Photo of Giovanni Parmigiani, PhD

Giovanni Parmigiani, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 632-3012
Fax: (617) 632-2444


gp@jimmy.harvard.edu

Photo of Giovanni Parmigiani, PhD

Dana-Farber Cancer Institute
Phone: (617) 632-3012
Fax: (617) 632-2444


gp@jimmy.harvard.edu

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Giovanni Parmigiani, PhD

Dana-Farber Cancer Institute

EDUCATIONAL TITLES

  • Professor, Biostatistics, Harvard T.H. Chan School Of Public Health
  • Chair and Professor, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute

DF/HCC PROGRAM AFFILIATION

DF/HCC ASSOCIATIONS

  • Member, Center Scientific Council
  • Associate Director, Population Science, Executive Committee

Research Abstract

Models and software for predicting who is at risk of carrying genetic variants that confer susceptibility to cancer. Application to breast, ovarian, colorectal, pancreatic and skin cancer.

Statistical methods for the analysis of high throughput genomic data: analysis of cancer genome sequencing projects; integration of genomic information across technologies; cross-study validation of genomics results.

Statistical methods for complex medical decisions: comprehensive models for lifetime history of chronic disease outcomes; decision trees and dynamic programming.

Bayesian modeling and computation: multilevel models; decision theoretic approaches to inference; sequential experimental design, Markov chain Monte Carlo methods.

