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Giovanni Parmigiani, PhD


Researcher

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Researcher

  • Professor of Biostatistics

Contact Information

  • Office Phone Number617-632-5323
  • Fax617-632-2444

Bio

Giovanni Parmigiani, PhD, is a professor of Biostatistics at Harvard TH Chan School of Public Health and Dana-Farber Cancer Institute and Associate Director for Population Sciences at the Dana-Farber/Harvard Cancer Center. He received his undergraduate degree in economics and social sciences at Università L. Bocconi, and a Masters and PhD in statistics from Carnegie Mellon University. He has held faculty positions at Carnegie Mellon, Duke and Johns Hopkins, before joining the faculty at the Harvard TH Chan School of Public Health in 2009 and becoming the Chair of the Department of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute.

Dr. Parmigiani is the recipient of numerous awards for his contributions to both science and teaching, including the Advising, Mentoring, and Teaching Recognition Award from the Johns Hopkins School of Public Health Student Assembly. He was named a Fellow of the American Statistical Association in 1999. While completing graduate studies at Carnegie Mellon, he received the Leonard J. Savage Dissertation Prize. His 2009 book on “Decision Theory” received the DeGroot prize. Dr. Parmigiani’s work has been published in the Journal of the American Medical Association, Science, Cancer Research, the Journal of the American Statistical Association, the Journal of Clinical Oncology, and the American Journal of Human Genetics.

Recent Awards:

  • Casty Award 2020
  • Junior Faculty Mentoring Award, Harvard T.H. Chan School of Public Health 2016
  • DeGroot Prize for Decision Theory, by Giovanni Parmigiani and Lurdes Y T Inoue, with contributions by Hedibert Freitas Lopes 2009
  • Advising, Mentoring, and Teaching Recognition Award. Johns Hopkins School of Public Health Student Assembly 2002

Research

Professor of Biostatistics at Harvard TH Chan School of Public Health and Dana Farber Cancer Institute. Professor Parmigiani is a statistician whose work creates statistical tools for understanding cancer data, with particular focus on genetic epidemiology and genomics. For example he uses Bayesian modeling and machine learning concepts for predicting who is at risk of carrying genetic variants that confer susceptibility to cancer.  For another example, he is interested in addressing the challenges of cross-study replication of predictions by constructing predictors that learn replicability from multiple studies. His overarching goals are to increase the rigor end efficiency with which we leverage the vast and complex information generated in today’s cancer research; and to foster the use of data sciences as a common thread to facilitate interactions between fields and academic cultures.

Influenza Vaccination and COVID-19 Mortality in the USA: An Ecological Study. Vaccines (Basel). 2021 Apr 24; 9(5).
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Gene Expression Pathways in Prostate Tissue Associated with Vigorous Physical Activity in Prostate Cancer. Cancer Epidemiol Biomarkers Prev. 2021 Apr; 30(4):751-756.
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Robustifying Genomic Classifiers To Batch Effects Via Ensemble Learning. Bioinformatics. 2020 Nov 27.
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A likelihood-based approach to assessing frequency of pathogenicity among variants of unknown significance in susceptibility genes. Stat Med. 2021 Feb 10; 40(3):593-606.
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Variation in cancer risk among families with genetic susceptibility. Genet Epidemiol. 2021 Mar; 45(2):209-221.
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Statistical approaches for meta-analysis of genetic mutation prevalence. Genet Epidemiol. 2021 Mar; 45(2):154-170.
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ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genom Bioinform. 2020 Sep; 2(3):lqaa078.
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Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tumor Tissue to Identify Single-Cell-Level PI3K Pathway Activation. Clin Cancer Res. 2020 Nov 15; 26(22):5903-5913.
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Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma. Cancer Res. 2020 10 15; 80(20):4335-4345.
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Genome-Wide Somatic Alterations in Multiple Myeloma Reveal a Superior Outcome Group. J Clin Oncol. 2020 09 20; 38(27):3107-3118.
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Influenza Vaccination and COVID19 Mortality in the USA. medRxiv. 2020 Jun 26.
