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Giovanni Parmigiani, Ph.D.

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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.

Research
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.
  1. R21CA177233 (PARMIGIANI, GIOVANNI LUIGI) Mar 1, 2013 - Feb 28, 2015
    NIH/NCI
    Novel Tools for Familial Risk Prediction
    Role: Principal Investigator
  2. 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
  3. T32GM074906 (IRIZARRY, RAFAEL ANGEL) Aug 1, 2006 - Sep 30, 2011
    NIH/NIGMS
    Predoctoral Biostatistics Training in Genetics/Genomics
    Role: Co-Principal Investigator
  4. R01CA105090 (PARMIGIANI, GIOVANNI) Sep 30, 2004 - Jun 30, 2010
    NIH/NCI
    Statistical Methods for Cancer Genes
    Role: Principal Investigator
  5. P50CA088843 (SUKUMAR, SARA) Sep 30, 2000 - Mar 29, 2013
    NIH/NCI
    SPORE in Breast Cancer
    Role: Co-Principal Investigator

Bibliographic
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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Huang T, Braun D, Lynch HT, Parmigiani G. Variation in cancer risk among families with genetic susceptibility. Genet Epidemiol. 2020 Oct 08. PMID: 33030277.
    Citations:    
  2. Hujoel MLA, Parmigiani G, Braun D. Statistical approaches for meta-analysis of genetic mutation prevalence. Genet Epidemiol. 2020 Sep 30. PMID: 33000511.
    Citations:    
  3. Zhang Y, Parmigiani G, Johnson WE. ComBat-seq: batch effect adjustment for RNA-seq count data. NAR Genom Bioinform. 2020 Sep; 2(3):lqaa078. PMID: 33015620.
    Citations:    
  4. 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 Sep 10. PMID: 32913135.
    Citations:    
  5. 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 Aug 03. PMID: 32747365.
    Citations:    
  6. 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 Sep 20; 38(27):3107-3118. PMID: 32687451.
    Citations:    
  7. Zanettini C, Omar M, Dinalankara W, Imada EL, Colantuoni E, Parmigiani G, Marchionni L. Influenza Vaccination and COVID19 Mortality in the USA. medRxiv. 2020 Jun 26. PMID: 32607525.
    Citations:    
  8. Huang T, Gorfine M, Hsu L, Parmigiani G, Braun D. Practical implementation of frailty models in Mendelian risk prediction. Genet Epidemiol. 2020 Sep; 44(6):564-578. PMID: 32506746.
    Citations:    
  9. Parmigiani G. Receiver Operating Characteristic Curves with an Indeterminacy Zone. Pattern Recognit Lett. 2020 Aug; 136:94-100. PMID: 32655204.
    Citations:    
  10. 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. J Natl Cancer Inst. 2020 May 01; 112(5):489-497. PMID: 31556450.
    Citations:    
  11. 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 Jul; 27(7):2212-2220. PMID: 32342295.
    Citations:    
  12. 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 BRCA1/2 Mutation and Do Not Use Risk-Reducing Salpingo-Oophorectomy: An Updated Meta-Analysis. JNCI Cancer Spectr. 2020 Aug; 4(4):pkaa029. PMID: 32676552.
    Citations:    
  13. 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 Aug; 4(5):pkaa027. PMID: 32923933.
    Citations:    
  14. Zhang Y, Bernau C, Parmigiani G, Waldron L. The impact of different sources of heterogeneity on loss of accuracy from genomic prediction models. Biostatistics. 2020 04 01; 21(2):253-268. PMID: 30202918.
    Citations:    Fields:    
  15. Spring LM, Fell G, Arfe A, Sharma C, Greenup R, Reynolds KL, Smith BL, Alexander B, Moy B, Isakoff SJ, Parmigiani G, Trippa L, Bardia A. Pathologic Complete Response after Neoadjuvant Chemotherapy and Impact on Breast Cancer Recurrence and Survival: A Comprehensive Meta-analysis. Clin Cancer Res. 2020 Jun 15; 26(12):2838-2848. PMID: 32046998.
