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.

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.

Ding J, Trippa L, Zhong X, Parmigiani G. Hierarchical bayesian analysis of somatic mutation data in cancer. Annals of Applied Statistics accepted 2012.

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.

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.

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 chromo- somal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 4; 162ra154 Nov 2012.

Telesca D, Muller P, Parmigiani G, Freedman RS. Modeling dependent gene expression. The Annals of Applied Statistics 6; 542–60 2012.

Mazzola E, Cheng SC, Parmigiani G. The penetrance of ductal carcinoma in situ among BRCA1 and BRCA2 mutation carriers. Breast Cancer Res Treat 137; 315–318 Jan 2013.

Thompson JR, Ggele M, Weichenberger CX, Modenese M, Attia J, Barrett JH, Boehnke M, Grandi AD, Domingues FS, Hicks AA, Marroni F, Pattaro C, Ruggeri F, Borsani G, Casari G, Parmigiani G, Pastore A, Pfeufer A, Schwienbacher C, Taliun D, Consortium C, Fox CS, Pramstaller PP, Minelli C. SNP prioritization using a bayesian probability of association. Genet Epidemiol 37; 214–221 Feb 2013.

Minelli C, Grandi AD, Weichenberger CX, Ggele 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 37; 205–213 Feb 2013.

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