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Practical implementation of frailty models in Mendelian risk prediction. Genet Epidemiol. 2020 Sep; 44(6):564-578.
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Receiver Operating Characteristic Curves with an Indeterminacy Zone. Pattern Recognit Lett. 2020 Aug; 136:94-100.
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Performance of Breast Cancer Risk-Assessment Models in a Large Mammography Cohort. J Natl Cancer Inst. 2020 05 01; 112(5):489-497.
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Legacy Genetic Testing Results for Cancer Susceptibility: How Common are Conflicting Classifications in a Large Variant Dataset from Multiple Practices? Ann Surg Oncol. 2020 Jul; 27(7):2212-2220.
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Penetrance of Colorectal Cancer Among Mismatch Repair Gene Mutation Carriers: A Meta-Analysis. JNCI Cancer Spectr. 2020 Aug; 4(5):pkaa027.
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Penetrance of Breast and Ovarian Cancer in Women Who Carry a BRCA1/2 Mutation and Do Not Use Risk-Reducing Salpingo-Oophorectomy: An Updated Meta-Analysis. JNCI Cancer Spectr. 2020 Aug; 4(4):pkaa029.
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The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models. Biostatistics. 2020 04 01; 21(2):253-268.
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Pathologic Complete Response after Neoadjuvant Chemotherapy and Impact on Breast Cancer Recurrence and Survival: A Comprehensive Meta-analysis. Clin Cancer Res. 2020 06 15; 26(12):2838-2848.
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Tree-Weighting for Multi-Study Ensemble Learners. Pac Symp Biocomput. 2020; 25:451-462.
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The Impact of Stroma Admixture on Molecular Subtypes and Prognostic Gene Signatures in Serous Ovarian Cancer. Cancer Epidemiol Biomarkers Prev. 2020 02; 29(2):509-519.
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Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes. JCO Clin Cancer Inform. 2019 09; 3:1-9.
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Validation of a Semiautomated Natural Language Processing-Based Procedure for Meta-Analysis of Cancer Susceptibility Gene Penetrance. JCO Clin Cancer Inform. 2019 08; 3:1-9.
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Family history of prostate cancer and the incidence of ERG- and phosphatase and tensin homolog-defined prostate cancer. Int J Cancer. 2020 05 15; 146(10):2694-2702.
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Clinical Factors Associated With Gastric Cancer in Individuals With Lynch Syndrome. Clin Gastroenterol Hepatol. 2020 04; 18(4):830-837.e1.
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Frequentist operating characteristics of Bayesian optimal designs via simulation. Stat Med. 2019 09 20; 38(21):4026-4039.
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High-Dimensional Confounding Adjustment Using Continuous Spike and Slab Priors. Bayesian Anal. 2019 Sep; 14(3):805-828.
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Deciphering the chronology of copy number alterations in Multiple Myeloma. Blood Cancer J. 2019 03 26; 9(4):39.
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Multi-study factor analysis. Biometrics. 2019 03; 75(1):337-346.
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Shared and Study-specific Dietary Patterns and Head and Neck Cancer Risk in an International Consortium. Epidemiology. 2019 01; 30(1):93-102.
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Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. iScience. 2018 Nov 30; 9:451-460.
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A Prospective Study of the Association between Physical Activity and Risk of Prostate Cancer Defined by Clinical Features and TMPRSS2:ERG. Eur Urol. 2019 07; 76(1):33-40.
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Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biol. 2018 09 25; 19(1):142.
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Family History of Breast or Prostate Cancer and Prostate Cancer Risk. Clin Cancer Res. 2018 12 01; 24(23):5910-5917.
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The clinical trials landscape for glioblastoma: is it adequate to develop new treatments? Neuro Oncol. 2018 07 05; 20(8):1034-1043.
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Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. Clin Cancer Res. 2018 10 15; 24(20):5037-5047.
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Efficient computation of the joint probability of multiple inherited risk alleles from pedigree data. Genet Epidemiol. 2018 09; 42(6):528-538.
