Program Official

Principal Investigator

Yingye
Zheng
Awardee Organization

Fred Hutchinson Cancer Center
United States

Fiscal Year
2023
Activity Code
U24
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

The Early Detection Research Network: Data Management and Coordinating Center

The key for the Early Detection Research Network (EDRN)'s success lies in good communication among scientists in multiple disciplines; efficient evaluation and prioritization of promising biomarkers; and rigorous validation studies to demonstrate their clinical utility. The overall aims of the proposed renewal of the Data Management and Coordinating Center (DMCC) are to (i) provide coordination of EDRN in order to enhance communication and collaboration among EDRN investigators and with general scientific communities; (ii) coordinate EDRN validation studies and provide leadership in data science; (iii) disseminate cancer biomarker information to broader scientific communities and the public; and (iv) manage the EDRN Core funds. Under the direction of the EDRN Steering Committee, the DMCC will 1) perform network coordination and outreach and promote collaborations among scientific investigators by providing support for EDRN meetings and workshops, developing and maintaining EDRN secure websites and listservs, producing and maintaining all EDRN documents, and maintaining the online review system for applications submitted to the EDRN; 2) support EDRN validation studies by developing and maintaining validation study data management systems; working with EDRN investigators on study design, protocol development, data forms, and study manuals; coordinating and monitoring studies; tracking specimens; and performing QA/QC and study evaluation; and provide and promote best statistical and computational practices to EDRN studies; 3) work with the NCI and JPL to provide informatics resources for the EDRN Secure Web site for data security, data warehousing, and data sharing, and a Public Web site for dissemination; and 4) work closely with the EDRN SC and the NCI Project Coordinator and Fred Hutch OSR to timely activate the core funds after the EDRN SC approval and ensure the compliance of all regulatory requirements for sub-award management.

Publications

  • Huang Y, Pepe MS. Semiparametric methods for evaluating the covariate-specific predictiveness of continuous markers in matched case-control studies. Journal of the Royal Statistical Society. Series C, Applied statistics. 2010;59(3):437-456. PMID: 21562626
  • Li W, Li R, Yan Q, Feng Z, Ning J. Conditional concordance-assisted learning under matched case-control design for combining biomarkers for population screening. Statistics in medicine. 2023 Apr 30;42(9):1398-1411. Epub 2023 Feb 2. PMID: 36733187
  • Wei JT, Feng Z, Partin AW, Brown E, Thompson I, Sokoll L, Chan DW, Lotan Y, Kibel AS, Busby JE, Bidair M, Lin DW, Taneja SS, Viterbo R, Joon AY, Dahlgren J, Kagan J, Srivastava S, Sanda MG. Can urinary PCA3 supplement PSA in the early detection of prostate cancer? Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2014 Dec 20;32(36):4066-72. Epub 2014 Nov 10. PMID: 25385735
  • Semmes OJ, Feng Z, Adam BL, Banez LL, Bigbee WL, Campos D, Cazares LH, Chan DW, Grizzle WE, Izbicka E, Kagan J, Malik G, McLerran D, Moul JW, Partin A, Prasanna P, Rosenzweig J, Sokoll LJ, Srivastava S, Srivastava S, Thompson I, Welsh MJ, White N, Winget M, Yasui Y, Zhang Z, Zhu L. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clinical chemistry. 2005 Jan;51(1):102-12. PMID: 15613711
  • Wang X, Grasso CS, Jordahl KM, Kolb S, Nyame YA, Wright JL, Ostrander EA, Troyer DA, Lance R, Feng Z, Dai JY, Stanford JL. Copy number alterations are associated with metastatic-lethal progression in prostate cancer. Prostate cancer and prostatic diseases. 2020 Sep;23(3):494-506. Epub 2020 Feb 18. PMID: 32071439
  • Singal AG, Hoshida Y, Pinato DJ, Marrero J, Nault JC, Paradis V, Tayob N, Sherman M, Lim YS, Feng Z, Lok AS, Rinaudo JA, Srivastava S, Llovet JM, Villanueva A. International Liver Cancer Association (ILCA) White Paper on Biomarker Development for Hepatocellular Carcinoma. Gastroenterology. 2021 Jun;160(7):2572-2584. Epub 2021 Mar 9. PMID: 33705745
  • Clark JP, Munson KW, Gu JW, Lamparska-Kupsik K, Chan KG, Yoshida JS, Kawachi MH, Crocitto LE, Wilson TG, Feng Z, Smith SS. Performance of a single assay for both type III and type VI TMPRSS2:ERG fusions in noninvasive prediction of prostate biopsy outcome. Clinical chemistry. 2008 Dec;54(12):2007-17. Epub 2008 Oct 23. PMID: 18948370