Publications from Harvard Catalyst Profiles

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  • Pernar CH, Chomistek AK, Barnett JB, Ivey K, Al-Shaar L, Roberts SB, Rood J, Fielding RA, Block J, Li R, Willett WC, Parmigiani G, Giovannucci EL, Mucci LA, Rimm EB. Validity and Relative Validity of Alternative Methods to Assess Physical Activity in Epidemiologic Studies: Findings from the Men's Lifestyle Validation Study. Am J Epidemiol 2022. PubMed
  • Bazarbachi AH, Avet-Loiseau H, Szalat R, Samur AA, Hunter Z, Shammas M, Corre J, Fulciniti M, Anderson KC, Parmigiani G, Treon SP, Mohty M, Munshi NC, Samur MK. IgM-MM is predominantly a pre-germinal center disorder and has a distinct genomic and transcriptomic signature from WM. Blood 2021; 138:1980-1985. PubMed
  • Blackford AL, Childs EJ, Porter N, Petersen GM, Rabe KG, Gallinger S, Borgida A, Syngal S, Cote ML, Schwartz AG, Goggins MG, Hruban RH, Parmigiani G, Klein AP. A risk prediction tool for individuals with a family history of breast, ovarian, or pancreatic cancer: BRCAPANCPRO. Br J Cancer 2021. PubMed
  • Huang T, Braun D, Lynch HT, Parmigiani G. Variation in cancer risk among families with genetic susceptibility. Genet Epidemiol 2021; 45:209-221. PubMed
  • Yang Y, Hong C, Liang JW, Gruber S, Parmigiani G, Idos G, Braun D. A likelihood-based approach to assessing frequency of pathogenicity among variants of unknown significance in susceptibility genes. Stat Med 2021; 40:593-606. PubMed
  • Pernar CH, Parmigiani G, Giovannucci EL, Rimm EB, Tyekucheva S, Loda M, Finn SP, Vander Heiden MG, Fiorentino M, Ebot EM, Mucci LA. Gene Expression Pathways in Prostate Tissue Associated with Vigorous Physical Activity in Prostate Cancer. Cancer Epidemiol Biomarkers Prev 2021. PubMed
  • Stopsack KH, Tyekucheva S, Wang M, Gerke TA, Vaselkiv JB, Penney KL, Kantoff PW, Finn SP, Fiorentino M, Loda M, Lotan TL, Parmigiani G, Mucci LA. Extent, impact, and mitigation of batch effects in tumor biomarker studies using tissue microarrays. Elife 2021. PubMed
  • Zhang Y, Patil P, Evan Johnson W, Parmigiani G. Robustifying Genomic Classifiers To Batch Effects Via Ensemble Learning. Bioinformatics 2020. PubMed
  • Hujoel MLA, Parmigiani G, Braun D. Statistical approaches for meta-analysis of genetic mutation prevalence. Genet Epidemiol 2020. PubMed
  • Samur MK, Aktas Samur A, Fulciniti M, Szalat R, Han T, Shammas M, Richardson P, Magrangeas F, Minvielle S, Corre J, Moreau P, Thakurta A, Anderson KC, Parmigiani G, Avet-Loiseau H, Munshi NC. Genome-Wide Somatic Alterations in Multiple Myeloma Reveal a Superior Outcome Group. J Clin Oncol 2020; 38:3107-3118. PubMed
  • Stopsack KH, Huang Y, Tyekucheva S, Gerke TA, Bango C, Elfandy H, Bowden M, Penney KL, Roberts TM, Parmigiani G, Kantoff PW, Mucci LA, Loda M. Multiplex immunofluorescence in formalin-fixed paraffin-embedded tumor tissue to identify single cell-level PI3K pathway activation. Clin Cancer Res 2020. PubMed
  • Zhang Y, Parmigiani G, Johnson WE. : batch effect adjustment for RNA-seq count data. NAR Genom Bioinform 2020; 2:lqaa078. PubMed
  • Geistlinger L, Oh S, Ramos M, Schiffer L, LaRue RS, Henzler CM, Munro SA, Daughters C, Nelson AC, Winterhoff BJ, Chang Z, Talukdar S, Shetty M, Mullany SA, Morgan M, Parmigiani G, Birrer MJ, Qin LX, Riester M, Starr TK, Waldron L. Multiomic Analysis of Subtype Evolution and Heterogeneity in High-Grade Serous Ovarian Carcinoma. Cancer Res 2020. PubMed
  • Parmigiani G. Receiver Operating Characteristic Curves with an Indeterminacy Zone. Pattern Recognit Lett 2020; 136:94-100. PubMed
  • Chen J, Bae E, Zhang L, Hughes K, Parmigiani G, Braun D, Rebbeck TR. Penetrance of Breast and Ovarian Cancer in Women Who Carry a Mutation and Do Not Use Risk-Reducing Salpingo-Oophorectomy: An Updated Meta-Analysis. JNCI Cancer Spectr 2020; 4:pkaa029. PubMed