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Precision Prevention and Early Detection of Cancer: Fundamental Principles. Cancer Discov. 2018 07; 8(7):803-811.
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Adding experimental arms to platform clinical trials: randomization procedures and interim analyses. Biostatistics. 2018 04 01; 19(2):199-215.
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Long intergenic non-coding RNAs have an independent impact on survival in multiple myeloma. Leukemia. 2018 12; 32(12):2626-2635.
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Training replicable predictors in multiple studies. Proc Natl Acad Sci U S A. 2018 03 13; 115(11):2578-2583.
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A Clinical Decision Support Tool to Predict Cancer Risk for Commonly Tested Cancer-Related Germline Mutations. J Genet Couns. 2018 09; 27(5):1187-1199.
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Expressed fusion gene landscape and its impact in multiple myeloma. Nat Commun. 2017 12 01; 8(1):1893.
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Propensity scores with misclassified treatment assignment: a likelihood-based adjustment. Biostatistics. 2017 Oct 01; 18(4):695-710.
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Nonparametric Adjustment for Measurement Error in Time-to-Event Data: Application to Risk Prediction Models. J Am Stat Assoc. 2018; 113(521):14-25.
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Stromal and epithelial transcriptional map of initiation progression and metastatic potential of human prostate cancer. Nat Commun. 2017 09 04; 8(1):420.
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Integrative factor analysis - An unsupervised method for quantifying cross-study consistency of gene expression data. Genomics. 2018 03; 110(2):80-88.
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Role of stem-cell divisions in cancer risk. Nature. 2017 08 09; 548(7666):E13-E14.
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Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma. Neuro Oncol. 2017 Jul 01; 19(7):908-917.
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Reassessing risk models for atypical hyperplasia: age may not matter. Breast Cancer Res Treat. 2017 Sep; 165(2):285-291.
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Designing Clinical Trials That Accept New Arms: An Example in Metastatic Breast Cancer. J Clin Oncol. 2017 Sep 20; 35(27):3160-3168.
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Bayesian response-adaptive designs for basket trials. Biometrics. 2017 09; 73(3):905-915.
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Combinatorial Mixtures of Multiparameter Distributions: An Application to Bivariate Data. Int J Biostat. 2017 02 16; 13(1).
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Model averaged double robust estimation. Biometrics. 2017 06; 73(2):410-421.
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Adaptive Randomization of Neratinib in Early Breast Cancer. N Engl J Med. 2016 10 20; 375(16):1593-4.
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I-SPY 2--A Glimpse of the Future of Phase 2 Drug Development? N Engl J Med. 2016 Jul 07; 375(1):7-9.
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The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles. J Natl Cancer Inst. 2016 11; 108(11).
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Penetrance of ATM Gene Mutations in Breast Cancer: A Meta-Analysis of Different Measures of Risk. Genet Epidemiol. 2016 07; 40(5):425-31.
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A two-stage approach to genetic risk assessment in primary care. Breast Cancer Res Treat. 2016 Jan; 155(2):375-83.
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Familial Risk and Heritability of Cancer Among Twins in Nordic Countries. JAMA. 2016 Jan 05; 315(1):68-76.
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Optimal Bayesian adaptive trials when treatment efficacy depends on biomarkers. Biometrics. 2016 06; 72(2):414-21.
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Evaluating a 4-marker signature of aggressive prostate cancer using time-dependent AUC. Prostate. 2015 Dec; 75(16):1926-33.
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Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO. Cancer Inform. 2015; 14(Suppl 2):147-57.
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Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues. J Mol Diagn. 2015 Jul; 17(4):374-81.
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Accounting for uncertainty in confounder and effect modifier selection when estimating average causal effects in generalized linear models. Biometrics. 2015 Sep; 71(3):654-65.
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BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol Cell. 2015 Feb 19; 57(4):636-647.
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Combining progression-free survival and overall survival as a novel composite endpoint for glioblastoma trials. Neuro Oncol. 2015 Aug; 17(8):1106-13.
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Only three driver gene mutations are required for the development of lung and colorectal cancers. Proc Natl Acad Sci U S A. 2015 Jan 06; 112(1):118-23.