  • Prentice RL, Qi L. Aspects of the design and analysis of high-dimensional SNP studies for disease risk estimation. Biostatistics (Oxford, England). 2006 Jul;7(3):339-54. Epub 2006 Jan 27. PMID: 16443924
  • Chekouo T, Stingo FC, Class CA, Yan Y, Bohannan Z, Wei Y, Garcia-Manero G, Hanash S, Do KA. Investigating protein patterns in human leukemia cell line experiments: A Bayesian approach for extremely small sample sizes. Statistical methods in medical research. 2020 Apr;29(4):1181-1196. Epub 2019 Jun 7. PMID: 31172886
  • Yang JD, Addissie BD, Mara KC, Harmsen WS, Dai J, Zhang N, Wongjarupong N, Ali HM, Ali HA, Hassan FA, Lavu S, Cvinar JL, Giama NH, Moser CD, Miyabe K, Allotey LK, Algeciras-Schimnich A, Theobald JP, Ward MM, Nguyen MH, Befeler AS, Reddy KR, Schwartz M, Harnois DM, Yamada H, Srivastava S, Rinaudo JA, Gores GJ, Feng Z, Marrero JA, Roberts LR. GALAD Score for Hepatocellular Carcinoma Detection in Comparison with Liver Ultrasound and Proposal of GALADUS Score. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2019 Mar;28(3):531-538. Epub 2018 Nov 21. PMID: 30464023
  • Pepe MS, Etzioni R, Feng Z, Potter JD, Thompson ML, Thornquist M, Winget M, Yasui Y. Phases of biomarker development for early detection of cancer. Journal of the National Cancer Institute. 2001 Jul 18;93(14):1054-61. PMID: 11459866
  • Gao C, Wisniewski L, Liu Y, Staal B, Beddows I, Plenker D, Aldakkak M, Hall J, Barnett D, Gouda MK, Allen P, Drake R, Zureikat A, Huang Y, Evans D, Singhi A, Brand RE, Tuveson DA, Tsai S, Haab BB. Detection of Chemotherapy-resistant Pancreatic Cancer Using a Glycan Biomarker, sTRA. Clinical cancer research : an official journal of the American Association for Cancer Research. 2021 Jan 1;27(1):226-236. Epub 2020 Oct 22. PMID: 33093149
  • Fahrmann JF, Bantis LE, Capello M, Scelo G, Dennison JB, Patel N, Murage E, Vykoukal J, Kundnani DL, Foretova L, Fabianova E, Holcatova I, Janout V, Feng Z, Yip-Schneider M, Zhang J, Brand R, Taguchi A, Maitra A, Brennan P, Max Schmidt C, Hanash S. A Plasma-Derived Protein-Metabolite Multiplexed Panel for Early-Stage Pancreatic Cancer. Journal of the National Cancer Institute. 2019 Apr 1;111(4):372-379. PMID: 30137376
  • Wang L, Huang Y. Evaluating classification performance of biomarkers in two-phase case-control studies. Statistics in medicine. 2019 Jan 15;38(1):100-114. Epub 2018 Sep 12. PMID: 30209824
  • Li F, Wei F, Huang WL, Lin CC, Li L, Shen MM, Yan Q, Liao W, Chia D, Tu M, Tang JH, Feng Z, Kim Y, Su WC, Wong DTW. Ultra-Short Circulating Tumor DNA (usctDNA) in Plasma and Saliva of Non-Small Cell Lung Cancer (NSCLC) Patients. Cancers. 2020 Jul 24;12. (8). PMID: 32722209
  • Pepe MS, Fan J, Seymour CW. Estimating the receiver operating characteristic curve in studies that match controls to cases on covariates. Academic radiology. 2013 Jul;20(7):863-73. Epub 2013 Apr 17. PMID: 23601953
  • Fong Y, Yin S, Huang Y. Combining biomarkers linearly and nonlinearly for classification using the area under the ROC curve. Statistics in medicine. 2016 Sep 20;35(21):3792-809. Epub 2016 Apr 5. PMID: 27058981
  • Zhang Y, Blomquist TM, Kusko R, Stetson D, Zhang Z, Yin L, Sebra R, Gong B, Lococo JS, Mittal VK, Novoradovskaya N, Yeo JY, Dominiak N, Hipp J, Raymond A, Qiu F, Arib H, Smith ML, Brock JE, Farkas DH, Craig DJ, Crawford EL, Li D, Morrison T, Tom N, Xiao W, Yang M, Mason CE, Richmond TA, Jones W, Johann DJ Jr, Shi L, Tong W, Willey JC, Xu J. Deep oncopanel sequencing reveals within block position-dependent quality degradation in FFPE processed samples. Genome biology. 2022 Jun 29;23(1):141. PMID: 35768876
  • Pepe MS, Fan J, Feng Z, Gerds T, Hilden J. The Net Reclassification Index (NRI): a Misleading Measure of Prediction Improvement Even with Independent Test Data Sets. Statistics in biosciences. 2015 Oct 1;7(2):282-295. Epub 2014 Aug 23. PMID: 26504496
  • Tayob N, Feng Z. Personalized statistical learning algorithms to improve the early detection of cancer using longitudinal biomarkers. Cancer biomarkers : section A of Disease markers. 2022;33(2):199-210. PMID: 35213362
  • Payne R, Yang M, Zheng Y, Jensen MK, Cai T. Robust risk prediction with biomarkers under two-phase stratified cohort design. Biometrics. 2016 Dec;72(4):1037-1045. Epub 2016 Apr 1. PMID: 27037494
  • Ostrin EJ, Bantis LE, Wilson DO, Patel N, Wang R, Kundnani D, Adams-Haduch J, Dennison JB, Fahrmann JF, Chiu HT, Gazdar A, Feng Z, Yuan JM, Hanash SM. Contribution of a Blood-Based Protein Biomarker Panel to the Classification of Indeterminate Pulmonary Nodules. Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer. 2021 Feb;16(2):228-236. Epub 2020 Oct 31. PMID: 33137463
