN score incorporates clonality and immunogenicity to predict immunotherapy outcomes. Science immunology 5 (44)

  23. Singla, N., Xie, Z., Zhang, Z., Gao, M., Yousuf, Q., Onabolu, O., McKenzie, T., Tcheuyap, V.T., Ma, Y., Choi, J., et al. (2020) Pancreatic tropism of metastatic renal cell carcinoma. JCI insight 5 (7)

  24. Lin, Y.H., Zhang, S., Zhu, M., Lu, T., Chen, K., Wen, Z., Wang, S., Xiao, G., Luo, D., Jia, Y., et al. (2020) Mice with increased numbers of polyploid hepatocytes maintain regenerative capacity but develop fewer hepatocellular carcinomas following chronic liver injury. Gastroenterology 158 (6), 1698-1712

  25. Park, S., Wang, X., Lim, J., Xiao, G., Lu, T., Wang, T. (2020) Bayesian multiple instance regression for modeling immunogenic neoantigens. Statistical methods in medical research 29 (10), 3032-3047

  26. Zhu, J., Kim, J., Xiao, X., Wang, Y., Luo, D., Jiang, S., Chen, R., Xu, L., Zhang, H., Moise, L., et al. (2020) The immune vulnerability landscape of the 2019 Novel Coronavirus, SARS-CoV-2. BioRxiv

  27. Hsiehchen, D., Hsieh, A., Samstein, R.M., Lu, T., Beg, M.S., Gerber, D.E., Wang, T., Morris, L.G., Zhu, H. (2020) DNA Repair Gene Mutations as Predictors of Immune Checkpoint Inhibitor Response beyond Tumor Mutation Burden. Cell Reports Medicine 1 (3), 100034

  28. Zhang, M., Sheffield, T., Zhan, X., Li, Q., Yang, D.M., Wang, Y., Wang, S., Xie, Y., Wang, T., Xiao, G. (2020) Spatial molecular profiling: platforms, applications and analysis tools. Briefings in Bioinformatics

  29. SoRelle, J.A., Chen, Z., Wang, J., Yue, T., Choi, J.H., Wang, K.w., Zhong, X., Hildebrand, S., Russell, J., Scott, L., et al. (2020) Dominant atopy risk mutations identified by mouse forward genetic analysis. Allergy

  30. Chung, A.S., Mettlen, M., Ganguly, D., Lu, T., Wang, T., Brekken, R.A., Hsiehchen, D., Zhu, H. (2020) Immune checkpoint inhibition is safe and effective for liver cancer prevention in a mouse model of hepatocellular carcinoma. Cancer Prevention Research 13 (11), 911-922

  31. Wang, Z., Chen, K., Jia, Y., Chuang, J.C., Sun, X., Lin, Y.H., Celen, C., Li, L., Huang, F., Liu, X., et al. (2020) Dual ARID1A/ARID1B loss leads to rapid carcinogenesis and disruptive redistribution of BAF complexes. Nature Cancer 1 (9), 909-922

  32. Reese, B., Silwal, A., Daugherity, E., Daugherity, M., Arabi, M., Daly, P., Paterson, Y., Woolford, L., Christie, A., Elias, R., et al. (2020) Complement as Prognostic Biomarker and Potential Therapeutic Target in Renal Cell Carcinoma. The Journal of Immunology 205 (11), 3218-3229

  33. Zheng, Y., Xu, L., Hassan, M., Zhou, X., Zhou, Q., Rakheja, D., Skapek, S.X. (2020) Bayesian modeling identifies PLAG1 as a key regulator of proliferation and survival in rhabdomyosarcoma cells. Molecular Cancer Research 18 (3), 364-374

  34. Bhargava, V., Goldstein, C.D., Russell, L., Xu, L., Ahmed, M., Li, W., Casey, A., Servage, K., Kollipara, R., Picciarelli, Z., et al. (2020) GCNA preserves genome integrity and fertility across species. Developmental cell 52 (1), 38-52

  35. Cui, M., Wang, Z., Chen, K., Shah, A.M., Tan, W., Duan, L., Sanchez-Ortiz, E., Li, H., Xu, L., Liu, N., et al. (2020) Dynamic transcriptional responses to injury of regenerative and non-regenerative cardiomyocytes revealed by single-nucleus RNA sequencing. Developmental cell 53 (1), 102-116

  36. Ci, B., Yang, D.M., Krailo, M., Xia, C., Yao, B., Luo, D., Zhou, Q., Xiao, G., Xu, L., Skapek, S.X., et al. (2020) Development of a Data Model and Data Commons for Germ Cell Tumors. JCO clinical cancer informatics 4, 555-566

  37. Butler, E., Schwettmann, B., Geboers, S., Hao, G., Kim, J., Nham, K., Sun, X., Laetsch, T.W., Xu, L., Williams, N.S., et al. (2020) Functional imaging of RAS pathway targeting in malignant peripheral nerve sheath tumor cells and xenografts. Pediatric Blood \& Cancer 67 (12), e28639

  38. Jiang, Y., Chen, S., Wang, X., Liu, M., Iacono, W.G., Hewitt, J.K., Hokanson, J.E., Krauter, K., Laakso, M., Li, K.W., et al. (2020) Association Analysis and Meta-Analysis of Multi-Allelic Variants for Large-Scale Sequence Data. Genes 11 (5), 586

  39. Erzurumluoglu, A.M., Liu, M., Jackson, V.E., Barnes, D.R., Datta, G., Melbourne, C.A., Young, R., Batini, C., Surendran, P., Jiang, T., et al. (2020) Meta-analysis of up to 622,409 individuals identifies 40 novel smoking behaviour associated genetic loci. Molecular psychiatry 25 (10), 2392-2409

