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Giovanni Parmigiani, PhD

Publications

  • 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-i112.
    24931973
  • Mazzola E, Chipman J, Cheng SC, Parmigiani G.Recent BRCAPRO upgrades significantly improve calibration.Cancer Epidemiol Biomarkers Prev. 2014 Jun 2.
    24891549
  • Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ.Risk Prediction for Late-Stage Ovarian Cancer by Meta-analysis of 1525 Patient Samples.Journal of the National Cancer Institute. 2014 Apr 3.
    24700803
  • Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G.Comparative Meta-analysis of Prognostic Gene Signatures for Late-Stage Ovarian Cancer.Journal of the National Cancer Institute. 2014 Apr 3.
    24700801
  • Gorfine M, Hsu L, Parmigiani G.Frailty Models for Familial Risk with Application to Breast Cancer.Journal of the American Statistical Association. 2013 Dec 1;108(504):1205-1215.
    24678132
  • Ho YY, Cope LM, Parmigiani G.Modular network construction using eQTL data: an analysis of computational costs and benefits.Front Genet. 2014;5:40.
    24616734
  • Tomasetti C, Demetri GD, Parmigiani G.Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors.F1000Res. 2013;2:152.
    24555070
  • 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.
    24429703
  • Biswas S, Arun B, Parmigiani G.Reclassification of predictions for uncovering subgroup specific improvement.Stat Med. 2013 Dec 18.
    24353130
  • Parmigiani G, Boca S, Ding J, Trippa L.Statistical tools and R software for cancer driver probabilities.Methods Mol Biol. 2014;1101:113-34.
    24233780
  • 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.
    23909925
  • 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.
    23901115
  • 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 1;29(15):1865-71.
    23712657
  • 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.
    23793601
  • Gorfine M, Hsu L, Zucker DM, Parmigiani G.Calibrated predictions for multivariate competing risks models.Lifetime Data Analysis. 2013 May 31.
    23737081
  • 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.
    23690142
  • 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 1;31(7):970-1.
    23565532
  • 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.
    23550061
  • 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 5;110(6):1999-2004.
    23345422
  • 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.
    23202128
  • 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.
    23184082
  • 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.
    23197571
  • 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):6136-6146.
    23136189
  • Victoria X, Blades N, Ding J, Sultana R, Parmigiani G.Estimation of sequencing error rates in short reads.BMC Bioinformatics. 2012;13(1):185.
    22846331
  • 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 Nov 2.
    23117858
  • 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.
    22649140
  • 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.
    21163964
  • Ho YY, Parmigiani G, Louis TA, Cope LM.Modeling Liquid Association.Biometrics. 2010 Jun 1.
    20528865
  • Boca SM, Kinzler K, Velculescu VE, Vogelstein B, Parmigiani G.Patient-oriented gene set analysis for cancer mutation data.Genome Biol. 2010 Nov 23;11(11):R112.
    21092299
  • Scharpf RB, Iacobuzio-Donahue CA, Cope L, Ruczinski I, Garrett-Mayer E, Lakkur S, Campagna D, Parmigiani G.Cross-platform Comparison of Two Pancreatic Cancer Phenotypes.Cancer Inform. 2010;9:257-64.
    21082040
  • 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 1;26(21):2792-3.
    20810601
  • 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.
    20068151
  • Lin X, Afsari B, Marchionni L, Cope L, Parmigiani G, Naiman D, Geman D.The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.BMC Bioinformatics. 2009;10:256.
    19695104
  • 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 4;106(31):12921-5.
    19617566
  • 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.
    19544456
  • 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.
    19584151
  • 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. Review.
    18692126
  • Tai YC, Chen S, Parmigiani G, Klein AP.Incorporating tumor immunohistochemical markers in BRCA1 and BRCA2 carrier prediction.Breast Cancer Res. 2008 Mar 20;10(2):401.
    18466632
  • 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 4;148(5):358-69. Review.
    18252678
  • Tai YC, Domchek S, Parmigiani G, Chen S.Breast cancer risk among male BRCA1 and BRCA2 mutation carriers.Journal of the National Cancer Institute. 2007 Dec 5;99(23):1811-4.
    18042939
  • Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B.The genomic landscapes of human breast and colorectal cancers.Science. 2007 Nov 16;318(5853):1108-13.
    17932254
  • Parmigiani G, Chen S, Iversen ES Jr, Friebel TM, Finkelstein DM, Anton-Culver H, Ziogas A, Weber BL, Eisen A, Malone KE, Daling JR, Hsu L, Ostrander EA, Peterson LE, Schildkraut JM, Isaacs C, Corio C, Leondaridis L, Tomlinson G, Amos CI, Strong LC, Berry DA, Weitzel JN, Sand S, Dutson D, Kerber R, Peshkin BN, Euhus DM.Validity of models for predicting BRCA1 and BRCA2 mutations.Ann Intern Med. 2007 Oct 2;147(7):441-50.
    17909205
  • 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.
    17693572
  • 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.
    17416862
  • Chen S, Parmigiani G.Meta-analysis of BRCA1 and BRCA2 penetrance.J Clin Oncol. 2007 Apr 10;25(11):1329-33.
    17416853
  • 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.
    16959974
  • 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.
    17003396