[70] Chen S, Wang W, Broman KW, Katki HA, Parmigiani G.
BayesMendel: an R environment for
Mendelian risk prediction.
Stat Appl Genet Mol Biol 3; Article 21 2004.
[71] 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 3; Article 29 2004.
[72] Garrett ES, Parmigiani G.
A nested unsupervised approach to identifying novel molecular subtypes
.
Bernoulli 10; 951–69 2004.
[73] 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 45; 2929–2942 Sep 2004.
[74] Kittleson MM, Ye SQ, Irizarry RA, Minhas KM, Edness G, Conte JV, Parmigiani G, Miller LW,
Chen Y, Hall JL, Garcia JGN, Hare JM.
Identification of a gene expression profile that differentiates
between ischemic and nonischemic cardiomyopathy.
Circulation 110; 3444–3451 Nov 2004.
[75] Iacobuzio-Donahue CA, Song J, Parmigiani G, Yeo CJ, Hruban RH, Kern SE. Missense mutations
of MADH4: characterization of the mutational hot spot and functional consequences in human
tumors. Clin Cancer Res 10; 1597–1604 Mar 2004.
[76] Parmigiani G, Garrett E, Azbazhagan B, Gabrielson E. Molecular classification of lung cancer - a
cross-platform comparison of gene epxression data sets. Chest 125(5); 103S 2004.
[77] Zhou X, Iversen Jr ES, Parmigiani G.
Classification of missense mutations of disease genes
. Journal
of the American Statistical Association 100; 51–60 2005. PMC2311507.
[78] Inoue L, Berry D, Parmigiani G.
Correspondences between bayesian and frequentist sample size
determination
. The American Statistician 59; 79–87 2005.
[79] M¨
uller P, Parmigiani G, Robert C, Rousseau J. Optimal sample size for multiple testing: the case
of gene expression microarrays. Journal of the American Statistical Association 99; 990–1001
2005.
[80] Shen Y, Parmigiani G.
A model-based comparison of breast cancer screening strategies: mam-
mograms and clinical breast examinations.
Cancer Epidemiol Biomarkers Prev 14; 529–532 Feb
2005.
[81] 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 77; 2739–2744
May 2005.
[82] 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 com-
plex diseases in humans.
Genetics 171; 2113–2121 Dec 2005. PMC1456130.
[83] Dettling M, Gabrielson E, Parmigiani G.
Searching for differentially expressed gene combinations.
Genome Biol 6; R88 2005. PMC1257471.
[84] Sugg Skinner C, 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
20; 360–365 Apr 2005. PMC1490091.
9
[85] 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 6; 450–464 Jul 2005.
[86] Chen S, Wang W, Lee S, Watson P, Gruber S, Romans K, Kinzler K, Giardiello F, Parmigiani G. A
mendelian model and software to compute the probability of carrying mlh1 and msh2 mutations.
Cancer Epidemiology Biomarkers and Prevention 13(11); 1894S 2004.
[87] Shih IM, Sheu JJC, 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 102; 14004–14009 Sep 2005.
PMC1236547.
[88] 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 24; 863–871 Feb 2006. PMC232978.
[89] Dominici F, Zeger SL, Parmigiani G, Katz J, Christian P.
Estimating percentile-specific treatment
effects in counterfactual models: a case-study of micronutrient supplementation, birth weight and
infant mortality
. Journal of the Royal Statistical Society Series C Applied Statistics 55; 261–280
2006.
[90] Sj¨
oblom 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
JKV, 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 314; 268–274 Oct 2006.
[91] Gandhi TKB, 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 38; 285–
293 Mar 2006.
[92] 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 103; 3363–3368 Feb
2006. PMC1413941.
[93] Favorova OO, Favorov AV, Boiko AN, Andreewski TV, Sudomoina MA, Alekseenkov AD, Ku-
lakova OG, Gusev EI, Parmigiani G, Ochs MF.
Three allele combinations associated with multiple
sclerosis.
BMC Med Genet 7; 63 2006. PMC1557481.
[94] 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, Colon
Cancer Family Registry.
Prediction of germline mutations and cancer risk in the Lynch syndrome.
JAMA 296; 1479–1487 Sep 2006. PMC2538673.
[95] 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 24; 1573–1580 Dec 2006.
10