Peng Wei

Peer-Reviewed Articles

1. Guo CC, Majewski T, Zhang L, Yao H, Bondaruk J, Wang Y, Zhang S, Wang Z, Lee JG, Lee S, Cogdell D, Zhang M, Wei P, Grossman HB, Kamat A, Duplisea JJ, Ferguson JE, Huang H, Dadhania V, Gao J, Dinney C, Weinstein JN, Baggerly K, McConkey D, Czerniak B. Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer. Cell Rep 27(6):1781-1793.e4, 2019. PMID: 31067463.
2. Ma Y, Wei P. FunSPU: a versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data. PLoS Genet 15(4):e1008081, 2019. e-Pub 2019. PMID: 31034468.
3. Yang T, Chen H, Tang H, Li D, Wei P. A powerful and data-adaptive test for rare-variant-based gene-environment interaction analysis. Stat Med 38(7):1230-1244, 2019. e-Pub 2018. PMID: 30460711.
4. Ok CY, Loghavi S, Sui D, Wei P, Kanagal-Shamanna R, Yin CC, Zuo Z, Routbort MJ, Tang G, Tang Z, Jorgensen JL, Luthra R, Ravandi F, Kantarjian HM, DiNardo CD, Medeiros LJ, Wang SA, Patel KP. Persistent IDH1/2 mutation in remission can predict relapse in patients with acute myeloid leukemia. Haematologica 104(2):305-311, 2019. e-Pub 2018. PMID: 30171025.
5. Majewski T, Yao H, Bondaruk J, Chung W, Lee S, Lee JG, Zhang S, Cogdell D, Yang G, Choi W, Dinney C, Grossman HB, Logothetis C, Scherer SE, Guo CC, Zhang L, Wei P, Weinstein JN, Issa JP, Baggerly K, McConkey DJ, Czerniak B. Whole-organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis. Cell Rep 26(8):2241-2256.e4, 2019. PMID: 30784602.
6. Xu X, Liu H, Gross N, Wei D, Qian Y, Li W, Wei P, Li G, Zhang F, Yang Z, Lei D, Pan X. Overexpression of miRNA 4451 is Associated With a Poor Survival of Patients With Hypopharyngeal Cancer After Surgery With Postoperative Radiotherapy. Transl Oncol 11(5):1244-1250, 2018. e-Pub 2018. PMID: 30103154.
7. Loghavi S, Sui D, Wei P, Garcia-Manero G, Pierce S, Routbort MJ, Jabbour EJ, Pemmaraju N, Kanagal-Shamanna R, Gur HD, Hu S, Zuo Z, Medeiros LJ, Kantarjian HM, Khoury JD. Validation of the 2017 revision of the WHO chronic myelomonocytic leukemia categories. Blood Adv 2(15):1807-1816, 2018. PMID: 30054307.
8. Tao Y, Sturgis EM, Huang Z, Wang Y, Wei P, Wang JR, Wei Q, Li G. TGFβ1Genetic Variants Predict Clinical Outcomes of HPV-Positive Oropharyngeal Cancer Patients after Definitive Radiotherapy. Clin Cancer Res 24(9):2225-2233, 2018. e-Pub 2018. PMID: 29463556.
9. Lu Z, Sturgis EM, Zhu L, Zhang H, Tao Y, Wei P, Wei Q, Li G. Mouse double minute 4 variants modify susceptibility to risk of recurrence in patients with squamous cell carcinoma of the oropharynx. Mol Carcinog 57(3):361-369, 2018. e-Pub 2017. PMID: 29073727.
10. Jiang C, Nischal H, Sun H, Li L, Cao Y, Wei P, Chang JY, Teng BB. Non-Native Conformational Isomers of the Catalytic Domain of PCSK9 Induce an Immune Response, Reduce Lipids and Increase LDL Receptor Levels. Int J Mol Sci 19(2), 2018. e-Pub 2018. PMID: 29495280.