  • Cheng A, Zhao S, FitzGerald LM, Wright JL, Kolb S, Karnes RJ, Jenkins RB, Davicioni E, Ostrander EA, Feng Z, Fan JB, Dai JY, Stanford JL. A four-gene transcript score to predict metastatic-lethal progression in men treated for localized prostate cancer: Development and validation studies. The Prostate. 2019 Oct;79(14):1589-1596. Epub 2019 Aug 2. PMID: 31376183
  • Hanash S. Lung cancer susceptibility beyond smoking history: opportunities and challenges. Translational lung cancer research. 2022 Jul;11(7):1230-1232. PMID: 35958329
  • Willey JC, Morrison TB, Austermiller B, Crawford EL, Craig DJ, Blomquist TM, Jones WD, Wali A, Lococo JS, Haseley N, Richmond TA, Novoradovskaya N, Kusko R, Chen G, Li QZ, Johann DJ Jr, Deveson IW, Mercer TR, Wu L, Xu J. Advancing NGS quality control to enable measurement of actionable mutations in circulating tumor DNA. Cell reports methods. 2021 Nov 3;1(7):100106. doi: 10.1016/j.crmeth.2021.100106. eCollection 2021 Nov 22. PMID: 35475002
  • Wang L, Huang Y, Feng Z. Strategies for validating biomarkers using data from a reference set. Biostatistics (Oxford, England). 2021 Apr 10;22(2):298-314. PMID: 31420985
  • Huang Y, Gilbert PB, Janes H. Assessing treatment-selection markers using a potential outcomes framework. Biometrics. 2012 Sep;68(3):687-96. Epub 2012 Feb 2. PMID: 22299708
  • Liu D, Cai T, Lok A, Zheng Y. Nonparametric Maximum Likelihood Estimators of Time-Dependent Accuracy Measures for Survival Outcome Under Two-Stage Sampling Designs. Journal of the American Statistical Association. 2018;113(522):882-892. Epub 2017 Feb 28. PMID: 30555194
  • Thompson ML. Assessing the diagnostic accuracy of a sequence of tests. Biostatistics (Oxford, England). 2003 Jul;4(3):341-51. PMID: 12925502
  • Tayob N, Stingo F, Do KA, Lok ASF, Feng Z. A Bayesian screening approach for hepatocellular carcinoma using multiple longitudinal biomarkers. Biometrics. 2018 Mar;74(1):249-259. Epub 2017 May 8. PMID: 28482112
  • Gao X, Shen W, Ning J, Feng Z, Hu J. Addressing patient heterogeneity in disease predictive model development. Biometrics. 2022 Sep;78(3):1045-1055. Epub 2021 Aug 1. PMID: 34184256
  • Bansal A, Pepe MS. When does combining markers improve classification performance and what are implications for practice? Statistics in medicine. 2013 May 20;32(11):1877-92. Epub 2013 Jan 24. PMID: 23348801
  • Cao Y, Haneuse S, Zheng Y, Chen J. Two-phase stratified sampling and analysis for predicting binary outcomes. Biostatistics (Oxford, England). 2023 Jul 14;24(3):585-602. PMID: 34923588
  • Zhou QM, Wang X, Zheng Y, Cai T. New weighting methods when cases are only a subset of events in a nested case-control study. Biometrical journal. Biometrische Zeitschrift. 2022 Oct;64(7):1240-1259. Epub 2022 Jun 26. PMID: 35754309
  • Maziarz M, Heagerty P, Cai T, Zheng Y. On longitudinal prediction with time-to-event outcome: Comparison of modeling options. Biometrics. 2017 Mar;73(1):83-93. Epub 2016 Jul 20. PMID: 27438160
  • McLerran D, Grizzle WE, Feng Z, Thompson IM, Bigbee WL, Cazares LH, Chan DW, Dahlgren J, Diaz J, Kagan J, Lin DW, Malik G, Oelschlager D, Partin A, Randolph TW, Sokoll L, Srivastava S, Srivastava S, Thornquist M, Troyer D, Wright GL, Zhang Z, Zhu L, Semmes OJ. SELDI-TOF MS whole serum proteomic profiling with IMAC surface does not reliably detect prostate cancer. Clinical chemistry. 2008 Jan;54(1):53-60. Epub 2007 Nov 16. PMID: 18024530
  • Williamson BD, Huang Y. Flexible variable selection in the presence of missing data. The international journal of biostatistics. 2024 Feb 13. Epub 2024 Feb 13. PMID: 38348882
  • Wang CY, Hsu L. Multinomial logistic regression with missing outcome data: An application to cancer subtypes. Statistics in medicine. 2020 Oct 30;39(24):3299-3312. Epub 2020 Jul 6. PMID: 32628308
  • Ankerst DP, Goros M, Tomlins SA, Patil D, Feng Z, Wei JT, Sanda MG, Gelfond J, Thompson IM, Leach RJ, Liss MA. Incorporation of Urinary Prostate Cancer Antigen 3 and TMPRSS2:ERG into Prostate Cancer Prevention Trial Risk Calculator. European urology focus. 2019 Jan;5(1):54-61. Epub 2018 Feb 13. PMID: 29422418
  • Pepe MS, Longton G, Anderson GL, Schummer M. Selecting differentially expressed genes from microarray experiments. Biometrics. 2003 Mar;59(1):133-42. PMID: 12762450