  40. Kim, J., Greenberg, D.E., Pifer, R., Jiang, S., Xiao, G., Shelburne, S.A., Koh, A., Xie, Y., Zhan, X. (2020) VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning. PLoS computational biology 16 (1), e1007511

  41. Pattee, J., Zhan, X., Xiao, G., Pan, W. (2020) Integrating germline and somatic genetics to identify genes associated with lung cancer. Genetic epidemiology 44 (3), 233-247

  42. Lu, T., Park, S., Zhu, J., Zhan, X., Wang, X., Zhu, H., Wang, T. (2020) Overcoming genetic drop-outs in variants-based lineage tracing from single-cell RNA sequencing data. bioRxiv

  43. Jiang, S., Xiao, G., Koh, A.Y., Chen, Y., Yao, B., Li, Q., Zhan, X. (2020) HARMONIES: A Hybrid Approach for Microbiome Networks Inference via Exploiting Sparsity. Frontiers in Genetics 11, 445

  44. Ramanand, S.G., Chen, Y., Yuan, J., Daescu, K., Lambros, M.B., Houlahan, K.E., Carreira, S., Yuan, W., Baek, G., Sharp, A., et al. (2020) The landscape of RNA polymerase II--associated chromatin interactions in prostate cancer. The Journal of clinical investigation 130 (8)

  45. Yang, L., Jiang, S., Jiang, B., Liu, D.J., Zhan, X. (2020) Seqminer2: an efficient tool to query and retrieve genotypes for statistical genetics analyses from biobank scale sequence dataset. Bioinformatics 36 (19), 4951-4954

  46. Jiang, S., Zhou, Q., Zhan, X., Li, Q. (2020) BayesSMILES: Bayesian segmentation modeling for longitudinal epidemiological studies. medRxiv

  47. Yan, J., Rong, R., Xiao, G., Zhan, X. (2020) HiddenVis: a Hidden State Visualization Toolkit to Visualize and Interpret Deep Learning Models for Time Series Data. bioRxiv

  48. Hasan, R.A., Coughlin, L., Poulides, N., Zhan, X., Zia, A., Koh, A.Y. (2020) Gut Microbiota Dysbiosis and Elevated Lipopolysaccharide Serum Levels Are Associated with Venous Thromboembolism in Pediatric Patients. 136

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2019

  1. Duan L, Chen Z, Lu J, Liang Y, Wang M, Roggero CM, Zhang QJ, Gao J, Fang Y, Cao J, Lu J, Zhao H, Dang A, Pong RC, Hernandez E, Chang CM, Hoang DT, Ahn JM, Xiao G, Wang RT, Yu KJ, Kapur P, Rizo J, Hsieh JT, Luo J, Liu ZP (2019) Histone lysine demethylase KDM4B regulates the alternative splicing of the androgen receptor in response to androgen deprivation. Nucleic acids research, 47(22), pp.11623-11636.

  2. Cai, L., Luo, D., Yao, B., Yang, D.M., Lin, S., Girard, L., DeBerardinis, R.J., Minna, J.D., Xie, Y. and Xiao, G.* (2019) Systematic Analysis of Gene Expression in Lung Adenocarcinoma and Squamous Cell Carcinoma with a Case Study of FAM83A and FAM83B. Cancers, 11(6), p.886.

  3. Wang, S., Lai, S., von Itzstein, M.S., Yang, L., Yang, D.M., Zhan, X., Xiao, G., Halm, E.A., Gerber, D.E. and Xie, Y.* (2019) Type and case volume of health care facility influences survival and surgery selection in cases with early‐stage non–small cell lung cancer. Cancer, 125(23), pp.4252-4259.

  4. Zhang, M., Lee, S., Yao, B., Xiao, G., Xu, L. and Xie, Y.*, (2019) DIGREM: an integrated web-based platform for detecting effective multi-drug combinations. Bioinformatics, 35(10), pp.1792-1794.

  5. Xie, Y., Lu, W., Wang, S., Tang, X., Tang, H., Zhou, Y., Moran, C., Behrens, C., Roth, J., Johnson, D. and Swisher, S., (2017) Validation of the 12-gene predictive signature for adjuvant chemotherapy response in lung cancer. Journal of Thoracic Oncology, 12(8), p.S1544.

  6. Li, Q., Wang, X., Liang, F., Yi, F., Xie, Y., Gazdar, A. and Xiao, G.*, (2019) A Bayesian hidden Potts mixture model for analyzing lung cancer pathology images. Biostatistics, 20(4), pp.565-581.

  7. Li, X., Wang, X. and Xiao, G., (2019) A comparative study of rank aggregation methods for partial and top ranked lists in genomic applications. Briefings in bioinformatics, 20(1), pp.178-189.

  8. Luo, X., Yin, S., Yang, L., Fujimoto, J., Yang, Y., Moran, C., Kalhor, N., Weissferdt, A., Xie, Y., Gazdar, A. and Minna, J., (2019) Development and Validation of a pathology Image Analysis-based predictive Model for Lung Adenocarcinoma prognosis-A Multi-cohort study. Scientific reports, 9(1), pp.1-6.

  9. Zhao, J., Lee, E.E., Kim, J., Yang, R., Chamseddin, B., Ni, C., Gusho, E., Xie, Y., Chiang, C.M., Buszczak, M. and Zhan, X., (2019) Transforming activity of an oncoprotein-encoding circular RNA from human papillomavirus. Nature communications, 10(1), pp.1-12.

  10. Kopp, F., Elguindy, M.M., Yalvac, M.E., Zhang, H., Chen, B., Gillett, F.A., Lee, S., Sivakumar, S., Yu, H., Xie, Y. and Mishra, P., (2019) PUMILIO hyperactivity drives premature aging of Norad-deficient mice. Elife, 8, p.e42650.

