Yingye Zheng

Yingye Zheng

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Evaluating longitudinal markers under two-phase study designs.

Biostatistics 2019 07;20(3):485-498

Department of Biostatistics, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA.

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http://dx.doi.org/10.1093/biostatistics/kxy013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6587940PMC
July 2019

Study Design Considerations for Cancer Biomarker Discoveries.

Authors:
Yingye Zheng

J Appl Lab Med 2018 Sep;3(2):282-289

Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-B500, Seattle, Washington 98109,

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http://dx.doi.org/10.1373/jalm.2017.025809DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391721PMC
September 2018

Robust Dynamic Risk Prediction with Longitudinal Studies.

Stat Theory Relat Fields 2017 27;1(2):159-170. Epub 2017 Nov 27.

Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA, 02115.

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http://dx.doi.org/10.1080/24754269.2017.1400418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5766050PMC
November 2017

IMPROVING EFFICIENCY IN BIOMARKER INCREMENTAL VALUE EVALUATION UNDER TWO-PHASE DESIGNS.

Ann Appl Stat 2017 Jun 20;11(2):638-654. Epub 2017 Jul 20.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115.

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http://dx.doi.org/10.1214/16-AOAS997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604898PMC
June 2017

Timing of Adverse Prostate Cancer Reclassification on First Surveillance Biopsy: Results from the Canary Prostate Cancer Active Surveillance Study.

J Urol 2017 04 1;197(4):1026-1033. Epub 2016 Nov 1.

University of Washington School of Medicine, Seattle, Washington; Seattle Puget Sound Health Care System, Veterans Affairs Hospital, Seattle, Washington; Fred Hutchinson Cancer Research Center, Seattle, Washington. Electronic address:

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http://dx.doi.org/10.1016/j.juro.2016.10.090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5571762PMC
April 2017

On longitudinal prediction with time-to-event outcome: Comparison of modeling options.

Biometrics 2017 03 20;73(1):83-93. Epub 2016 Jul 20.

Fred Hutchinson Cancer Research Center 1100 Fairview Ave N., M2-B500, Seattle, Washington 98109, U.S.A.

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http://dx.doi.org/10.1111/biom.12562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5250577PMC
March 2017

Racial/ethnic differences in obesity and comorbidities between safety-net- and non safety-net integrated health systems.

Medicine (Baltimore) 2017 Mar;96(11):e6326

aDepartment of Epidemiology, Human Genetics, and Environmental Sciences, UTHealth School of Public Health in Dallas bHarold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX cDivision of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA dDivision of Research, Kaiser Permanente Northern California, Oakland, CA eDepartment of Family Medicine and Community Health, and the Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA fDivision of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA gGroup Health Research Institute, Seattle, WA hResearch & Evaluation Department, Kaiser Permanente Southern California, Pasadena, CA iDepartment of Biostatistics and Biomathematics, Division of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, WA jDepartment of Clinical Sciences and Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical School, Dallas, TX.

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http://dx.doi.org/10.1097/MD.0000000000006326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5369907PMC
March 2017

Nonparametric Maximum Likelihood Estimators of Time-Dependent Accuracy Measures for Survival Outcome Under Two-Stage Sampling Designs.

J Am Stat Assoc 2018 28;113(522):882-892. Epub 2017 Feb 28.

Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.

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http://dx.doi.org/10.1080/01621459.2017.1295866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6291304PMC
February 2017

Robust risk prediction with biomarkers under two-phase stratified cohort design.

Biometrics 2016 12 1;72(4):1037-1045. Epub 2016 Apr 1.

Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, U.S.A.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045782PMC
http://dx.doi.org/10.1111/biom.12515DOI Listing
December 2016

Racial/Ethnic Disparities in Colorectal Cancer Screening Across Healthcare Systems.

Am J Prev Med 2016 10 1;51(4):e107-15. Epub 2016 Apr 1.

Department of Family Medicine and Community Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.

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http://dx.doi.org/10.1016/j.amepre.2016.02.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5030113PMC
October 2016

Validation of a Novel Biomarker Panel for the Detection of Ovarian Cancer.

Cancer Epidemiol Biomarkers Prev 2016 09 22;25(9):1333-40. Epub 2016 Jul 22.

