PubMed

The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations.

Lin X, Afsari B, Marchionni L, Cope L, Parmigiani G, Naiman D, Geman D.

BMC Bioinformatics. 2009 Aug 20;10:256.PMID: 19695104 [PubMed - in process]Related articlesFree article

Inactivating germ-line and somatic mutations in polypeptide N-acetylgalactosaminyltransferase 12 in human colon cancers.

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.

Proc Natl Acad Sci U S A. 2009 Aug 4;106(31):12921-5. Epub 2009 Jul 17.PMID: 19617566 [PubMed - indexed for MEDLINE]Related articles

Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays.

Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I.

Ann Appl Stat. 2008 Jun 1;2(2):687-713.PMID: 19609370 [PubMed]Related articlesFree article

SMAD4 gene mutations are associated with poor prognosis in pancreatic cancer.

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.

Clin Cancer Res. 2009 Jul 15;15(14):4674-9. Epub 2009 Jul 7.PMID: 19584151 [PubMed - indexed for MEDLINE]Related articles

Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma.

He X, Marchionni L, Hansel DE, Yu W, Sood A, Yang J, Parmigiani G, Matsui W, Berman DM.

Stem Cells. 2009 Jul;27(7):1487-95.PMID: 19544456 [PubMed - indexed for MEDLINE]Related articles

A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro.

Daniel VC, Marchionni L, Hierman JS, Rhodes JT, Devereux WL, Rudin CM, Yung R, Parmigiani G, Dorsch M, Peacock CD, Watkins DN.

Cancer Res. 2009 Apr 15;69(8):3364-73. Epub 2009 Apr 7.PMID: 19351829 [PubMed - indexed for MEDLINE]Related articles

Genetic mutations associated with cigarette smoking in pancreatic cancer.

Blackford A, Parmigiani G, Kensler TW, Wolfgang C, Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Eshleman JR, Goggins M, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Klein A, Cameron JL, Olino K, Schulick R, Winter J, Vogelstein B, Velculescu VE, Kinzler KW, Hruban RH.

Cancer Res. 2009 Apr 15;69(8):3681-8. Epub 2009 Apr 7.PMID: 19351817 [PubMed - indexed for MEDLINE]Related articles

Exomic sequencing identifies PALB2 as a pancreatic cancer susceptibility gene.

Jones S, Hruban RH, Kamiyama M, Borges M, Zhang X, Parsons DW, Lin JC, Palmisano E, Brune K, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Parmigiani G, Kern SE, Velculescu VE, Kinzler KW, Vogelstein B, Eshleman JR, Goggins M, Klein AP.

Science. 2009 Apr 10;324(5924):217. Epub 2009 Mar 5.PMID: 19264984 [PubMed - indexed for MEDLINE]Related articles

Tailoring BRCAPRO to Asian-Americans.

Chen S, Blackford AL, Parmigiani G.

J Clin Oncol. 2009 Feb 1;27(4):642-3; author reply 643-4. Epub 2008 Dec 15. No abstract available. PMID: 19075251 [PubMed - indexed for MEDLINE]Related articles

Identifying differential correlation in gene/pathway combinations.

Braun R, Cope L, Parmigiani G.

BMC Bioinformatics. 2008 Nov 18;9:488.PMID: 19017408 [PubMed - indexed for MEDLINE]Related articlesFree article

A multiple-loop, double-cube microarray design applied to prostate cancer cell lines with variable sensitivity to histone deacetylase inhibitors.

Kortenhorst MS, Zahurak M, Shabbeer S, Kachhap S, Galloway N, Parmigiani G, Verheul HM, Carducci MA.

Clin Cancer Res. 2008 Nov 1;14(21):6886-94.PMID: 18980983 [PubMed - indexed for MEDLINE]Related articlesFree article

Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers.

Leary RJ, Lin JC, Cummins J, Boca S, Wood LD, Parsons DW, Jones S, Sjöblom T, Park BH, Parsons R, Willis J, Dawson D, Willson JK, Nikolskaya T, Nikolsky Y, Kopelovich L, Papadopoulos N, Pennacchio LA, Wang TL, Markowitz SD, Parmigiani G, Kinzler KW, Vogelstein B, Velculescu VE.

