Giovanni Parmigiani, PhD

Giovanni Parmigiani, PhD


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Giovanni Parmigiani, PhD

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.



Professor of Biostatistics

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


    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.

    Research Departments

    Support my research


      • Meta-Analysis of Breast Cancer Risk for Individuals with PALB2 Pathogenic Variants. medRxiv. 2023 Jun 04. View in: Pubmed

      • Clinical implications of conflicting variant interpretations in the cancer genetics clinic. Genet Med. 2023 Jul; 25(7):100837. View in: Pubmed

      • High-dose melphalan treatment significantly increases mutational burden at relapse in multiple myeloma. Blood. 2023 04 06; 141(14):1724-1736. View in: Pubmed

      • Variant-specific Mendelian Risk Prediction Model. bioRxiv. 2023 Mar 08. View in: Pubmed

      • Combining Breast Cancer Risk Prediction Models. Cancers (Basel). 2023 Feb 08; 15(4). View in: Pubmed

      • MyLynch: A Patient-Facing Clinical Decision Support Tool for Genetically-Guided Personalized Medicine in Lynch Syndrome. Cancers (Basel). 2023 Jan 06; 15(2). View in: Pubmed

      • In-depth analysis of alternative splicing landscape in multiple myeloma and potential role of dysregulated splicing factors. Blood Cancer J. 2022 12 20; 12(12):171. View in: Pubmed

      • Loss of ribonuclease DIS3 hampers genome integrity in myeloma by disrupting DNA:RNA hybrid metabolism. EMBO J. 2022 Nov 17; 41(22):e108040. View in: Pubmed

      • Hierarchical resampling for bagging in multistudy prediction with applications to human neurochemical sensing. Ann Appl Stat. 2022 Dec; 16(4):2145-2165. View in: Pubmed

      • A validation of models for prediction of pathogenic variants in mismatch repair genes. Genet Med. 2022 10; 24(10):2155-2166. View in: Pubmed

      • Validity and Relative Validity of Alternative Methods of Assessing Physical Activity in Epidemiologic Studies: Findings From the Men's Lifestyle Validation Study. Am J Epidemiol. 2022 06 27; 191(7):1307-1322. View in: Pubmed

      • Statistical methods for Mendelian models with multiple genes and cancers. Genet Epidemiol. 2022 10; 46(7):395-414. View in: Pubmed

      • Association of COVID-19 Vaccination With SARS-CoV-2 Infection in Patients With Cancer: A US Nationwide Veterans Affairs Study. JAMA Oncol. 2022 02 01; 8(2):281-286. View in: Pubmed

      • Validation of Breast Cancer Risk Models by Race/Ethnicity, Family History and Molecular Subtypes. Cancers (Basel). 2021 Dec 23; 14(1). View in: Pubmed

      • Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays. Elife. 2021 12 23; 10. View in: Pubmed

      • IgM-MM is predominantly a pre-germinal center disorder and has a distinct genomic and transcriptomic signature from WM. Blood. 2021 11 18; 138(20):1980-1985. View in: Pubmed

      • A risk prediction tool for individuals with a family history of breast, ovarian, or pancreatic cancer: BRCAPANCPRO. Br J Cancer. 2021 12; 125(12):1712-1717. View in: Pubmed

      • Multi-syndrome, multi-gene risk modeling for individuals with a family history of cancer with the novel R package PanelPRO. Elife. 2021 08 18; 10. View in: Pubmed

      • Robustifying genomic classifiers to batch effects via ensemble learning. Bioinformatics. 2021 07 12; 37(11):1521-1527. View in: Pubmed

      • covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data. Database (Oxford). 2021 05 15; 2021. View in: Pubmed

      • Influenza Vaccination and COVID-19 Mortality in the USA: An Ecological Study. Vaccines (Basel). 2021 Apr 24; 9(5). View in: Pubmed

      • Gene Expression Pathways in Prostate Tissue Associated with Vigorous Physical Activity in Prostate Cancer. Cancer Epidemiol Biomarkers Prev. 2021 04; 30(4):751-756. View in: Pubmed

