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profileGiovanni Parmigiani, Ph.D.

TitleProfessor of Biostatistics
InstitutionHarvard T.H. Chan School of Public Health
DepartmentBiostatistics
AddressHarvard, FAS Freshman Seminar Program
Morton Prince House
6 Prescott St
Cambridge MA 02138
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Other Positions
TitleProfessor of Biostatistics
InstitutionFaculty of Arts & Sciences
DepartmentFreshman Seminar


Collapse Overview 
Collapse overview
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 comparative effectiveness research: comprehensive models for lifetime history of chronic disease outcomes; Bayesian meta-analysis; Bayesian causal inference; decision analysis.

Bayesian modeling and computation: multilevel models; decision theoretic approaches to inference; sequential experimental design and their application to adaptive and multistage studies in clinical and epidemiological research.


Collapse Research 
Collapse research activities and funding
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
R21CA177233     (PARMIGIANI, GIOVANNI LUIGI)Mar 1, 2013 - Feb 28, 2015
NIH/NCI
Novel Tools for Familial Risk Prediction
Role: Principal Investigator

R01CA174206     (PARMIGIANI, GIOVANNI LUIGI)Feb 1, 2013 - Jan 31, 2018
NIH/NCI
Bioinformatics Tools for Genomic Analysis of Tumor and Stromal Pathways in Cancer
Role: Principal Investigator

T32GM074906     (IRIZARRY, RAFAEL ANGEL)Aug 1, 2006 - Sep 30, 2011
NIH/NIGMS
Predoctoral Biostatistics Training in Genetics/Genomics
Role: Co-Principal Investigator

R01CA105090     (PARMIGIANI, GIOVANNI)Sep 30, 2004 - Jun 30, 2010
NIH/NCI
Statistical Methods for Cancer Genes
Role: Principal Investigator

P50CA088843     (SUKUMAR, SARA)Sep 30, 2000 - Mar 29, 2013
NIH/NCI
SPORE in Breast Cancer
Role: Co-Principal Investigator

Collapse Bibliographic 
Collapse selected publications
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Tomasetti C, Durrett R, Kimmel M, Lambert A, Parmigiani G, Zauber A, Vogelstein B. Role of stem-cell divisions in cancer risk. Nature. 2017 Aug 09; 548(7666):E13-E14. PMID: 28796214.
    View in: PubMed
  2. 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. Neuro Oncol. 2017 Jul 01; 19(7):908-917. PMID: 28339723.
    View in: PubMed
  3. 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 Sep; 165(2):285-291. PMID: 28589368.
    View in: PubMed
  4. 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 May 22; JCO2016701169. PMID: 28530853.
    View in: PubMed
  5. Braun D, Gorfine M, Parmigiani G, Arvold ND, Dominici F, Zigler C. Propensity scores with misclassified treatment assignment: a likelihood-based adjustment. Biostatistics. 2017 Apr 17. PMID: 28419189.
    View in: PubMed
  6. Ventz S, Barry WT, Parmigiani G, Trippa L. Bayesian response-adaptive designs for basket trials. Biometrics. 2017 Feb 17. PMID: 28211944.
    View in: PubMed
  7. Edefonti V, Parmigiani G. Combinatorial Mixtures of Multiparameter Distributions: An Application to Bivariate Data. Int J Biostat. 2017 Feb 16; 13(1). PMID: 28207413.
    View in: PubMed
  8. Cefalu M, Dominici F, Arvold N, Parmigiani G. Model averaged double robust estimation. Biometrics. 2017 Jun; 73(2):410-421. PMID: 27893927.
    View in: PubMed
  9. Harrington D, Parmigiani G. Adaptive Randomization of Neratinib in Early Breast Cancer. N Engl J Med. 2016 10 20; 375(16):1593-4. PMID: 28103002.
    View in: PubMed
  10. Harrington D, Parmigiani G. I-SPY 2--A Glimpse of the Future of Phase 2 Drug Development? N Engl J Med. 2016 Jul 07; 375(1):7-9. PMID: 27406345.
    View in: PubMed
  11. Waldron L, Riester M, Ramos M, Parmigiani G, Birrer M. The Doppelgänger Effect: Hidden Duplicates in Databases of Transcriptome Profiles. J Natl Cancer Inst. 2016 Nov; 108(11). PMID: 27381624.
    View in: PubMed
  12. 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 07; 40(5):425-31. PMID: 27112364.
    View in: PubMed
  13. 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 Jan; 155(2):375-83. PMID: 26786860; PMCID: PMC4742331 [Available on 01/19/17].
  14. 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 Jan 05; 315(1):68-76. PMID: 26746459.
    View in: PubMed
  15. Zhang Y, Trippa L, Parmigiani G. Optimal Bayesian adaptive trials when treatment efficacy depends on biomarkers. Biometrics. 2016 Jun; 72(2):414-21. PMID: 26575199.
    View in: PubMed
  16. 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 Dec; 75(16):1926-33. PMID: 26469352; PMCID: PMC4831584 [Available on 12/01/16].
  17. Mazzola E, Blackford A, Parmigiani G, Biswas S. Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO. Cancer Inform. 2015; 14(Suppl 2):147-57. PMID: 25983549; PMCID: PMC4428390.
  18. 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 Jul; 17(4):374-81. PMID: 25937617; PMCID: PMC4483460.
  19. Wang C, Dominici F, Parmigiani G, Zigler CM. 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. PMID: 25899155; PMCID: PMC4575246.