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Differential and limited expression of mutant alleles in multiple myeloma. Blood. 2014 Nov 13; 124(20):3110-7.
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Misreported family histories and underestimation of risk. J Clin Oncol. 2014 Nov 10; 32(32):3682-3.
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Cost-effectiveness of alternative strategies for integrating MRI into breast cancer screening for women at high risk. Br J Cancer. 2014 Oct 14; 111(8):1542-51.
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Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics. 2014 Nov 01; 30(21):3062-9.
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Cross-study validation for the assessment of prediction algorithms. Bioinformatics. 2014 Jun 15; 30(12):i105-12.
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Recent BRCAPRO upgrades significantly improve calibration. Cancer Epidemiol Biomarkers Prev. 2014 Aug; 23(8):1689-95.
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Completing the results of the 2013 Boston marathon. PLoS One. 2014; 9(4):e93800.
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Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. J Natl Cancer Inst. 2014 Apr 03; 106(5).
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Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. J Natl Cancer Inst. 2014 Apr 03; 106(5).
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Modular network construction using eQTL data: an analysis of computational costs and benefits. Front Genet. 2014; 5:40.
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Integrative correlation: Properties and relation to canonical correlations. J Multivar Anal. 2014 Jan 01; 123:270-280.
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Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun. 2014; 5:2997.
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Statistical tools and R software for cancer driver probabilities. Methods Mol Biol. 2014; 1101:113-34.
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Reclassification of predictions for uncovering subgroup specific improvement. Stat Med. 2014 May 20; 33(11):1914-27.
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Frailty Models for Familial Risk with Application to Breast Cancer. J Am Stat Assoc. 2013 Dec 01; 108(504):1205-1215.
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A decision-theory approach to interpretable set analysis for high-dimensional data. Biometrics. 2013 Sep; 69(3):614-23.
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Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A. 2013 Aug 13; 110(33):13481-6.
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Biomarker-based adaptive trials for patients with glioblastoma--lessons from I-SPY 2. Neuro Oncol. 2013 Aug; 15(8):972-8.
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Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors. F1000Res. 2013; 2:152.
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Providing access to risk prediction tools via the HL7 XML-formatted risk web service. Breast Cancer Res Treat. 2013 Jul; 140(1):187-93.
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Calibrated predictions for multivariate competing risks models. Lifetime Data Anal. 2014 Apr; 20(2):234-51.
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DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics. 2013 Aug 01; 29(15):1865-71.
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Simplifying clinical use of the genetic risk prediction model BRCAPRO. Breast Cancer Res Treat. 2013 Jun; 139(2):571-9.
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curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database (Oxford). 2013; 2013:bat013.
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Reply to B. Freidlin et al. J Clin Oncol. 2013 Mar 01; 31(7):970-1.
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Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. Genet Epidemiol. 2013 Feb; 37(2):205-13.
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Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation. Proc Natl Acad Sci U S A. 2013 Feb 05; 110(6):1999-2004.
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SNP prioritization using a Bayesian probability of association. Genet Epidemiol. 2013 Feb; 37(2):214-21.
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Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. Nat Genet. 2013 Jan; 45(1):12-7.
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Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med. 2012 Nov 28; 4(162):162ra154.
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The penetrance of ductal carcinoma in situ among BRCA1 and BRCA2 mutation carriers. Breast Cancer Res Treat. 2013 Jan; 137(1):315-8.
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Expression profiling of archival tumors for long-term health studies. Clin Cancer Res. 2012 Nov 15; 18(22):6136-46.
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The role of chemoprevention in modifying the risk of breast cancer in women with atypical breast lesions. Breast Cancer Res Treat. 2012 Dec; 136(3):627-33.
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Estimation of sequencing error rates in short reads. BMC Bioinformatics. 2012 Jul 30; 13:185.
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MODELING DEPENDENT GENE EXPRESSION. Ann Stat. 2012; 6(2):542-560.
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Bayesian adaptive randomized trial design for patients with recurrent glioblastoma. J Clin Oncol. 2012 Sep 10; 30(26):3258-63.