      • A likelihood-based approach to assessing frequency of pathogenicity among variants of unknown significance in susceptibility genes. Stat Med. 2021 02 10; 40(3):593-606. View in: Pubmed

      • Variation in cancer risk among families with genetic susceptibility. Genet Epidemiol. 2021 03; 45(2):209-221. View in: Pubmed

      • Statistical approaches for meta-analysis of genetic mutation prevalence. Genet Epidemiol. 2021 03; 45(2):154-170. View in: Pubmed

      • ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genom Bioinform. 2020 Sep; 2(3):lqaa078. View in: Pubmed

      • Multiplex Immunofluorescence in Formalin-Fixed Paraffin-Embedded Tumor Tissue to Identify Single-Cell-Level PI3K Pathway Activation. Clin Cancer Res. 2020 11 15; 26(22):5903-5913. View in: Pubmed

      • Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma. Cancer Res. 2020 10 15; 80(20):4335-4345. View in: Pubmed

      • Genome-Wide Somatic Alterations in Multiple Myeloma Reveal a Superior Outcome Group. J Clin Oncol. 2020 09 20; 38(27):3107-3118. View in: Pubmed

      • Influenza Vaccination and COVID19 Mortality in the USA. medRxiv. 2020 Jun 26. View in: Pubmed

      • Practical implementation of frailty models in Mendelian risk prediction. Genet Epidemiol. 2020 09; 44(6):564-578. View in: Pubmed

      • Receiver Operating Characteristic Curves with an Indeterminacy Zone. Pattern Recognit Lett. 2020 Aug; 136:94-100. View in: Pubmed

      • Performance of Breast Cancer Risk-Assessment Models in a Large Mammography Cohort. J Natl Cancer Inst. 2020 05 01; 112(5):489-497. View in: Pubmed

      • 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. View in: Pubmed

      • Penetrance of Colorectal Cancer Among Mismatch Repair Gene Mutation Carriers: A Meta-Analysis. JNCI Cancer Spectr. 2020 Aug; 4(5):pkaa027. View in: Pubmed

      • 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. View in: Pubmed

      • The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models. Biostatistics. 2020 04 01; 21(2):253-268. View in: Pubmed

      • 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. View in: Pubmed

      • Tree-Weighting for Multi-Study Ensemble Learners. Pac Symp Biocomput. 2020; 25:451-462. View in: Pubmed

      • 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. View in: Pubmed

      • 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. View in: Pubmed

      • 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. View in: Pubmed

      • 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. View in: Pubmed

      • Clinical Factors Associated With Gastric Cancer in Individuals With Lynch Syndrome. Clin Gastroenterol Hepatol. 2020 04; 18(4):830-837.e1. View in: Pubmed

      • Frequentist operating characteristics of Bayesian optimal designs via simulation. Stat Med. 2019 09 20; 38(21):4026-4039. View in: Pubmed

      • High-Dimensional Confounding Adjustment Using Continuous Spike and Slab Priors. Bayesian Anal. 2019 Sep; 14(3):805-828. View in: Pubmed

      • Deciphering the chronology of copy number alterations in Multiple Myeloma. Blood Cancer J. 2019 03 26; 9(4):39. View in: Pubmed

      • Multi-study factor analysis. Biometrics. 2019 03; 75(1):337-346. View in: Pubmed

      • Shared and Study-specific Dietary Patterns and Head and Neck Cancer Risk in an International Consortium. Epidemiology. 2019 01; 30(1):93-102. View in: Pubmed

      • Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. iScience. 2018 Nov 30; 9:451-460. View in: Pubmed

      • 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. View in: Pubmed

      • Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biol. 2018 09 25; 19(1):142. View in: Pubmed

      • Family History of Breast or Prostate Cancer and Prostate Cancer Risk. Clin Cancer Res. 2018 12 01; 24(23):5910-5917. View in: Pubmed

      • The clinical trials landscape for glioblastoma: is it adequate to develop new treatments? Neuro Oncol. 2018 07 05; 20(8):1034-1043. View in: Pubmed

      • Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. Clin Cancer Res. 2018 10 15; 24(20):5037-5047. View in: Pubmed

