Peng Wei

Peer-Reviewed Articles

1. El Hussein S, Medeiros LJ, Gruschkus SK, Wei P, Schlette E, Fang H, Jelloul FZ, Wang W, Fiskus W, Kanagal-Shamanna R, Loghavi S, Yang H, Li S, Xu J, Tang Z, Thakral B, Jain N, Wierda WG, Patel K, Bhalla KN, Khoury JD. Immune evasion phenotype is common in Richter transformation diffuse large B-cell lymphoma variant. Virchows Arch. e-Pub 2023. PMID: 36864257.
2. Kwan SY, Slayden AN, Coronado AR, Marquez RC, Chen H, Wei P, Savage MI, Vornik LA, Fox JT, Sei S, Liang D, Stevenson HL, Wilkerson GK, Gagea M, Brown PH, Beretta L. Treatment strategies and mechanisms associated with the prevention of NASH-associated HCC by a toll-like receptor 4 inhibitor. Cancer Prev Res (Phila) 16(1):17-28, 2023. e-Pub 2022. PMID: 36162136.
3. Zhou Z, Adrada BE, Candelaria RP, Elshafeey NA, Boge M, Mohamed RM, Pashapoor S, Sun J, Xu Z, Panthi B, Son JB, Guirguis MS, Patel MM, Whitman GJ, Moseley TW, Scoggins ME, White JB, Litton JK, Valero V, Hunt KK, Tripathy D, Yang W, Wei P, Yam C, Pagel MD, Rauch GM, Ma J. Prediction of pathologic complete response to neoadjuvant systemic therapy in triple negative breast cancer using deep learning on multiparametric MRI. Sci Rep 13(1):1171, 2023. e-Pub 2023. PMID: 36670144.
4. Panthi B, Adrada BE, Candelaria RP, Guirguis MS, Yam C, Boge M, Chen H, Hunt KK, Huo L, Hwang K-P, Korkut A, Lane DL, Le-Petross HC, Leung JWT, Litton JK, Mohamed RM, Musall BC, Pashapoor S, Patel MM, Perez F, Son JB, Thompson A, Valero V, Wei P, White J, Xu Z, Pinsky L, Tripathy D, Yang W, Ma J, Rauch GM. Assessment of Response to Neoadjuvant Systemic Treatment in Triple-Negative Breast Cancer Using Functional Tumor Volumes from Longitudinal Dynamic Contrast-Enhanced MRI. Cancers 15(4):2023, 2023.
5. Musall BC, Adrada BE, Candelaria RP, Mohamed RMM, Abdelhafez AH, Son JB, Sun J, Santiago L, Whitman GJ, Moseley TW, Scoggins ME, Mahmoud HS, White JB, Hwang KP, Elshafeey NA, Boge M, Zhang S, Litton JK, Valero V, Tripathy D, Thompson AM, Yam C, Wei P, Moulder SL, Pagel MD, Yang WT, Ma J, Rauch GM. Quantitative Apparent Diffusion Coefficients from Peritumoral Regions as Early Predictors of Response to Neoadjuvant Systemic Therapy in Triple-Negative Breast Cancer. J Magn Reson Imaging 56(6):1901-1909, 2022. e-Pub 2022. PMID: 35499264.
6. Xu Y, Wang Z, Wei P, Gairola R, Kelsey KT, Sikora AG, Li G, Gu J. Hypermethylation of nc886 in HPV-positive oropharyngeal cancer and its clinical implications: An epigenome-wide association study. Mol Ther Nucleic Acids 30:596-605, 2022. e-Pub 2022. PMID: 36514351.
7. Wang Z, Lu Y, Fornage M, Jiao L, Shen J, Li D, Wei P. Identification of novel susceptibility methylation loci for pancreatic cancer in a two-phase epigenome-wide association study. Epigenetics 17(11):1-16, 2022. e-Pub 2022. PMID: 35030986.
8. Pankratz N, Wei P, Brody JA, Chen MH, de Vries PS, Huffman JE, Stimson MR, Auer PL, Boerwinkle E, Cushman M, de Maat MPM, Folsom AR, Franco OH, Gibbs RA, Haagenson KK, Hofman A, Johnsen JM, Kovar CL, Kraaij R, McKnight B, Metcalf GA, Muzny D, Psaty BM, Tang W, Uitterlinden AG, van Rooij JGJ, Dehghan A, O'Donnell CJ, Reiner AP, Morrison AC, Smith NL. Whole exome sequencing of 14389 individuals from the ESP and CHARGE consortia identifies novel rare variation associated with hemostatic factors. Hum Mol Genet 31(18):3120-3132, 2022. e-Pub 2022. PMID: 35552711.