  11. Ting, T.C., Goralski, M., Klein, K., Wang, B., Kim, J., Xie, Y. and Nijhawan, D., (2019) Aryl Sulfonamides Degrade RBM39 and RBM23 by Recruitment to CRL4-DCAF15. Cell reports, 29(6), pp.1499-1510.

  12. Khan, S.A., Ci, B., Xie, Y., Gerber, D.E., Beg, M.S., Sherman, S.I., Cabanillas, M.E., Busaidy, N.L., Burtness, B.A., Heilmann, A.M. and Bailey, M., (2019) Unique mutation patterns in anaplastic thyroid cancer identified by comprehensive genomic profiling. Head & neck, 41(6), pp.1928-1934.

  13. Hsiehchen, D., Watters, M.K., Lu, R., Xie, Y. and Gerber, D.E., (2019) Variation in the Assessment of Immune-Related Adverse Event Occurrence, Grade, and Timing in Patients Receiving Immune Checkpoint Inhibitors. JAMA network open, 2(9), pp.e1911519-e1911519.

  14. Khan, S., Khan, S.A., Luo, X., Fattah, F.J., Saltarski, J., Gloria-McCutchen, Y., Lu, R., Xie, Y., Li, Q., Wakeland, E. and Gerber, D.E., (2019) Immune dysregulation in cancer patients developing immune-related adverse events. British journal of cancer, 120(1), pp.63-68.

  15. Povedano, J.M., Liou, J., Wei, D., Srivatsav, A., Kim, J., Xie, Y., Nijhawan, D. and McFadden, D.G., (2019) Engineering Forward Genetics into Cultured Cancer Cells for Chemical Target Identification. Cell chemical biology, 26(9), pp.1315-1321.

  16. Chen PH, Cai L, Huffman K, Yang C, Kim J, Faubert B, Boroughs L, Ko B, Sudderth J, McMillan EA, Girard L, Chen D, Peyton M, Shields MD, Yao B, Shames DS, Kim HS, Timmons B, Sekine I, Britt R, Weber S, Byers LA, Heymach JV, Chen J, White MA, Minna JD, Xiao G, DeBerardinis RJ. (2019) Metabolic diversity in human non-small cell lung cancer cells. Molecular Cell, 76(5), pp.838-851.

  17. Wang S, Yang DM, Rong R, Zhan X, Fujimoto J, Liu H, Minna J, Wistuba II, Xie Y, Xiao G* (2019) Artificial Intelligence in Lung Cancer Pathology Image Analysis. Cancers 11 (11), 1673

  18. Wang,S, Wang,T* Yang L,et al.(2019) ConvPath: A Software Tool for Lung Adenocarcinoma Digital Pathological Image Analysis Aided by Convolutional Neural Network. EBioMedicine 50, 103-110

  19. T Wang*, Lu, R, Lai S, Schiller JH, Zhou FL,Ci,B ,Wang,S, Gao, X, Yao, B, Gerber DE, Johnson DH, Xiao G, Xie Y* (2019) Development and Validation of a Nomogram Prognostic Model for Patients With Advanced Non-Small-Cell Lung Cancer,Cancer Inform 5;18:1176935119837547. PMID: 31057324

  20. Zhang,H, Liang.F, Zhan,X, Brugarolas J, Xie, Y* (2019) DEFOR: Depth- and Frequency-Based Somatic Copy Number Alteration Detector, Biostatistics, pii: btz170. doi: 10.1093/bioinformatics/btz170.PMID: 30860569

  21. Zhang.M, Wang, T*, Sirianni R, Shaul PW, Xie, Y * (2019) Identifying genes with tri-modal association with survival and tumor grade in cancer patients., BMC Bioinformatics. 20(1):13. doi: 10.1186/s12859-018-2582-7. PMID: 30621577

  22. Cai, L, Lin, S, Girard L, Zhou, Y, Yang L, Ci, B, Zhou Q, Luo D, Yao B,Tang H, Allen J, Huffman K, Gazdar A, Heymach J, Wistuba I, Xiao G*, Minna J, Xie Y* (2019) LCE: an open web portal to explore gene expression and clinical associations in lung cancer, Oncogene 38(14):2551-2564. doi: 10.1038/s41388-018-0588-2. Epub 2018 Dec 7. PMID: 30532070

  23. Jia G, Wang X, Li Q, Lu W, Tang X, Wistuba I,Xie,Y* (2019) RCRnorm: An integrated system of random-coefficient hierarchical regression models for normalizing NanoString nCounter data from FFPE samples, Annals of Applied Statistics 13 (3), 1617-1647

  24. Zhang,M, Li Q, Yu D, Yao, B, Guo W,Xiao,G*, Xie,Y* (2019) GeNeCK: a web server for gene network construction and visualization, BMC Bioinformatics 2019 Jan 7;20(1):12. PMID: 30616521

  25. Li Q, Wang X, Liang F, Xiao,G* (2019) A Bayesian mark interaction model for analysis of tumor pathology images, Annals of Applied Statistics. 13 (3), 1708-1732

  26. Wang S, Yang D, Rong R, Zhan X, Xiao G* (2019) Pathology image analysis using segmentation deep learning algorithms, The American Journal of Pathology. 2020-09-01 PMID:31199919

  27. Ze Zhang, Danni Luo, Xue Zhong, Jin Choi, Yuanqing Ma, Elena Mahrt, Wei Guo, Eric Stawiski, Stacy Wang, Zora Modrusan, Somasekar Seshagiri, Payal Kapur, Gary Hon, James Brugarolas, Tao Wang * (2019) SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples, Genes 2019

  28. Min Zhu, Tianshi Lu, Yuemeng Jia, Xin Luo, Purva Gopal, Lin Li, Mobolaji Odewole, Veronica Renteria, Amit G. Singal, Younghoon Jang, Kai Ge, Sam C. Wang, Mahsa Sorouri, Justin R. Parekh, Malcolm P. MacConmara, Adam C. Yopp, Tao Wang*, Hao Zhu (2019) Somatic mutations increase hepatic clonal fitness and regeneration in chronic liver disease, Cell 2019.