  • Qu Y, Adam BL, Thornquist M, Potter JD, Thompson ML, Yasui Y, Davis J, Schellhammer PF, Cazares L, Clements M, Wright GL Jr, Feng Z. Data reduction using a discrete wavelet transform in discriminant analysis of very high dimensionality data. Biometrics. 2003 Mar;59(1):143-51. PMID: 12762451
  • Chan S, Wang X, Jazić I, Peskoe S, Zheng Y, Cai T. Developing and evaluating risk prediction models with panel current status data. Biometrics. 2021 Jun;77(2):599-609. Epub 2020 Jul 8. PMID: 32562264
  • Tayob N, Do KA, Feng Z. Unbiased estimation of biomarker panel performance when combining training and testing data in a group sequential design. Biometrics. 2016 Sep;72(3):888-96. Epub 2016 Feb 4. PMID: 26845527
  • Borges KA, Dai J, Parikh ND, Schwartz M, Nguyen MH, Roberts LR, Befeler AS, Srivastava S, Rinaudo JA, Feng Z, Marrero JA, Reddy KR. Rationale and design of the Hepatocellular carcinoma Early Detection Strategy study: A multi-center longitudinal initiative of the National Cancer Institute's Early Detection Research Network. Contemporary clinical trials. 2019 Jan;76:49-54. Epub 2018 Nov 12. PMID: 30439517
  • Liu Y, Kaur S, Huang Y, Fahrmann JF, Rinaudo JA, Hanash SM, Batra SK, Singhi AD, Brand RE, Maitra A, Haab BB. Biomarkers and Strategy to Detect Preinvasive and Early Pancreatic Cancer: State of the Field and the Impact of the EDRN. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2020 Dec;29(12):2513-2523. Epub 2020 Jun 12. PMID: 32532830
  • Zheng C, Zheng Y. Calibrate Variations in Biomarker Measures for Improving Prediction with Time-to-event Outcomes. Statistics in biosciences. 2019 Dec;11(3):477-503. Epub 2019 Apr 5. PMID: 33833826
  • Wang P, Tang H, Zhang H, Whiteaker J, Paulovich AG, Mcintosh M. Normalization regarding non-random missing values in high-throughput mass spectrometry data. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 2006: 315-26. PMID: 17094249
  • Kerr KF, Bansal A, Pepe MS. Further insight into the incremental value of new markers: the interpretation of performance measures and the importance of clinical context. American journal of epidemiology. 2012 Sep 15;176(6):482-7. Epub 2012 Aug 8. PMID: 22875756
  • Wang CY, Feng Z. A Flexible Method for Diagnostic Accuracy with Biomarker Measurement Error. Mathematics (Basel, Switzerland). 2023 Feb 1;11. (3). Epub 2023 Jan 19. PMID: 37251695
  • Huang Y, Laber EB, Janes H. Characterizing expected benefits of biomarkers in treatment selection. Biostatistics (Oxford, England). 2015 Apr;16(2):383-99. Epub 2014 Sep 3. PMID: 25190512
  • Kim S, Huang Y. Combining biomarkers for classification with covariate adjustment. Statistics in medicine. 2017 Jul 10;36(15):2347-2362. Epub 2017 Mar 9. PMID: 28276080
  • Marks JR, Anderson KS, Engstrom P, Godwin AK, Esserman LJ, Longton G, Iversen ES, Mathew A, Patriotis C, Pepe MS. Construction and analysis of the NCI-EDRN breast cancer reference set for circulating markers of disease. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2015 Feb;24(2):435-41. Epub 2014 Dec 3. PMID: 25471344
  • Ransohoff DF. Evaluating a New Cancer Screening Blood Test: Unintended Consequences and the Need for Clarity in Policy Making. Journal of the National Cancer Institute. 2021 Feb 1;113(2):109-111. PMID: 32761203
  • Kearns JT, Faino AV, Newcomb LF, Brooks JD, Carroll PR, Dash A, Ellis WJ, Fabrizio M, Gleave ME, Morgan TM, Nelson PS, Thompson IM, Wagner AA, Zheng Y, Lin DW. Role of Surveillance Biopsy with No Cancer as a Prognostic Marker for Reclassification: Results from the Canary Prostate Active Surveillance Study. European urology. 2018 May;73(5):706-712. Epub 2018 Feb 9. PMID: 29433973
  • Zhao S, Zheng Y, Prentice RL, Feng Z. Two-stage biomarker panel study and estimation allowing early termination for futility. Biostatistics (Oxford, England). 2015 Oct;16(4):799-812. Epub 2015 May 11. PMID: 25964662
  • Cooperberg MR, Brooks JD, Faino AV, Newcomb LF, Kearns JT, Carroll PR, Dash A, Etzioni R, Fabrizio MD, Gleave ME, Morgan TM, Nelson PS, Thompson IM, Wagner AA, Lin DW, Zheng Y. Refined Analysis of Prostate-specific Antigen Kinetics to Predict Prostate Cancer Active Surveillance Outcomes. European urology. 2018 Aug;74(2):211-217. Epub 2018 Feb 9. PMID: 29433975
  • Zheng Y, Brown M, Lok A, Cai T. IMPROVING EFFICIENCY IN BIOMARKER INCREMENTAL VALUE EVALUATION UNDER TWO-PHASE DESIGNS. The annals of applied statistics. 2017 Jun;11(2):638-654. Epub 2017 Jul 20. PMID: 28943991
