[96] 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 24; 5079–5090 Nov 2006.
[97] Salvatori R, Serpa MG, Parmigiani G, Britto AVO, Oliveira JLM, Oliveira CRP, Prado CM, Farias
CT, Almeida JC, Vicente TAR, Aguiar-Oliveira MH.
GH response to hypoglycemia and clonidine
in the GH-releasing hormone resistance syndrome.
J Endocrinol Invest 29; 805–808 Oct 2006.
[98] Dominici F, Zeger SL, Parmigiani G, Katz J, Christian P.
Does the effect of micronutrient
supplementation on neonatal survival vary with respect to the percentiles of the birth weight
distribution?
Bayesian Analysis 2; 1–30 2007.
[99] Emerick MC, Parmigiani G, Agnew WS.
Multivariate analysis and visualization of splicing corre-
lations in single-gene transcriptomes.
BMC Bioinformatics 8; 16 2007. PMC1785386.
[100] Dahinden C, Parmigiani G, Emerick MC, B¨
uhlmann P.
Penalized likelihood for sparse contin-
gency tables with an application to full-length cDNA libraries.
BMC Bioinformatics 8; 476 2007.
PMC2233645.
[101] Parmigiani G, Lin J, Boca S, Sj¨
oblom T, Jones S, Wood LD, Parsons DW, Barber T, Buckhaults
P, Markowitz SD, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu
VE.
Response to comments on ’The consensus coding sequences of breast and colorectal cancers’
.
Science 317 (5844); 1500d 2007.
[102] Wood LD, Parsons DW, Jones S, Lin J, Sjblom 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 JKV, Sukumar S,
Polyak K, Park BH, Pethiyagoda CL, Pant PVK, 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 318;
1108–1113 Nov 2007.
[103] 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 25; 1417–1422 Apr 2007.
[104] Scharpf RB, Iacobuzio-Donahue CA, Sneddon JB, Parmigiani G.
When should one subtract
background fluorescence in 2-color microarrays?
Biostatistics 8; 695–707 Oct 2007.
[105] 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 13;
807–821 Jul 2007.
[106] Oliveira JLM, Aguiar-Oliveira MH, D’Oliveira A, Pereira RMC, Oliveira CRP, 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 92; 4664–4670 Dec 2007.
[107] Chen S, Parmigiani G.
Meta-analysis of BRCA1 and BRCA2 penetrance.
J Clin Oncol 25;
1329–1333 Apr 2007. PMC2267287.
11
[108] Chen S, Euhus DM, Parmigiani G.
Quantitative models for predicting mutations in Lynch syndrome
genes
. Current Colorectal Cancer Reports 3(4); 206–211 2007.
[109] Zahurak M, Parmigiani G, Yu W, Scharpf RB, Berman D, Schaeffer E, Shabbeer S, Cope L.
Pre-processing agilent microarray data.
BMC Bioinformatics 8; 142 2007. PMC1876252.
[110] 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 1–105 Dec 2007.
[111] Ho YY, Cope L, Dettling M, Parmigiani G. Statistical methods for identifying differentially ex-
pressed gene combinations. Methods Mol Biol 408; 171–191 2007.
[112] Lin J, Gan CM, Zhang X, Jones S, Sjblom 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 17; 1304–1318 Sep 2007. PMC1950899.
[113] 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 147; 441–450 Oct 2007. PMC2423214.
[114] Tai YC, Domchek S, Parmigiani G, Chen S.
Breast cancer risk among male BRCA1 and BRCA2
mutation carriers.
J Natl Cancer Inst 99; 1811–1814 Dec 2007. PMC2267289.
[115] Iversen ES, Katki HA, Chen S, Berry DA, Parmigiani G.
Limited family structure and breast
cancer risk.
JAMA 298; 2007 Nov 2007.
[116] Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I.
Hidden Markov models for the assessment
of chromosomal alterations using high-throughput SNP arrays
. Annals of Applied Statistics 2;
687–713 2008. PMC2710854.
[117] 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
148; 358–369 Mar 2008.
[118] 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 105; 4283–4288
Mar 2008. PMC2393770.
[119] Jones S, Zhang X, Parsons DW, Lin JCH, 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 321; 1801–1806 Sep 2008.
PMC2848990.
[120] Garrett-Mayer E, Parmigiani G, Zhong X, Cope L, Gabrielson E.
Cross-study validation and
combined analysis of gene expression microarray data.
Biostatistics 9; 333–354 Apr 2008.
12