  • Wang C, Wang Y, Hughes KS, Parmigiani G, Braun D. Penetrance of Colorectal Cancer Among Mismatch Repair Gene Mutation Carriers: A Meta-Analysis. JNCI Cancer Spectr 2020; 4:pkaa027. PubMed
  • Yin K, Liu Y, Lamichhane B, Sandbach JF, Patel G, Compagnoni G, Kanak RH, Rosen B, Ondrula DP, Smith L, Brown E, Gold L, Whitworth P, App C, Euhus D, Semine A, Dwight Lyons S, Lazarte MAC, Parmigiani G, Braun D, Hughes KS. Legacy Genetic Testing Results for Cancer Susceptibility: How Common are Conflicting Classifications in a Large Variant Dataset from Multiple Practices? Ann Surg Oncol 2020; 27:2212-2220. PubMed
  • Huang T, Gorfine M, Hsu L, Parmigiani G, Braun D. Practical implementation of frailty models in Mendelian risk prediction. Genet Epidemiol 2020. PubMed
  • Spring LM, Fell G, Arfe A, Sharma C, Greenup RA, Reynolds KL, Smith BL, Alexander BM, Moy B, Isakoff SJ, Parmigiani G, Trippa L, Bardia A. Pathological complete response after neoadjuvant chemotherapy and impact on breast cancer recurrence and survival: a comprehensive meta-analysis. Clin Cancer Res 2020. PubMed
  • Ramchandran M, Patil P, Parmigiani G. Tree-Weighting for Multi-Study Ensemble Learners. Pac Symp Biocomput 2020; 25:451-462. PubMed
  • Schwede M, Waldron L, Mok SC, Wei W, Basunia A, Merritt MA, Mitsiades CS, Parmigiani G, Harrington DP, Quackenbush J, Birrer MJ, Culhane AC. The impact of stroma admixture on molecular subtypes and prognostic gene signatures in serous ovarian cancer. Cancer Epidemiol Biomarkers Prev 2019. PubMed
  • McCarthy AM, Guan Z, Welch M, Griffin ME, Sippo DA, Deng Z, Coopey SB, Acar A, Semine A, Parmigiani G, Braun D, Hughes KS. Performance of breast cancer risk assessment models in a large mammography cohort. Journal of the National Cancer Institute 2019. PubMed
  • Bao Y, Deng Z, Wang Y, Kim H, Armengol VD, Acevedo F, Ouardaoui N, Wang C, Parmigiani G, Barzilay R, Braun D, Hughes KS. Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes. JCO Clin Cancer Inform 2019; 3:1-9. PubMed
  • Hashim D, Gonzalez-Feliciano AG, Ahearn TU, Pettersson A, Barber L, Pernar CH, Ebot EM, Isikbay M, Finn SP, Giovannucci EL, Lis RT, Loda M, Parmigiani G, Lotan T, Kantoff PW, Mucci LA, Graff RE. Family history of prostate cancer and the incidence of ERG- and phosphatase and tensin homolog-defined prostate cancer. Int. J. Cancer 2019. PubMed
  • Zhang Y, Trippa L, Parmigiani G. Frequentist operating characteristics of Bayesian optimal designs via simulation. Stat Med 2019. PubMed
  • Aktas Samur A, Minvielle S, Shammas M, Fulciniti M, Magrangeas F, Richardson PG, Moreau P, Attal M, Anderson KC, Parmigiani G, Avet-Loiseau H, Munshi NC, Samur MK. Deciphering the chronology of copy number alterations in Multiple Myeloma. Blood Cancer J 2019; 9:39. PubMed
  • Deng Z, Yin K, Bao Y, Armengol VD, Wang C, Tiwari A, Barzilay R, Parmigiani G, Braun D, Hughes KS. Validation of a Semiautomated Natural Language Processing-Based Procedure for Meta-Analysis of Cancer Susceptibility Gene Penetrance. JCO Clin Cancer Inform 2019; 3:1-9. PubMed
  • Wang Z, Cao S, Morris JS, Ahn J, Liu R, Tyekucheva S, Gao F, Li B, Lu W, Tang X, Wistuba II, Bowden M, Mucci L, Loda M, Parmigiani G, Holmes CC, Wang W. Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. iScience 2018; 9:451-460. PubMed
  • Pernar CH, Ebot EM, Pettersson A, Graff RE, Giunchi F, Ahearn TU, Gonzalez-Feliciano AG, Markt SC, Wilson KM, Stopsack KH, Gazeeva E, Lis RT, Parmigiani G, Rimm EB, Finn SP, Giovannucci EL, Fiorentino M, Mucci LA. A Prospective Study of the Association between Physical Activity and Risk of Prostate Cancer Defined by Clinical Features and TMPRSS2:ERG. Eur Urol 2018. PubMed
  • De Vito R, Bellio R, Trippa L, Parmigiani G. Multi-study Factor Analysis. Biometrics 2018. PubMed
  • Ma S, Ogino S, Parsana P, Nishihara R, Qian Z, Shen J, Mima K, Masugi Y, Cao Y, Nowak JA, Shima K, Hoshida Y, Giovannucci EL, Gala MK, Chan AT, Fuchs CS, Parmigiani G, Huttenhower C, Waldron L. Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis. Genome Biol 2018; 19:142. PubMed
