[145] Blackford A, Serrano OK, Wolfgang CL, Parmigiani G, Jones S, Zhang X, Parsons DW, Lin
JCH, 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 15; 4674–4679 Jul 2009. PMCID: PMC2819274.
[146] 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 5; Article 18 2009.
PMC2827886.
[147] Guda K, Moinova H, He J, Jamison O, Ravi L, Natale L, Lutterbaugh J, Lawrence E, Lewis S,
Willson JKV, 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 106(31); 12921–25 Jul 2009. PMC2722285.
[148] Scharpf RB, Tjelmeland H, Parmigiani G, Nobel A. A Bayesian model for cross-study differential
gene expression. JASA 104 (488); 1295–1310 2009. PMCID: PMC2994029.
[149] Scharpf RB, Tjelmeland H, Parmigiani G, Nobel A. A Bayesian model for cross-study differential
gene expression rejoinder. JASA 104 (488); 1318–1323 2009. PMCID: PMC2994029.
[150] 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 70; 552–559 Jan 2010. PMC2947347.
[151] 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
9; 257–264 2010. PMC2978933.
[152] 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 26; 2792–2793 Nov
2010. PMC3025742.
[153] Boca SM, Kinzler KW, Velculescu VE, Vogelstein B, Parmigiani G.
Patient-oriented gene set
analysis for cancer mutation data.
Genome Biol 11; R112 2010. PMC3156951.
[154] Joshu C, Parmigiani G, Colditz GA, Platz E. The prevalence of colorectal cancer risk factors
in the United States, 1999-2008. In: Cancer Prevention Research, vol. 3(supplement 12), B83
December 2010.
[155] Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JCH, 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 SKN, Shinjo SMO, 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, Parmi-
giani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE.
The
genetic landscape of the childhood cancer medulloblastoma.
Science 331; 435–439 Jan 2011.
PMC3110744.
[156] Ho YY, Parmigiani G, Louis TA, Cope LM.
Modeling liquid association.
Biometrics 67; 133–141
Mar 2011.
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[157] Trippa L, Parmigiani G. False discovery rates in somatic mutation studies of cancer. The Annals
of Applied Statistics 5(2B); 1360–1378 2011.
[158] Favorov A, Lvovs D, Speier W, Parmigiani G, Ochs MF. Oniontree XML: A format to exchange
gene-related probabilities. Journal of Biomolecular Structure Dynamics 29; 417–23 2011.
[159] Tyekucheva S, Marchionni L, Karchin R, Parmigiani G. Integrating diverse genomic data using
gene sets. Genome Biology 12(10); R105 2011. PMC3333775.
[160] Joshu CE, Parmigiani G, Colditz GA, Platz EA.
Opportunities for the primary prevention of
colorectal cancer in the united states.
Cancer Prev Res Phila 5; 138–145 Jan 2012. PMC3252472.
[161] Wang C, Parmigiani G, Dominici F.
Bayesian effect estimation accounting for adjustment uncer-
tainty.
Biometrics 68; 661–71 Feb 2012.
[162] Biswas S, Tankhiwale N, Blackford A, Barrera AMG, 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 133; 347–355 Jan 2012.
[163] Roberts N, Vogelstein J, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE. The predictive
capacity of personal genome sequencing. Nature Translational Medicine 4(133); 133ra58 2012.
PMCID: PMC3741669.
[164] Waldron L, Simpson PT, Parmigiani G, Huttenhower C. Report on emerging technologies for
translational bioinformatics: a symposium on gene expression profiling for archival tissues. BMC
Cancer 12; 124 2012. PMC3342119.
[165] 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 30; 3258–
63 May 2012. PMC3434985.
[166] Wang XV, Blades N, Ding J, Sultana R, Parmigiani. G. Estimation of sequencing error rates in
short reads. BMC Bioinformatics 13(1); 185 Jul 2012 2012. PMC3495688.
[167] Waldron L, Ogino S, Hoshida Y, Shima K, Reed A, Simpson P, Baba Y, Nosho K, Segata N,
Vargas AC, Cummings M, Lakhani S, Kirkner G, Giovannucci E, Quackenbush J, Golub T, Fuchs
C, Parmigiani G, Huttenhower C. Expression profiling of archival tumors for long-term health
studies. Clin Cancer Res 18; 6136–46 2012. PMC3500412.
[168] Coopey SB, Mazzola E, Buckley JM, Sharko J, Belli AK, Kim EMH, 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 136; 627–33 Nov 2012.
[169] Sausen M, Leary RJ, Jones S, Wu J, Reynolds CP, Liu X, Blackford A, Parmigiani G, Luis A. Diaz
J, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE, Hogarty MD. Integrated genomic
analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. Nature
Genetics 45; 12–7 2012. PMCID: PMC3557959.
[170] 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 4; 162ra154
Nov 2012. PMCID: PMC3641759.
16