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada. Department of Clinical Biochemistry, University Health Network, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/1055-9965.EPI-15-1299DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5010461PMC
September 2016

Assessing incremental value of biomarkers with multi-phase nested case-control studies.

Biometrics 2015 Dec 20;71(4):1139-49. Epub 2015 Jul 20.

Department of Biostatistics, Harvard University, Boston, MA, USA.

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http://dx.doi.org/10.1111/biom.12344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819437PMC
December 2015

Two-stage biomarker panel study and estimation allowing early termination for futility.

Biostatistics 2015 Oct 11;16(4):799-812. Epub 2015 May 11.

Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

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http://dx.doi.org/10.1093/biostatistics/kxv017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570581PMC
October 2015

Estimated intake of vitamin D and its interaction with vitamin A on lung cancer risk among smokers.

Int J Cancer 2014 Nov 24;135(9):2135-45. Epub 2014 Mar 24.

Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Epidemiology, University of Washington, Seattle, WA.

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http://dx.doi.org/10.1002/ijc.28846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4293152PMC
November 2014

Estimating Risk with Time-to-Event Data: An Application to the Women's Health Initiative.

J Am Stat Assoc 2014 Jun;109(506):514-524

Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109.

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http://dx.doi.org/10.1080/01621459.2014.881739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091861PMC
June 2014

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

Lifetime Data Anal 2013 Oct 27;19(4):568-88. Epub 2013 Jun 27.

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, 98109, USA,

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http://dx.doi.org/10.1007/s10985-013-9270-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3903399PMC
October 2013

Vitamin D intake and lung cancer risk in the Women's Health Initiative.

Am J Clin Nutr 2013 Oct 21;98(4):1002-11. Epub 2013 Aug 21.

Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA and Biostatistics, University of Washington, Seattle, WA; Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA.

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http://dx.doi.org/10.3945/ajcn.112.055905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778856PMC
October 2013

Assessment of biomarkers for risk prediction with nested case-control studies.

Clin Trials 2013 Oct 6;10(5):677-9. Epub 2013 Sep 6.

aDepartment of Statistics and Actuarial Science, Simon Fraser University, Burnaby, BC, Canada.

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http://dx.doi.org/10.1177/1740774513498321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3800233PMC
October 2013

Evaluating incremental values from new predictors with net reclassification improvement in survival analysis.

Lifetime Data Anal 2013 Jul 20;19(3):350-70. Epub 2012 Dec 20.

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1007/s10985-012-9239-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3686882PMC
July 2013

Biomarkers of inflammation are associated with colorectal cancer risk in women but are not suitable as early detection markers.

Int J Cancer 2013 Jun 5;132(11):2648-58. Epub 2012 Dec 5.

Division of Preventive Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany.

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http://dx.doi.org/10.1002/ijc.27942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3609926PMC
June 2013

A unified mixed-effects model for rare-variant association in sequencing studies.

Genet Epidemiol 2013 May 9;37(4):334-44. Epub 2013 Mar 9.

Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.1002/gepi.21717DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740585PMC
May 2013

Subgroup specific incremental value of new markers for risk prediction.

Lifetime Data Anal 2013 Apr 23;19(2):142-69. Epub 2012 Dec 23.

Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.

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http://dx.doi.org/10.1007/s10985-012-9235-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633735PMC
April 2013

Resampling Procedures for Making Inference under Nested Case-control Studies.

J Am Stat Assoc 2013 Jan;108(504):1532-1544

Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

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http://dx.doi.org/10.1080/01621459.2013.856715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3891801PMC
January 2013

Evaluating the predictive value of biomarkers with stratified case-cohort design.

Biometrics 2012 Dec 22;68(4):1219-27. Epub 2012 Nov 22.

Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2012.01787.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3718317PMC
December 2012

Evaluating prognostic accuracy of biomarkers under competing risk.

Biometrics 2012 Jun 7;68(2):388-96. Epub 2011 Dec 7.

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2011.01671.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694786PMC
June 2012

Evaluating prognostic accuracy of biomarkers in nested case-control studies.

Biostatistics 2012 Jan 19;13(1):89-100. Epub 2011 Aug 19.

Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/biostatistics/kxr021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3276269PMC
January 2012

The association between worksite social support, diet, physical activity and body mass index.