  20. 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 Feb 19; 57(4):636-47. PMID: 25699710; PMCID: PMC4351672 [Available on 02/19/16].
  21. 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. Neuro Oncol. 2015 Aug; 17(8):1106-13. PMID: 25568226; PMCID: PMC4490868.
  22. 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 Jan 06; 112(1):118-23. PMID: 25535351; PMCID: PMC4291633.
  23. 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 Nov 13; 124(20):3110-7. PMID: 25237203; PMCID: PMC4231420.
  24. Braun D, Gorfine M, Parmigiani G. Misreported family histories and underestimation of risk. J Clin Oncol. 2014 Nov 10; 32(32):3682-3. PMID: 25199751.
    View in: PubMed
  25. Ahern CH, Shih YC, Dong W, Parmigiani G, Shen Y. 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. PMID: 25137022; PMCID: PMC4200098.
  26. Zhao SD, Parmigiani G, Huttenhower C, Waldron L. Más-o-menos: a simple sign averaging method for discrimination in genomic data analysis. Bioinformatics. 2014 Nov 01; 30(21):3062-9. PMID: 25061068; PMCID: PMC4201155.
  27. 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 Jun 15; 30(12):i105-12. PMID: 24931973; PMCID: PMC4058929.
  28. Mazzola E, Chipman J, Cheng SC, Parmigiani G. Recent BRCAPRO upgrades significantly improve calibration. Cancer Epidemiol Biomarkers Prev. 2014 Aug; 23(8):1689-95. PMID: 24891549; PMCID: PMC4119541.
  29. Hammerling D, Cefalu M, Cisewski J, Dominici F, Parmigiani G, Paulson C, Smith RL. Completing the results of the 2013 Boston marathon. PLoS One. 2014; 9(4):e93800. PMID: 24727904; PMCID: PMC3984103.
  30. 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. J Natl Cancer Inst. 2014 Apr 03; 106(5). PMID: 24700801; PMCID: PMC4580554.
  31. 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. J Natl Cancer Inst. 2014 Apr 03; 106(5). PMID: 24700803; PMCID: PMC4580556.
  32. Ho YY, Cope LM, Parmigiani G. Modular network construction using eQTL data: an analysis of computational costs and benefits. Front Genet. 2014; 5:40. PMID: 24616734; PMCID: PMC3935177.
  33. Cope L, Naiman DQ, Parmigiani G. Integrative correlation: Properties and relation to canonical correlations. J Multivar Anal. 2014 Jan 01; 123:270-280. PMID: 26028790.
    View in: PubMed
  34. Parmigiani G, Boca S, Ding J, Trippa L. Statistical tools and R software for cancer driver probabilities. Methods Mol Biol. 2014; 1101:113-34. PMID: 24233780.
    View in: PubMed
  35. 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. PMID: 24429703; PMCID: PMC3905727.
  36. Biswas S, Arun B, Parmigiani G. Reclassification of predictions for uncovering subgroup specific improvement. Stat Med. 2014 May 20; 33(11):1914-27. PMID: 24353130; PMCID: PMC4008681.
  37. Gorfine M, Hsu L, Parmigiani G. Frailty Models for Familial Risk with Application to Breast Cancer. J Am Stat Assoc. 2013 Dec 01; 108(504):1205-1215. PMID: 24678132.
    View in: PubMed
  38. Boca SM, Bravo HC, Caffo B, Leek JT, Parmigiani G. A decision-theory approach to interpretable set analysis for high-dimensional data. Biometrics. 2013 Sep; 69(3):614-23. PMID: 23909925; PMCID: PMC3927844.
  39. 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 Aug 13; 110(33):13481-6. PMID: 23901115; PMCID: PMC3746936.
  40. Alexander BM, Wen PY, Trippa L, Reardon DA, Yung WK, Parmigiani G, Berry DA. Biomarker-based adaptive trials for patients with glioblastoma--lessons from I-SPY 2. Neuro Oncol. 2013 Aug; 15(8):972-8. PMID: 23857706; PMCID: PMC3714161.
  41. Tomasetti C, Demetri GD, Parmigiani G. Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors. F1000Res. 2013; 2:152. PMID: 24555070; PMCID: PMC3892920.
  42. 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 Jul; 140(1):187-93. PMID: 23793601; PMCID: PMC3760685.
  43. Gorfine M, Hsu L, Zucker DM, Parmigiani G. Calibrated predictions for multivariate competing risks models. Lifetime Data Anal. 2014 Apr; 20(2):234-51. PMID: 23737081; PMCID: PMC3884047.
  44. 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 Aug 01; 29(15):1865-71. PMID: 23712657; PMCID: PMC3841439.
  45. 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 Jun; 139(2):571-9. PMID: 23690142; PMCID: PMC3699331.
  46. 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. PMID: 23550061; PMCID: PMC3625954.
  47. Trippa L, Lee EQ, Wen PY, Batchelor TT, Cloughesy T, Parmigiani G, Alexander BM. Reply to B. Freidlin et al. J Clin Oncol. 2013 Mar 01; 31(7):970-1. PMID: 23565532.
    View in: PubMed
  48. Minelli C, De Grandi A, Weichenberger CX, Gögele M, Modenese M, Attia J, Barrett JH, Boehnke M, Borsani G, Casari G, Fox CS, Freina T, Hicks AA, Marroni F, Parmigiani G, Pastore A, Pattaro C, Pfeufer A, Ruggeri F, Schwienbacher C, Taliun D, Pramstaller PP, Domingues FS, Thompson JR. Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. Genet Epidemiol. 2013 Feb; 37(2):205-13. PMID: 23307621; PMCID: PMC3725558.