    Citations:    
  16. Ramchandran M, Patil P, Parmigiani G. Tree-Weighting for Multi-Study Ensemble Learners. Pac Symp Biocomput. 2020; 25:451-462. PMID: 31797618.
    Citations:    
  17. 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. 2020 02; 29(2):509-519. PMID: 31871106.
    Citations:    
  18. 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 09; 3:1-9. PMID: 31545655.
    Citations:    
  19. 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 08; 3:1-9. PMID: 31419182.
    Citations:    
  20. 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. 2020 05 15; 146(10):2694-2702. PMID: 31318977.
    Citations:    
  21. Kim J, Braun D, Ukaegbu C, Dhingra TG, Kastrinos F, Parmigiani G, Syngal S, Yurgelun MB. Clinical Factors Associated With Gastric Cancer in Individuals With Lynch Syndrome. Clin Gastroenterol Hepatol. 2020 Apr; 18(4):830-837.e1. PMID: 31319185.
    Citations:    
  22. Zhang Y, Trippa L, Parmigiani G. Frequentist operating characteristics of Bayesian optimal designs via simulation. Stat Med. 2019 09 20; 38(21):4026-4039. PMID: 31215685.
    Citations:    
  23. Antonelli J, Parmigiani G, Dominici F. High-Dimensional Confounding Adjustment Using Continuous Spike and Slab Priors. Bayesian Anal. 2019 Sep; 14(3):805-828. PMID: 32431779.
    Citations:    
  24. 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 03 26; 9(4):39. PMID: 30914633.
    Citations:    
  25. De Vito R, Bellio R, Trippa L, Parmigiani G. Multi-study factor analysis. Biometrics. 2019 03; 75(1):337-346. PMID: 30289163.
    Citations:    Fields:    
  26. De Vito R, Lee YCA, Parpinel M, Serraino D, Olshan AF, Zevallos JP, Levi F, Zhang ZF, Morgenstern H, Garavello W, Kelsey K, McClean M, Schantz S, Yu GP, Boffetta P, Chuang SC, Hashibe M, La Vecchia C, Parmigiani G, Edefonti V. Shared and Study-specific Dietary Patterns and Head and Neck Cancer Risk in an International Consortium. Epidemiology. 2019 01; 30(1):93-102. PMID: 30063539.
    Citations:    Fields:    
  27. 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 Nov 30; 9:451-460. PMID: 30469014.
    Citations:    
  28. 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. 2019 07; 76(1):33-40. PMID: 30301696.
    Citations:    Fields:    
  29. 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 09 25; 19(1):142. PMID: 30253799.
    Citations:    Fields:    Translation:HumansCells
  30. Barber L, Gerke T, Markt SC, Peisch SF, Wilson KM, Ahearn T, Giovannucci E, Parmigiani G, Mucci LA. Family History of Breast or Prostate Cancer and Prostate Cancer Risk. Clin Cancer Res. 2018 12 01; 24(23):5910-5917. PMID: 30082473.
    Citations:    Fields:    
  31. 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? Neuro Oncol. 2018 07 05; 20(8):1034-1043. PMID: 29518210.
    Citations:    
  32. 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 10 15; 24(20):5037-5047. PMID: 30084834.
    Citations:    Fields:    
  33. 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 09; 42(6):528-538. PMID: 29943416.
    Citations:    Fields:    Translation:Humans
  34. Rebbeck TR, Burns-White K, Chan AT, Emmons K, Freedman M, Hunter DJ, Kraft P, Laden F, Mucci L, Parmigiani G, Schrag D, Syngal S, Tamimi RM, Viswanath K, Yurgelun MB, Garber JE. Precision Prevention and Early Detection of Cancer: Fundamental Principles. Cancer Discov. 2018 07; 8(7):803-811. PMID: 29907587.