Proc Natl Acad Sci U S A. 2008 Oct 21;105(42):16224-9. Epub 2008 Oct 13.PMID: 18852474 [PubMed - indexed for MEDLINE]Related articlesFree article

Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer.

Schaeffer EM, Marchionni L, Huang Z, Simons B, Blackman A, Yu W, Parmigiani G, Berman DM.

Oncogene. 2008 Dec 4;27(57):7180-91. Epub 2008 Sep 15.PMID: 18794802 [PubMed - indexed for MEDLINE]Related articlesFree article

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

Jones S, Zhang X, Parsons DW, Lin JC, 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.

Science. 2008 Sep 26;321(5897):1801-6. Epub 2008 Sep 4.PMID: 18772397 [PubMed - indexed for MEDLINE]Related articlesFree article

An integrated genomic analysis of human glioblastoma multiforme.

Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW.

Science. 2008 Sep 26;321(5897):1807-12. Epub 2008 Sep 4.PMID: 18772396 [PubMed - indexed for MEDLINE]Related articlesFree article

Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies.

Pattaro C, Ruczinski I, Fallin DM, Parmigiani G.

BMC Genomics. 2008 Aug 29;9:405.PMID: 18759977 [PubMed - indexed for MEDLINE]Related articlesFree article

Toll-like receptor 3 and geographic atrophy in age-related macular degeneration.

Yang Z, Stratton C, Francis PJ, Kleinman ME, Tan PL, Gibbs D, Tong Z, Chen H, Constantine R, Yang X, Chen Y, Zeng J, Davey L, Ma X, Hau VS, Wang C, Harmon J, Buehler J, Pearson E, Patel S, Kaminoh Y, Watkins S, Luo L, Zabriskie NA, Bernstein PS, Cho W, Schwager A, Hinton DR, Klein ML, Hamon SC, Simmons E, Yu B, Campochiaro B, Sunness JS, Campochiaro P, Jorde L, Parmigiani G, Zack DJ, Katsanis N, Ambati J, Zhang K.

N Engl J Med. 2008 Oct 2;359(14):1456-63. Epub 2008 Aug 27. Erratum in: N Engl J Med. 2008 Oct 23;359(17):1859. N Engl J Med. 2009 Jul 23;361(4):431. PMID: 18753640 [PubMed - indexed for MEDLINE]Related articlesFree article

Design and analysis issues in genome-wide somatic mutation studies of cancer.

Parmigiani G, Boca S, Lin J, Kinzler KW, Velculescu V, Vogelstein B.

Genomics. 2009 Jan;93(1):17-21. Epub 2008 Aug 23. Review.PMID: 18692126 [PubMed - indexed for MEDLINE]Related articles

Model selection and health effect estimation in environmental epidemiology.

Dominici F, Wang C, Crainiceanu C, Parmigiani G.

Epidemiology. 2008 Jul;19(4):558-60.PMID: 18552590 [PubMed - indexed for MEDLINE]Related articles

Incorporating tumor immunohistochemical markers in BRCA1 and BRCA2 carrier prediction.

Tai YC, Chen S, Parmigiani G, Klein AP.

Breast Cancer Res. 2008;10(2):401. Epub 2008 Mar 20. No abstract available. PMID: 18466632 [PubMed - indexed for MEDLINE]Related articlesFree article

Impact of gene expression profiling tests on breast cancer outcomes.

Marchionni L, Wilson RF, Marinopoulos SS, Wolff AC, Parmigiani G, Bass EB, Goodman SN.

Evid Rep Technol Assess (Full Rep). 2007 Dec;(160):1-105. Review.PMID: 18457476 [PubMed - indexed for MEDLINE]Related articles

Classification of Missense Mutations of Disease Genes.

Zhou X, Iversen ES, Parmigiani G.

J Am Stat Assoc. 2005;100:51-60.PMID: 18418466 [PubMed]Related articlesFree article

Multiple diseases in carrier probability estimation: accounting for surviving all cancers other than breast and ovary in BRCAPRO.

Katki HA, Blackford A, Chen S, Parmigiani G.

