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  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


  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

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  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

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  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


  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

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