  29. Lodhi H, Peri-Okonny P, Schesing K, Phelps K, Ngo C, Evans H, Arbique D, Price A, Vernino S, Phillips L, Mitchell J, Smith S, Yano Y, Das S, Wang T* , Vongpatanasin W (2019) Usefulness of Blood Pressure Variability Indices Derived from 24-hour Ambulatory Blood Pressure Monitoring in Detecting Autonomic Failure, Journal of the American Heart Association. 2019

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2018

  1. Jiang, S., Xiao, G., Koh, A.Y., Kim, J., Li, Q. and Zhan, X.*, (2018) A Bayesian zero-inflated negative binomial regression model for the integrative analysis of microbiome data. Biostatistics.

  2. Yang.L, Wang,S, Gerber DE, Zhou Y, Xu F, Liu J, Liang H, Xiao G*, Zhou Q, Gazdar A, Xie Y* (2018) Main bronchus location is a predictor for metastasis and prognosis in lung adenocarcinoma: A large cohort analysis., Lung Cancer Volume 120,22-26

  3. MacLean M, Luo X, Wang,S, Kernstine K, Gerber DE, Xie Y* (2018) Outcomes of neoadjuvant and adjuvant chemotherapy in stage 2 and 3 non-small cell lung cancer: an analysis of the National Cancer Database, Oncotarget 9(36):24470-24479.

  4. Wang,S, Yang L, Ci B, Maclean M, Gerber D, Xiao G*, Xie Y* (2018) Development and Validation of a Nomogram Prognostic Model for SCLC Patients, Journal of Thoracic Oncology PMID: 29902534.

  5. Wang,S, Khera R, Das SR, Vigen R, Wang T*, Luo X, Lu R, Zhan X, Xiao G*, Vongpatanasin W, Xie, Y* (2018) Usefulness of a Simple Algorithm to Identify Hypertensive Patients Who Benefit from Intensive Blood Pressure Lowering, The American Journal of Cardiology 122(2):248-254. doi: 10.1016/j.amjcard.2018.03.361. Epub 2018 Apr 11. PMID: 29880288

  6. Xie Y*, Lu W, Wang S, Tang X, Tang H, Zhou Y, Moran C, Behrens C, Roth JA, Zhou Q, Johnson DH, Swisher SG, Heymach JV, Papadimitrakopoulou VA, Xiao G*, Minna JD, Wistuba II. (2018) Validation of the 12-gene Predictive Signature for Adjuvant Chemotherapy Response in Lung Cancer, Clin Cancer Res pii: clincanres.2543.2017. doi: 10.1158/1078-0432.CCR-17-2543.PMID: 30287547

  7. Zhang M, Lee S, Yao B, Xiao G*, Xu L, Xie Y* (2018) DIGREM: an integrated web-based platform for detecting effective multi-drug combinations, Bioinformatics PMID: 30295728

  8. Qiwei Li, Xinlei Wang, Faming Liang, Faliu Yi, Xie Yang* ,Adi Gazdar, Guanghua Xiao* (2018) A Bayesian hidden Potts mixture model for analyzing lung cancer pathology images, Biostatistics. 2018 May 18. doi: 10.1093/biostatistics/kxy019

  9. Shidan, Wang, Alyssa Chen, Lin Yang, Ling Cai, Yang Xie* , Junya Fujimoto, Adi Gazdar, Guanghua Xiao* (2018) Comprehensive analysis of lung cancer pathology images to discover tumor shape and boundary features that predict survival outcome, Scientific report 2018 Jul 10;8(1):10393. doi: 10.1038/s41598-018-27707-4. PMID: 29991684

  10. Silvia Vega-Rubín-de-Celis, Zhongju Zou, Álvaro F Fernández, Bo,Ci, Min Kim, Guanghua, Xiao*, Beth Levine Yang Xie,* (2018) Increased autophagy blocks HER2-mediated breast tumorigenesis, PNAS 2018. 115 (16) 4176-4181

  11. Faliu Yi, Lin Yang, Shidan Wang, Lei Guo, Chenglong Huang, Yang Xie* , Guanghua Xiao* (2018) Microvessel prediction in H&E Stained Pathology Images using fully convolutional neural networks, BMC Bioinformatics 64 (2018)

  12. Wang T*, Lu R, Kapur P, Jaiswal BS, Hannan R, Zhang Z, Pedrosa I, Luke JJ, Zhang H, Goldstein LD, Yousuf Q, Gu YF, McKenzie T, Joyce A, Kim MS, Wang X, Luo D, Onabolu O, Stevens C, Xie Z, Chen M, Filatenkov A, Torrealba J, Luo X, Guo W, He J, Stawiski E, Modrusan Z, Durinck S, Seshagiri S, Brugarolas J. Xiao G* (2018) An Empirical Approach Leveraging Tumorgrafts to Dissect the Tumor Microenvironment in Renal Cell Carcinoma Identifies Missing Link to Prognostic Inflammatory Factors. Cancer discovery, Cancer discovery. 2018; 8(9):1142-1155.