9. Gregg JR, Kim J, Logothetis C, Hanash S, Zhang X, Manyam G, Muir K, UKGPCS Collaborative Group, Giles GG, Stanford JL, Berndt SI, Kogevinas M, Brenner H, Eeles RA, PRACTICAL Consortium, Wei P, Daniel CR. Coffee Intake, Caffeine Metabolism Genotype, and Survival Among Men with Prostate Cancer. Eur Urol Oncol. e-Pub 2022. PMID: 35995710.
10. Tashakori M, Kadia T, Loghavi S, Daver N, Kanagal-Shamanna R, Pierce S, Sui D, Wei P, Khodakarami F, Tang Z, Routbort M, Bivins CA, Jabbour EJ, Medeiros LJ, Bhalla K, Kantarjian HM, Ravandi F, Khoury JD. TP53 Copy Number and Protein Expression Inform Mutation Status across Risk Categories in Acute Myeloid Leukemia. Blood 140(1):58-72, 2022. e-Pub 2022. PMID: 35390143.
11. Bondaruk J, Jaksik R, Wang Z, Cogdell D, Lee S, Chen Y, Dinh KN, Majewski T, Zhang L, Cao S, Tian F, Yao H, Kus P, Chen H, Weinstein JN, Navai N, Dinney C, Gao J, Theodorescu D, Logothetis C, Guo CC, Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. The origin of bladder cancer from mucosal field effects. iScience 25(7):104551, 2022. e-Pub 2022. PMID: 35747385.
12. Kwan SY, Sabotta CM, Joon A, Wei P, Petty LE, Below JE, Wu X, Zhang J, Jenq RR, Hawk ET, McCormick JB, Fisher-Hoch SP, Beretta L. Gut microbiome alterations associated with diabetes in Mexican Americans in South Texas. mSystems 7(3):e0003322, 2022. e-Pub 2022. PMID: 35477306.
13. Kwan SY, Jiao J, Joon A, Wei P, Petty LE, Below JE, Daniel CR, Wu X, Zhang J, Jenq RR, Futreal PA, Hawk ET, McCormick JB, Fisher-Hoch SP, Beretta L. Gut Microbiome Features Associated with Liver Fibrosis in Hispanics, a Population at High Risk for Fatty Liver Disease. Hepatology 75(4):955-967, 2022. e-Pub 2021. PMID: 34633706.
14. Jimenez JE, Abdelhafez A, Mittendorf EA, Elshafeey N, Yung JP, Litton JK, Adrada BE, Candelaria RP, White J, Thompson AM, Huo L, Wei P, Tripathy D, Valero V, Yam C, Hazle JD, Moulder SL, Yang WT, Rauch GM. A model combining pretreatment MRI radiomic features and tumor-infiltrating lymphocytes to predict response to neoadjuvant systemic therapy in triple-negative breast cancer. Eur J Radiol 149:110220, 2022. e-Pub 2022. PMID: 35193025.
15. Zhou J, Jiang X, Xia HA, Wei P, Hobbs BP. Predicting outcomes of phase III oncology trials with Bayesian mediation modeling of tumor response. Stat Med 41(4):751-768, 2022. e-Pub 2021. PMID: 34888892.
16. Sabotta CM, Kwan SY, Petty LE, Below JE, Joon A, Wei P, Fisher-Hoch SP, McCormick JB, Beretta L. Genetic variants associated with circulating liver injury markers in Mexican Americans, a population at risk for non-alcoholic fatty liver disease. Front Genet 13:995488:995488, 2022. e-Pub 2022. PMID: 36386790.
17. Zhou J, Jiang X, Xia HA, Hobbs BP, Wei P. Landmark mediation survival analysis using longitudinal surrogate. Front Oncol 12:999324, 2022. e-Pub 2023. PMID: 36733365.
18. Nguyen TT, Bhosale PR, Xu G, Pan T, Wei P, Lu Y. Comparison of PSMA-based 18F-DCFPyL PET/CT and pelvic multiparametric MRI for lesion detection in the pelvis in patients with prostate cancer. Am J Nucl Med Mol Imaging 12(6):166-179, 2022. e-Pub 2022. PMID: 36636233.