  • Chari ST, Maitra A, Matrisian LM, Shrader EE, Wu BU, Kambadakone A, Zhao YQ, Kenner B, Rinaudo JAS, Srivastava S, Huang Y, Feng Z, Early Detection Initiative Consortium. Early Detection Initiative: A randomized controlled trial of algorithm-based screening in patients with new onset hyperglycemia and diabetes for early detection of pancreatic ductal adenocarcinoma. Contemporary clinical trials. 2022 Feb;113:106659. Epub 2021 Dec 23. PMID: 34954100
  • Tayob N, Lok ASF, Feng Z. A multivariate parametric empirical Bayes screening approach for early detection of hepatocellular carcinoma using multiple longitudinal biomarkers. Statistics in medicine. 2022 Jun 15;41(13):2338-2353. Epub 2022 Feb 23. PMID: 35199349
  • Park Y, Yuan Y, Ning J, Liu S, Feng Z. Hybrid design evaluating new biomarkers when there is an existing screening test. Statistics in medicine. 2021 Apr 15;40(8):2037-2054. Epub 2021 Feb 4. PMID: 33540472
  • Sanda MG, Feng Z, Howard DH, Tomlins SA, Sokoll LJ, Chan DW, Regan MM, Groskopf J, Chipman J, Patil DH, Salami SS, Scherr DS, Kagan J, Srivastava S, Thompson IM Jr, Siddiqui J, Fan J, Joon AY, Bantis LE, Rubin MA, Chinnayian AM, Wei JT, and the EDRN-PCA3 Study Group, Bidair M, Kibel A, Lin DW, Lotan Y, Partin A, Taneja S. Association Between Combined TMPRSS2:ERG and PCA3 RNA Urinary Testing and Detection of Aggressive Prostate Cancer. JAMA oncology. 2017 Aug 1;3(8):1085-1093. PMID: 28520829
  • Buas MF, Li CI, Anderson GL, Pepe MS. Recommendation to use exact P-values in biomarker discovery research in place of approximate P-values. Cancer epidemiology. 2018 Oct;56:83-89. Epub 2018 Aug 10. PMID: 30099328
  • Zhou QM, Dai W, Zheng Y, Cai T. Robust Dynamic Risk Prediction with Longitudinal Studies. Statistical theory and related fields. 2017;1(2):159-170. Epub 2017 Nov 27. PMID: 29335682
  • Kerr KF, Pepe MS. Joint modeling, covariate adjustment, and interaction: contrasting notions in risk prediction models and risk prediction performance. Epidemiology (Cambridge, Mass.). 2011 Nov;22(6):805-12. PMID: 21968770
  • Fu R, Wang P, Ma W, Taguchi A, Wong CH, Zhang Q, Gazdar A, Hanash SM, Zhou Q, Zhong H, Feng Z. A statistical method for detecting differentially expressed SNVs based on next-generation RNA-seq data. Biometrics. 2017 Mar;73(1):42-51. Epub 2016 Jun 8. PMID: 27276420
  • Winget MD, Baron JA, Spitz MR, Brenner DE, Warzel D, Kincaid H, Thornquist M, Feng Z. Development of common data elements: the experience of and recommendations from the early detection research network. International journal of medical informatics. 2003 Apr;70(1):41-8. PMID: 12706181
  • Pepe MS, Cai T. The analysis of placement values for evaluating discriminatory measures. Biometrics. 2004 Jun;60(2):528-35. PMID: 15180681
  • Tayob N, Lok AS, Do KA, Feng Z. Improved Detection of Hepatocellular Carcinoma by Using a Longitudinal Alpha-Fetoprotein Screening Algorithm. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2016 Mar;14(3):469-475.e2. Epub 2015 Aug 7. PMID: 26260109
  • Pepe MS, Kerr KF, Longton G, Wang Z. Testing for improvement in prediction model performance. Statistics in medicine. 2013 Apr 30;32(9):1467-82. Epub 2013 Jan 7. PMID: 23296397
  • Prentice RL. Observational studies, clinical trials, and the women's health initiative. Lifetime data analysis. 2007 Dec;13(4):449-62. Epub 2007 Oct 18. PMID: 17943443
  • Pepe MS, Janes H, Li CI, Bossuyt PM, Feng Z, Hilden J. Early-Phase Studies of Biomarkers: What Target Sensitivity and Specificity Values Might Confer Clinical Utility? Clinical chemistry. 2016 May;62(5):737-42. Epub 2016 Mar 21. PMID: 27001493
  • Feng Z, Pepe MS. Adding Rigor to Biomarker Evaluations-EDRN Experience. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2020 Dec;29(12):2575-2582. Epub 2020 Nov 10. PMID: 33172885
  • Zheng Y. Study Design Considerations for Cancer Biomarker Discoveries. The journal of applied laboratory medicine. 2018 Sep;3(2):282-289. PMID: 30828695
  • Randolph TW, Mitchell BL, McLerran DF, Lampe PD, Feng Z. Quantifying peptide signal in MALDI-TOF mass spectrometry data. Molecular & cellular proteomics : MCP. 2005 Dec;4(12):1990-9. Epub 2005 Sep 29. PMID: 16195224
  • Huang Y, Pepe MS, Feng Z. LOGISTIC REGRESSION ANALYSIS WITH STANDARDIZED MARKERS. The annals of applied statistics. 2013 Sep 1;7. (3). PMID: 24204441
  • Li R, Ning J, Feng Z. Estimation and inference of predictive discrimination for survival outcome risk prediction models. Lifetime data analysis. 2022 Apr;28(2):219-240. Epub 2022 Jan 21. PMID: 35061146
  • Huang Y, Pepe MS. Biomarker evaluation and comparison using the controls as a reference population. Biostatistics (Oxford, England). 2009 Apr;10(2):228-44. Epub 2008 Aug 28. PMID: 18755739