  49. 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 Feb 05; 110(6):1999-2004. PMID: 23345422; PMCID: PMC3568331.
  50. Thompson JR, Gögele M, Weichenberger CX, Modenese M, Attia J, Barrett JH, Boehnke M, De Grandi A, Domingues FS, Hicks AA, Marroni F, Pattaro C, Ruggeri F, Borsani G, Casari G, Parmigiani G, Pastore A, Pfeufer A, Schwienbacher C, Taliun D, Fox CS, Pramstaller PP, Minelli C. SNP prioritization using a Bayesian probability of association. Genet Epidemiol. 2013 Feb; 37(2):214-21. PMID: 23280596; PMCID: PMC3725584.
  51. 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 Jan; 45(1):12-7. PMID: 23202128; PMCID: PMC3557959.
  52. 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 Nov 28; 4(162):162ra154. PMID: 23197571; PMCID: PMC3641759.
  53. Mazzola E, Cheng SC, Parmigiani G. The penetrance of ductal carcinoma in situ among BRCA1 and BRCA2 mutation carriers. Breast Cancer Res Treat. 2013 Jan; 137(1):315-8. PMID: 23184082; PMCID: PMC3836600.
  54. 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 Nov 15; 18(22):6136-46. PMID: 23136189; PMCID: PMC3500412.
  55. 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 Dec; 136(3):627-33. PMID: 23117858.
    View in: PubMed
  56. Wang XV, Blades N, Ding J, Sultana R, Parmigiani G. Estimation of sequencing error rates in short reads. BMC Bioinformatics. 2012 Jul 30; 13:185. PMID: 22846331; PMCID: PMC3495688.
  57. 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 Sep 10; 30(26):3258-63. PMID: 22649140; PMCID: PMC3434985.
  58. Vogelstein B, Roberts NJ, Vogelstein JT, Parmigiani G, Kinzler KW, Velculescu VE. Response to comments on "the predictive capacity of personal genome sequencing". Sci Transl Med. 2012 May 23; 4(135):135lr3. PMID: 22623739.
    View in: PubMed
  59. Roberts NJ, Vogelstein JT, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. The predictive capacity of personal genome sequencing. Sci Transl Med. 2012 May 09; 4(133):133ra58. PMID: 22472521; PMCID: PMC3741669.
  60. Waldron L, Simpson P, Parmigiani G, Huttenhower C. Report on emerging technologies for translational bioinformatics: a symposium on gene expression profiling for archival tissues. BMC Cancer. 2012 Mar 29; 12:124. PMID: 22458912; PMCID: PMC3342119.
  61. Wang C, Parmigiani G, Dominici F. Bayesian effect estimation accounting for adjustment uncertainty. Biometrics. 2012 Sep; 68(3):661-71. PMID: 22364439.
    View in: PubMed
  62. Biswas S, Tankhiwale N, Blackford A, Barrera AM, Ready K, Lu K, Amos CI, Parmigiani G, Arun B. Assessing the added value of breast tumor markers in genetic risk prediction model BRCAPRO. Breast Cancer Res Treat. 2012 May; 133(1):347-55. PMID: 22270937.
    View in: PubMed
  63. Tyekucheva S, Marchionni L, Karchin R, Parmigiani G. Integrating diverse genomic data using gene sets. Genome Biol. 2011 Oct 21; 12(10):R105. PMID: 22018358; PMCID: PMC3333775.
  64. Favorov A, Lvovs D, Speier W, Parmigiani G, Ochs MF. OnionTree XML: a format to exchange gene-related probabilities. J Biomol Struct Dyn. 2011 Oct; 29(2):417-23. PMID: 21875159; PMCID: PMC4856015.
  65. Joshu CE, Parmigiani G, Colditz GA, Platz EA. Opportunities for the primary prevention of colorectal cancer in the United States. Cancer Prev Res (Phila). 2012 Jan; 5(1):138-45. PMID: 21955521; PMCID: PMC3252472.
  66. Arun B, Biswas S, Tankhiwale N, Blackford AL, Gutierrez-Barrera AM, Litton JK, Hortobagyi GN, Amos CI, Parmigiani G. 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. PMID: 27957957.
    View in: PubMed
  67. Ho YY, Parmigiani G, Louis TA, Cope LM. Modeling liquid association. Biometrics. 2011 Mar; 67(1):133-41. PMID: 20528865.
    View in: PubMed
  68. 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 Jan 28; 331(6016):435-9. PMID: 21163964; PMCID: PMC3110744.
  69. Boca SM, Kinzler KW, Velculescu VE, Vogelstein B, Parmigiani G. Patient-oriented gene set analysis for cancer mutation data. Genome Biol. 2010; 11(11):R112. PMID: 21092299; PMCID: PMC3156951.
  70. 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 Nov 01; 9:257-64. PMID: 21082040; PMCID: PMC2978933.
  71. 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 Nov 01; 26(21):2792-3. PMID: 20810601; PMCID: PMC3025742.
  72. 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 Jan 15; 70(2):552-9. PMID: 20068151; PMCID: PMC2947347.
  73. Scharpf RB, Tjelmeland H, Parmigiani G, Nobel AB. Rejoinder. J Am Stat Assoc. 2009 Dec; 104(488):1318-1323. PMID: 21904418.