  13. Wang Y, Cao L, Lee C, Matsuo T, Wu K, Asher G, Tang L, Saitoh T, Russell J, Klewe-Nebenius D, Wang L, Soya S, Hasegawa E, Chérasse Y, Zhou J, Li Y, Wang T*, Zhan X, Miyoshi C, Irukayama Y, Cao J, Meeks J, Gautron L, Wang Z, Sakurai K, Funato H, Sakurai T, Yanagisawa M, Nagase H, Kobayakawa R, Kobayakawa K, Beutler B, Liu Q. (2018) Large-scale forward genetics screening identifies Trpa1 as a chemosensor for predator odor-evoked innate fear behaviors, Nature Communications. 2018; 9(1)

  14. Wang T*, Bu CH, Hildebrand S, Jia G, Siggs OM, Lyon S, Pratt D, Scott L, Russell J, Ludwig S, Murray AR, Moresco EMY, Beutler B. * (2018) Probability of phenotypically detectable protein damage by ENU-induced mutations in the Mutagenetix database, Nature communications. 2018; 9(1):441.

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2017

  1. Luo, X., Zang, X., Yang, L., Huang, J., Liang, F., Rodriguez, C.J., Wistuba, II, Gazdar, A., Xie, Y., Xiao, G.* (2017) Comprehensive Computational Pathological Image Analysis Predicts Lung Cancer Prognosis, Journal of Thoracic Oncology 12:3, 501-509

  2. Lee, S., Liang, F., Cai, L., Xiao, G.* (2017) A two-stage approach of gene network analysis for high-dimensional heterogeneous data, Biostatistics (In Press)

  3. Wang, T., Yun, J., Xie, Y., Xiao, G. (2017) Finding RNA-Protein Interaction Sites Using HMMs, Methods Mol Biol 1552:177-184. PMID: 28224499

  4. Yu, D., Lim, J., Wang, X., Liang, F., Xiao, G. (2017) Enhanced construction of gene regulatory networks using hub gene information, BMC Bioinformatics 23;18(1):186. PMID: 28335719

  5. 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)

  6. Jia, G., Wang, X.*, Xiao, G*. (2017) A permutation-based non-parametric analysis of CRISPR screen data, BMC Genomics 19;18(1):545. PMID: 28724352

  7. Yi, F., Huang, J., Yang, L., Xie, Y., Xiao, G.* (2017) Automatic extraction of cell nuclei from H&E-stained histopathological images, J Med Imaging Apr;4(2):027502. PMID: 28653017

  8. 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, VS., Chen, Z.J., Xie, Y., Mendell, J.T. (2017) An Argonaute phosphorylation cycle promotes microRNA-mediated silencing, Nature

  9. Guinney, J., Wang, T., Laajala, T.D., Winner, K.K., Bare, J.C., Neto, E.C., et al, Xie, Y., Aittokallio, T., Zhou, F.L., Costello, J.C. (2017) Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data, The Lancet Oncology 18(1):132-42.

  10. Tang, H., Wang, S., Xiao, G., Schiller, J., Papadimitrakopoulou, V., Minna, J., Wistuba, I.I., Xie, Y. Comprehensive evaluation of published gene expression prognostic signatures for biomarker-based lung cancer clinical studies, Annals of Oncology (in press).

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2016

  1. Lee, S., Liang, F., Cai, Ling., Xiao, G.* (2016) Integrative analysis of gene networks and their application to lung adenocarcinoma studies, Cancer Informatics (In press).

  2. Lee, S., Kopp, F., Chang, T.C., Sataluri, A., Chen, B., Sivakumar, S., Yu, H., Xie, Y., Mendell, J.T. (2016) Noncoding RNA NORAD Regulates Genomic Stability by Sequestering PUMILIO Proteins, Cell Jan 14;164(1-2):69-80. Epub 2015 Dec 24. PMID: 26724866

  3. Chen, W., Hill, H., Christie, A., Kim, M.S., Holloman, E., et. al., Xie, Y., Xie, X.J., Kapur, P., McKay, RM., Brugarolas, J. (2016) Targeting renal cell carcinoma with a HIF-2 antagonist, Nature 539(7627):112-7.

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2015

  1. Wang, T., Xiao, G., Chu, Y., Zhang, M.Q., Corey, D.R., Xie, Y.* (2015) Design and bioinformatics analysis of genome-wide CLIP experiments, Nucleic Acids Research 43(11):5263-74. PMID: 25958398

  2. Yang, J., Tang, H., Li, Y., Zhong, R., Wang, T., Wong, S., Xiao, G., and Xie, Y.* (2015) DIGRE: Drug Induced Genomic Residual Effect Model for Successful Prediction of Multidrug Effects, CPT: Pharmacometrics & Systems Pharmacology DOI: 10.1002/psp4.1.

  3. Yu, D., Won, S., Lim, J., and Xiao, G* (2015) Statistical completion of a partially identified graph with applications for the estimation of gene regulatory networks, Biostatistics pii: kxv013. [Epub ahead of print].

  4. Zhong, R., Dong, X., Levine, B., Xie, Y., and Xiao, G.* (2015) iScreen: Image-Based High-Content RNAi Screening Analysis Tools, J Biomol Screen pii: 1087057114564348. [Epub ahead of print].

  5. Sei, E.#, Wang, T.#, Hunter, O.V., Xie, Y.*, and Conrad, N.K.* (2015) HITS-CLIP Analysis Uncovers a Link between the Kaposi's Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism, PLoS Pathogens 24;11(2):e1004652.

  6. Tang, H., Sebti, S., Titone, R., Zhou, Y., Isidoro, C., Ross, T., Hibshoosh, H., Xiao, G., Packer, M., Xie, Y.*, and Levine, B.* (2015) Decreased BECN1 mRNA Expression in Human Breast Cancer is Associated with Estrogen Receptor-Negative Subtypes and Poor Prognosis, EBioMedicine 2, 255-263.