Prev Med 2011 Jul-Aug;53(1-2):53-6. Epub 2011 May 4.

Harvard School of Public Health, Department of Society, Human Development, and Health, 67 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.ypmed.2011.04.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143200PMC
December 2011

Exploring the role of co-worker social support on health care utilization and sickness absence.

J Occup Environ Med 2011 Jul;53(7):751-7

Department of Society, Human Development, and Health, Harvard School of Public Health, Boston, MA 02115, USA.

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http://dx.doi.org/10.1097/JOM.0b013e318223d42fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3132298PMC
July 2011

Robust prediction of t-year survival with data from multiple studies.

Biometrics 2011 Jun 28;67(2):436-44. Epub 2010 Jul 28.

Department of Biostatistics, Harvard University, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2010.01462.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2987565PMC
June 2011

Non-parametric Evaluation of Biomarker Accuracy under Nested Case-control Studies.

J Am Stat Assoc 2011 Jan 24;106(494):569-580. Epub 2012 Jan 24.

Department of Biostatistics, Harvard University, Boston, MA, USA.

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http://dx.doi.org/10.1198/jasa.2011.tm09807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3404857PMC
January 2011

On combining family-based and population-based case-control data in association studies.

Biometrics 2010 Dec;66(4):1024-33

Biostatistics and Biomathematics Program, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2010.01393.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3038246PMC
December 2010

Semiparametric models of time-dependent predictive values of prognostic biomarkers.

Biometrics 2010 Mar 13;66(1):50-60. Epub 2009 Apr 13.

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2009.01246.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2875380PMC
March 2010

Nidogen-2: a new serum biomarker for ovarian cancer.

Clin Biochem 2010 Mar 31;43(4-5):355-61. Epub 2009 Oct 31.

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.

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http://dx.doi.org/10.1016/j.clinbiochem.2009.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109863PMC
March 2010

Activated leukocyte cell adhesion molecule: a novel biomarker for breast cancer.

Int J Cancer 2009 Jul;125(1):9-14

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1002/ijc.24292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3743675PMC
July 2009

The relationship between gravidity and parity and colorectal cancer risk.

J Womens Health (Larchmt) 2009 Jul;18(7):995-1001

Fred Hutchinson Cancer Research Center, Seattle, Washington 98109-1024, USA.

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http://dx.doi.org/10.1089/jwh.2008.1068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851134PMC
July 2009

On combining triads and unrelated subjects data in candidate gene studies: an application to data on testicular cancer.

Hum Hered 2009 12;67(2):88-103. Epub 2008 Dec 12.

Biostatistics and Biomathematics Program, Fred Hutchinson Cancer Research Center, Seattle, Wash., USA.

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http://dx.doi.org/10.1159/000179557DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763779PMC
March 2009

The association of tumor microsatellite instability phenotype with family history of colorectal cancer.

Cancer Epidemiol Biomarkers Prev 2009 Mar 3;18(3):967-75. Epub 2009 Mar 3.

Department of Pathology and Lab Medicine, Mount Sinai Hospital, and Samuel Lunenfeld Research Institute, University of Toronto, 60 Murray Street, Box 30, Toronto, M5T 3L9, Ontario, Canada.

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http://dx.doi.org/10.1158/1055-9965.EPI-08-0878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2763617PMC
March 2009

Reproducibility of serum leptin, insulin-like growth factor-I, and insulin-like growth factor-binding protein-3 measurements.

Horm Res 2008 6;69(5):295-300. Epub 2008 Feb 6.

Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Wash. 98109, USA.

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http://dx.doi.org/10.1159/000114861DOI Listing
July 2008

Evaluating the ROC performance of markers for future events.

Lifetime Data Anal 2008 Mar 7;14(1):86-113. Epub 2007 Dec 7.

Biostatistics and Biomathematics, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., M2-B500, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1007/s10985-007-9073-xDOI Listing
March 2008

A multiparametric serum kallikrein panel for diagnosis of non-small cell lung carcinoma.

Clin Cancer Res 2008 Mar;14(5):1355-62

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1158/1078-0432.CCR-07-4117DOI Listing
March 2008

Integrating the predictiveness of a marker with its performance as a classifier.