    View in: PubMed
  74. 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 Aug 20; 10:256. PMID: 19695104; PMCID: PMC2745389.
  75. 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 Aug 04; 106(31):12921-5. PMID: 19617566; PMCID: PMC2722285.
  76. 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 Jul 15; 15(14):4674-9. PMID: 19584151; PMCID: PMC2819274.
  77. 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 Jul; 27(7):1487-95. PMID: 19544456; PMCID: PMC3060766.
  78. Caffo BS, Liu D, Scharpf RB, Parmigiani G. Likelihood estimation of conjugacy relationships in linear models with applications to high-throughput genomics. Int J Biostat. 2009 May 29; 5(1):Article 18. PMID: 20224629.
    View in: PubMed
  79. Blackford A, Parmigiani G, Kensler TW, Wolfgang C, Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Eshleman JR, Goggins M, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Klein A, Cameron JL, Olino K, Schulick R, Winter J, Vogelstein B, Velculescu VE, Kinzler KW, Hruban RH. Genetic mutations associated with cigarette smoking in pancreatic cancer. Cancer Res. 2009 Apr 15; 69(8):3681-8. PMID: 19351817; PMCID: PMC2669837.
  80. Daniel VC, Marchionni L, Hierman JS, Rhodes JT, Devereux WL, Rudin CM, Yung R, Parmigiani G, Dorsch M, Peacock CD, Watkins DN. 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. PMID: 19351829; PMCID: PMC2821899.
  81. Jones S, Hruban RH, Kamiyama M, Borges M, Zhang X, Parsons DW, Lin JC, Palmisano E, Brune K, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Parmigiani G, Kern SE, Velculescu VE, Kinzler KW, Vogelstein B, Eshleman JR, Goggins M, Klein AP. Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene. Science. 2009 Apr 10; 324(5924):217. PMID: 19264984; PMCID: PMC2684332.
  82. Favorova OO, Favorov AV, Boiko AN, Sudomoina MA, Andreevskii TV, Alekseenkov AD, Kulakova OG, Gusev EI, Parmigiani G, Ochs MF. [Genetic predisposition to multiple sclerosis as a polygenic autoimmune disease]. Zh Nevrol Psikhiatr Im S S Korsakova. 2009; 109(7 Suppl 2):16-22. PMID: 19894308.
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  83. Scharpf RB, Tjelmeland H, Parmigiani G, Nobel AB. A Bayesian model for cross-study differential gene expression. J Am Stat Assoc. 2009; 104(488):1295-1310. PMID: 21127725.
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  84. Chen S, Blackford AL, Parmigiani G. Tailoring BRCAPRO to Asian-Americans. J Clin Oncol. 2009 Feb 01; 27(4):642-3; author reply 643-4. PMID: 19075251; PMCID: PMC4877690.
  85. Braun R, Cope L, Parmigiani G. Identifying differential correlation in gene/pathway combinations. BMC Bioinformatics. 2008 Nov 18; 9:488. PMID: 19017408; PMCID: PMC2613418.
  86. Kortenhorst MS, Zahurak M, Shabbeer S, Kachhap S, Galloway N, Parmigiani G, Verheul HM, Carducci MA. 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. PMID: 18980983; PMCID: PMC2603330.
  87. Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, Parsons DW, Jones S, Sjöblom T, Park BH, Parsons R, Willis J, Dawson D, Willson JK, Nikolskaya T, Nikolsky Y, Kopelovich L, Papadopoulos N, Pennacchio LA, Wang TL, Markowitz SD, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. 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. PMID: 18852474; PMCID: PMC2571022.
  88. Katki HA, Blackford A, Chen S, Parmigiani G. 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. PMID: 18407567; PMCID: PMC2562929.
  89. Schaeffer EM, Marchionni L, Huang Z, Simons B, Blackman A, Yu W, Parmigiani G, Berman DM. 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. PMID: 18794802; PMCID: PMC2676849.
  90. Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Kamiyama H, Jimeno A, Hong SM, Fu B, Lin MT, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, Iacobuzio-Donahue C, Eshleman JR, Kern SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science. 2008 Sep 26; 321(5897):1801-6. PMID: 18772397; PMCID: PMC2848990.
  91. Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008 Sep 26; 321(5897):1807-12. PMID: 18772396; PMCID: PMC2820389.
  92. Pattaro C, Ruczinski I, Fallin DM, Parmigiani G. Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies. BMC Genomics. 2008 Aug 29; 9:405. PMID: 18759977; PMCID: PMC2547855.
  93. Yang Z, Stratton C, Francis PJ, Kleinman ME, Tan PL, Gibbs D, Tong Z, Chen H, Constantine R, Yang X, Chen Y, Zeng J, Davey L, Ma X, Hau VS, Wang C, Harmon J, Buehler J, Pearson E, Patel S, Kaminoh Y, Watkins S, Luo L, Zabriskie NA, Bernstein PS, Cho W, Schwager A, Hinton DR, Klein ML, Hamon SC, Simmons E, Yu B, Campochiaro B, Sunness JS, Campochiaro P, Jorde L, Parmigiani G, Zack DJ, Katsanis N, Ambati J, Zhang K. Toll-like receptor 3 and geographic atrophy in age-related macular degeneration. N Engl J Med. 2008 Oct 02; 359(14):1456-63. PMID: 18753640; PMCID: PMC2573951.
  94. 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 Jan; 93(1):17-21. PMID: 18692126; PMCID: PMC2820387.