  7. Wang, T., Zhan, X., Bu, CH., Lyon, S., Pratt, D., Hildebrand, S., Choi, J.H., Zhang, Z., Zeng, M., Wang, K.W., Turer, E., Chen, Z., Zhang, D., Yue, T., Wang, Y., Shi, H., Wang, J., Sun, L., SoRelle, J., McAlpine, W., Hutchins, N., Zhan, X., Fina, M., Gobert, R., Quan, J., Kreutzer, M., Arnett, S., Hawkins, K., Leach, A., Tate, C., Daniel, C., Reyna, C., Prince, L., Davis, S., Purrington, J., Bearden, R., Weatherly, J., White, D., Russell, J., Sun, Q., Tang, M., Li, X., Scott, L., Moresco, E.M., McInerney, G.M., Karlsson, Hedestam, G.B., Xie, Y., Beutler, B. (2015) Real-time resolution of point mutations that cause phenovariance in mice, Proc Natl Acad Sci U S A 112(5):E440-9.

  8. Zang, X., Chen, M., Zhou, Y., Xiao, G., Xie, Y.*, and Wang, X.* (2015) Meta-analysis Identification of CDKN3 Gene Expression as a Prognostic Biomarker in Lung Adenocarcinoma, Cancer Informatics (In Press)

  9. Chu, Y.#, Wang, T.#, Dodd, D., Xie, Y., Janowski, A.B. and Corey, D.R. (2015) Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells, Nucleic Acid Research DOI: 10.1093/nar/gkv213

  10. Eduati, F.#, Mangravite, L.#, Wang, T.#, Tang, H.#, Bare, C., Huang, R., Norman, T., Kellen, M., Menden, M., Yang, J., Zhan, X., Zhong, R., Xiao, G., Xia, M., the NIEHS-NATS-UNC DREAM Toxicogenetics Collaboration, Friend, S., Dearry, A., Simeonov, A., Tice, R., Rusyn, I., Wright, F., Stolovitzky, G., Xie, Y.*, and Saez-Rodriguez, J.* (2015) Opportunities and limitations in the prediction of population responses to toxic compounds assessed through a collaborative competition, Nature Biotechnology (In Press)


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2014

  1. Wang, T., Xie, Y., and Xiao, G.* (2014) dCLIP: a computational approach for comparative CLIP-seq analyses, Genome biology 15, R11.

  2. Xiao, G., Ma, S., Minna, J., and Xie, Y.* (2014) Adaptive prediction model in prospective molecular signature-based clinical studies, Clin Cancer Res 20, 531-539.

  3. Chen, B., Yun, J., Kim, M. S., Mendell, J. T., and Xie, Y.* (2014) PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis, Genome biology 15, R18.

  4. Yun, J., Wang, T., and Xiao, G. (2014) Bayesian hidden Markov models to identify RNA-protein interaction sites in PAR-CLIP, Biometrics 70, 430-440.

  5. Zhong, R., Kim, J., Kim, H. S., Kim, M., Lum, L., Levine, B., Xiao, G., White, M. A., and Xie, Y.* (2014) Computational detection and suppression of sequence-specific off-target phenotypes from whole genome RNAi screens, Nucleic acids research 42, 8214-8222.

  6. Wang, T., Chen, B., Kim, M., Xie, Y., and Xiao, G.* (2014) A model-based approach to identify binding sites in CLIP-Seq data, PloS one 9, e93248.

  7. Kwon, I., Xiang, S., Kato, M., Wu, L., Theodoropoulos, P., Wang, T., Kim, J., Yun, J., Xie, Y., and McKnight, S. L. (2014) Poly-dipeptides encoded by the C9ORF72 repeats bind nucleoli, impede RNA biogenesis, and kill cells, Science.

  8. Yang, J., Tang, H., Li, Y., Zhong, R., Wang, T., Wong, S., Xiao, G., and Xie, Y.* (2014) DIGRE: Drug Induced Genomic Residual Effect Model for Successful Prediction of Multidrug Effects, Nature CPT: Pharmacometrics & Systems Pharmacology. (In Press)

  9. Xue, Z., Ye, Q., Anson, S. R., Yang, J., Xiao, G., Kowbel, D., Glass, N. L., Crosthwaite, S. K., Liu, Y. (2014) Transcriptional interference by antisense RNA is required for circadian clock function, Nature. Oct 30;514(7524):650-3

  10. Sean Landman Tae Hyun Hwang*, Kevin Silverstein, Yingming Li, Scott Dehm, Michael Steinbach, and Vipin Kumar, SHEAR: sample heterogeneity estimation and assembly by reference, BMC Genomics. 2014 Jan 29;15(1):84.

  11. Wang, C.*, X. Zhan*, J. Bragg-Gresham, H. M. Kang, D. Stambolian, E. Y. Chew, K. E. Branham, J. Heckenlively, R. Fulton, R. K. Wilson, E. R. Mardis, X. Lin, A. Swaroop, S. Zollner, and G. R. Abecasis. 2014. "Ancestry estimation and control of population stratification for sequence-based association studies." Nat Genet. doi: 10.1038/ng.2924.

  12. Liu, D. J.*, G. M. Peloso*, X. Zhan*, O. L. Holmen*, M. Zawistowski, S. Feng, M. Nikpay, P. L. Auer, A. Goel, H. Zhang, U. Peters, M. Farrall, M. Orho-Melander, C. Kooperberg, R. McPherson, H. Watkins, C. J. Willer, K. Hveem, O. Melander, S. Kathiresan, and G. R. Abecasis. 2014. "Meta-analysis of gene-level tests for rare variant association." Nat Genet no. 46 (2):200-4. doi: 10.1038/ng.2852. Li, M., Z. He, M. Zhang, X. Zhan, C. Wei, R. C. Elston, and Q. Lu. 2014. "A generalized genetic random field method for the genetic association analysis of sequencing data." Genet Epidemiol no. 38 (3):242-53. doi: 10.1002/gepi.21790.