Am J Epidemiol 2008 Feb 2;167(3):362-8. Epub 2007 Nov 2.

Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1093/aje/kwm305DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939738PMC
February 2008

A practical multifaceted approach to selecting differentially expressed genes.

Cancer Inform 2008 Jan 15;3:203-12. Epub 2008 Jan 15.

Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675859PMC
January 2008

Time-dependent Predictive Values of Prognostic Biomarkers with Failure Time Outcome.

J Am Stat Assoc 2008 ;103(481):362-368

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109.

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http://dx.doi.org/10.1198/016214507000001481DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2719907PMC
January 2008

Changes in cancer worry associated with participation in ovarian cancer screening.

Psychooncology 2007 Sep;16(9):814-20

Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA.

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http://dx.doi.org/10.1002/pon.1151DOI Listing
September 2007

Estrogen plus progestin use, microsatellite instability, and the risk of colorectal cancer in women.

Cancer Res 2007 Aug;67(15):7534-9

Fred Hutchinson Cancer Research Center and Department of Epidemiology, University of Washington, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1158/0008-5472.CAN-06-4275DOI Listing
August 2007

Prospective accuracy for longitudinal markers.

Biometrics 2007 Jun;63(2):332-41

Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., M2-B500, P.O. Box 19024, Seattle, Washington 98109-1024, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2006.00726.xDOI Listing
June 2007

Application of a methylation gene panel by quantitative PCR for lung cancers.

Cancer Lett 2007 Mar 27;247(1):56-71. Epub 2006 Apr 27.

Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.

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http://dx.doi.org/10.1016/j.canlet.2006.03.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3379713PMC
March 2007

Model checking for ROC regression analysis.

Biometrics 2007 Mar;63(1):152-63

Department of Biostatistics, Harvard University, Boston, Massachusetts 02115, USA.

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http://doi.wiley.com/10.1111/j.1541-0420.2006.00620.x
Publisher Site
http://dx.doi.org/10.1111/j.1541-0420.2006.00620.xDOI Listing
March 2007

The sensitivity and specificity of markers for event times.

Biostatistics 2006 Apr 3;7(2):182-97. Epub 2005 Aug 3.

Department of Biostatistics, Harvard University, Boston, MA 02115, USA.

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http://dx.doi.org/10.1093/biostatistics/kxi047DOI Listing
April 2006

Application of the time-dependent ROC curves for prognostic accuracy with multiple biomarkers.

Biometrics 2006 Mar;62(1):279-87

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1111/j.1541-0420.2005.00441.xDOI Listing
March 2006

Aberrant promoter methylation of multiple genes during multistep pathogenesis of colorectal cancers.

Int J Cancer 2006 Feb;118(4):924-31

Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-8593, USA.

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http://dx.doi.org/10.1002/ijc.21453DOI Listing
February 2006

Partly conditional survival models for longitudinal data.

Biometrics 2005 Jun;61(2):379-91

Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N., M2-B230, P.O. Box 19024, Seattle, Washington 98109-1024, USA.

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http://www.jstor.org/stable/pdf/3695957.pdf
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http://biostat.mc.vanderbilt.edu/wiki/pub/Main/MSJournalClub
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http://doi.wiley.com/10.1111/j.1541-0420.2005.00323.x
Publisher Site
http://dx.doi.org/10.1111/j.1541-0420.2005.00323.xDOI Listing
June 2005

Survival model predictive accuracy and ROC curves.

Biometrics 2005 Mar;61(1):92-105

Department of Biostatistics, University of Washington, P.O. Box 357232, Seattle, Washington 98195-7232, USA.

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http://dx.doi.org/10.1111/j.0006-341X.2005.030814.xDOI Listing
March 2005

Assessing accuracy of mammography in the presence of verification bias and intrareader correlation.

Biometrics 2005 Mar;61(1):259-68

Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, North Seattle, Washington 98109, USA.

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http://dx.doi.org/10.1111/j.0006-341X.2005.031139.xDOI Listing
March 2005

Semiparametric estimation of time-dependent ROC curves for longitudinal marker data.

Biostatistics 2004 Oct;5(4):615-32

Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA.

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http://dx.doi.org/10.1093/biostatistics/kxh013DOI Listing
October 2004