19. Wei P. Radiomics, Deep Learning and Early Diagnosis in Oncology. Emerg Top Life Sci 5(6):829-835, 2021. PMID: 34874454.
20. Zhou J, Jiang X, Amy Xia H, Wei P, Hobbs BP. A Survival Mediation Model with Bayesian Model Averaging. Stat Methods Med Res 30(11):9622802211037069, 2021. e-Pub 2021. PMID: 34448657.
21. Sanchez JI, Jiao J, Kwan SY, Veillon L, Warmoes MO, Tan L, Odewole M, Rich NE, Wei P, Lorenzi PL, Singal AG, Beretta L. Lipidomic Profiles of Plasma Exosomes Identify Candidate Biomarkers for Early Detection of Hepatocellular Carcinoma in Patients with Cirrhosis. Cancer Prev Res (Phila) 14(10):955-962, 2021. e-Pub 2021. PMID: 34253566.
22. Jiao J, Kwan SY, Sabotta CM, Tanaka H, Veillon L, Warmoes MO, Lorenzi PL, Wang Y, Wei P, Hawk ET, Almeda JL, McCormick JB, Fisher-Hoch SP, Beretta L. Circulating Fatty Acids Associated with Advanced Liver Fibrosis and Hepatocellular Carcinoma in South Texas Hispanics. Cancer Epidemiol Biomarkers Prev 30(9):1643-1651, 2021. e-Pub 2021. PMID: 34155064.
23. Zhang S, Rauch GM, Adrada BE, Boge M, Mohamed RMM, Abdelhafez AH, Son JB, Sun J, Elshafeey NA, White JB, Musall BC, Miyoshi M, Wang X, Kotrotsou A, Wei P, Hwang KP, Ma J, Pagel MD. Assessment of Early Response to Neoadjuvant Systemic Therapy in Triple-Negative Breast Cancer Using Amide Proton Transfer-weighted Chemical Exchange Saturation Transfer MRI: A Pilot Study. Radiol Imaging Cancer 3(5):e200155, 2021. PMID: 34477453.
24. Yang T, Jackson VE, Smith AV, Chen H, Bartz TM, Sitlani CM, Psaty BM, Gharib SA, O'Connor GT, Dupuis J, Xu J, Lohman K, Liu Y, Kritchevsky SB, Cassano PA, Flexeder C, Gieger C, Karrasch S, Peters A, Schulz H, Harris SE, Starr JM, Deary IJ, Manichaikul A, Oelsner EC, Barr RG, Taylor KD, Rich SS, Bonten TN, Mook-Kanamori DO, Noordam R, Li-Gao R, Jarvelin MR, Wielscher M, Terzikhan N, Lahousse L, Brusselle G, Weiss S, Ewert R, Gläser S, Homuth G, Shrine N, Hall IP, Tobin M, London SJ, Wei P, Morrison AC. Rare and low-frequency exonic variants and gene-by-smoking interactions in pulmonary function. Sci Rep 11(1):19365, 2021. e-Pub 2021. PMID: 34588469.
25. Qin Y, Wang JR, Wang Y, Iyer P, Cote GJ, Busaidy NL, Dadu R, Zafereo M, Williams MD, Ferrarotto R, Gunn GB, Wei P, Patel K, Hofmann MC, Cabanillas ME. Clinical Utility of Circulating Cell-free DNA Mutations in Anaplastic Thyroid Carcinoma. Thyroid 31(8):1235-1243, 2021. e-Pub 2021. PMID: 33599171.
26. Adrada BE, Candelaria R, Moulder S, Thompson A, Wei P, Whitman GJ, Valero V, Litton JK, Santiago L, Scoggins ME, Moseley TW, White JB, Ravenberg EE, Yang WT, Rauch GM. Early ultrasound evaluation identifies excellent responders to neoadjuvant systemic therapy among patients with triple-negative breast cancer. Cancer 127(16):2880-2887, 2021. e-Pub 2021. PMID: 33878210.
27. Yang T, Niu J, Chen H, Wei P. Estimation of Total Mediation Effect for High-dimensional Omics Mediators. BMC Bioinformatics 22(414):1-17, 2021. e-Pub 2021. PMID: 34425752.
28. Shu H, Chiang T, Wei P, Do KA, Lesslie MD, Cohen EO, Srinivasan A, Moseley TW, Chang Sen LQ, Leung JWT, Dennison JB, Hanash SM, Weaver OO. A Deep-Learning Approach to Recreate Raw Full-Field Digital Mammograms for Breast Density and Texture Analysis. Radiol Artif Intell 3(4):e200097, 2021. e-Pub 2021. PMID: 34350403.