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2013

  1. Zhong, R., Kim, M. S., White, M. A., Xie, Y., and Xiao, G.* (2013) SbacHTS: spatial background noise correction for high-throughput RNAi screening, Bioinformatics (Oxford, England) 29, 2218-2220.

  2. Yang, J., Wang, X., Kim, M., Xie, Y., and Xiao, G.* (2013) Detection of candidate tumor driver genes using a fully integrated Bayesian approach, Statistics in medicine 33, 1784-1800.

  3. Wei, Y., Zou, Z., Becker, N., Anderson, M., Sumpter, R., Xiao, G., Kinch, L., Koduru, P., Christudass, C. S., Veltri, R. W., Grishin, N. V., Peyton, M., Minna, J., Bhagat, G., and Levine, B. (2013) EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance, Cell 154, 1269-1284.

  4. Wang, X., Zang, M., and Xiao, G.* (2013) Epigenetic change detection and pattern recognition via Bayesian hierarchical hidden Markov models, Statistics in medicine 32, 2292-2307.

  5. 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, Clin Cancer Res 19, 1577-1586.

  6. Potts, M. B., Kim, H. S., Fisher, K. W., Hu, Y., Carrasco, Y. P., Bulut, G. B., Ou, Y. H., Herrera-Herrera, M. L., Cubillos, F., Mendiratta, S., Xiao, G., Hofree, M., Ideker, T., Xie, Y., Huang, L. J., Lewis, R. E., MacMillan, J. B., and White, M. A. (2013) Using functional signature ontology (FUSION) to identify mechanisms of action for natural products, Science signaling 6, ra90.

  7. He, C., Wei, Y., Sun, K., Li, B., Dong, X., Zou, Z., Liu, Y., Kinch, L. N., Khan, S., Sinha, S., Xavier, R. J., Grishin, N. V., Xiao, G., Eskelinen, E. L., Scherer, P. E., Whistler, J. L., and Levine, B. (2013) Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism, Cell 154, 1085-1099.

  8. Xiao, G., Wang X., Quincey L., Nestler E. J., and Xie, Y.* (2013) Detection of epigenetic changes using ANOVA with spatially varying coefficients, Statistical applications in genetics and molecular biology 12, 189-205.

  9. Chen, M., Zang, M., Wang, X., and Xiao, G.* (2013) A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies, Bioinformatics (Oxford, England) 29, 862-869.

  10. Donghyeon Yu, MinSoo Kim, Xiao, G. and Tae Hyun Hwang*, Review of Biological Network Data and its Applications, Genomics Inform. 2013 Dec;11(4):200-210.

  11. Tae Hyun Hwang*, Gowtham Atluri, Rui Kuang, Timothy Starr, Kevin AT Silverstein, Peter Haverty, Zemin Zhang, and Jinfeng Liu*, Large-scale Integrative Network-based analysis Identifies Common Pathways Disrupted by Copy Number Alterations across Cancers, BMC Genomics, 2013 14:440. DOI: 10.1186/1471-2164-14-440

  12. He, Z., M. Zhang, X. Zhan, and Q. Lu. 2014. "Modeling and testing for joint association using a genetic random field model." Biometrics. doi: 10.1111/biom.12160.

  13. Zhan, X.*, D. E. Larson*, C. Wang*, et al, and G. R. Abecasis. 2013. "Identification of a rare coding variant in complement 3 associated with age-related macular degeneration." Nat Genet no. 45 (11):1375-9. doi: 10.1038/ng.2758.

  14. Li, B.*, X. Zhan*, M. K. Wing, P. Anderson, H. M. Kang, and G. R. Abecasis. 2013. "QPLOT: a quality assessment tool for next generation sequencing data." Biomed Res Int no. 2013:865181. doi: 10.1155/2013/865181.

  15. Hu, Y., C. Willer, X. Zhan, H. M. Kang, and G. R. Abecasis. 2013. "Accurate local-ancestry inference in exome-sequenced admixed individuals via off-target sequence reads." Am J Hum Genet no. 93 (5):891-9. doi: 10.1016/j.ajhg.2013.10.008.


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2012

  1. Xie, Y., and Minna, J. D. (2012) A lung cancer molecular prognostic test ready for prime time, Lancet 379, 785-787.

  2. Wang, R. C., Wei, Y., An, Z., Zou, Z., Xiao, G., Bhagat, G., White, M., Reichelt, J., and Levine, B. (2012) Akt-mediated regulation of autophagy and tumorigenesis through Beclin 1 phosphorylation, Science 338, 956-959.

  3. Zhang, Y., Xie, Y., Berglund, E.D., Coate, K.C., He, T.T., Katafuchi, T., Xiao, G., Potthoff, M.J., Wei, W., Wan, Y., Yu, R.T., Evans, R.M., Kliewer, S.A., Mangelsdorf, D.J. (2012) The starvation hormone, fibroblast growth factor-21, extends lifespan in mice, eLife 1:e00065. PMCID: 3466591.

  4. Wang, X., Chen, M., Khodursky, A. B., and Xiao, G.*. (2012) Bayesian Joint Analysis of Gene Expression Data and Gene Functional Annotations, Statistics in Biosciences 4, 300-318.

  5. Ma, S., Dai, Y., Huang, J., and Xie, Y.* (2012) Identification of Breast Cancer Prognosis Markers via Integrative Analysis, Computational statistics & data analysis 56, 2718-2728.