  95. Dominici F, Wang C, Crainiceanu C, Parmigiani G. Model selection and health effect estimation in environmental epidemiology. Epidemiology. 2008 Jul; 19(4):558-60. PMID: 18552590.
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  96. Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I. Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Ann Appl Stat. 2008 Jun 01; 2(2):687-713. PMID: 19609370.
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  97. Tai YC, Chen S, Parmigiani G, Klein AP. Incorporating tumor immunohistochemical markers in BRCA1 and BRCA2 carrier prediction. Breast Cancer Res. 2008; 10(2):401. PMID: 18466632; PMCID: PMC2397515.
  98. Parmigiani G, Chen S. TRAB: testing whether mutation frequencies are above an unknown background. Stat Appl Genet Mol Biol. 2008; 7(1):Article11. PMID: 18384264.
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  99. Jones S, Chen WD, Parmigiani G, Diehl F, Beerenwinkel N, Antal T, Traulsen A, Nowak MA, Siegel C, Velculescu VE, Kinzler KW, Vogelstein B, Willis J, Markowitz SD. Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci U S A. 2008 Mar 18; 105(11):4283-8. PMID: 18337506; PMCID: PMC2393770.
  100. Barber TD, McManus K, Yuen KW, Reis M, Parmigiani G, Shen D, Barrett I, Nouhi Y, Spencer F, Markowitz S, Velculescu VE, Kinzler KW, Vogelstein B, Lengauer C, Hieter P. 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. PMID: 18299561; PMCID: PMC2265152.
  101. 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 Mar 04; 148(5):358-69. PMID: 18252678.
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  102. Marchionni L, Wilson RF, Marinopoulos SS, Wolff AC, Parmigiani G, Bass EB, Goodman SN. Impact of gene expression profiling tests on breast cancer outcomes. Evid Rep Technol Assess (Full Rep). 2008 Jan; (160):1-105. PMID: 20629480.
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  103. Dahinden C, Parmigiani G, Emerick MC, Bühlmann P. Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries. BMC Bioinformatics. 2007 Dec 11; 8:476. PMID: 18072965; PMCID: PMC2233645.
  104. Marchionni L, Wilson RF, Marinopoulos SS, Wolff AC, Parmigiani G, Bass EB, Goodman SN. Impact of gene expression profiling tests on breast cancer outcomes. Evid Rep Technol Assess (Full Rep). 2007 Dec; (160):1-105. PMID: 18457476; PMCID: PMC4781418.
  105. Tai YC, Domchek S, Parmigiani G, Chen S. Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. J Natl Cancer Inst. 2007 Dec 05; 99(23):1811-4. PMID: 18042939; PMCID: PMC2267289.
  106. Iversen ES, Katki HA, Chen S, Berry DA, Parmigiani G. Limited family structure and breast cancer risk. JAMA. 2007 Nov 07; 298(17):2007; author reply 2007-8. PMID: 17986693.
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  107. Wood LD, Parsons DW, Jones S, Lin J, Sjöblom 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 Nov 16; 318(5853):1108-13. PMID: 17932254.
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  108. Parmigiani G, Chen S, Iversen ES, 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 Oct 02; 147(7):441-50. PMID: 17909205; PMCID: PMC2423214.
  109. Oliveira JL, Aguiar-Oliveira MH, D'Oliveira A, Pereira RM, Oliveira CR, Farias CT, Barreto-Filho JA, Anjos-Andrade FD, Marques-Santos C, Nascimento-Junior AC, Alves EO, Oliveira FT, Campos VC, Ximenes R, Blackford A, Parmigiani G, Salvatori R. 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. PMID: 17911170.
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  110. Garrett-Mayer E, Parmigiani G, Zhong X, Cope L, Gabrielson E. Cross-study validation and combined analysis of gene expression microarray data. Biostatistics. 2008 Apr; 9(2):333-54. PMID: 17873151.
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  111. 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 Sep; 17(9):1304-18. PMID: 17693572; PMCID: PMC1950899.
  112. Wu F, Dassopoulos T, Cope L, Maitra A, Brant SR, Harris ML, Bayless TM, Parmigiani G, Chakravarti S. 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. PMID: 17262812.
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  113. Zahurak M, Parmigiani G, Yu W, Scharpf RB, Berman D, Schaeffer E, Shabbeer S, Cope L. Pre-processing Agilent microarray data. BMC Bioinformatics. 2007 May 01; 8:142. PMID: 17472750; PMCID: PMC1876252.
  114. Chen S, Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007 Apr 10; 25(11):1329-33. PMID: 17416853; PMCID: PMC2267287.
  115. 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 Apr 10; 25(11):1417-22. PMID: 17416862; PMCID: PMC2267288.
  116. Emerick MC, Parmigiani G, Agnew WS. Multivariate analysis and visualization of splicing correlations in single-gene transcriptomes. BMC Bioinformatics. 2007 Jan 18; 8:16. PMID: 17233916; PMCID: PMC1785386.
  117. Ho YY, Cope L, Dettling M, Parmigiani G. Statistical methods for identifying differentially expressed gene combinations. Methods Mol Biol. 2007; 408:171-91. PMID: 18314583.
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  118. Scharpf RB, Iacobuzio-Donahue CA, Sneddon JB, Parmigiani G. When should one subtract background fluorescence in 2-color microarrays? Biostatistics. 2007 Oct; 8(4):695-707. PMID: 17164465.