11. Xu Z, Wu C, Wei P, Pan W. A Powerful Framework for Integrating eQTL and GWAS Summary Data. Genetics 207(3):893-902, 2017. e-Pub 2017. PMID: 28893853.
12. McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, Conti D, Gauderman WJ, Hsu L, Hutter CM, Jankowska MM, Kerr J, Kraft P, Montgomery SB, Mukherjee B, Papanicolaou GJ, Patel CJ, Ritchie MD, Ritz BR, Thomas DC, Wei P, Witte JS. Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. Am J Epidemiol 186(7):753-761, 2017. PMID: 28978193.
13. Ritchie MD, Davis JR, Aschard H, Battle A, Conti D, Du M, Eskin E, Fallin MD, Hsu L, Kraft P, Moore JH, Pierce BL, Bien SA, Thomas DC, Wei P, Montgomery SB. Incorporation of Biological Knowledge Into the Study of Gene-Environment Interactions. Am J Epidemiol 186(7):771-777, 2017. PMID: 28978191.
14. Tang H, Wei P, Chang P, Li Y, Yan D, Liu C, Hassan M, Li D. Genetic polymorphisms associated with pancreatic cancer survival: A genome-wide association study. Int J Cancer 141(4):678-686, 2017. e-Pub 2017. PMID: 28470677.
15. Hong C, Ning Y, Wei P , Cao Y, Chen Y. A semiparametric model for vQTL mapping. Biometrics 73(2):571-581, 2017. e-Pub 2016. PMID: 27861717.
16. Simon DK, Wu C, Tilley BC, Lohmann K, Klein C, Payami H, Wills AM, Aminoff MJ, Bainbridge J, Dewey R, Hauser RA, Schaake S, Schneider JS, Sharma S, Singer C, Tanner CM, Truong D, Wei P, Wong PS, Yang T. Caffeine, creatine, GRIN2A and Parkinson's disease progression. J Neurol Sci 375:355-359, 2017. e-Pub 2017. PMID: 28320167.
17. Zhu L, Sturgis EM, Lu Z, Zhang H, Wei P, Wei Q, Li G. Association between miRNA-binding site polymorphisms in double-strand break repair genes and risk of recurrence in patients with squamous cell carcinomas of the nonoropharynx. Carcinogenesis 38(4):432-438, 2017. e-Pub 2017. PMID: 28334093.
18. Cao Y, Rajan SS, Wei P . Mendelian randomization analysis of a time-varying exposure for binary disease outcomes using functional data analysis methods. Genet Epidemiol 40(8):744-755, 2016. e-Pub 2016. PMID: 27813215.
19. Wei P , Cao Y, Zhang Y, Xu Z, Kwak IY, Boerwinkle E, Pan W. On robust association testing for quantitative traits and rare variants. G3 (Bethesda) 6(12):3941-3950, 2016. e-Pub 2016. PMID: 27678522.
20. Ogunwale AN, Morrison AC, Sun W, Dodge RC, Virani SS, Taylor A, Gottesman RF, Yang E, Wei P, McEvoy JW, Heiss G, Boerwinkle E, Ballantyne CM, Nambi V. The impact of multiple single day blood pressure readings on cardiovascular risk estimation: The Atherosclerosis Risk in Communities study. Eur J Prev Cardiol 23(14):1529-36, 2016. e-Pub 2016. PMID: 26869459.
21. Xu G, Lin L, Wei P, Pan W. An adaptive two-sample test for high-dimensional means. Biometrika 103(3):609-624, 2016.
22. Wei P, Yang Y, Guo X, Hei N, Lai S, Assassi S, Liu M, Tan F, Zhou X. Identification of an Association of TNFAIP3 Polymorphisms With Matrix Metalloproteinase Expression in Fibroblasts in an Integrative Study of Systemic Sclerosis-Associated Genetic and Environmental Factors. Arthritis Rheumatol 68(3):749-60, 2016. PMID: 26474180.