    Citations:    Fields:    
  35. Ventz S, Cellamare M, Parmigiani G, Trippa L. Adding experimental arms to platform clinical trials: randomization procedures and interim analyses. Biostatistics. 2018 04 01; 19(2):199-215. PMID: 29036330.
    Citations:    Fields:    
  36. 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 12; 32(12):2626-2635. PMID: 29749396.
    Citations: 1     Fields:    
  37. Patil P, Parmigiani G. Training replicable predictors in multiple studies. Proc Natl Acad Sci U S A. 2018 03 13; 115(11):2578-2583. PMID: 29531060.
    Citations: 1     Fields:    Translation:Humans
  38. 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 09; 27(5):1187-1199. PMID: 29500626.
    Citations: 1     Fields:    
  39. Cleynen A, Szalat R, Kemal Samur M, Robiou du Pont S, Buisson L, Boyle E, Chretien ML, Anderson K, Minvielle S, Moreau P, Attal M, Parmigiani G, Corre J, Munshi N, Avet-Loiseau H. Expressed fusion gene landscape and its impact in multiple myeloma. Nat Commun. 2017 12 01; 8(1):1893. PMID: 29196615.
    Citations: 4     Fields:    Translation:Humans
  40. Braun D, Gorfine M, Parmigiani G, Arvold ND, Dominici F, Zigler C. Propensity scores with misclassified treatment assignment: a likelihood-based adjustment. Biostatistics. 2017 Oct 01; 18(4):695-710. PMID: 28419189.
    Citations:    Fields:    Translation:Humans
  41. 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. J Am Stat Assoc. 2018; 113(521):14-25. PMID: 30093737.
    Citations:    
  42. Tyekucheva S, Bowden M, Bango C, Giunchi F, Huang Y, Zhou C, Bondi A, Lis R, Van Hemelrijck M, Andrén O, Andersson SO, Watson RW, Pennington S, Finn SP, Martin NE, Stampfer MJ, Parmigiani G, Penney KL, Fiorentino M, Mucci LA, Loda M. Stromal and epithelial transcriptional map of initiation progression and metastatic potential of human prostate cancer. Nat Commun. 2017 09 04; 8(1):420. PMID: 28871082.
    Citations: 4     Fields:    Translation:HumansCells
  43. Wang XV, Parmigiani G. Integrative factor analysis - An unsupervised method for quantifying cross-study consistency of gene expression data. Genomics. 2018 03; 110(2):80-88. PMID: 28882735.
    Citations:    Fields:    
  44. Tomasetti C, Durrett R, Kimmel M, Lambert A, Parmigiani G, Zauber A, Vogelstein B. Role of stem-cell divisions in cancer risk. Nature. 2017 08 09; 548(7666):E13-E14. PMID: 28796214.
    Citations: 1     Fields:    
  45. 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.
    Citations: 3     Fields:    Translation:HumansCells
  46. 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.
    Citations: 1     Fields:    Translation:Humans
  47. 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 Sep 20; 35(27):3160-3168. PMID: 28530853.
    Citations:    Fields:    Translation:Humans
  48. Ventz S, Barry WT, Parmigiani G, Trippa L. Bayesian response-adaptive designs for basket trials. Biometrics. 2017 09; 73(3):905-915. PMID: 28211944.
    Citations: 3     Fields:    Translation:Humans
  49. Edefonti V, Parmigiani G. Combinatorial Mixtures of Multiparameter Distributions: An Application to Bivariate Data. Int J Biostat. 2017 02 16; 13(1). PMID: 28207413.
    Citations:    Fields:    Translation:Humans
  50. Cefalu M, Dominici F, Arvold N, Parmigiani G. Model averaged double robust estimation. Biometrics. 2017 06; 73(2):410-421. PMID: 27893927.
    Citations: 3     Fields:    Translation:Humans
  51. 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.
    Citations:    Fields:    
  52. 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.
    Citations: 2     Fields:    Translation:Cells
  53. 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 11; 108(11). PMID: 27381624.