  • Zhang Y, Bernau C, Parmigiani G, Waldron L. The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models. Biostatistics 2018. PubMed
  • Barber LE, Gerke T, Markt SC, Peisch SF, Wilson KM, Ahearn TU, Giovannucci EL, Parmigiani G, Mucci LA. Family history of breast or prostate cancer and prostate cancer risk. Clin Cancer Res 2018. PubMed
  • Chen GM, Kannan L, Geistlinger L, Kofia V, Safikhani Z, Gendoo DMA, Parmigiani G, Birrer M, Haibe-Kains B, Waldron L. Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. Clin Cancer Res 2018. PubMed
  • Madsen T, Braun D, Peng G, Parmigiani G, Trippa L. Efficient computation of the joint probability of multiple inherited risk alleles from pedigree data. Genet Epidemiol 2018. PubMed
  • Samur MK, Minvielle S, Gulla A, Fulciniti M, Cleynen A, Aktas Samur A, Szalat R, Shammas M, Magrangeas F, Tai YT, Auclair D, Keats J, Richardson P, Attal M, Moreau P, Anderson KC, Parmigiani G, Avet-Loiseau H, Munshi NC. Long intergenic non-coding RNAs have an independent impact on survival in multiple myeloma. Leukemia 2018. PubMed
  • Patil P, Parmigiani G. Training replicable predictors in multiple studies. Proc Natl Acad Sci U S A 2018; 115:2578-2583. PubMed
  • Vanderbeek AM, Rahman R, Fell G, Ventz S, Chen T, Redd R, Parmigiani G, Cloughesy TF, Wen PY, Trippa L, Alexander BM. The clinical trials landscape for glioblastoma: is it adequate to develop new treatments? 2018. PubMed
  • Braun D, Yang J, Griffin M, Parmigiani G, Hughes KS. A Clinical Decision Support Tool to Predict Cancer Risk for Commonly Tested Cancer-Related Germline Mutations. J Genet Couns 2018. PubMed
  • Braun D, Gorfine M, Katki HA, Ziogas A, Parmigiani G. Nonparametric Adjustment for Measurement Error in Time-to-Event Data: Application to Risk Prediction Models. Journal of the American Statistical Association 2018; 113:14-25. PubMed
  • Wang XV, Parmigiani G. Integrative factor analysis - An unsupervised method for quantifying cross-study consistency of gene expression data. Genomics 2017. PubMed
  • Tomasetti C, Durrett R, Kimmel M, Lambert A, Parmigiani G, Zauber A, Vogelstein B. Role of stem-cell divisions in cancer risk. Nature 2017; 548:E13-E14. PubMed
  • Ventz S, Cellamare M, Parmigiani G, Trippa L. Adding experimental arms to platform clinical trials: randomization procedures and interim analyses. Biostatistics 2017. PubMed
  • Tanguturi SK, Trippa L, Ramkissoon SH, Pelton K, Knoff D, Sandak D, Lindeman NI, Ligon AH, Beroukhim R, Parmigiani G, Wen PY, Ligon KL, Alexander BM. Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma. 2017. PubMed
  • Mazzola E, Coopey SB, Griffin M, Polubriaginof F, Buckley JM, Parmigiani G, Garber JE, Smith BL, Gadd MA, Specht MC, Guidi A, Hughes KS. Reassessing risk models for atypical hyperplasia: age may not matter. Breast Cancer Res Treat 2017. PubMed
  • Ventz S, Alexander BM, Parmigiani G, Gelber RD, Trippa L. Designing Clinical Trials That Accept New Arms: An Example in Metastatic Breast Cancer. J Clin Oncol 2017. PubMed
  • Braun D, Gorfine M, Parmigiani G, Arvold ND, Dominici F, Zigler C. Propensity scores with misclassified treatment assignment: a likelihood-based adjustment. Biostatistics 2017. PubMed
  • Ventz S, Barry WT, Parmigiani G, Trippa L. Bayesian response-adaptive designs for basket trials. Biometrics 2017. PubMed
  • Edefonti V, Parmigiani G. Combinatorial Mixtures of Multiparameter Distributions: An Application to Bivariate Data. Int J Biostat 2017. PubMed
  • Cefalu M, Dominici F, Arvold N, Parmigiani G. Model averaged double robust estimation. Biometrics 2016. PubMed
  • Waldron L, Riester M, Ramos M, Parmigiani G, Birrer M. The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles. Journal of the National Cancer Institute 2016. PubMed
  • Harrington D, Parmigiani G. I-SPY 2--A Glimpse of the Future of Phase 2 Drug Development? N Engl J Med 2016; 375:7-9. PubMed
