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Statistical inference for net benefit measures in biomarker validation studies.

Marsh TL, Janes H, Pepe MS.

Biometrics. 2019 Nov 16. doi: 10.1111/biom.13190. [Epub ahead of print]


Assessment of Second-Opinion Strategies for Diagnoses of Cutaneous Melanocytic Lesions.

Piepkorn MW, Longton GM, Reisch LM, Elder DE, Pepe MS, Kerr KF, Tosteson ANA, Nelson HD, Knezevich S, Radick A, Shucard H, Onega T, Carney PA, Elmore JG, Barnhill RL.

JAMA Netw Open. 2019 Oct 2;2(10):e1912597. doi: 10.1001/jamanetworkopen.2019.12597.


Concordance and Reproducibility of Melanoma Staging According to the 7th vs 8th Edition of the AJCC Cancer Staging Manual.

Elmore JG, Elder DE, Barnhill RL, Knezevich SR, Longton GM, Titus LJ, Weinstock MA, Pepe MS, Nelson HD, Reisch LM, Radick AC, Piepkorn MW.

JAMA Netw Open. 2018 May;1(1). pii: e180083. doi: 10.1001/jamanetworkopen.2018.0083.


Combined use of ELISA and Western blot with recombinant N protein is a powerful tool for the immunodiagnosis of avian infectious bronchitis.

Finger PF, Pepe MS, Dummer LA, Magalhães CG, de Castro CC, de Oliveira Hübner S, Leite FPL, Ritterbusch GA, Esteves PA, Conceição FR.

Virol J. 2018 Dec 12;15(1):189. doi: 10.1186/s12985-018-1096-2.


Recommendation to use exact P-values in biomarker discovery research in place of approximate P-values.

Buas MF, Li CI, Anderson GL, Pepe MS.

Cancer Epidemiol. 2018 Oct;56:83-89. doi: 10.1016/j.canep.2018.07.014. Epub 2018 Aug 10.


Pathologist characteristics associated with accuracy and reproducibility of melanocytic skin lesion interpretation.

Elder DE, Piepkorn MW, Barnhill RL, Longton GM, Nelson HD, Knezevich SR, Pepe MS, Carney PA, Titus LJ, Onega T, Tosteson ANA, Weinstock MA, Elmore JG.

J Am Acad Dermatol. 2018 Jul;79(1):52-59.e5. doi: 10.1016/j.jaad.2018.02.070. Epub 2018 Mar 7.


Pathologists' diagnosis of invasive melanoma and melanocytic proliferations: observer accuracy and reproducibility study.

Elmore JG, Barnhill RL, Elder DE, Longton GM, Pepe MS, Reisch LM, Carney PA, Titus LJ, Nelson HD, Onega T, Tosteson ANA, Weinstock MA, Knezevich SR, Piepkorn MW.

BMJ. 2017 Jun 28;357:j2813. doi: 10.1136/bmj.j2813. Erratum in: BMJ. 2017 Aug 8;358:j3798.


The diagnostic challenge of low-grade ductal carcinoma in situ.

Onega T, Weaver DL, Frederick PD, Allison KH, Tosteson ANA, Carney PA, Geller BM, Longton GM, Nelson HD, Oster NV, Pepe MS, Elmore JG.

Eur J Cancer. 2017 Jul;80:39-47. doi: 10.1016/j.ejca.2017.04.013. Epub 2017 May 20.


A Randomized Study Comparing Digital Imaging to Traditional Glass Slide Microscopy for Breast Biopsy and Cancer Diagnosis.

Elmore JG, Longton GM, Pepe MS, Carney PA, Nelson HD, Allison KH, Geller BM, Onega T, Tosteson AN, Mercan E, Shapiro LG, Brunyé TT, Morgan TR, Weaver DL.

J Pathol Inform. 2017 Mar 10;8:12. doi: 10.4103/2153-3539.201920. eCollection 2017.


Diagnostic Reproducibility: What Happens When the Same Pathologist Interprets the Same Breast Biopsy Specimen at Two Points in Time?

Jackson SL, Frederick PD, Pepe MS, Nelson HD, Weaver DL, Allison KH, Carney PA, Geller BM, Tosteson AN, Onega T, Elmore JG.

Ann Surg Oncol. 2017 May;24(5):1234-1241. doi: 10.1245/s10434-016-5695-0. Epub 2016 Dec 2.


Evaluation of 12 strategies for obtaining second opinions to improve interpretation of breast histopathology: simulation study.

Elmore JG, Tosteson AN, Pepe MS, Longton GM, Nelson HD, Geller B, Carney PA, Onega T, Allison KH, Jackson SL, Weaver DL.

BMJ. 2016 Jun 22;353:i3069. doi: 10.1136/bmj.i3069.


Early-Phase Studies of Biomarkers: What Target Sensitivity and Specificity Values Might Confer Clinical Utility?

Pepe MS, Janes H, Li CI, Bossuyt PM, Feng Z, Hilden J.