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  119. Bettegowda C, Huang X, Lin J, Cheong I, Kohli M, Szabo SA, Zhang X, Diaz LA, Velculescu VE, Parmigiani G, Kinzler KW, Vogelstein B, Zhou S. The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT. Nat Biotechnol. 2006 Dec; 24(12):1573-80. PMID: 17115055.
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  120. Hayes DN, Monti S, Parmigiani G, Gilks CB, Naoki K, Bhattacharjee A, Socinski MA, Perou C, Meyerson M. Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts. J Clin Oncol. 2006 Nov 01; 24(31):5079-90. PMID: 17075127.
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  121. Salvatori R, Serpa MG, Parmigiani G, Britto AV, Oliveira JL, Oliveira CR, Prado CM, Farias CT, Almeida JC, Vicente TA, Aguiar-Oliveira MH. GH response to hypoglycemia and clonidine in the GH-releasing hormone resistance syndrome. J Endocrinol Invest. 2006 Oct; 29(9):805-8. PMID: 17114911.
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  122. 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 Sep 27; 296(12):1479-87. PMID: 17003396; PMCID: PMC2538673.
  123. 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 Oct 13; 314(5797):268-74. PMID: 16959974.
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  124. Favorova OO, Favorov AV, Boiko AN, Andreewski TV, Sudomoina MA, Alekseenkov AD, Kulakova OG, Gusev EI, Parmigiani G, Ochs MF. Three allele combinations associated with multiple sclerosis. BMC Med Genet. 2006 Jul 26; 7:63. PMID: 16872485; PMCID: PMC1557481.
  125. Gandhi TK, Zhong J, Mathivanan S, Karthick L, Chandrika KN, Mohan SS, Sharma S, Pinkert S, Nagaraju S, Periaswamy B, Mishra G, Nandakumar K, Shen B, Deshpande N, Nayak R, Sarker M, Boeke JD, Parmigiani G, Schultz J, Bader JS, Pandey A. Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat Genet. 2006 Mar; 38(3):285-93. PMID: 16501559.
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  126. Zilliox MJ, Parmigiani G, Griffin DE. 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. PMID: 16492729; PMCID: PMC1413941.
  127. Chen S, Iversen ES, Friebel T, Finkelstein D, Weber BL, Eisen A, Peterson LE, Schildkraut JM, Isaacs C, Peshkin BN, Corio C, Leondaridis L, Tomlinson G, Dutson D, Kerber R, Amos CI, Strong LC, Berry DA, Euhus DM, Parmigiani G. Characterization of BRCA1 and BRCA2 mutations in a large United States sample. J Clin Oncol. 2006 Feb 20; 24(6):863-71. PMID: 16484695; PMCID: PMC2323978.
  128. Dettling M, Gabrielson E, Parmigiani G. Searching for differentially expressed gene combinations. Genome Biol. 2005; 6(10):R88. PMID: 16207359; PMCID: PMC1257471.
  129. Shih IeM, Sheu JJ, Santillan A, Nakayama K, Yen MJ, Bristow RE, Vang R, Parmigiani G, Kurman RJ, Trope CG, Davidson B, Wang TL. 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. PMID: 16172393; PMCID: PMC1236547.
  130. Favorov AV, Andreewski TV, Sudomoina MA, Favorova OO, Parmigiani G, Ochs MF. 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. PMID: 16118183; PMCID: PMC1456130.
  131. Molina H, Parmigiani G, Pandey A. 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. PMID: 15859588.
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  132. Chen S, Watson P, Parmigiani G. 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. PMID: 15831578; PMCID: PMC2274000.
  133. Skinner CS, Rawl SM, Moser BK, Buchanan AH, Scott LL, Champion VL, Schildkraut JM, Parmigiani G, Clark S, Lobach DF, Bastian LA. 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. PMID: 15857495; PMCID: PMC1490091.
  134. Shen Y, Parmigiani G. A model-based comparison of breast cancer screening strategies: mammograms and clinical breast examinations. Cancer Epidemiol Biomarkers Prev. 2005 Feb; 14(2):529-32. PMID: 15734983.
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  135. Zhou X, Iversen ES, Parmigiani G. Classification of Missense Mutations of Disease Genes. J Am Stat Assoc. 2005; 100:51-60. PMID: 18418466.
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  136. Kittleson MM, Ye SQ, Irizarry RA, Minhas KM, Edness G, Conte JV, Parmigiani G, Miller LW, Chen Y, Hall JL, Garcia JG, Hare JM. Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation. 2004 Nov 30; 110(22):3444-51. PMID: 15557369.
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  137. Marroni F, Aretini P, D'Andrea E, Caligo MA, Cortesi L, Viel A, Ricevuto E, Montagna M, Cipollini G, Federico M, Santarosa M, Marchetti P, Bailey-Wilson JE, Bevilacqua G, Parmigiani G, Presciuttini S. 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. PMID: 15340362.
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  138. Cope L, Zhong X, Garrett E, Parmigiani G. MergeMaid: R tools for merging and cross-study validation of gene expression data. Stat Appl Genet Mol Biol. 2004; 3:Article29. PMID: 16646808.
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  139. Chen S, Wang W, Broman KW, Katki HA, Parmigiani G. BayesMendel: an R environment for Mendelian risk prediction. Stat Appl Genet Mol Biol. 2004; 3:Article21. PMID: 16646800; PMCID: PMC2274007.
  140. Hackam AS, Strom R, Liu D, Qian J, Wang C, Otteson D, Gunatilaka T, Farkas RH, Chowers I, Kageyama M, Leveillard T, Sahel JA, Campochiaro PA, Parmigiani G, Zack DJ. 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. PMID: 15326104.