Stat Med. 2008 Sep 30;27(22):4532-48.PMID: 18407567 [PubMed - indexed for MEDLINE]Related articlesFree article

TRAB: testing whether mutation frequencies are above an unknown background.

Parmigiani G, Chen S.

Stat Appl Genet Mol Biol. 2008;7(1):Article11. Epub 2008 Mar 14.PMID: 18384264 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative lesion sequencing provides insights into tumor evolution.

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.

Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4283-8. Epub 2008 Mar 12.PMID: 18337506 [PubMed - indexed for MEDLINE]Related articlesFree article

Statistical methods for identifying differentially expressed gene combinations.

Ho YY, Cope L, Dettling M, Parmigiani G.

Methods Mol Biol. 2007;408:171-91.PMID: 18314583 [PubMed - indexed for MEDLINE]Related articles

Chromatid cohesion defects may underlie chromosome instability in human colorectal cancers.

Barber TD, McManus K, Yuen KW, Reis M, Parmigiani G, Shen D, Barrett I, Nouhi Y, Spencer F, Markowitz S, Velculescu VE, Kinzler KW, Vogelstein B, Lengauer C, Hieter P.

Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3443-8. Epub 2008 Feb 25.PMID: 18299561 [PubMed - indexed for MEDLINE]Related articlesFree article

Systematic review: gene expression profiling assays in early-stage breast cancer.

Marchionni L, Wilson RF, Wolff AC, Marinopoulos S, Parmigiani G, Bass EB, Goodman SN.

Ann Intern Med. 2008 Mar 4;148(5):358-69. Epub 2008 Feb 4. Review.PMID: 18252678 [PubMed - indexed for MEDLINE]Related articlesFree article

Penalized likelihood for sparse contingency tables with an application to full-length cDNA libraries.

Dahinden C, Parmigiani G, Emerick MC, Bühlmann P.

BMC Bioinformatics. 2007 Dec 11;8:476.PMID: 18072965 [PubMed - indexed for MEDLINE]Related articlesFree article

Breast cancer risk among male BRCA1 and BRCA2 mutation carriers.

Tai YC, Domchek S, Parmigiani G, Chen S.

J Natl Cancer Inst. 2007 Dec 5;99(23):1811-4. Epub 2007 Nov 27.PMID: 18042939 [PubMed - indexed for MEDLINE]Related articlesFree article

Limited family structure and breast cancer risk.

Iversen ES Jr, Katki HA, Chen S, Berry DA, Parmigiani G.

JAMA. 2007 Nov 7;298(17):2007; author reply 2007-8. No abstract available. PMID: 17986693 [PubMed - indexed for MEDLINE]Related articles

The genomic landscapes of human breast and colorectal cancers.

Wood LD, Parsons DW, Jones S, Lin J, Sjöblom 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.

Science. 2007 Nov 16;318(5853):1108-13. Epub 2007 Oct 11.PMID: 17932254 [PubMed - indexed for MEDLINE]Related articlesFree article

Congenital growth hormone (GH) deficiency and atherosclerosis: effects of GH replacement in GH-naive adults.

Oliveira JL, Aguiar-Oliveira MH, D'Oliveira A Jr, Pereira RM, Oliveira CR, 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.

J Clin Endocrinol Metab. 2007 Dec;92(12):4664-70. Epub 2007 Oct 2.PMID: 17911170 [PubMed - indexed for MEDLINE]Related articlesFree article

Validity of models for predicting BRCA1 and BRCA2 mutations.

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.

Ann Intern Med. 2007 Oct 2;147(7):441-50.PMID: 17909205 [PubMed - indexed for MEDLINE]Related articlesFree article

Cross-study validation and combined analysis of gene expression microarray data.

Garrett-Mayer E, Parmigiani G, Zhong X, Cope L, Gabrielson E.

Biostatistics. 2008 Apr;9(2):333-54. Epub 2007 Sep 14.PMID: 17873151 [PubMed - indexed for MEDLINE]Related articles

A multidimensional analysis of genes mutated in breast and colorectal cancers.

Lin J, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE.

Genome Res. 2007 Sep;17(9):1304-18. Epub 2007 Aug 10.PMID: 17693572 [PubMed - indexed for MEDLINE]Related articlesFree article

Pre-processing Agilent microarray data.