29. Musall BC, Abdelhafez AH, Adrada BE, Candelaria RP, Mohamed RMM, Boge M, Le-Petross H, Arribas E, Lane DL, Spak DA, Leung JWT, Hwang KP, Son JB, Elshafeey NA, Mahmoud HS, Wei P, Sun J, Zhang S, White JB, Ravenberg EE, Litton JK, Damodaran S, Thompson AM, Moulder SL, Yang WT, Pagel MD, Rauch GM, Ma J. Functional Tumor Volume by Fast Dynamic Contrast-Enhanced MRI for Predicting Neoadjuvant Systemic Therapy Response in Triple-Negative Breast Cancer. J Magn Reson Imaging 54(1):251-260, 2021. e-Pub 2021. PMID: 33586845.
30. Fang H, Yabe M, Zhang X, Kim Y, Wu X, Wei P, Chi S, Zheng L, Garcia-Manero G, Shao L, Yuan J, Shen Y, Zheng G, Tang G, Wang W, Loghavi S, Shen Q, Yuan Y, He R, Chen D, Medeiros LJ, Hu S. Myelodysplastic Syndrome with t(6;9)(p22;q34.1)/DEK-NUP214 Better Classified as Acute Myeloid Leukemia? A Multicenter Study of 107 Cases. Mod Pathol 34(6):1143-1152, 2021. e-Pub 2021. PMID: 33558656.
31. Khan IM, Gjuka D, Jiao J, Song X, Wang Y, Wang J, Wei P, El-Serag HB, Marrero JA, Beretta L. A Novel Biomarker Panel for the Early Detection and Risk Assessment of Hepatocellular Carcinoma in Patients with Cirrhosis. Cancer Prev Res (Phila) 14(6):667-674, 2021. e-Pub 2021. PMID: 33685927.
32. Malec SA, Wei P, Bernstam EV, Boyce RD, Cohen T. Using computable knowledge mined from the literature to elucidate confounders for EHR-based pharmacovigilance. J Biomed Inform 117:103719, 2021. e-Pub 2021. PMID: 33716168.
33. Wang Z, Wei P. IMIX: A multivariate mixture model approach to association analysis through multi-omics data integration. Bioinformatics 36(22-23):5439-5447, 2021. e-Pub 2020. PMID: 33258948.
34. Zhang X, Hoffman KL, Wei P, Elhor Gbito KY, Joseph R, Li F, Scheet P, Chang S, Petrosino JF, Daniel CR. Baseline oral microbiome and all-cancer incidence in a cohort of non-smoking Mexican American women. Cancer Prev Res (Phila) 14(3):383-392, 2021. e-Pub 2020. PMID: 33277317.
35. Shi B, Wei P, Huang X. Functional principal component based landmark analysis for the effects of longitudinal cholesterol profiles on the risk of coronary heart disease. Stat Med 40(3):650-667, 2021. e-Pub 2020. PMID: 33155338.
36. Abdelhafez AH, Musall BC, Adrada BE, Hess K, Son JB, Hwang KP, Candelaria RP, Santiago L, Whitman GJ, Le-Petross HT, Moseley TW, Arribas E, Lane DL, Scoggins ME, Leung JWT, Mahmoud HS, White JB, Ravenberg EE, Litton JK, Valero V, Wei P, Thompson AM, Moulder SL, Pagel MD, Ma J, Yang WT, Rauch GM. Tumor necrosis by pretreatment breast MRI: association with neoadjuvant systemic therapy (NAST) response in triple-negative breast cancer (TNBC). Breast Cancer Res Treat 185(1):1-12, 2021. e-Pub 2020. PMID: 32920733.
37. Yang T, Wei P, Pan W. Integrative analysis of multi-omics data for discovering low-frequency variants associated with low-density lipoprotein cholesterol levels. Bioinformatics 36(21):5223-5228, 2021. e-Pub 2020. PMID: 33070182.
38. Zheng J, Hoffman KL, Chen JS, Shivappa N, Sood A, Browman GJ, Dirba DD, Hanash S, Wei P, Hebert JR, Petrosino JF, Schembre SM, Daniel CR. Dietary inflammatory potential in relation to the gut microbiome: results from a cross-sectional study. Br J Nutr 124(9):1-31, 2020. e-Pub 2020. PMID: 32475373.