23. Huang J, Wang K, Wei P, Liu X, Liu X, Tan K, Boerwinkle E, Potash JB, Han S. FLAGS: A Flexible and Adaptive Association Test for Gene Sets Using Summary Statistics. Genetics 202(3):919-29, 2016. e-Pub 2016. PMID: 26773050.
24. Liu X, White S, Peng B, Johnson AD, Brody JA, Li AH, Huang Z, Carroll A, Wei P, Gibbs R, Klein RJ, Boerwinkle E. WGSA: an annotation pipeline for human genome sequencing studies. J Med Genet 53(2):111-2, 2016. e-Pub 2015. PMID: 26395054.
25. Ware RE, Davis BR, Schultz WH, Brown RC, Aygun B, Sarnaik S, Odame I, Fuh B, George A, Owen W, Luchtman-Jones L, Rogers ZR, Hilliard L, Gauger C, Piccone C, Lee MT, Kwiatkowski JL, Jackson S, Miller ST, Roberts C, Heeney MM, Kalfa TA, Nelson S, Imran H, Nottage K, Alvarez O, Rhodes M, Thompson AA, Rothman JA, Helton KJ, Roberts D, Coleman J, Bonner MJ, Kutlar A, Patel N, Wood J, Piller L, Wei P, Luden J, Mortier NA, Stuber SE, Luban NL, Cohen AR, Pressel S, Adams RJ. Hydroxycarbamide versus chronic transfusion for maintenance of transcranial doppler flow velocities in children with sickle cell anaemia-TCD With Transfusions Changing to Hydroxyurea (TWiTCH): a multicentre, open-label, phase 3, non-inferiority trial. Lancet 387(10019):661-70, 2016. e-Pub 2015. PMID: 26670617.
26. Malec SA, Wei P, Xu H, Bernstam EV, Myneni S, Cohen T. Literature-based discovery of confounding in observational clinical data. AMIA Annu Symp Proc 2016:1920-1929, 2016.
27. Kim T, Wei P . Incorporating ENCODE information into association analysis of whole genome sequencing data. BMC Proc 10(Suppl 7):257-261, 2016. e-Pub 2016. PMID: 27980646.
28. Pan W, Kwak IY, Wei P . A Powerful Pathway-Based Adaptive Test for Genetic Association with Common or Rare Variants. Am J Hum Genet 97(1):86-98, 2015. e-Pub 2015. PMID: 26119817.
29. Pan W, Chen YM, Wei P . Testing for polygenic effects in genome-wide association studies. Genet Epidemiol 39(4):306-16, 2015. e-Pub 2015. PMID: 25847094.
30. Yu B, Li AH, Muzny D, Veeraraghavan N, de Vries PS, Bis JC, Musani SK, Alexander D, Morrison AC, Franco OH, Uitterlinden A, Hofman A, Dehghan A, Wilson JG, Psaty BM, Gibbs R, Wei P, Boerwinkle E. Association of Rare Loss-Of-Function Alleles in HAL, Serum Histidine: Levels and Incident Coronary Heart Disease. Circ Cardiovasc Genet 8(2):351-5, 2015. e-Pub 2015. PMID: 25575548.
31. Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, Liu X. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet 24(8):2125-37, 2015. e-Pub 2014. PMID: 25552646.
32. Cao Y, Maxwell TJ, Wei P. A family-based joint test for mean and variance heterogeneity for quantitative traits. Ann Hum Genet 79(1):46-56, 2015. e-Pub 2014. PMID: 25393880.
33. Wang Y, Li D, Wei P. Powerful Tukey's One Degree-of-Freedom Test for Detecting Gene-Gene and Gene-Environment Interactions. Cancer Inform 14(Suppl 2):209-18, 2015. e-Pub 2015. PMID: 26064040.