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  141. Hackam AS, Qian J, Liu D, Gunatilaka T, Farkas RH, Chowers I, Kageyama M, Parmigiani G, Zack DJ. Comparative gene expression analysis of murine retina and brain. Mol Vis. 2004 Aug 31; 10:637-49. PMID: 15359217.
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  142. Wang Z, Shen D, Parsons DW, Bardelli A, Sager J, Szabo S, Ptak J, Silliman N, Peters BA, van der Heijden MS, Parmigiani G, Yan H, Wang TL, Riggins G, Powell SM, Willson JK, Markowitz S, Kinzler KW, Vogelstein B, Velculescu VE. Mutational analysis of the tyrosine phosphatome in colorectal cancers. Science. 2004 May 21; 304(5674):1164-6. PMID: 15155950.
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  143. Parmigiani G, Garrett-Mayer ES, Anbazhagan R, Gabrielson E. 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. PMID: 15131026.
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  144. Parmigiani G, Garrett E, Anbazhagan R, Gabrielson E. Molecular classification of lung cancer: a cross-platform comparison of gene expression data sets. Chest. 2004 May; 125(5 Suppl):103S. PMID: 15136439.
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  145. Marroni F, Aretini P, D'Andrea E, Caligo MA, Cortesi L, Viel A, Ricevuto E, Montagna M, Cipollini G, Ferrari S, Santarosa M, Bisegna R, Bailey-Wilson JE, Bevilacqua G, Parmigiani G, Presciuttini S. Evaluation of widely used models for predicting BRCA1 and BRCA2 mutations. J Med Genet. 2004 Apr; 41(4):278-85. PMID: 15060102; PMCID: PMC1735736.
  146. Parmigiani G. 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. PMID: 14981678.
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  147. Mehrotra J, Ganpat MM, Kanaan Y, Fackler MJ, McVeigh M, Lahti-Domenici J, Polyak K, Argani P, Naab T, Garrett E, Parmigiani G, Broome C, Sukumar S. 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. PMID: 15041725.
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  148. Dang LH, Bettegowda C, Agrawal N, Cheong I, Huso D, Frost P, Loganzo F, Greenberger L, Barkoczy J, Pettit GR, Smith AB, Gurulingappa H, Khan S, Parmigiani G, Kinzler KW, Zhou S, Vogelstein B. Targeting vascular and avascular compartments of tumors with C. novyi-NT and anti-microtubule agents. Cancer Biol Ther. 2004 Mar; 3(3):326-37. PMID: 14739784.
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  149. Wang TL, Diaz LA, Romans K, Bardelli A, Saha S, Galizia G, Choti M, Donehower R, Parmigiani G, Shih IeM, Iacobuzio-Donahue C, Kinzler KW, Vogelstein B, Lengauer C, Velculescu VE. 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. PMID: 14970324; PMCID: PMC420348.
  150. Chowers I, Liu D, Farkas RH, Gunatilaka TL, Hackam AS, Bernstein SL, Campochiaro PA, Parmigiani G, Zack DJ. Gene expression variation in the adult human retina. Hum Mol Genet. 2003 Nov 15; 12(22):2881-93. PMID: 14519682.
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  151. Cappola TP, Cope L, Cernetich A, Barouch LA, Minhas K, Irizarry RA, Parmigiani G, Durrani S, Lavoie T, Hoffman EP, Ye SQ, Garcia JG, Hare JM. Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy. Physiol Genomics. 2003 Jun 24; 14(1):25-34. PMID: 12709511.
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  152. Bardelli A, Parsons DW, Silliman N, Ptak J, Szabo S, Saha S, Markowitz S, Willson JK, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. Mutational analysis of the tyrosine kinome in colorectal cancers. Science. 2003 May 09; 300(5621):949. PMID: 12738854.
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  153. Scharpf R, Garrett ES, Hu J, Parmigiani G. Statistical modeling and visualization of molecular profiles in cancer. Biotechniques. 2003 Mar; Suppl:22-9. PMID: 12664681.
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  154. Parmigiani G. Measuring uncertainty in complex decision analysis models. Stat Methods Med Res. 2002 Dec; 11(6):513-37. PMID: 12516987.
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  155. Symer DE, Connelly C, Szak ST, Caputo EM, Cost GJ, Parmigiani G, Boeke JD. Human l1 retrotransposition is associated with genetic instability in vivo. Cell. 2002 Aug 09; 110(3):327-38. PMID: 12176320.
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  156. Kauff ND, Perez-Segura P, Robson ME, Scheuer L, Siegel B, Schluger A, Rapaport B, Frank TS, Nafa K, Ellis NA, Parmigiani G, Offit K. 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. PMID: 12161607; PMCID: PMC1735198.
  157. Berry DA, Iversen ES, Gudbjartsson DF, Hiller EH, Garber JE, Peshkin BN, Lerman C, Watson P, Lynch HT, Hilsenbeck SG, Rubinstein WS, Hughes KS, Parmigiani G. 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. PMID: 12039933.
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  158. Parmigiani G, Skates S, Zelen M. Modeling and optimization in early detection programs with a single exam. Biometrics. 2002 Mar; 58(1):30-6. PMID: 11890325.
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  159. Wang TL, Rago C, Silliman N, Ptak J, Markowitz S, Willson JK, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. Prevalence of somatic alterations in the colorectal cancer cell genome. Proc Natl Acad Sci U S A. 2002 Mar 05; 99(5):3076-80. PMID: 11867767; PMCID: PMC122475.