  • Barnett D, Liu Y, Partyka K, Huang Y, Tang H, Hostetter G, Brand RE, Singhi AD, Drake RR, Haab BB. The CA19-9 and Sialyl-TRA Antigens Define Separate Subpopulations of Pancreatic Cancer Cells. Scientific reports. 2017 Jun 22;7(1):4020. PMID: 28642461
  • Danaher P, Wang P, Witten DM. The joint graphical lasso for inverse covariance estimation across multiple classes. Journal of the Royal Statistical Society. Series B, Statistical methodology. 2014 Mar;76(2):373-397. PMID: 24817823
  • Pepe MS, Janes HE. Gauging the performance of SNPs, biomarkers, and clinical factors for predicting risk of breast cancer. Journal of the National Cancer Institute. 2008 Jul 16;100(14):978-9. Epub 2008 Jul 8. PMID: 18612128
  • Bantis LE, Feng Z. Comparison of two correlated ROC curves at a given specificity or sensitivity level. Statistics in medicine. 2016 Oct 30;35(24):4352-4367. Epub 2016 Jun 20. PMID: 27324068
  • Huang Y, Pepe MS. Assessing risk prediction models in case-control studies using semiparametric and nonparametric methods. Statistics in medicine. 2010 Jun 15;29(13):1391-410. PMID: 20527013
  • Irajizad E, Fahrmann JF, Marsh T, Vykoukal J, Dennison JB, Long JP, Do KA, Feng Z, Hanash S, Ostrin EJ. Mortality Benefit of a Blood-Based Biomarker Panel for Lung Cancer on the Basis of the Prostate, Lung, Colorectal, and Ovarian Cohort. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2023 Sep 20;41(27):4360-4368. Epub 2023 Jun 28. PMID: 37379494
  • Yan Q, Bantis LE, Stanford JL, Feng Z. Combining multiple biomarkers linearly to maximize the partial area under the ROC curve. Statistics in medicine. 2018 Feb 20;37(4):627-642. Epub 2017 Oct 30. PMID: 29082535
  • Zhong H, Prentice RL. Bias-reduced estimators and confidence intervals for odds ratios in genome-wide association studies. Biostatistics (Oxford, England). 2008 Oct;9(4):621-34. Epub 2008 Feb 28. PMID: 18310059
  • Newman LA, Stark A, Chitale D, Pepe M, Longton G, Worsham MJ, Nathanson SD, Miller P, Bensenhaver JM, Proctor E, Swain M, Patriotis C, Engstrom PF. Association Between Benign Breast Disease in African American and White American Women and Subsequent Triple-Negative Breast Cancer. JAMA oncology. 2017 Aug 1;3(8):1102-1106. PMID: 28006062
  • Huang Y, Gilbert PB, Wolfson J. Design and estimation for evaluating principal surrogate markers in vaccine trials. Biometrics. 2013 Jun;69(2):301-9. Epub 2013 Feb 14. PMID: 23409839
  • Zheng Y, Cai T, Jin Y, Feng Z. Evaluating prognostic accuracy of biomarkers under competing risk. Biometrics. 2012 Jun;68(2):388-96. Epub 2011 Dec 7. PMID: 22150576
  • Cheng J, Levina E, Wang P, Zhu J. A sparse Ising model with covariates. Biometrics. 2014 Dec;70(4):943-53. Epub 2014 Aug 5. PMID: 25099186
  • Jung Y, Hu J. A K-fold Averaging Cross-validation Procedure. Journal of nonparametric statistics. 2015;27(2):167-179. Epub 2015 Feb 26. PMID: 27630515
  • Janssens AC, Ioannidis JP, Bedrosian S, Boffetta P, Dolan SM, Dowling N, Fortier I, Freedman AN, Grimshaw JM, Gulcher J, Gwinn M, Hlatky MA, Janes H, Kraft P, Melillo S, O'Donnell CJ, Pencina MJ, Ransohoff D, Schully SD, Seminara D, Winn DM, Wright CF, van Duijn CM, Little J, Khoury MJ. Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration. European journal of epidemiology. 2011 Apr;26(4):313-37. PMID: 21424820
  • Zhang L, Yang N, Park JW, Katsaros D, Fracchioli S, Cao G, O'Brien-Jenkins A, Randall TC, Rubin SC, Coukos G. Tumor-derived vascular endothelial growth factor up-regulates angiopoietin-2 in host endothelium and destabilizes host vasculature, supporting angiogenesis in ovarian cancer. Cancer research. 2003 Jun 15;63(12):3403-12. PMID: 12810677
  • Ha MJ, Banerjee S, Akbani R, Liang H, Mills GB, Do KA, Baladandayuthapani V. Personalized Integrated Network Modeling of the Cancer Proteome Atlas. Scientific reports. 2018 Oct 8;8(1):14924. PMID: 30297783
  • Fahrmann JF, Marsh T, Irajizad E, Patel N, Murage E, Vykoukal J, Dennison JB, Do KA, Ostrin E, Spitz MR, Lam S, Shete S, Meza R, Tammemägi MC, Feng Z, Hanash SM. Blood-Based Biomarker Panel for Personalized Lung Cancer Risk Assessment. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2022 Mar 10;40(8):876-883. Epub 2022 Jan 7. PMID: 34995129
  • Huang Y. Evaluating and comparing biomarkers with respect to the area under the receiver operating characteristics curve in two-phase case-control studies. Biostatistics (Oxford, England). 2016 Jul;17(3):499-522. Epub 2016 Feb 16. PMID: 26883772