    Citations: 2     Fields:    Translation:HumansCells
  54. 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.
    Citations: 8     Fields:    Translation:Humans
  55. 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.
    Citations: 1     Fields:    Translation:Humans
  56. 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.
    Citations: 52     Fields:    Translation:Humans
  57. Zhang Y, Trippa L, Parmigiani G. Optimal Bayesian adaptive trials when treatment efficacy depends on biomarkers. Biometrics. 2016 06; 72(2):414-21. PMID: 26575199.
    Citations:    Fields:    Translation:Humans
  58. 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.
    Citations:    Fields:    Translation:Humans
  59. 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.
    Citations: 6     
  60. 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.
    Citations: 5     Fields:    Translation:Humans
  61. 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.
    Citations: 3     Fields:    Translation:Humans
  62. 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):636-647. PMID: 25699710.
    Citations: 66     Fields:    Translation:HumansCells
  63. 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.
    Citations: 5     Fields:    Translation:Humans
  64. 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.
    Citations: 61     Fields:    Translation:HumansCells
  65. 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.
    Citations: 17     Fields:    Translation:Humans
  66. 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.
    Citations: 1     Fields:    Translation:Humans
  67. 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.
    Citations: 4     Fields:    Translation:HumansPHPublic Health
  68. 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.
    Citations: 9     Fields:    Translation:Humans
  69. 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.
    Citations: 6     Fields:    Translation:Humans
  70. 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.
    Citations: 6     Fields:    Translation:Humans
  71. 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.
    Citations: 1     Fields:    Translation:Humans
  72. 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.
    Citations: 28     Fields:    Translation:HumansCells
  73. 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.
    Citations: 38     Fields:    Translation:HumansCells
  74. 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.
    Citations: 3     
  75. 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.
    Citations:    
  76. 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.
    Citations:    Fields:    Translation:Humans
  77. 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.
    Citations: 172     Fields:    Translation:Humans
  78. 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.
    Citations: 3     Fields:    Translation:Humans
  79. 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.
    Citations: 3     
  80. 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.
    Citations: 1     Fields:    Translation:Humans
  81. 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.
    Citations: 53     Fields:    Translation:HumansCells
  82. 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.
    Citations: 8     Fields:    Translation:Humans
  83. Tomasetti C, Demetri GD, Parmigiani G. Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors. F1000Res. 2013; 2:152. PMID: 24555070.
    Citations: 2     
  84. 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.
    Citations: 3     Fields:    Translation:Humans
  85. 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.
    Citations: 1     Fields:    Translation:Humans
  86. 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.
    Citations: 18     Fields:    Translation:HumansAnimals
  87. 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.
    Citations: 7     Fields:    Translation:Humans
  88. 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.
    Citations: 43     Fields:    Translation:HumansCells
  89. 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.
    Citations: 2     Fields:    Translation:Humans
  90. 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.
    Citations: 6     Fields:    Translation:Humans
  91. 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.
    Citations: 95     Fields:    Translation:HumansCells
  92. 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.
    Citations: 5     Fields:    Translation:Humans
  93. 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.
    Citations: 148     Fields:    Translation:HumansCells
  94. 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.
    Citations: 153     Fields:    Translation:Humans
  95. 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.
    Citations:    Fields:    Translation:Humans
  96. 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.
    Citations: 12     Fields:    Translation:HumansCells
  97. 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.
    Citations: 22     Fields:    Translation:Humans
  98. 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.
    Citations: 20     Fields:    Translation:Humans
  99. Telesca D, Müller P, Parmigiani G, Freedman RS. MODELING DEPENDENT GENE EXPRESSION. Ann Stat. 2012; 6(2):542-560. PMID: 28473730.
    Citations: 1     
  100. 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.
    Citations: 13     Fields:    Translation:Humans
  101. 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.
    Citations:    
  102. 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.
    Citations: 52     Fields:    Translation:Humans
  103. 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.