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Response to comments on "the predictive capacity of personal genome sequencing". Sci Transl Med. 2012 May 23; 4(135):135lr3.
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The predictive capacity of personal genome sequencing. Sci Transl Med. 2012 May 09; 4(133):133ra58.
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Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. BMC Cancer. 2012 Mar 29; 12:124.
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Bayesian effect estimation accounting for adjustment uncertainty. Biometrics. 2012 Sep; 68(3):661-71.
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Assessing the added value of breast tumor markers in genetic risk prediction model BRCAPRO. Breast Cancer Res Treat. 2012 May; 133(1):347-55.
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Integrating diverse genomic data using gene sets. Genome Biol. 2011 Oct 21; 12(10):R105.
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OnionTree XML: a format to exchange gene-related probabilities. J Biomol Struct Dyn. 2011 Oct; 29(2):417-23.
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Opportunities for the primary prevention of colorectal cancer in the United States. Cancer Prev Res (Phila). 2012 Jan; 5(1):138-45.
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Assessing the added value of breast tumor markers in breast cancer genetic risk prediction model BRCAPRO. J Clin Oncol. 2011 Sep 20; 29(27_suppl):164.
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Modeling liquid association. Biometrics. 2011 Mar; 67(1):133-41.
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The genetic landscape of the childhood cancer medulloblastoma. Science. 2011 Jan 28; 331(6016):435-9.
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Patient-oriented gene set analysis for cancer mutation data. Genome Biol. 2010; 11(11):R112.
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Cross-platform Comparison of Two Pancreatic Cancer Phenotypes. Cancer Inform. 2010 Nov 01; 9:257-64.
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CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinformatics. 2010 Nov 01; 26(21):2792-3.
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Estimating CDKN2A carrier probability and personalizing cancer risk assessments in hereditary melanoma using MelaPRO. Cancer Res. 2010 Jan 15; 70(2):552-9.
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Rejoinder. J Am Stat Assoc. 2009 12; 104(488):1318-1323.
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The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. BMC Bioinformatics. 2009 Aug 20; 10:256.
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Inactivating germ-line and somatic mutations in polypeptide N-acetylgalactosaminyltransferase 12 in human colon cancers. Proc Natl Acad Sci U S A. 2009 Aug 04; 106(31):12921-5.
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SMAD4 gene mutations are associated with poor prognosis in pancreatic cancer. Clin Cancer Res. 2009 Jul 15; 15(14):4674-9.
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Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma. Stem Cells. 2009 Jul; 27(7):1487-95.
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Likelihood estimation of conjugacy relationships in linear models with applications to high-throughput genomics. Int J Biostat. 2009 May 29; 5(1):Article 18.
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A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. Cancer Res. 2009 Apr 15; 69(8):3364-73.
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Genetic mutations associated with cigarette smoking in pancreatic cancer. Cancer Res. 2009 Apr 15; 69(8):3681-8.
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Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science. 2009 Apr 10; 324(5924):217.
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A Bayesian model for cross-study differential gene expression. J Am Stat Assoc. 2009; 104(488):1295-1310.
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[Genetic predisposition to multiple sclerosis as a polygenic autoimmune disease]. Zh Nevrol Psikhiatr Im S S Korsakova. 2009; 109(7 Suppl 2):16-22.
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Tailoring BRCAPRO to Asian-Americans. J Clin Oncol. 2009 Feb 01; 27(4):642-3; author reply 643-4.
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Identifying differential correlation in gene/pathway combinations. BMC Bioinformatics. 2008 Nov 18; 9:488.
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A multiple-loop, double-cube microarray design applied to prostate cancer cell lines with variable sensitivity to histone deacetylase inhibitors. Clin Cancer Res. 2008 Nov 01; 14(21):6886-94.
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Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A. 2008 Oct 21; 105(42):16224-9.
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Multiple diseases in carrier probability estimation: accounting for surviving all cancers other than breast and ovary in BRCAPRO. Stat Med. 2008 Sep 30; 27(22):4532-48.