34. Schick UM, Auer PL, Bis JC, Lin H, Wei P, Pankratz N, Lange LA, Brody J, Stitziel NO, Kim DS, Carlson CS, Fornage M, Haessler J, Hsu L, Jackson RD, Kooperberg C, Leal SM, Psaty BM, Boerwinkle E, Tracy R, Ardissino D, Shah S, Willer C, Loos R, Melander O, Mcpherson R, Hovingh K, Reilly M, Watkins H, Girelli D, Fontanillas P, Chasman DI, Gabriel SB, Gibbs R, Nickerson DA, Kathiresan S, Peters U, Dupuis J, Wilson JG, Rich SS, Morrison AC, Benjamin EJ, Gross MD, Reiner AP, Cohorts for Heart and Aging Research in Genomic Epidemiology, National Heart, Lung, and Blood Institute GO Exome Sequencing Project. Association of exome sequences with plasma C-reactive protein levels in >9000 participants. Hum Mol Genet 24(2):559-71, 2015. e-Pub 2014. PMID: 25187575.
35. Sun Y, Yu W, Sturgis EM, Wei P, Lei D, Wei Q, Song X, Li G. Site disparities in apoptotic variants as predictors of risk for second primary malignancy in patients with squamous cell carcinoma of the head and neck. BMC Cancer 16:70, 2015. e-Pub 2016. PMID: 26858129.
36. Wei P, Tang H, Li D. Functional logistic regression approach to detecting gene by longitudinal environmental exposure interaction in a case-control study. Genet Epidemiol 38(7):638-51, 2014. e-Pub 2014. PMID: 25219575.
37. Pan W, Kim J, Zhang Y, Shen X, Wei P. A powerful and adaptive association test for rare variants. Genetics 197(4):1081-95, 2014. e-Pub 2014. PMID: 24831820.
38. Tang H, Wei P, Duell EJ, Risch HA, Olson SH, Bueno-de-Mesquita HB, Gallinger S, Holly EA, Petersen G, Bracci PM, McWilliams RR, Jenab M, Riboli E, Tjønneland A, Boutron-Ruault MC, Kaaks R, Trichopoulos D, Panico S, Sund M, Peeters PH, Khaw KT, Amos CI, Li D. Axonal guidance signaling pathway interacting with smoking in modifying the risk of pancreatic cancer: a gene- and pathway-based interaction analysis of GWAS data. Carcinogenesis 35(5):1039-45, 2014. e-Pub 2014. PMID: 24419231.
39. Zhang C, Sturgis EM, Zheng H, Song X, Wei P, Jin L, Chao L, Wei Q, Li G. Genetic variants in TNF-α promoter are predictors of recurrence in patients with squamous cell carcinoma of oropharynx after definitive radiotherapy. Int J Cancer 134(8):1907-15, 2014. e-Pub 2013. PMID: 24122460.
40. Tang H, Wei P, Duell EJ, Risch HA, Olson SH, Bueno-de-Mesquita HB, Gallinger S, Holly EA, Petersen GM, Bracci PM, McWilliams RR, Jenab M, Riboli E, Tjønneland A, Boutron-Ruault MC, Kaaks R, Trichopoulos D, Panico S, Sund M, Peeters PH, Khaw KT, Amos CI, Li D. Genes-environment interactions in obesity- and diabetes-associated pancreatic cancer: a GWAS data analysis. Cancer Epidemiol Biomarkers Prev 23(1):98-106, 2014. e-Pub 2013. PMID: 24136929.
41. Cao Y, Wei P, Bailey M, Kauwe JS, Maxwell TJ, Alzheimer's Disease Neuroimaging Initiative. A versatile omnibus test for detecting mean and variance heterogeneity. Genet Epidemiol 38(1):51-9, 2014. PMID: 24482837.
42. Yang Y, Wei P, Guo XJ, Zhou D, Zhang WZ, Assassi S, Zhou XD. Impact of Age and Autoantibody Status on the Gene Expression of Scleroderma Fibroblasts in Response to Silica Stimulation. Eur J Inflamm 11(3):631-639, 2013. PMID: 25435887.