  • Marabelli M, Cheng SC, Parmigiani G. Penetrance of ATM Gene Mutations in Breast Cancer: A Meta-Analysis of Different Measures of Risk. Genet Epidemiol 2016. PubMed
  • Mucci LA, Hjelmborg JB, Harris JR, Czene K, Havelick DJ, Scheike T, Graff RE, Holst K, Möller S, Unger RH, McIntosh C, Nuttall E, Brandt I, Penney KL, Hartman M, Kraft P, Parmigiani G, Christensen K, Koskenvuo M, Holm NV, Heikkilä K, Pukkala E, Skytthe A, Adami HO, Kaprio J, . Familial Risk and Heritability of Cancer Among Twins in Nordic Countries. JAMA 2016; 315:68-76. PubMed
  • Biswas S, Atienza P, Chipman J, Blackford AL, Arun B, Hughes K, Parmigiani G. A two-stage approach to genetic risk assessment in primary care. Breast Cancer Res Treat 2016; 155:375-83. PubMed
  • Harrington D, Parmigiani G. Adaptive Randomization of Neratinib in Early Breast Cancer. N Engl J Med 2016; 375:1593-4. PubMed
  • Gerke TA, Martin NE, Ding Z, Nuttall EJ, Stack EC, Giovannucci E, Lis RT, Stampfer MJ, Kantoff PW, Parmigiani G, Loda M, Mucci LA. Evaluating a 4-marker signature of aggressive prostate cancer using time-dependent AUC. Prostate 2015; 75:1926-33. PubMed
  • Zhang Y, Trippa L, Parmigiani G. Optimal Bayesian adaptive trials when treatment efficacy depends on biomarkers. Biometrics 2015. PubMed
  • Trippa L, Wen PY, Parmigiani G, Berry DA, Alexander BM. Combining progression-free survival and overall survival as a novel composite endpoint for glioblastoma trials. 2015. PubMed
  • Tyekucheva S, Martin NE, Stack EC, Wei W, Vathipadiekal V, Waldron L, Fiorentino M, Lis RT, Stampfer MJ, Loda M, Parmigiani G, Mucci LA, Birrer M. Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues. J Mol Diagn 2015; 17:374-81. PubMed
  • Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, Dimitrov S, Pathania S, McKinney KM, Eaton ML, Kellis M, Hill SJ, Parmigiani G, Proudfoot NJ, Livingston DM. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol Cell 2015; 57:636-47. PubMed
  • Tomasetti C, Marchionni L, Nowak MA, Parmigiani G, Vogelstein B. Only three driver gene mutations are required for the development of lung and colorectal cancers. Proc Natl Acad Sci U S A 2015; 112:118-23. PubMed
  • Rashid NU, Sperling AS, Bolli N, Wedge DC, Van Loo P, Tai YT, Shammas MA, Fulciniti M, Samur MK, Richardson PG, Magrangeas F, Minvielle S, Futreal PA, Anderson KC, Avet-Loiseau H, Campbell PJ, Parmigiani G, Munshi NC. Differential and limited expression of mutant alleles in multiple myeloma. Blood 2014. PubMed
  • Braun D, Gorfine M, Parmigiani G. Misreported family histories and underestimation of risk. J Clin Oncol 2014. PubMed
  • Mazzola E, Chipman J, Cheng SC, Parmigiani G. Recent BRCAPRO upgrades significantly improve calibration. Cancer Epidemiol Biomarkers Prev 2014. PubMed
  • Bernau C, Riester M, Boulesteix AL, Parmigiani G, Huttenhower C, Waldron L, Trippa L. Cross-study validation for the assessment of prediction algorithms. Bioinformatics 2014; 30:i105-12. PubMed
  • Biswas S, Arun B, Parmigiani G. Reclassification of predictions for uncovering subgroup specific improvement. Stat Med 2014. PubMed
  • Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G. Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. Journal of the National Cancer Institute 2014. PubMed
  • Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. Journal of the National Cancer Institute 2014. PubMed
  • Gorfine M, Hsu L, Zucker DM, Parmigiani G. Calibrated predictions for multivariate competing risks models. Lifetime Data Analysis 2014. PubMed
  • Parmigiani G, Boca S, Ding J, Trippa L. Statistical tools and R software for cancer driver probabilities. Methods Mol Biol 2014; 1101:113-34. PubMed
  • Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, O' Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun 2014; 5:2997. PubMed
  • Ho YY, Cope LM, Parmigiani G. Modular network construction using eQTL data: an analysis of computational costs and benefits. Front Genet 2014; 5:40. PubMed