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Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer. Oncogene. 2008 Dec 04; 27(57):7180-91.
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Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26; 321(5897):1801-6.
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An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26; 321(5897):1807-12.
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Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies. BMC Genomics. 2008 Aug 29; 9:405.
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Toll-like receptor 3 and geographic atrophy in age-related macular degeneration. N Engl J Med. 2008 Oct 02; 359(14):1456-63.
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Design and analysis issues in genome-wide somatic mutation studies of cancer. Genomics. 2009 Jan; 93(1):17-21.
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Model selection and health effect estimation in environmental epidemiology. Epidemiology. 2008 Jul; 19(4):558-60.
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Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Ann Appl Stat. 2008 Jun 01; 2(2):687-713.
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Incorporating tumor immunohistochemical markers in BRCA1 and BRCA2 carrier prediction. Breast Cancer Res. 2008; 10(2):401.
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TRAB: testing whether mutation frequencies are above an unknown background. Stat Appl Genet Mol Biol. 2008; 7(1):Article11.
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Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci U S A. 2008 Mar 18; 105(11):4283-8.
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Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers. Proc Natl Acad Sci U S A. 2008 Mar 04; 105(9):3443-8.
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Systematic review: gene expression profiling assays in early-stage breast cancer. Ann Intern Med. 2008 Mar 04; 148(5):358-69.
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Impact of gene expression profiling tests on breast cancer outcomes. Evid Rep Technol Assess (Full Rep). 2008 Jan; (160):1-105.
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Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries. BMC Bioinformatics. 2007 Dec 11; 8:476.
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Impact of gene expression profiling tests on breast cancer outcomes. Evid Rep Technol Assess (Full Rep). 2007 Dec; (160):1-105.
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Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. J Natl Cancer Inst. 2007 Dec 05; 99(23):1811-4.
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Limited family structure and breast cancer risk. JAMA. 2007 Nov 07; 298(17):2007; author reply 2007-8.
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The genomic landscapes of human breast and colorectal cancers. Science. 2007 Nov 16; 318(5853):1108-13.
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Congenital growth hormone (GH) deficiency and atherosclerosis: effects of GH replacement in GH-naive adults. J Clin Endocrinol Metab. 2007 Dec; 92(12):4664-70.
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Validity of models for predicting BRCA1 and BRCA2 mutations. Ann Intern Med. 2007 Oct 02; 147(7):441-50.
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Cross-study validation and combined analysis of gene expression microarray data. Biostatistics. 2008 Apr; 9(2):333-54.
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A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res. 2007 Sep; 17(9):1304-18.
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Genome-wide gene expression differences in Crohn's disease and ulcerative colitis from endoscopic pinch biopsies: insights into distinctive pathogenesis. Inflamm Bowel Dis. 2007 Jul; 13(7):807-21.
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Pre-processing Agilent microarray data. BMC Bioinformatics. 2007 May 01; 8:142.
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PancPRO: risk assessment for individuals with a family history of pancreatic cancer. J Clin Oncol. 2007 Apr 10; 25(11):1417-22.
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Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007 Apr 10; 25(11):1329-33.
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Multivariate analysis and visualization of splicing correlations in single-gene transcriptomes. BMC Bioinformatics. 2007 Jan 18; 8:16.
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Statistical methods for identifying differentially expressed gene combinations. Methods Mol Biol. 2007; 408:171-91.
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When should one subtract background fluorescence in 2-color microarrays? Biostatistics. 2007 Oct; 8(4):695-707.
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The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT. Nat Biotechnol. 2006 Dec; 24(12):1573-80.
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Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. J Clin Oncol. 2006 Nov 01; 24(31):5079-90.
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GH response to hypoglycemia and clonidine in the GH-releasing hormone resistance syndrome. J Endocrinol Invest. 2006 Oct; 29(9):805-8.
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Prediction of germline mutations and cancer risk in the Lynch syndrome. JAMA. 2006 Sep 27; 296(12):1479-87.
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The consensus coding sequences of human breast and colorectal cancers. Science. 2006 Oct 13; 314(5797):268-74.