  • Zheng J, Zheng Y, Hsu L. Risk Projection for Time-to-event Outcome Leveraging Summary Statistics With Source Individual-level Data. Journal of the American Statistical Association. 2022;117(540):2043-2055. Epub 2021 Apr 22. PMID: 36687294
  • Vykoukal J, Fahrmann JF, Patel N, Shimizu M, Ostrin EJ, Dennison JB, Ivan C, Goodman GE, Thornquist MD, Barnett MJ, Feng Z, Calin GA, Hanash SM. Contributions of Circulating microRNAs for Early Detection of Lung Cancer. Cancers. 2022 Aug 30;14. (17). PMID: 36077759
  • Hemken PM, Sokoll LJ, Yang X, Dai J, Elliott D, Gawel SH, Lucht M, Feng Z, Marrero JA, Srivastava S, Chan DW, Davis GJ. Validation of a novel model for the early detection of hepatocellular carcinoma. Clinical proteomics. 2019 Jan 16;16:2. doi: 10.1186/s12014-018-9222-0. eCollection 2019. PMID: 30675135
  • Zhao YQ, Zhu R, Chen G, Zheng Y. Constructing dynamic treatment regimes with shared parameters for censored data. Statistics in medicine. 2020 Apr 30;39(9):1250-1263. Epub 2020 Jan 17. PMID: 31951041
  • Dong X, Zheng Y, Lin DW, Newcomb L, Zhao YQ. Constructing time-invariant dynamic surveillance rules for optimal monitoring schedules. Biometrics. 2023 Dec;79(4):3895-3906. Epub 2023 Jul 21. PMID: 37479875
  • Etzioni R, Gulati R, Patriotis C, Rutter C, Zheng Y, Srivastava S, Feng Z. Revisiting the standard blueprint for biomarker development to address emerging cancer early detection technologies. Journal of the National Cancer Institute. 2024 Feb 8;116(2):189-193. PMID: 37941446
  • Wang Y, Zhao Y, Zheng Y. Targeted Search for Individualized Clinical Decision Rules to Optimize Clinical Outcomes. Statistics in biosciences. 2022 Dec;14(3):564-581. Epub 2022 May 28. PMID: 37323466
  • Wang X, Zheng Y, Jensen MK, He Z, Cai T. Biomarker evaluation under imperfect nested case-control design. Statistics in medicine. 2021 Aug 15;40(18):4035-4052. Epub 2021 Apr 29. PMID: 33915597
  • Bantis LE, Yan Q, Tsimikas JV, Feng Z. Estimation of smooth ROC curves for biomarkers with limits of detection. Statistics in medicine. 2017 Oct 30;36(24):3830-3843. Epub 2017 Aug 7. PMID: 28786136
  • Wang Y, Zhao YQ, Zheng Y. Learning-based biomarker-assisted rules for optimized clinical benefit under a risk constraint. Biometrics. 2020 Sep;76(3):853-862. Epub 2019 Dec 25. PMID: 31833561
  • Tosoian JJ, Sessine MS, Trock BJ, Ross AE, Xie C, Zheng Y, Samora NL, Siddiqui J, Niknafs Y, Chopra Z, Tomlins S, Kunju LP, Palapattu GS, Morgan TM, Wei JT, Salami SS, Chinnaiyan AM. MyProstateScore in men considering repeat biopsy: validation of a simple testing approach. Prostate cancer and prostatic diseases. 2023 Sep;26(3):563-567. Epub 2022 Dec 30. PMID: 36585434
  • Koopmeiners JS, Feng Z. Group sequential testing of the predictive accuracy of a continuous biomarker with unknown prevalence. Statistics in medicine. 2016 Apr 15;35(8):1267-80. Epub 2015 Nov 4. PMID: 26537180
  • Wang X, Qin L, Zhang H, Zhang Y, Hsu L, Wang P. A regularized multivariate regression approach for eQTL analysis. Statistics in biosciences. 2015 May 1;7(1):129-146. Epub 2013 Nov 21. PMID: 26085849
  • Gu W, Pepe MS. Estimating the capacity for improvement in risk prediction with a marker. Biostatistics (Oxford, England). 2009 Jan;10(1):172-86. Epub 2008 Aug 19. PMID: 18714084
  • Li S, Hsu L, Peng J, Wang P. BOOTSTRAP INFERENCE FOR NETWORK CONSTRUCTION WITH AN APPLICATION TO A BREAST CANCER MICROARRAY STUDY. The annals of applied statistics. 2013 Mar 1;7(1):391-417. PMID: 24563684
  • Class CA, Ha MJ, Baladandayuthapani V, Do KA. iDINGO-integrative differential network analysis in genomics with Shiny application. Bioinformatics (Oxford, England). 2018 Apr 1;34(7):1243-1245. PMID: 29194470
  • Feng Z, Kagan J, Pepe M, Thornquist M, Ann Rinaudo J, Dahlgren J, Krueger K, Zheng Y, Patriotis C, Huang Y, Sorbara L, Thompson I, Srivastava S. The Early Detection Research Network's Specimen reference sets: paving the way for rapid evaluation of potential biomarkers. Clinical chemistry. 2013 Jan;59(1):68-74. Epub 2012 Nov 27. PMID: 23193062
  • McLerran D, Grizzle WE, Feng Z, Bigbee WL, Banez LL, Cazares LH, Chan DW, Diaz J, Izbicka E, Kagan J, Malehorn DE, Malik G, Oelschlager D, Partin A, Randolph T, Rosenzweig N, Srivastava S, Srivastava S, Thompson IM, Thornquist M, Troyer D, Yasui Y, Zhang Z, Zhu L, Semmes OJ. Analytical validation of serum proteomic profiling for diagnosis of prostate cancer: sources of sample bias. Clinical chemistry. 2008 Jan;54(1):44-52. Epub 2007 Nov 2. PMID: 17981926