  • Gorfine M, Hsu L, Parmigiani G. Frailty Models for Familial Risk with Application to Breast Cancer. Journal of the American Statistical Association 2013; 108:1205-1215. PubMed
  • Boca SM, Bravo HC, Caffo B, Leek JT, Parmigiani G. A decision-theory approach to interpretable set analysis for high-dimensional data. Biometrics 2013; 69:614-23. PubMed
  • Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, , Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A 2013; 110:13481-6. PubMed
  • Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W. DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics 2013; 29:1865-71. PubMed
  • Chipman J, Drohan B, Blackford A, Parmigiani G, Hughes K, Bosinoff P. Providing access to risk prediction tools via the HL7 XML-formatted risk web service. Breast Cancer Res Treat 2013; 140:187-93. PubMed
  • Biswas S, Atienza P, Chipman J, Hughes K, Barrera AM, Amos CI, Arun B, Parmigiani G. Simplifying clinical use of the genetic risk prediction model BRCAPRO. Breast Cancer Res Treat 2013; 139:571-9. PubMed
  • Trippa L, Lee EQ, Wen PY, Batchelor TT, Cloughesy T, Parmigiani G, Alexander BM. Reply to B. Freidlin et al. J Clin Oncol 2013; 31:970-1. PubMed
  • Tomasetti C, Vogelstein B, Parmigiani G. 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; 110:1999-2004. PubMed
  • Tomasetti C, Demetri GD, Parmigiani G. Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors. F1000Res 2013; 2:152. PubMed
  • Mazzola E, Cheng SC, Parmigiani G. The penetrance of ductal carcinoma in situ among BRCA1 and BRCA2 mutation carriers. Breast Cancer Res Treat 2013; 137:315-8. PubMed
  • Sausen M, Leary RJ, Jones S, Wu J, Reynolds CP, Liu X, Blackford A, Parmigiani G, Diaz LA, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE, Hogarty MD. Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. Nat Genet 2013; 45:12-7. PubMed
  • Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L. curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database (Oxford) 2013; 2013:bat013. PubMed
  • Coopey SB, Mazzola E, Buckley JM, Sharko J, Belli AK, Kim EM, Polubriaginof F, Parmigiani G, Garber JE, Smith BL, Gadd MA, Specht MC, Guidi AJ, Roche CA, Hughes KS. The role of chemoprevention in modifying the risk of breast cancer in women with atypical breast lesions. Breast Cancer Res Treat 2012. PubMed
  • Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, O'Shaughnessy J, Kinzler KW, Parmigiani G, Vogelstein B, Diaz LA, Velculescu VE. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 2012; 4:162ra154. PubMed
  • Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, Golub TR, Fuchs CS, Parmigiani G, Huttenhower C. Expression profiling of archival tumors for long-term health studies. Clin Cancer Res 2012; 18:6136-46. PubMed
  • Trippa L, Lee EQ, Wen PY, Batchelor TT, Cloughesy T, Parmigiani G, Alexander BM. Bayesian adaptive randomized trial design for patients with recurrent glioblastoma. J Clin Oncol 2012; 30:3258-63. PubMed
  • Wang XV, Blades N, Ding J, Sultana R, Parmigiani G. Estimation of sequencing error rates in short reads. BMC Bioinformatics 2012; 13:185. PubMed
  • Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The genetic landscape of the childhood cancer medulloblastoma. Science 2011; 331:435-9. PubMed
  • Boca SM, Kinzler K, Velculescu VE, Vogelstein B, Parmigiani G. Patient-oriented gene set analysis for cancer mutation data. Genome Biol 2010; 11:R112. PubMed
  • Fertig EJ, Ding J, Favorov AV, Parmigiani G, Ochs MF. CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinformatics 2010; 26:2792-3. PubMed
  • Ho YY, Parmigiani G, Louis TA, Cope LM. Modeling Liquid Association. Biometrics 2010. PubMed
  • Wang W, Niendorf KB, Patel D, Blackford A, Marroni F, Sober AJ, Parmigiani G, Tsao H. Estimating CDKN2A carrier probability and personalizing cancer risk assessments in hereditary melanoma using MelaPRO. Cancer Res 2010; 70:552-9. PubMed