      • Efficient computation of the joint probability of multiple inherited risk alleles from pedigree data. Genet Epidemiol. 2018 09; 42(6):528-538. View in: Pubmed

      • Precision Prevention and Early Detection of Cancer: Fundamental Principles. Cancer Discov. 2018 07; 8(7):803-811. View in: Pubmed

      • Adding experimental arms to platform clinical trials: randomization procedures and interim analyses. Biostatistics. 2018 04 01; 19(2):199-215. View in: Pubmed

      • Long intergenic non-coding RNAs have an independent impact on survival in multiple myeloma. Leukemia. 2018 12; 32(12):2626-2635. View in: Pubmed

      • Training replicable predictors in multiple studies. Proc Natl Acad Sci U S A. 2018 03 13; 115(11):2578-2583. View in: Pubmed

      • 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. View in: Pubmed

      • Expressed fusion gene landscape and its impact in multiple myeloma. Nat Commun. 2017 12 01; 8(1):1893. View in: Pubmed

      • Propensity scores with misclassified treatment assignment: a likelihood-based adjustment. Biostatistics. 2017 Oct 01; 18(4):695-710. View in: Pubmed

      • Nonparametric Adjustment for Measurement Error in Time-to-Event Data: Application to Risk Prediction Models. J Am Stat Assoc. 2018; 113(521):14-25. View in: Pubmed

      • Stromal and epithelial transcriptional map of initiation progression and metastatic potential of human prostate cancer. Nat Commun. 2017 09 04; 8(1):420. View in: Pubmed

      • Integrative factor analysis - An unsupervised method for quantifying cross-study consistency of gene expression data. Genomics. 2018 03; 110(2):80-88. View in: Pubmed

      • Role of stem-cell divisions in cancer risk. Nature. 2017 08 09; 548(7666):E13-E14. View in: Pubmed

      • Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma. Neuro Oncol. 2017 Jul 01; 19(7):908-917. View in: Pubmed

      • Reassessing risk models for atypical hyperplasia: age may not matter. Breast Cancer Res Treat. 2017 Sep; 165(2):285-291. View in: Pubmed

      • Designing Clinical Trials That Accept New Arms: An Example in Metastatic Breast Cancer. J Clin Oncol. 2017 Sep 20; 35(27):3160-3168. View in: Pubmed

      • Bayesian response-adaptive designs for basket trials. Biometrics. 2017 09; 73(3):905-915. View in: Pubmed

      • Combinatorial Mixtures of Multiparameter Distributions: An Application to Bivariate Data. Int J Biostat. 2017 02 16; 13(1). View in: Pubmed

      • Model averaged double robust estimation. Biometrics. 2017 06; 73(2):410-421. View in: Pubmed

      • Adaptive Randomization of Neratinib in Early Breast Cancer. N Engl J Med. 2016 10 20; 375(16):1593-4. View in: Pubmed

      • I-SPY 2--A Glimpse of the Future of Phase 2 Drug Development? N Engl J Med. 2016 Jul 07; 375(1):7-9. View in: Pubmed

      • The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles. J Natl Cancer Inst. 2016 11; 108(11). View in: Pubmed

      • Penetrance of ATM Gene Mutations in Breast Cancer: A Meta-Analysis of Different Measures of Risk. Genet Epidemiol. 2016 07; 40(5):425-31. View in: Pubmed

      • A two-stage approach to genetic risk assessment in primary care. Breast Cancer Res Treat. 2016 Jan; 155(2):375-83. View in: Pubmed

      • Familial Risk and Heritability of Cancer Among Twins in Nordic Countries. JAMA. 2016 Jan 05; 315(1):68-76. View in: Pubmed

      • Optimal Bayesian adaptive trials when treatment efficacy depends on biomarkers. Biometrics. 2016 06; 72(2):414-21. View in: Pubmed

      • Evaluating a 4-marker signature of aggressive prostate cancer using time-dependent AUC. Prostate. 2015 Dec; 75(16):1926-33. View in: Pubmed

      • Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO. Cancer Inform. 2015; 14(Suppl 2):147-57. View in: Pubmed

      • Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues. J Mol Diagn. 2015 Jul; 17(4):374-81. View in: Pubmed

      • 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. View in: Pubmed

      • BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol Cell. 2015 Feb 19; 57(4):636-647. View in: Pubmed

      • Combining progression-free survival and overall survival as a novel composite endpoint for glioblastoma trials. Neuro Oncol. 2015 Aug; 17(8):1106-13. View in: Pubmed

      • 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. View in: Pubmed

      • Differential and limited expression of mutant alleles in multiple myeloma. Blood. 2014 Nov 13; 124(20):3110-7. View in: Pubmed

      • Misreported family histories and underestimation of risk. J Clin Oncol. 2014 Nov 10; 32(32):3682-3. View in: Pubmed

      • 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. View in: Pubmed

      • Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics. 2014 Nov 01; 30(21):3062-9. View in: Pubmed

      • Cross-study validation for the assessment of prediction algorithms. Bioinformatics. 2014 Jun 15; 30(12):i105-12. View in: Pubmed

      • Recent BRCAPRO upgrades significantly improve calibration. Cancer Epidemiol Biomarkers Prev. 2014 Aug; 23(8):1689-95. View in: Pubmed

      • Completing the results of the 2013 Boston marathon. PLoS One. 2014; 9(4):e93800. View in: Pubmed

      • Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. J Natl Cancer Inst. 2014 Apr 03; 106(5). View in: Pubmed

      • Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. J Natl Cancer Inst. 2014 Apr 03; 106(5). View in: Pubmed

      • Modular network construction using eQTL data: an analysis of computational costs and benefits. Front Genet. 2014; 5:40. View in: Pubmed

      • Integrative correlation: Properties and relation to canonical correlations. J Multivar Anal. 2014 Jan 01; 123:270-280. View in: Pubmed

      • Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun. 2014; 5:2997. View in: Pubmed

      • Statistical tools and R software for cancer driver probabilities. Methods Mol Biol. 2014; 1101:113-34. View in: Pubmed

      • Reclassification of predictions for uncovering subgroup specific improvement. Stat Med. 2014 May 20; 33(11):1914-27. View in: Pubmed

      • Frailty Models for Familial Risk with Application to Breast Cancer. J Am Stat Assoc. 2013 Dec 01; 108(504):1205-1215. View in: Pubmed

      • A decision-theory approach to interpretable set analysis for high-dimensional data. Biometrics. 2013 Sep; 69(3):614-23. View in: Pubmed

      • 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. View in: Pubmed

      • Biomarker-based adaptive trials for patients with glioblastoma--lessons from I-SPY 2. Neuro Oncol. 2013 Aug; 15(8):972-8. View in: Pubmed

      • Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors. F1000Res. 2013; 2:152. View in: Pubmed

      • Providing access to risk prediction tools via the HL7 XML-formatted risk web service. Breast Cancer Res Treat. 2013 Jul; 140(1):187-93. View in: Pubmed

      • Calibrated predictions for multivariate competing risks models. Lifetime Data Anal. 2014 Apr; 20(2):234-51. View in: Pubmed

      • DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics. 2013 Aug 01; 29(15):1865-71. View in: Pubmed

      • Simplifying clinical use of the genetic risk prediction model BRCAPRO. Breast Cancer Res Treat. 2013 Jun; 139(2):571-9. View in: Pubmed

      • curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database (Oxford). 2013; 2013:bat013. View in: Pubmed

      • Reply to B. Freidlin et al. J Clin Oncol. 2013 Mar 01; 31(7):970-1. View in: Pubmed

      • Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. Genet Epidemiol. 2013 Feb; 37(2):205-13. View in: Pubmed

      • 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. View in: Pubmed

      • SNP prioritization using a Bayesian probability of association. Genet Epidemiol. 2013 Feb; 37(2):214-21. View in: Pubmed

      • Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. Nat Genet. 2013 Jan; 45(1):12-7. View in: Pubmed

      • Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med. 2012 Nov 28; 4(162):162ra154. View in: Pubmed