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Three allele combinations associated with multiple sclerosis. BMC Med Genet. 2006 Jul 26; 7:63.
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Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet. 2006 Mar; 38(3):285-93.
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Gene expression patterns in dendritic cells infected with measles virus compared with other pathogens. Proc Natl Acad Sci U S A. 2006 Feb 28; 103(9):3363-8.
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Characterization of BRCA1 and BRCA2 mutations in a large United States sample. J Clin Oncol. 2006 Feb 20; 24(6):863-71.
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Amplification of a chromatin remodeling gene, Rsf-1/HBXAP, in ovarian carcinoma. Proc Natl Acad Sci U S A. 2005 Sep 27; 102(39):14004-9.
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Searching for differentially expressed gene combinations. Genome Biol. 2005; 6(10):R88.
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A Markov chain Monte Carlo technique for identification of combinations of allelic variants underlying complex diseases in humans. Genetics. 2005 Dec; 171(4):2113-21.
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Assessing reproducibility of a protein dynamics study using in vivo labeling and liquid chromatography tandem mass spectrometry. Anal Chem. 2005 May 01; 77(9):2739-44.
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Accuracy of MSI testing in predicting germline mutations of MSH2 and MLH1: a case study in Bayesian meta-analysis of diagnostic tests without a gold standard. Biostatistics. 2005 Jul; 6(3):450-64.
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Impact of the Cancer Risk Intake System on patient-clinician discussions of tamoxifen, genetic counseling, and colonoscopy. J Gen Intern Med. 2005 Apr; 20(4):360-5.
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A model-based comparison of breast cancer screening strategies: mammograms and clinical breast examinations. Cancer Epidemiol Biomarkers Prev. 2005 Feb; 14(2):529-32.
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Classification of Missense Mutations of Disease Genes. J Am Stat Assoc. 2005; 100(469):51-60.
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Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation. 2004 Nov 30; 110(22):3444-51.
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Penetrances of breast and ovarian cancer in a large series of families tested for BRCA1/2 mutations. Eur J Hum Genet. 2004 Nov; 12(11):899-906.
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MergeMaid: R tools for merging and cross-study validation of gene expression data. Stat Appl Genet Mol Biol. 2004; 3:Article29.
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BayesMendel: an R environment for Mendelian risk prediction. Stat Appl Genet Mol Biol. 2004; 3:Article21.
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Identification of gene expression changes associated with the progression of retinal degeneration in the rd1 mouse. Invest Ophthalmol Vis Sci. 2004 Sep; 45(9):2929-42.
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Comparative gene expression analysis of murine retina and brain. Mol Vis. 2004 Aug 31; 10:637-49.
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Mutational analysis of the tyrosine phosphatome in colorectal cancers. Science. 2004 May 21; 304(5674):1164-6.
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Molecular classification of lung cancer: a cross-platform comparison of gene expression data sets. Chest. 2004 May; 125(5 Suppl):103S.
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A cross-study comparison of gene expression studies for the molecular classification of lung cancer. Clin Cancer Res. 2004 May 01; 10(9):2922-7.
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Evaluation of widely used models for predicting BRCA1 and BRCA2 mutations. J Med Genet. 2004 Apr; 41(4):278-85.
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Uncertainty and the value of diagnostic information, with application to axillary lymph node dissection in breast cancer. Stat Med. 2004 Mar 15; 23(5):843-55.
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Estrogen receptor/progesterone receptor-negative breast cancers of young African-American women have a higher frequency of methylation of multiple genes than those of Caucasian women. Clin Cancer Res. 2004 Mar 15; 10(6):2052-7.
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Targeting vascular and avascular compartments of tumors with C. novyi-NT and anti-microtubule agents. . 2004 Mar; 3(3):326-37.
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Digital karyotyping identifies thymidylate synthase amplification as a mechanism of resistance to 5-fluorouracil in metastatic colorectal cancer patients. Proc Natl Acad Sci U S A. 2004 Mar 02; 101(9):3089-94.
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Gene expression variation in the adult human retina. Hum Mol Genet. 2003 Nov 15; 12(22):2881-93.