Clin Chem. 2016 May;62(5):737-42. doi: 10.1373/clinchem.2015.252163. Epub 2016 Mar 21.


Variability in Pathologists' Interpretations of Individual Breast Biopsy Slides: A Population Perspective.

Elmore JG, Nelson HD, Pepe MS, Longton GM, Tosteson AN, Geller B, Onega T, Carney PA, Jackson SL, Allison KH, Weaver DL.

Ann Intern Med. 2016 May 17;164(10):649-55. doi: 10.7326/M15-0964. Epub 2016 Mar 22.


The Net Reclassification Index (NRI): a Misleading Measure of Prediction Improvement Even with Independent Test Data Sets.

Pepe MS, Fan J, Feng Z, Gerds T, Hilden J.

Stat Biosci. 2015 Oct 1;7(2):282-295. Epub 2014 Aug 23.


Discordant Interpretations of Breast Biopsy Specimens by Pathologists--Reply.

Elmore JG, Pepe MS, Weaver DL.

JAMA. 2015 Jul 7;314(1):83-4. doi: 10.1001/jama.2015.6239. No abstract available.


Designing a study to evaluate the benefit of a biomarker for selecting patient treatment.

Janes H, Brown MD, Pepe MS.

Stat Med. 2015 Nov 30;34(27):3503-15. doi: 10.1002/sim.6564. Epub 2015 Jun 25.


The Fundamental Difficulty With Evaluating the Accuracy of Biomarkers for Guiding Treatment.

Janes H, Pepe MS, McShane LM, Sargent DJ, Heagerty PJ.

J Natl Cancer Inst. 2015 Jun 24;107(8). pii: djv157. doi: 10.1093/jnci/djv157. Print 2015 Aug.


Improving the quality of biomarker discovery research: the right samples and enough of them.

Pepe MS, Li CI, Feng Z.

Cancer Epidemiol Biomarkers Prev. 2015 Jun;24(6):944-50. doi: 10.1158/1055-9965.EPI-14-1227. Epub 2015 Apr 2.


Diagnostic concordance among pathologists interpreting breast biopsy specimens.

Elmore JG, Longton GM, Carney PA, Geller BM, Onega T, Tosteson AN, Nelson HD, Pepe MS, Allison KH, Schnitt SJ, O'Malley FP, Weaver DL.

JAMA. 2015 Mar 17;313(11):1122-32. doi: 10.1001/jama.2015.1405.


Construction and analysis of the NCI-EDRN breast cancer reference set for circulating markers of disease.

Marks JR, Anderson KS, Engstrom P, Godwin AK, Esserman LJ, Longton G, Iversen ES, Mathew A, Patriotis C, Pepe MS.

Cancer Epidemiol Biomarkers Prev. 2015 Feb;24(2):435-41. doi: 10.1158/1055-9965.EPI-14-1178. Epub 2014 Dec 3.



Pepe MS.

J Natl Cancer Inst. 2014 Nov 27;107(1):356. doi: 10.1093/jnci/dju356. Print 2015 Jan. No abstract available.


An approach to evaluating and comparing biomarkers for patient treatment selection.

Janes H, Brown MD, Huang Y, Pepe MS.

Int J Biostat. 2014;10(1):99-121. doi: 10.1515/ijb-2012-0052.


Net risk reclassification p values: valid or misleading?

Pepe MS, Janes H, Li CI.

J Natl Cancer Inst. 2014 Apr;106(4):dju041. doi: 10.1093/jnci/dju041. Epub 2014 Mar 28.


Vertical transmission of Toxocara canis in successive generations of mice.

Schoenardie ER, Scaini CJ, Pepe MS, Borsuk S, de Avila LF, Villela M, Berne ME.

Rev Bras Parasitol Vet. 2013 Oct-Dec;22(4):623-6. doi: 10.1590/S1984-29612013000400030.


Net reclassification indices for evaluating risk prediction instruments: a critical review.

Kerr KF, Wang Z, Janes H, McClelland RL, Psaty BM, Pepe MS.

Epidemiology. 2014 Jan;25(1):114-21. doi: 10.1097/EDE.0000000000000018. Review.



Huang Y, Pepe MS, Feng Z.

Ann Appl Stat. 2013 Sep 1;7(3). doi: 10.1214/13-AOAS634SUPP.


A framework for evaluating markers used to select patient treatment.

Janes H, Pepe MS, Huang Y.

Med Decis Making. 2014 Feb;34(2):159-67. doi: 10.1177/0272989X13493147. Epub 2013 Jun 27.


Adopting nested case-control quota sampling designs for the evaluation of risk markers.

Zheng Y, Cai T, Pepe MS.

Lifetime Data Anal. 2013 Oct;19(4):568-88. doi: 10.1007/s10985-013-9270-8. Epub 2013 Jun 27.


Seroprevalence of Toxocara infection in children from southern Brazil.