  160. Ryu B, Jones J, Blades NJ, Parmigiani G, Hollingsworth MA, Hruban RH, Kern SE. 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. PMID: 11830538.
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  161. Bova GS, Parmigiani G, Epstein JI, Wheeler T, Mucci NR, Rubin MA. Web-based tissue microarray image data analysis: initial validation testing through prostate cancer Gleason grading. Hum Pathol. 2001 Apr; 32(4):417-27. PMID: 11331959.
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  162. Dominici F, Parmigiani G. Bayesian semiparametric analysis of developmental toxicology data. Biometrics. 2001 Mar; 57(1):150-7. PMID: 11252591.
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  163. Jones JB, Song JJ, Hempen PM, Parmigiani G, Hruban RH, Kern SE. 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. PMID: 11245424.
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  164. Müller P, Parmigiani G, Schildkraut J, Tardella L. A Bayesian hierarchical approach for combining case-control and prospective studies. Biometrics. 1999 Sep; 55(3):858-66. PMID: 11315018.
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  165. Parmigiani G, Berry DA, Winer EP, Tebaldi C, Iglehart JD, Prosnitz LR. Is axillary lymph node dissection indicated for early-stage breast cancer? A decision analysis. J Clin Oncol. 1999 May; 17(5):1465-73. PMID: 10334532.
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  166. Samsa GP, Reutter RA, Parmigiani G, Ancukiewicz M, Abrahamse P, Lipscomb J, Matchar DB. 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. PMID: 10210244.
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  167. Claus EB, Schildkraut J, Iversen ES, Berry D, Parmigiani G. 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. PMID: 9839523.
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  168. Clyde MA, Parmigiani G. Protein construct storage: Bayesian variable selection and prediction with mixtures. J Biopharm Stat. 1998 Jul; 8(3):431-43. PMID: 9741858.
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  169. Petersen GM, Parmigiani G, Thomas D. Missense mutations in disease genes: a Bayesian approach to evaluate causality. Am J Hum Genet. 1998 Jun; 62(6):1516-24. PMID: 9585599; PMCID: PMC1377150.
  170. Lipscomb J, Ancukiewicz M, Parmigiani G, Hasselblad V, Samsa G, Matchar DB. Predicting the cost of illness: a comparison of alternative models applied to stroke. Med Decis Making. 1998 Apr-Jun; 18(2 Suppl):S39-56. PMID: 9566466.
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  171. Berry DA, Parmigiani G. Assessing the benefits of testing for breast cancer susceptibility genes: a decision analysis. Breast Dis. 1998 Apr; 10(1-2):115-25. PMID: 15687554.
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  172. Parmigiani G, Berry D, Aguilar O. Determining carrier probabilities for breast cancer-susceptibility genes BRCA1 and BRCA2. Am J Hum Genet. 1998 Jan; 62(1):145-58. PMID: 9443863; PMCID: PMC1376797.
  173. Matchar DB, Samsa GP, Matthews JR, Ancukiewicz M, Parmigiani G, Hasselblad V, Wolf PA, D'Agostino RB, Lipscomb J. The Stroke Prevention Policy Model: linking evidence and clinical decisions. Ann Intern Med. 1997 Oct 15; 127(8 Pt 2):704-11. PMID: 9382384.
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  174. Parmigiani G, Samsa GP, Ancukiewicz M, Lipscomb J, Hasselblad V, Matchar DB. Assessing uncertainty in cost-effectiveness analyses: application to a complex decision model. Med Decis Making. 1997 Oct-Dec; 17(4):390-401. PMID: 9343797.
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  175. Weinstein MP, Towns ML, Quartey SM, Mirrett S, Reimer LG, Parmigiani G, Reller LB. 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. PMID: 9145732.
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  176. Berry DA, Parmigiani G, Sanchez J, Schildkraut J, Winer E. 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. PMID: 9017003.
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  177. Parmigiani G, Migliorini D, Bertazzoni A, Caprio G. [Immunoglobulins in lymphomas: quantitative determinations and detection of molecular dysmetabolic changes]. Ann Sclavo. 1972 Jan-Feb; 14(1):85-98. PMID: 4592016.
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  178. Caprio G, Lusian F, Migliorini D, Parmigiani G. [Screening for serum hepatitis in a non-ambulatory hospital population]. Boll Ist Sieroter Milan. 1971 Nov-Dec; 50(6):514-9. PMID: 5005966.
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  179. Caprio G, Parmigiani G. [Further simplification of the method of immunoelectrophoresis]. Haematol Lat. 1971 Jul-Sep; 13(3):223-31. PMID: 5097062.
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  180. Bertazzoni A, Caprio G, Migliorini D, Mortillaro F, Parmigiani G. [Report on 6-month use of the Coulter Counter, model S]. Ann Ist Super Sanita. 1971; 7(2):484-90. PMID: 5154677.
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  181. Parmigiani G. [Clinico-statistical note on 2000 cesarean sections for 1954 to 1964]. Ann Ostet Ginecol Med Perinat. 1966 Sep; 88(9):713-28. PMID: 5992010.
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  182. MAGNI A, PARMIGIANI G. [Effect of heparin therapy on blood and bone marrow levels of cells with basophilic granulations]. Boll Soc Med Chir Cremona. 1956 May-Jun; 10(5):92-101. PMID: 13364079.
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