    Citations: 9     Fields:    Translation:Humans
  104. Wang C, Parmigiani G, Dominici F. Bayesian effect estimation accounting for adjustment uncertainty. Biometrics. 2012 Sep; 68(3):661-71. PMID: 22364439.
    Citations: 25     Fields:    Translation:HumansPHPublic Health
  105. 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.
    Citations: 11     Fields:    Translation:Humans
  106. 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.
    Citations: 25     Fields:    Translation:HumansCells
  107. 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.
    Citations:    Fields:    
  108. 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.
    Citations: 9     Fields:    Translation:Humans
  109. 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.
    Citations:    
  110. Ho YY, Parmigiani G, Louis TA, Cope LM. Modeling liquid association. Biometrics. 2011 Mar; 67(1):133-41. PMID: 20528865.
    Citations: 8     Fields:    Translation:Humans
  111. 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.
    Citations: 317     Fields:    Translation:HumansCells
  112. 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.
    Citations: 23     Fields:    Translation:Humans
  113. 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.
    Citations: 1     
  114. 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.
    Citations: 13     Fields:    
  115. 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.
    Citations: 11     Fields:    Translation:Humans
  116. Scharpf RB, Tjelmeland H, Parmigiani G, Nobel AB. Rejoinder. J Am Stat Assoc. 2009 12; 104(488):1318-1323. PMID: 21904418.
    Citations:    
  117. 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.
    Citations: 12     Fields:    Translation:Humans
  118. 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.
    Citations: 55     Fields:    Translation:HumansAnimalsCells
  119. 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.
    Citations: 105     Fields:    Translation:Humans
  120. 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.
    Citations: 38     Fields:    Translation:HumansAnimalsCells
  121. 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.
    Citations:    Fields:    
  122. 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.
    Citations: 35     Fields:    Translation:Humans
  123. 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.
    Citations: 149     Fields:    Translation:HumansAnimalsCells
  124. 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.
    Citations: 257     Fields:    Translation:Humans
  125. 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.
    Citations:    Fields:    Translation:Humans
  126. 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.
    Citations: 15     
  127. 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.
    Citations: 9     Fields:    Translation:Humans
  128. Braun R, Cope L, Parmigiani G. Identifying differential correlation in gene/pathway combinations. BMC Bioinformatics. 2008 Nov 18; 9:488. PMID: 19017408.
    Citations: 9     Fields:    Translation:Humans
  129. 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.
    Citations: 7     Fields:    Translation:HumansCells
  130. 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.
    Citations: 124     Fields:    Translation:Cells
  131. 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.
    Citations: 9     Fields:    Translation:Humans
  132. 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.
    Citations: 72     Fields:    Translation:AnimalsCells
  133. 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.
    Citations: 1342     Fields:    Translation:HumansCells
  134. 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.
    Citations: 1786     Fields:    Translation:HumansCells
  135. 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.
    Citations: 6     Fields:    Translation:Humans
  136. 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.
    Citations: 87     Fields:    Translation:HumansAnimalsCells
  137. 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.
    Citations: 29     Fields:    Translation:Humans
  138. 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.
    Citations: 10     Fields:    Translation:Humans
  139. 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.
    Citations: 32     
  140. 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.
    Citations: 13     Fields:    Translation:Humans
  141. 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.
    Citations: 2     Fields:    
  142. 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.
    Citations: 275     Fields:    Translation:HumansAnimalsCells
  143. 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.
    Citations: 148     Fields:    Translation:HumansCells
  144. 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.
    Citations: 50     Fields:    Translation:Humans
  145. 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.
    Citations:    
  146. 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.
    Citations: 2     Fields:    
  147. 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.
    Citations: 23     Fields:    Translation:Humans
  148. 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.
    Citations: 59     Fields:    Translation:Humans
  149. 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.
    Citations:    Fields:    Translation:Humans
  150. 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.
    Citations: 1200     Fields:    Translation:HumansAnimalsCells
  151. 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.