43. Jin L, Sturgis EM, Zhang Y, Huang Z, Wei P, Guo W, Wang Z, Wei Q, Song X, Li G. Genetic variants in p53-related genes confer susceptibility to second primary malignancy in patients with index squamous cell carcinoma of head and neck. Carcinogenesis 34(7):1551-7, 2013. e-Pub 2013. PMID: 23508638.
44. Johnsen JM, Auer PL, Morrison AC, Jiao S, Wei P, Haessler J, Fox K, McGee SR, Smith JD, Carlson CS, Smith N, Boerwinkle E, Kooperberg C, Nickerson DA, Rich SS, Green D, Peters U, Cushman M, Reiner AP, NHLBI Exome Sequencing Project. Common and rare von Willebrand factor (VWF) coding variants, VWF levels, and factor VIII levels in African Americans: the NHLBI Exome Sequencing Project. Blood 122(4):590-7, 2013. e-Pub 2013. PMID: 23690449.
45. Chen Y, Luo S, Chu H, Wei P. Bayesian inference on risk differences: an application to multivariate meta-analysis of adverse events in clinical trials. Stat Biopharm Res 5(2):142-155, 2013. PMID: 23853700.
46. Grimes CZ, Hwang LY, Wei P, Shah DP, Volcik KA, Brown EL. Differentially regulated gene expression associated with hepatitis C virus clearance. J Gen Virol 94(Pt 3):534-42, 2013. e-Pub 2012. PMID: 23152368.
47. Nischal H, Sun H, Wang Y, Ford DA, Cao Y, Wei P, Teng BB. Long-term Expression of Apolipoprotein B mRNA-specific Hammerhead Ribozyme via scAAV8.2 Vector Inhibits Atherosclerosis in Mice. Mol Ther Nucleic Acids 2:e125, 2013. e-Pub 2013. PMID: 24084845.
48. Wei P, Pan W. Bayesian Joint Modeling of Multiple Gene Networks and Diverse Genomic Data to Identify Target Genes of a Transcription Factor. Ann Appl Stat 6(1):334-355, 2012. PMID: 22408712.
49. Wei P, Tang H, Li D. Insights into pancreatic cancer etiology from pathway analysis of genome-wide association study data. PLoS One 7(10):e46887, 2012. e-Pub 2012. PMID: 23056513.
50. Wei P, Liu X, Fu YX. Incorporating predicted functions of nonsynonymous variants into gene-based analysis of exome sequencing data: a comparative study. BMC Proc 5 Suppl 9:S20, 2011. e-Pub 2011. PMID: 22373178.
51. Chen GK, Wei P, DeStefano AL. Incorporating biological information into association studies of sequencing data. Genet Epidemiol 35 Suppl 1:S29-34, 2011. PMID: 22128055.
52. Wei P, Milbauer LC, Enenstein J, Nguyen J, Pan W, Hebbel RP. Differential endothelial cell gene expression by African Americans versus Caucasian Americans: a possible contribution to health disparity in vascular disease and cancer. BMC Med 9:2, 2011. e-Pub 2011. PMID: 21223544.
53. Enenstein J, Milbauer L, Domingo E, Wells A, Roney M, Kiley J, Wei P, Hebbel RP. Proinflammatory phenotype with imbalance of KLF2 and RelA: risk of childhood stroke with sickle cell anemia. Am J Hematol 85(1):18-23, 2010. PMID: 19957349.
54. Wei P, Pan W. Network-based genomic discovery: application and comparison of Markov random field models. J R Stat Soc Ser C Appl Stat 59(1):105-125, 2010. PMID: 21373371.
55. John R, Panch S, Hrabe J, Wei P, Solovey A, Joyce L, Hebbel R. Activation of endothelial and coagulation systems in left ventricular assist device recipients. Ann Thorac Surg 88(4):1171-9, 2009. PMID: 19766802.