39. Yang T, Tang H, Risch HA, Olson SH, Peterson G, Bracci PM, Gallinger S, Hung RJ, Neale RE, Scelo G, Duell EJ, Kurtz RC, Khaw KT, Severi G, Sund M, Wareham N, Amos CI, Li D, Wei P. Incorporating multiple sets of eQTL weights into gene-by-environment interaction analysis identifies novel susceptibility loci for pancreatic cancer. Genet Epidemiol 44(8):880-892, 2020. e-Pub 2020. PMID: 32779232.
40. Tang H, Jiang L, Stolzenberg-Solomon RZ, Arslan AA, Beane Freeman LE, Bracci PM, Brennan P, Canzian F, Du M, Gallinger S, Giles GG, Goodman PJ, Kooperberg C, Le Marchand L, Neale RE, Shu XO, Visvanathan K, White E, Zheng W, Albanes D, Andreotti G, Babic A, Bamlet WR, Berndt SI, Blackford A, Bueno-de-Mesquita B, Buring JE, Campa D, Chanock SJ, Childs E, Duell EJ, Fuchs C, Gaziano JM, Goggins M, Hartge P, Hassam MH, Holly EA, Hoover RN, Hung RJ, Kurtz RC, Lee IM, Malats N, Milne RL, Ng K, Oberg AL, Orlow I, Peters U, Porta M, Rabe KG, Rothman N, Scelo G, Sesso HD, Silverman DT, Thompson IM, Tjønneland A, Trichopoulou A, Wactawski-Wende J, Wentzensen N, Wilkens LR, Yu H, Zeleniuch-Jacquotte A, Amundadottir LT, Jacobs EJ, Petersen GM, Wolpin BM, Risch HA, Chatterjee N, Klein AP, Li D, Kraft P, Wei P. Genome-wide gene-diabetes and gene-obesity interaction scan in 8,255 cases and 11,900 controls from the PanScan and PanC4 Consortia. Cancer Epidemiol Biomarkers Prev 29(9):1784-1791, 2020. e-Pub 2020. PMID: 32546605.
41. Teyateeti A, Khan B, Teyateeti A, Chen B, Bridhikitti J, Pan T, Wei P, Macapinlac HA, Lu Y. Diagnostic performance of F-18 fluciclovine PET/CT in post-radical prostatectomy prostate cancer patients with rising prostate-specific antigen level =0.5?ng/mL. Nucl Med Commun 41(9):906-915, 2020. PMID: 32796479.
42. Shuai W, Lin P, Strati P, Patel KP, Routbort MJ, Hu S, Wei P, Khoury JD, You MJ, Loghavi S, Tang Z, Fang H, Thakral B, Medeiros LJ, Wang W. Clinicopathological characterization of chronic lymphocytic leukemia with MYD88 mutations: L265P and non-L265P mutations are associated with different features. Blood Cancer J 10(8):86, 2020. e-Pub 2020. PMID: 32848129.
43. Hebbel RP, Wei P, Milbauer L, Corban MT, Solovey A, Kiley J, Pattee J, Lerman LO, Pan W, Lerman A. Abnormal Endothelial Gene Expression Associated With Early Coronary Atherosclerosis. J Am Heart Assoc 9(14):e016134, 2020. e-Pub 2020. PMID: 32673514.
44. Guo CC, Bondaruk J, Yao H, Wang Z, Zhang L, Lee S, Lee JG, Cogdell D, Zhang M, Yang G, Dadhania V, Choi W, Wei P, Gao J, Theodorescu D, Logothetis C, Dinney C, Kimmel M, Weinstein JN, McConkey DJ, Czerniak B. Assessment of luminal and basal phenotypes in bladder cancer. Sci Rep 10(1):9743, 2020. e-Pub 2020. PMID: 32546765.
45. Yang G, Bondaruk J, Cogdell D, Wang Z, Lee S, Lee JG, Zhang S, Choi W, Wang Y, Liang Y, Wang G, Wang Y, Yao H, Dadhania V, Gao J, Logothetis C, Siefker-Radtke A, Kamat A, Dinney C, Theodorescu D, Kimmel M, Wei P, Guo CC, Weinstein JN, McConkey DJ, Czerniak B. Urothelial-to-Neural Plasticity Drives Progression to Small Cell Bladder Cancer. iScience 23(6):101201, 2020. e-Pub 2020. PMID: 32521509.