    Citations: 25     Fields:    Translation:Humans
  152. 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.
    Citations: 19     Fields:    Translation:Humans
  153. 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.
    Citations: 13     Fields:    Translation:Humans
  154. 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.
    Citations: 56     Fields:    Translation:HumansCells
  155. 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.
    Citations: 91     Fields:    Translation:Humans
  156. 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.
    Citations: 77     Fields:    Translation:HumansAnimalsCells
  157. Chen S, Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol. 2007 Apr 10; 25(11):1329-33. PMID: 17416853.
    Citations: 369     Fields:    Translation:Humans
  158. 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.
    Citations: 62     Fields:    Translation:Humans
  159. 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.
    Citations: 5     Fields:    Translation:HumansCells
  160. 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.
    Citations: 7     Fields:    
  161. 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.
    Citations: 12     Fields:    Translation:Humans
  162. 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.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  163. 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.
    Citations: 74     Fields:    Translation:Humans
  164. 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.
    Citations: 2     Fields:    Translation:HumansCTClinical Trials
  165. 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.
    Citations: 108     Fields:    Translation:Humans
  166. 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.
    Citations: 1274     Fields:    Translation:HumansCells
  167. 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.
    Citations: 5     Fields:    Translation:Humans
  168. 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.
    Citations: 172     Fields:    Translation:HumansAnimals
  169. 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.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  170. 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.
    Citations: 86     Fields:    Translation:Humans
  171. Dettling M, Gabrielson E, Parmigiani G. Searching for differentially expressed gene combinations. Genome Biol. 2005; 6(10):R88. PMID: 16207359.
    Citations: 23     Fields:    Translation:Humans
  172. 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.
    Citations: 61     Fields:    Translation:HumansCells
  173. 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.
    Citations: 15     Fields:    Translation:Humans
  174. 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.
    Citations: 5     Fields:    Translation:HumansCells
  175. 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.
    Citations: 6     Fields:    Translation:HumansCells
  176. 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.
    Citations: 13     Fields:    Translation:Humans
  177. 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.
    Citations: 5     Fields:    Translation:HumansPHPublic Health
  178. Zhou X, Iversen ES, Parmigiani G. Classification of Missense Mutations of Disease Genes. J Am Stat Assoc. 2005; 100(469):51-60. PMID: 18418466.
    Citations: 6     
  179. 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.
    Citations: 40     Fields:    Translation:HumansCells
  180. 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.
    Citations: 11     Fields:    Translation:Humans
  181. 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.
    Citations: 11     Fields:    
  182. 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.
    Citations: 32     Fields:    
  183. 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.
    Citations: 36     Fields:    Translation:AnimalsCells
  184. 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.
    Citations: 9     Fields:    Translation:AnimalsCells
  185. 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.
    Citations: 177     Fields:    Translation:HumansCells
  186. 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.
    Citations: 80     Fields:    Translation:Humans
  187. 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.
    Citations: 1     Fields:    Translation:Humans
  188. 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.
    Citations: 17     Fields:    Translation:Humans
  189. 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.
    Citations: 1     Fields:    Translation:Humans
  190. 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.
    Citations: 28     Fields:    Translation:HumansCells
  191. 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. . 2004 Mar; 3(3):326-37. PMID: 14739784.
    Citations: 16     Fields:    Translation:AnimalsCells
  192. 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.
    Citations: 50     Fields:    Translation:HumansCells
  193. 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.
    Citations: 23     Fields:    Translation:HumansCells
  194. 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.
    Citations: 13     Fields:    Translation:AnimalsCells
  195. 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.
    Citations: 134     Fields:    Translation:HumansCells
  196. 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.
    Citations: 2     Fields:    Translation:Humans
  197. Parmigiani G. Measuring uncertainty in complex decision analysis models. Stat Methods Med Res. 2002 Dec; 11(6):513-37. PMID: 12516987.
    Citations: 5