  • Huang Y, Laber E. Personalized Evaluation of Biomarker Value: A Cost-Benefit Perspective. Statistics in biosciences. 2016;8(1):43-65. Epub 2014 Nov 21. PMID: 27446505
  • Marsh TL, Janes H, Pepe MS. Statistical inference for net benefit measures in biomarker validation studies. Biometrics. 2020 Sep;76(3):843-852. Epub 2019 Nov 28. PMID: 31732971
  • Ankerst DP, Koniarski T, Liang Y, Leach RJ, Feng Z, Sanda MG, Partin AW, Chan DW, Kagan J, Sokoll L, Wei JT, Thompson IM. Updating risk prediction tools: a case study in prostate cancer. Biometrical journal. Biometrische Zeitschrift. 2012 Jan;54(1):127-42. Epub 2011 Nov 17. PMID: 22095849
  • Shaukat A, Marsh TL, Crockett SD, Syngal S, Bresalier RS, Brenner DE. Low Prevalence of Screen-Detected Colorectal Cancer in an Average-Risk Population: The New Normal. Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association. 2022 Nov;20(11):2650-2652.e1. Epub 2021 Sep 20. PMID: 34547437
  • Dasgupta S, Huang Y. Selecting Biomarkers for building optimal treatment selection rules using Kernel Machines. Journal of the Royal Statistical Society. Series C, Applied statistics. 2020 Jan 1;69(1):69-88. Epub 2019 Sep 18. PMID: 32921837
  • Ladabaum U, Church TR, Feng Z, Ransohoff DF, Schoen RE. Counting Advanced Precancerous Lesions as True Positives When Determining Colorectal Cancer Screening Test Specificity. Journal of the National Cancer Institute. 2022 Jul 11;114(7):1040-1043. PMID: 35134969
  • Pepe MS, Li CI, Feng Z. Improving the quality of biomarker discovery research: the right samples and enough of them. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology. 2015 Jun;24(6):944-50. Epub 2015 Apr 2. PMID: 25837819
  • Kashiro A, Kobayashi M, Oh T, Miyamoto M, Atsumi J, Nagashima K, Takeuchi K, Nara S, Hijioka S, Morizane C, Kikuchi S, Kato S, Kato K, Ochiai H, Obata D, Shizume Y, Konishi H, Nomura Y, Matsuyama K, Xie C, Wong C, Huang Y, Jung G, Srivastava S, Kutsumi H, Honda K. Clinical development of a blood biomarker using apolipoprotein-A2 isoforms for early detection of pancreatic cancer. Journal of gastroenterology. 2024 Mar;59(3):263-278. Epub 2024 Jan 23. PMID: 38261000
  • Bantis LE, Tsimikas JV, Chambers GR, Capello M, Hanash S, Feng Z. The length of the receiver operating characteristic curve and the two cutoff Youden index within a robust framework for discovery, evaluation, and cutoff estimation in biomarker studies involving improper receiver operating characteristic curves. Statistics in medicine. 2021 Mar 30;40(7):1767-1789. Epub 2021 Feb 2. PMID: 33530129
  • Huang Y, Fong Y, Wei J, Feng Z. Borrowing Information across Populations in Estimating Positive and Negative Predictive Values. Journal of the Royal Statistical Society. Series C, Applied statistics. 2011 Nov 1;60(5):633-653. PMID: 22021938
  • Prentice RL. Epidemiologic methods developments: a look forward to the year 2032. Annals of epidemiology. 2007 Nov;17(11):906-10. Epub 2007 Sep 14. PMID: 17855116
  • Pepe MS, Longton G. Standardizing diagnostic markers to evaluate and compare their performance. Epidemiology (Cambridge, Mass.). 2005 Sep;16(5):598-603. PMID: 16135934
  • Kim J, Do KA, Ha MJ, Peterson CB. Bayesian inference of hub nodes across multiple networks. Biometrics. 2019 Mar;75(1):172-182. Epub 2018 Aug 23. PMID: 30051914
  • Hwang WH, Stoklosa J, Wang CY. Population Size Estimation using Zero-truncated Poisson Regression with Measurement Error. Journal of agricultural, biological, and environmental statistics. 2022 Jun;27(2):303-320. Epub 2022 Jan 12. PMID: 35813491
  • Besasie BD, Sunnapwar AG, Gao F, Troyer D, Clarke GD, White H, Fox PT, Dale A, Wheeler A, Liss MA. Restriction Spectrum Imaging-Magnetic Resonance Imaging to Improve Prostate Cancer Imaging in Men on Active Surveillance. The Journal of urology. 2021 Jul;206(1):44-51. Epub 2021 Feb 22. PMID: 33617334
  • Huang Y, Fong Y. Identifying optimal biomarker combinations for treatment selection via a robust kernel method. Biometrics. 2014 Dec;70(4):891-901. Epub 2014 Aug 14. PMID: 25124089
  • Huang Y, Pepe MS. A parametric ROC model-based approach for evaluating the predictiveness of continuous markers in case-control studies. Biometrics. 2009 Dec;65(4):1133-44. PMID: 19459841
  • Maziarz M, Cai T, Qi L, Lok AS, Zheng Y. Evaluating longitudinal markers under two-phase study designs. Biostatistics (Oxford, England). 2019 Jul 1;20(3):485-498. PMID: 29912281
  • Wang L, Luedtke AR, Huang Y. Assessing the incremental value of new biomarkers based on OR rules. Biostatistics (Oxford, England). 2020 Jul 1;21(3):594-609. PMID: 30590454