      • The penetrance of ductal carcinoma in situ among BRCA1 and BRCA2 mutation carriers. Breast Cancer Res Treat. 2013 Jan; 137(1):315-8. View in: Pubmed

      • Expression profiling of archival tumors for long-term health studies. Clin Cancer Res. 2012 Nov 15; 18(22):6136-46. View in: Pubmed

      • 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. View in: Pubmed

      • Estimation of sequencing error rates in short reads. BMC Bioinformatics. 2012 Jul 30; 13:185. View in: Pubmed

      • MODELING DEPENDENT GENE EXPRESSION. Ann Stat. 2012; 6(2):542-560. View in: Pubmed

      • Bayesian adaptive randomized trial design for patients with recurrent glioblastoma. J Clin Oncol. 2012 Sep 10; 30(26):3258-63. View in: Pubmed

      • Response to comments on "the predictive capacity of personal genome sequencing". Sci Transl Med. 2012 May 23; 4(135):135lr3. View in: Pubmed

      • The predictive capacity of personal genome sequencing. Sci Transl Med. 2012 May 09; 4(133):133ra58. View in: Pubmed

      • Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. BMC Cancer. 2012 Mar 29; 12:124. View in: Pubmed

      • Bayesian effect estimation accounting for adjustment uncertainty. Biometrics. 2012 Sep; 68(3):661-71. View in: Pubmed

      • Assessing the added value of breast tumor markers in genetic risk prediction model BRCAPRO. Breast Cancer Res Treat. 2012 May; 133(1):347-55. View in: Pubmed

      • Integrating diverse genomic data using gene sets. Genome Biol. 2011 Oct 21; 12(10):R105. View in: Pubmed

      • OnionTree XML: a format to exchange gene-related probabilities. J Biomol Struct Dyn. 2011 Oct; 29(2):417-23. View in: Pubmed

      • Opportunities for the primary prevention of colorectal cancer in the United States. Cancer Prev Res (Phila). 2012 Jan; 5(1):138-45. View in: Pubmed

      • 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. View in: Pubmed

      • Modeling liquid association. Biometrics. 2011 Mar; 67(1):133-41. View in: Pubmed

      • The genetic landscape of the childhood cancer medulloblastoma. Science. 2011 Jan 28; 331(6016):435-9. View in: Pubmed

      • Patient-oriented gene set analysis for cancer mutation data. Genome Biol. 2010; 11(11):R112. View in: Pubmed

      • Cross-platform Comparison of Two Pancreatic Cancer Phenotypes. Cancer Inform. 2010 Nov 01; 9:257-64. View in: Pubmed

      • CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinformatics. 2010 Nov 01; 26(21):2792-3. View in: Pubmed

      • Estimating CDKN2A carrier probability and personalizing cancer risk assessments in hereditary melanoma using MelaPRO. Cancer Res. 2010 Jan 15; 70(2):552-9. View in: Pubmed

      • Rejoinder. J Am Stat Assoc. 2009 12; 104(488):1318-1323. View in: Pubmed

      • The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. BMC Bioinformatics. 2009 Aug 20; 10:256. View in: Pubmed

      • 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. View in: Pubmed

      • SMAD4 gene mutations are associated with poor prognosis in pancreatic cancer. Clin Cancer Res. 2009 Jul 15; 15(14):4674-9. View in: Pubmed

      • Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma. Stem Cells. 2009 Jul; 27(7):1487-95. View in: Pubmed

      • Likelihood estimation of conjugacy relationships in linear models with applications to high-throughput genomics. Int J Biostat. 2009 May 29; 5(1):Article 18. View in: Pubmed

      • 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. View in: Pubmed

      • Genetic mutations associated with cigarette smoking in pancreatic cancer. Cancer Res. 2009 Apr 15; 69(8):3681-8. View in: Pubmed

      • Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science. 2009 Apr 10; 324(5924):217. View in: Pubmed

      • A Bayesian model for cross-study differential gene expression. J Am Stat Assoc. 2009; 104(488):1295-1310. View in: Pubmed