  6. He, C., Bassik, M. C., Moresi, V., Sun, K., Wei, Y., Zou, Z., An, Z., Loh, J., Fisher, J., Sun, Q., Korsmeyer, S., Packer, M., May, H. I., Hill, J. A., Virgin, H. W., Gilpin, C., Xiao, G., Bassel-Duby, R., Scherer, P. E., and Levine, B. (2012) Exercise-induced BCL2-regulated autophagy is required for muscle glucose homeostasis, Nature 481, 511-515.

  7. Han, T. W., Kato, M., Xie, S., Wu, L. C., Mirzaei, H., Pei, J., Chen, M., Xie, Y., Allen, J., Xiao, G., and McKnight, S. L. (2012) Cell-free formation of RNA granules: bound RNAs identify features and components of cellular assemblies, Cell 149, 768-779.

  8. Allen, J. D., Xie, Y., Chen, M., Girard, L., and Xiao, G.* (2012) Comparing statistical methods for constructing large scale gene networks, PloS one 7, e29348.

  9. Allen, J. D., Wang, S., Chen, M., Girard, L., Minna, J. D., Xie, Y., and Xiao, G.* (2012) Probe mapping across multiple microarray platforms, Briefings in bioinformatics 13, 547-554.

  10. Tang, H., Wang, X. S., Hsieh, J-H. and Tropsha, A. Do crystal structures obviate the need for theoretical models of GPCRs for structure based virtual screening. Proteins. (2012) Jan 17. doi: 10.1002/prot.24035

  11. Tae Hyun Hwang, Maoqiang Xie, Gowtham Atluri, Sanjoy Dey, Changjin Hong, Vipin Kumar, and Rui Kuang., Co-clustering Phenome-genome for Phenotype Classification and Disease Gene Discovery, Nucleic Acids Research, 2012 Jun., doi: 10.1093/nar/gks615.

  12. Young-Mi Kim, Matthew Stone, Tae Hyun Hwang, Yeon-Gil Kim, Timothy J. Griffin, and Do-Hyung Kim, SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1, Molecular Cell, 2012 May, doi:10.1016/j.molcel.2012.04.007.

  13. Yingming Li*, Tae Hyun Hwang*, LeAnn Oseth, Betsy Hirsch, Robert Vessella, Kenny Beckman, Kevin Silverstein, and Scott Dehm, AR intragenic deletions linked to Androgen Receptor Splice Variant Expression and Activity in Models of Prostate Cancer Progression, Oncogene, 2012 Jan., doi:10.1038/onc.2011.637.

  14. Tae Hyun Hwang, Wei Zhang, Maoqiang Xie, Jinfeng Liu, and Rui Kuang, Inferring Disease and Gene Set Associations with Rank Coherence in Networks, Bioinformatics 2011 1;27(19):2692-9. Epub 2011 Aug 8.

  15. Li B, Chen W, Zhan X, Busonero F, Sanna S, et al. (2012) A likelihood-based framework for variant calling and de novo mutation detection in families. PLoS Genet 8(10): e1002944.


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2011

  1. 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, Clin Cancer Res 17, 5705-5714.

  2. Xiao, G., Wang, X., and Khodursky, A. B. (2011) Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data, Journal of the American Statistical Association 106, 61-72.

  3. Wang, S., Wang, Y., Xie, Y., and Xiao, G.* (2011) A novel approach to DNA copy number data segmentation, Journal of bioinformatics and computational biology 9, 131-148.

  4. Orvedahl, A., Sumpter, R., Jr., Xiao, G., Ng, A., Zou, Z., Tang, Y., Narimatsu, M., Gilpin, C., Sun, Q., Roth, M., Forst, C. V., Wrana, J. L., Zhang, Y. E., Luby-Phelps, K., Xavier, R. J., Xie, Y., and Levine, B. (2011) Image-based genome-wide siRNA screen identifies selective autophagy factors, Nature 480, 113-117.


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2010

  1. Jeong Y, Xie, Y., Xiao, G., Behrens C, Girard L, Wistuba II, Minna JD, Mangelsdorf DJ, Nuclear receptor expression defines a set of prognostic biomarkers for lung cancer. PLoS Med, 2010. 7(12): p. e1000378.

  2. Xie, Y. and J.D. Minna, Non-small-cell lung cancer mRNA expression signature predicting response to adjuvant chemotherapy. J Clin Oncol, 2010. 28(29): p. 4404-7.

  3. Xie, Y. and C. Ahn, Statistical methods for integrating multiple types of high-throughput data. Methods Mol Biol, 2010. 620: p. 511-29.

  4. Xie, Y., JK, Pan W, Xiao, G., Khodursky A. A Bayesian Approach to Joint Modeling of Protein-DNA Binding, Gene Expression and Sequence Data. Statistics in Medicine. 2010 Feb 20;29(4):489-503.PMID:20049751.

  5. Laplant Q, Vialou V, Covington HE 3rd, Dumitriu D, Feng J, Warren BL, Maze I, Dietz DM, Watts EL, Iñiguez SD, Koo JW, Mouzon E, Renthal W, Hollis F, Wang H, Noonan MA, Ren Y, Eisch AJ, Bolaños CA, Kabbaj M, Xiao, G., Neve RL, Hurd YL, Oosting RS, Fan G, Morrison JH, Nestler EJ. Dnmt3a regulates emotional behavior and spine plasticity in the nucleus accumbens. Nature Neuroscience. 2010 Sep 13(9):1137-43.

  6. Xie, Y., et al., A Bayesian approach to joint modeling of protein-DNA binding, gene expression and sequence data. Stat Med, 2010. 29(4): p. 489-503.

  7. Lu, H., U.S. Yezhuvath, and Xiao, G.*, Improving fMRI sensitivity by normalization of basal physiologic state. Hum Brain Mapp, 2010. 31(1): p. 80-7.


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