56. Wei P, Pan W. Incorporating gene functions into regression analysis of DNA-protein binding data and gene expression data to construct transcriptional networks. IEEE/ACM Trans Comput Biol Bioinform 5(3):401-15, 2008. PMID: 18670043.
57. Chang Milbauer L, Wei P, Enenstein J, Jiang A, Hillery CA, Scott JP, Nelson SC, Bodempudi V, Topper JN, Yang RB, Hirsch B, Pan W, Hebbel RP. Genetic endothelial systems biology of sickle stroke risk. Blood 111(7):3872-9, 2008. e-Pub 2007. PMID: 18156497.
58. Wei P, Pan W. Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model. Bioinformatics 24(3):404-11, 2008. e-Pub 2007. PMID: 18083717.
59. Pan W, Wei P, Khodursky A. A parametric joint model of DNA-protein binding, gene expression and DNA sequence data to detect target genes of a transcription factor. Pac Symp Biocomput:465-76, 2008. PMID: 18229708.
60. Li N, Wu B, Wei P, Xie B, Xie Y, Xiao G, Pan W. Functional group-based linkage analysis of gene expression trait loci. BMC Proc 1 Suppl 1:S117, 2007. e-Pub 2007. PMID: 18466458.
61. Huang D, Wei P , Pan W. Combining gene annotations and gene expression data in model-based clustering: weighted method. OMICS 10(1):28-39, 2006. PMID: 16584316.
62. Quesada AE, Medeiros LJ, Desai PA, Lin P, Westin JR, Hawsawi HM, Wei P, Tang G, Seegmiller AC, Reddy NM, Yin CC, Wang W, Xu J, Miranda RN, Zuo Z, Li S. Increased MYC copy number is an independent prognostic factor in patients with diffuse large B-cell lymphoma. Mod Pathol. e-Pub 2017. PMID: 28776574.
63. Khogeer H, Rahman H, Jain N, Angelova EA, Yang H, Quesada A, Ok CY, Sui D, Wei P, Al Fattani A, Pierce S, Loghavi S, Lamb A, Hu P, Thakral B, Kanagal-Shamanna R, Jorgensen JL, Jabbour EJ, Kantarjian HM, Medeiros LJ, Khoury JD. Early T precursor acute lymphoblastic leukaemia/lymphoma shows differential immunophenotypic characteristics including frequent CD33 expression and in vitro response to targeted CD33 therapy. Br J Haematol. e-Pub 2019. PMID: 31115909.
64. Yang Z, Zhang Y, Wang X, Huang J, Guo W, Wei P, Li G, Wang Z, Huang Z, Zhang L. Putative biomarkers of malignant transformation of sinonasal inverted papilloma into squamous cell carcinoma. J Int Med Res:300060519838385. e-Pub 2019. PMID: 30991875.
65. Luo X, Sturgis EM, Yang Z, Sun Y, Wei P, Liu Z, Wei Q, Li G. Lymphocyte Telomere Length Predicts Clinical Outcomes of HPV-Positive Oropharyngeal Cancer Patients after Definitive Radiotherapy. Carcinogenesis. e-Pub 2019. PMID: 30721961.
66. Li D, Tang H, Wei P, Zheng J, Daniel CR, Hassan MM. Vitamin C and vitamin E Mitigate the Risk of Pancreatic Ductal Adenocarcinoma from Meat-Derived Mutagen Exposure in Adults in a Case-Control Study. J Nutr. e-Pub 2019. PMID: 31100111.
67. Zhang S, Wang Y, Bondaruk J, Majewski T, Yao H, Lee S, Lee JG, Cogdell D, Lotan Y, Dinney C, Wei P, Baggerly K, Czerniak B. Detection of Bladder Cancer in Urine Sediments by a Novel Multicolor Fluorescence In Situ Hybridization (Quartet) Test. Eur Urol Focus. e-Pub 2018. PMID: 29428551.