      • [Genetic predisposition to multiple sclerosis as a polygenic autoimmune disease]. Zh Nevrol Psikhiatr Im S S Korsakova. 2009; 109(7 Suppl 2):16-22. View in: Pubmed

      • Tailoring BRCAPRO to Asian-Americans. J Clin Oncol. 2009 Feb 01; 27(4):642-3; author reply 643-4. View in: Pubmed

      • Identifying differential correlation in gene/pathway combinations. BMC Bioinformatics. 2008 Nov 18; 9:488. View in: Pubmed

      • 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. View in: Pubmed

      • 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. View in: Pubmed

      • 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. View in: Pubmed

      • 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. View in: Pubmed

      • Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26; 321(5897):1801-6. View in: Pubmed

      • An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26; 321(5897):1807-12. View in: Pubmed

      • Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies. BMC Genomics. 2008 Aug 29; 9:405. View in: Pubmed

      • Toll-like receptor 3 and geographic atrophy in age-related macular degeneration. N Engl J Med. 2008 Oct 02; 359(14):1456-63. View in: Pubmed

      • Design and analysis issues in genome-wide somatic mutation studies of cancer. Genomics. 2009 Jan; 93(1):17-21. View in: Pubmed

      • Model selection and health effect estimation in environmental epidemiology. Epidemiology. 2008 Jul; 19(4):558-60. View in: Pubmed

      • Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Ann Appl Stat. 2008 Jun 01; 2(2):687-713. View in: Pubmed

      • Incorporating tumor immunohistochemical markers in BRCA1 and BRCA2 carrier prediction. Breast Cancer Res. 2008; 10(2):401. View in: Pubmed

      • TRAB: testing whether mutation frequencies are above an unknown background. Stat Appl Genet Mol Biol. 2008; 7(1):Article11. View in: Pubmed

      • Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci U S A. 2008 Mar 18; 105(11):4283-8. View in: Pubmed

      • 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. View in: Pubmed

      • Systematic review: gene expression profiling assays in early-stage breast cancer. Ann Intern Med. 2008 Mar 04; 148(5):358-69. View in: Pubmed

      • Impact of gene expression profiling tests on breast cancer outcomes. Evid Rep Technol Assess (Full Rep). 2008 Jan; (160):1-105. View in: Pubmed

      • Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries. BMC Bioinformatics. 2007 Dec 11; 8:476. View in: Pubmed

      • Impact of gene expression profiling tests on breast cancer outcomes. Evid Rep Technol Assess (Full Rep). 2007 Dec; (160):1-105. View in: Pubmed

      • Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. J Natl Cancer Inst. 2007 Dec 05; 99(23):1811-4. View in: Pubmed

      • Limited family structure and breast cancer risk. JAMA. 2007 Nov 07; 298(17):2007; author reply 2007-8. View in: Pubmed

      • The genomic landscapes of human breast and colorectal cancers. Science. 2007 Nov 16; 318(5853):1108-13. View in: Pubmed

      • 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. View in: Pubmed

      • Validity of models for predicting BRCA1 and BRCA2 mutations. Ann Intern Med. 2007 Oct 02; 147(7):441-50. View in: Pubmed

      • Cross-study validation and combined analysis of gene expression microarray data. Biostatistics. 2008 Apr; 9(2):333-54. View in: Pubmed

      • A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res. 2007 Sep; 17(9):1304-18. View in: Pubmed

      • 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. View in: Pubmed

      • Pre-processing Agilent microarray data. BMC Bioinformatics. 2007 May 01; 8:142. View in: Pubmed

      • PancPRO: risk assessment for individuals with a family history of pancreatic cancer. J Clin Oncol. 2007 Apr 10; 25(11):1417-22. View in: Pubmed

      • Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007 Apr 10; 25(11):1329-33. View in: Pubmed

      • Multivariate analysis and visualization of splicing correlations in single-gene transcriptomes. BMC Bioinformatics. 2007 Jan 18; 8:16. View in: Pubmed

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      Dana-Farber Cancer Institute

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      Dana-Farber Cancer Institute

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      Dana-Farber Cancer Institute

      450 Brookline Avenue CLS 11043 Boston, MA 02215
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      42.3374, -71.1082