46. Wang Z, Wei P, Wei D, Cao S, Liu H, Chen L, Han X, Zhao X, Liu C, Li G, Yang J, Pan X, Lei D. Effect of upregulation of circMATR3 on the proliferation, metastasis, progression, and survival of hypopharyngeal carcinoma. J Cell Mol Med 24(8):4687-4697, 2020. e-Pub 2020. PMID: 32166857.
47. Kwan SY, Jiao J, Qi J, Wang Y, Wei P, McCormick JB, Fisher-Hoch SP, Beretta L. Bile Acid Changes Associated With Liver Fibrosis and Steatosis in the Mexican-American Population of South Texas. Hepatol Commun 4(4):555-568, 2020. e-Pub 2020. PMID: 32258950.
48. Yang T, Wu C, Wei P, Pan W. Integrating DNA sequencing and transcriptomic data for association analyses of low-frequency variants and lipid traits. Hum Mol Genet 29(3):515-526, 2020. PMID: 31919517.
49. Yang T, Kim J, Wu C, Ma Y, Wei P, Pan W. An Adaptive Test for Meta-analysis of Rare Variant Association Studies. Genet Epidemiol 44(1):104-116, 2020. e-Pub 2019. PMID: 31830326.
50. Zhu Y, Xia X, Gross N, Dahlstrom KR, Gao L, Liang Z, Gao Z, Wei P, Liu C, Li G, Li Y, Chen X. Prognostic implications of human papillomavirus status and p16 expression in laryngeal squamous cell carcinoma. Head Neck 41(12):4151-4163, 2019. e-Pub 2019. PMID: 31566825.
51. Zhang Y, Sturgis EM, Wei P, Liu H, Wang Z, Ma Y, Liu C, Gu KJ, Wei Q, Li G. A genetic variant within MDM4 3'UTR miRNA binding site is associated with HPV16-positive tumors and survival of oropharyngeal cancer. Mol Carcinog 58(12):2276-2285, 2019. e-Pub 2019. PMID: 31513313.
52. Chen B, Wei P, Macapinlac HA, Lu Y. Comparison of 18F-Fluciclovine PET/CT and 99mTc-MDP bone scan in detection of bone metastasis in prostate cancer. Nucl Med Commun 40(9):940-946, 2019. e-Pub 2019. PMID: 31343613.
53. 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 149(8):1443-1450, 2019. e-Pub 2019. PMID: 31100111.
54. 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 186(4):538-548, 2019. e-Pub 2019. PMID: 31115909.
55. 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 5(4):664-675, 2019. e-Pub 2018. PMID: 29428551.
56. 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 40(6):735-741, 2019. e-Pub 2019. PMID: 30721961.
57. 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 47(6):300060519838385, 2019. e-Pub 2019. PMID: 30991875.
58. 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.
59. 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.
60. 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.
61. 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.
62. 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.
63. 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.
64. 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.
65. 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.
66. 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.
67. 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.
68. 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.
69. 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.
70. 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.
71. 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.
72. 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.
73. 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.
74. 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.
75. 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.
76. 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.
77. 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.
78. 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.
79. Xu G, Lin L, Wei P, Pan W. An adaptive two-sample test for high-dimensional means. Biometrika 103(3):609-624, 2016.
80. 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.
81. 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.
82. 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.
83. 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.
84. 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.
85. 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.
86. 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.
87. 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.
88. 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.
89. 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.
90. 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.
91. 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.
92. 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.
93. 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.
94. 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.
95. 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.
96. 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.
97. 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.
98. 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.
99. 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.
100. 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.
101. 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.
102. 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.
103. 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.
104. 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.
105. 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.
106. 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.
107. 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.
108. 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.
109. 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.
110. 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.
111. 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.
112. 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.
113. 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.
114. 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.
115. 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.
116. 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.
117. 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.
118. 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.
119. 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.
120. El Hussein S, Medeiros LJ, Lyapichev KA, Fang H, Fiskus A, Chen J, Wei P, Schlette E, Xu J, Li S, Kanagal-Shamanna R, Yang H, Tang Z, Thakral B, Loghavi S, Jain N, Philip A. Thompson PA, Ferrajoli A, Wierda WG, Jabbour E, Patel KP, Dabaja BS, Bhalla KN, Khoury JD. Immunophenotypic and Genomic Landscape of Richter Transformation Diffuse Large B-cell Lymphoma. Pathology.

Book Chapters

1. Wei P, Shu H. Big Data and Machine Learning in Oncology. In: The MD Anderson Manual of Medical Oncology. 4th Edition. McGraw Hill: New York, 1593-1601, 2022.