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Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy. Physiol Genomics. 2003 Jun 24; 14(1):25-34.
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Mutational analysis of the tyrosine kinome in colorectal cancers. Science. 2003 May 09; 300(5621):949.
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Statistical modeling and visualization of molecular profiles in cancer. Biotechniques. 2003 Mar; Suppl:22-9.
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Measuring uncertainty in complex decision analysis models. Stat Methods Med Res. 2002 Dec; 11(6):513-37.
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Human l1 retrotransposition is associated with genetic instability in vivo. Cell. 2002 Aug 09; 110(3):327-38.
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Incidence of non-founder BRCA1 and BRCA2 mutations in high risk Ashkenazi breast and ovarian cancer families. J Med Genet. 2002 Aug; 39(8):611-4.
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BRCAPRO validation, sensitivity of genetic testing of BRCA1/BRCA2, and prevalence of other breast cancer susceptibility genes. J Clin Oncol. 2002 Jun 01; 20(11):2701-12.
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Modeling and optimization in early detection programs with a single exam. Biometrics. 2002 Mar; 58(1):30-6.
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Prevalence of somatic alterations in the colorectal cancer cell genome. Proc Natl Acad Sci U S A. 2002 Mar 05; 99(5):3076-80.
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Relationships and differentially expressed genes among pancreatic cancers examined by large-scale serial analysis of gene expression. Cancer Res. 2002 Feb 01; 62(3):819-26.
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Web-based tissue microarray image data analysis: initial validation testing through prostate cancer Gleason grading. Hum Pathol. 2001 Apr; 32(4):417-27.
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Bayesian semiparametric analysis of developmental toxicology data. Biometrics. 2001 Mar; 57(1):150-7.
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Detection of mitochondrial DNA mutations in pancreatic cancer offers a "mass"-ive advantage over detection of nuclear DNA mutations. Cancer Res. 2001 Feb 15; 61(4):1299-304.
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A Bayesian hierarchical approach for combining case-control and prospective studies. Biometrics. 1999 Sep; 55(3):858-66.
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Is axillary lymph node dissection indicated for early-stage breast cancer? A decision analysis. J Clin Oncol. 1999 May; 17(5):1465-73.
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Performing cost-effectiveness analysis by integrating randomized trial data with a comprehensive decision model: application to treatment of acute ischemic stroke. J Clin Epidemiol. 1999 Mar; 52(3):259-71.
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Effect of BRCA1 and BRCA2 on the association between breast cancer risk and family history. J Natl Cancer Inst. 1998 Dec 02; 90(23):1824-9.
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Protein construct storage: Bayesian variable selection and prediction with mixtures. J Biopharm Stat. 1998 Jul; 8(3):431-43.
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Missense mutations in disease genes: a Bayesian approach to evaluate causality. Am J Hum Genet. 1998 Jun; 62(6):1516-24.
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Assessing the benefits of testing for breast cancer susceptibility genes: a decision analysis. Breast Dis. 1998 Apr; 10(1-2):115-25.
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Predicting the cost of illness: a comparison of alternative models applied to stroke. Med Decis Making. 1998 Apr-Jun; 18(2 Suppl):S39-56.
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Determining carrier probabilities for breast cancer-susceptibility genes BRCA1 and BRCA2. Am J Hum Genet. 1998 Jan; 62(1):145-58.
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The Stroke Prevention Policy Model: linking evidence and clinical decisions. Ann Intern Med. 1997 Oct 15; 127(8 Pt 2):704-11.
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Assessing uncertainty in cost-effectiveness analyses: application to a complex decision model. Med Decis Making. 1997 Oct-Dec; 17(4):390-401.
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The clinical significance of positive blood cultures in the 1990s: a prospective comprehensive evaluation of the microbiology, epidemiology, and outcome of bacteremia and fungemia in adults. Clin Infect Dis. 1997 Apr; 24(4):584-602.
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Probability of carrying a mutation of breast-ovarian cancer gene BRCA1 based on family history. J Natl Cancer Inst. 1997 Feb 05; 89(3):227-38.
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