Schoenardie ER, Scaini CJ, Brod CS, Pepe MS, Villela MM, McBride AJ, Borsuk S, Berne ME.

J Parasitol. 2013 Jun;99(3):537-9. doi: 10.1645/GE-3182.


Estimating the receiver operating characteristic curve in studies that match controls to cases on covariates.

Pepe MS, Fan J, Seymour CW.

Acad Radiol. 2013 Jul;20(7):863-73. doi: 10.1016/j.acra.2013.03.004. Epub 2013 Apr 17.


Improving risk classification of critical illness with biomarkers: a simulation study.

Seymour CW, Cooke CR, Wang Z, Kerr KF, Yealy DM, Angus DC, Rea TD, Kahn JM, Pepe MS.

J Crit Care. 2013 Oct;28(5):541-8. doi: 10.1016/j.jcrc.2012.12.001. Epub 2013 Apr 6.


Estimating improvement in prediction with matched case-control designs.

Bansal A, Pepe MS.

Lifetime Data Anal. 2013 Apr;19(2):170-201. doi: 10.1007/s10985-012-9237-1. Epub 2013 Jan 29.


When does combining markers improve classification performance and what are implications for practice?

Bansal A, Pepe MS.

Stat Med. 2013 May 20;32(11):1877-92. doi: 10.1002/sim.5736. Epub 2013 Jan 24.


Testing for improvement in prediction model performance.

Pepe MS, Kerr KF, Longton G, Wang Z.

Stat Med. 2013 Apr 30;32(9):1467-82. doi: 10.1002/sim.5727. Epub 2013 Jan 7.


Biases introduced by choosing controls to match risk factors of cases in biomarker research.

Pepe MS, Fan J, Seymour CW, Li C, Huang Y, Feng Z.

Clin Chem. 2012 Aug;58(8):1242-51. doi: 10.1373/clinchem.2012.186007. Epub 2012 Jun 22.


Conditional estimation after a two-stage diagnostic biomarker study that allows early termination for futility.

Koopmeiners JS, Feng Z, Pepe MS.

Stat Med. 2012 Feb 28;31(5):420-35. doi: 10.1002/sim.4430. Epub 2012 Jan 12.


Improving biomarker identification with better designs and reporting.

Pepe MS, Feng Z.

Clin Chem. 2011 Aug;57(8):1093-5. doi: 10.1373/clinchem.2011.164657. No abstract available.


Commentary: Reporting standards are needed for evaluations of risk reclassification.

Pepe MS, Janes H.

Int J Epidemiol. 2011 Aug;40(4):1106-8. doi: 10.1093/ije/dyr083. Epub 2011 May 13. No abstract available.


Problems with risk reclassification methods for evaluating prediction models.

Pepe MS.

Am J Epidemiol. 2011 Jun 1;173(11):1327-35. doi: 10.1093/aje/kwr013. Epub 2011 May 9.


Measuring the performance of markers for guiding treatment decisions.

Janes H, Pepe MS, Bossuyt PM, Barlow WE.

Ann Intern Med. 2011 Feb 15;154(4):253-9. doi: 10.7326/0003-4819-154-4-201102150-00006.


Presence of Toxocara canis eggs on the hair of dogs: a risk factor for Visceral Larva Migrans.

Amaral HL, Rassier GL, Pepe MS, Gallina T, Villela MM, Nobre Mde O, Scaini CJ, Berne ME.

Vet Parasitol. 2010 Nov 24;174(1-2):115-8. doi: 10.1016/j.vetpar.2010.07.016. Epub 2010 Aug 6.


Estimating the diagnostic likelihood ratio of a continuous marker.

Gu W, Pepe MS.

Biostatistics. 2011 Jan;12(1):87-101. doi: 10.1093/biostatistics/kxq045. Epub 2010 Jul 16.


Assessing risk prediction models in case-control studies using semiparametric and nonparametric methods.

Huang Y, Pepe MS.

Stat Med. 2010 Jun 15;29(13):1391-410. doi: 10.1002/sim.3876.


The potential of genes and other markers to inform about risk.

Pepe MS, Gu JW, Morris DE.

Cancer Epidemiol Biomarkers Prev. 2010 Mar;19(3):655-65. doi: 10.1158/1055-9965.EPI-09-0510. Epub 2010 Feb 16.


Contrasting two frameworks for ROC analysis of ordinal ratings.

Morris DE, Pepe MS, Barlow WE.

Med Decis Making. 2010 Jul-Aug;30(4):484-98. doi: 10.1177/0272989X09357477. Epub 2010 Feb 10.


Methods for Assessing Improvement in Specificity when a Biomarker is Combined with a Standard Screening Test.

Shaw PA, Pepe MS, Alonzo TA, Etzioni R.

Stat Biopharm Res. 2009 Feb 1;1(1):18-25.


Semiparametric methods for evaluating risk prediction markers in case-control studies.

Huang Y, Pepe MS.

Biometrika. 2009 Dec;96(4):991-997. Epub 2009 Oct 12.

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