  • Scharpf RB, Iacobuzio-Donahue CA, Cope L, Ruczinski I, Garrett-Mayer E, Lakkur S, Campagna D, Parmigiani G. Cross-platform Comparison of Two Pancreatic Cancer Phenotypes. Cancer Inform 2010; 9:257-64. PubMed
  • Guda K, Moinova H, He J, Jamison O, Ravi L, Natale L, Lutterbaugh J, Lawrence E, Lewis S, Willson JK, Lowe JB, Wiesner GL, Parmigiani G, Barnholtz-Sloan J, Dawson DW, Velculescu VE, Kinzler KW, Papadopoulos N, Vogelstein B, Willis J, Gerken TA, Markowitz SD. Inactivating germ-line and somatic mutations in polypeptide N-acetylgalactosaminyltransferase 12 in human colon cancers. Proc Natl Acad Sci U S A 2009; 106:12921-5. PubMed
  • Blackford A, Serrano OK, Wolfgang CL, Parmigiani G, Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Eshleman JR, Goggins M, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Cameron JL, Olino K, Schulick R, Winter J, Herman JM, Laheru D, Klein AP, Vogelstein B, Kinzler KW, Velculescu VE, Hruban RH. SMAD4 gene mutations are associated with poor prognosis in pancreatic cancer. Clin Cancer Res 2009; 15:4674-9. PubMed
  • He X, Marchionni L, Hansel DE, Yu W, Sood A, Yang J, Parmigiani G, Matsui W, Berman DM. Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma. Stem Cells 2009; 27:1487-95. PubMed
  • Parmigiani G, Boca S, Lin J, Kinzler KW, Velculescu V, Vogelstein B. Design and analysis issues in genome-wide somatic mutation studies of cancer. Genomics 2009; 93:17-21. PubMed
  • Lin X, Afsari B, Marchionni L, Cope L, Parmigiani G, Naiman D, Geman D. The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. BMC Bioinformatics 2009; 10:256. PubMed
  • Tai YC, Chen S, Parmigiani G, Klein AP. Incorporating tumor immunohistochemical markers in BRCA1 and BRCA2 carrier prediction. Breast Cancer Res 2008; 10:401. PubMed
  • Marchionni L, Wilson RF, Wolff AC, Marinopoulos S, Parmigiani G, Bass EB, Goodman SN. Systematic review: gene expression profiling assays in early-stage breast cancer. Ann Intern Med 2008; 148:358-69. PubMed
  • Tai YC, Domchek S, Parmigiani G, Chen S. Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. Journal of the National Cancer Institute 2007; 99:1811-4. PubMed
  • Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science 2007; 318:1108-13. PubMed
  • Parmigiani G, Chen S, Iversen ES Jr, Friebel TM, Finkelstein DM, Anton-Culver H, Ziogas A, Weber BL, Eisen A, Malone KE, Daling JR, Hsu L, Ostrander EA, Peterson LE, Schildkraut JM, Isaacs C, Corio C, Leondaridis L, Tomlinson G, Amos CI, Strong LC, Berry DA, Weitzel JN, Sand S, Dutson D, Kerber R, Peshkin BN, Euhus DM. Validity of models for predicting BRCA1 and BRCA2 mutations. Ann Intern Med 2007; 147:441-50. PubMed
  • Lin J, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE. A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res 2007; 17:1304-18. PubMed
  • Chen S, Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol 2007; 25:1329-33. PubMed
  • Wang W, Chen S, Brune KA, Hruban RH, Parmigiani G, Klein AP. PancPRO: risk assessment for individuals with a family history of pancreatic cancer. J Clin Oncol 2007; 25:1417-22. PubMed
  • Sjöblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The consensus coding sequences of human breast and colorectal cancers. Science 2006; 314:268-74. PubMed
  • Chen S, Wang W, Lee S, Nafa K, Lee J, Romans K, Watson P, Gruber SB, Euhus D, Kinzler KW, Jass J, Gallinger S, Lindor NM, Casey G, Ellis N, Giardiello FM, Offit K, Parmigiani G, . Prediction of germline mutations and cancer risk in the Lynch syndrome. JAMA 2006; 296:1479-87. PubMed
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DF/HCC members that share similar concepts* with Giovanni Parmigiani, PhD but have yet to coauthor a publication with this researcher.

* Concepts are MeSH terms, automatically derived from member publications

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