Zahurak M, Parmigiani G, Yu W, Scharpf RB, Berman D, Schaeffer E, Shabbeer S, Cope L.

BMC Bioinformatics. 2007 May 1;8:142.PMID: 17472750 [PubMed - indexed for MEDLINE]Related articlesFree article

PancPRO: risk assessment for individuals with a family history of pancreatic cancer.

Wang W, Chen S, Brune KA, Hruban RH, Parmigiani G, Klein AP.

J Clin Oncol. 2007 Apr 10;25(11):1417-22.PMID: 17416862 [PubMed - indexed for MEDLINE]Related articlesFree article

Meta-analysis of BRCA1 and BRCA2 penetrance.

Chen S, Parmigiani G.

J Clin Oncol. 2007 Apr 10;25(11):1329-33.PMID: 17416853 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome-wide gene expression differences in Crohn's disease and ulcerative colitis from endoscopic pinch biopsies: insights into distinctive pathogenesis.

Wu F, Dassopoulos T, Cope L, Maitra A, Brant SR, Harris ML, Bayless TM, Parmigiani G, Chakravarti S.

Inflamm Bowel Dis. 2007 Jul;13(7):807-21.PMID: 17262812 [PubMed - indexed for MEDLINE]Related articlesFree article

Multivariate analysis and visualization of splicing correlations in single-gene transcriptomes.

Emerick MC, Parmigiani G, Agnew WS.

BMC Bioinformatics. 2007 Jan 18;8:16.PMID: 17233916 [PubMed - indexed for MEDLINE]Related articlesFree article

When should one subtract background fluorescence in 2-color microarrays?

Scharpf RB, Iacobuzio-Donahue CA, Sneddon JB, Parmigiani G.

Biostatistics. 2007 Oct;8(4):695-707. Epub 2006 Dec 12.PMID: 17164465 [PubMed - indexed for MEDLINE]Related articlesFree article

The genome and transcriptomes of the anti-tumor agent Clostridium novyi-NT.

Bettegowda C, Huang X, Lin J, Cheong I, Kohli M, Szabo SA, Zhang X, Diaz LA Jr, Velculescu VE, Parmigiani G, Kinzler KW, Vogelstein B, Zhou S.

Nat Biotechnol. 2006 Dec;24(12):1573-80. Epub 2006 Nov 19.PMID: 17115055 [PubMed - indexed for MEDLINE]Related articles

GH response to hypoglycemia and clonidine in the GH-releasing hormone resistance syndrome.

Salvatori R, Serpa MG, Parmigiani G, Britto AV, Oliveira JL, Oliveira CR, Prado CM, Farias CT, Almeida JC, Vicente TA, Aguiar-Oliveira MH.

J Endocrinol Invest. 2006 Oct;29(9):805-8.PMID: 17114911 [PubMed - indexed for MEDLINE]Related articles

Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts.

Hayes DN, Monti S, Parmigiani G, Gilks CB, Naoki K, Bhattacharjee A, Socinski MA, Perou C, Meyerson M.

J Clin Oncol. 2006 Nov 1;24(31):5079-90. Review.PMID: 17075127 [PubMed - indexed for MEDLINE]Related articles

Prediction of germline mutations and cancer risk in the Lynch syndrome.

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.

JAMA. 2006 Sep 27;296(12):1479-87.PMID: 17003396 [PubMed - indexed for MEDLINE]Related articlesFree article

The consensus coding sequences of human breast and colorectal cancers.

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.

Science. 2006 Oct 13;314(5797):268-74. Epub 2006 Sep 7.PMID: 16959974 [PubMed - indexed for MEDLINE]Related articlesFree article

Three allele combinations associated with multiple sclerosis.

Favorova OO, Favorov AV, Boiko AN, Andreewski TV, Sudomoina MA, Alekseenkov AD, Kulakova OG, Gusev EI, Parmigiani G, Ochs MF.

BMC Med Genet. 2006 Jul 26;7:63.PMID: 16872485 [PubMed - indexed for MEDLINE]Related articlesFree article

MergeMaid: R tools for merging and cross-study validation of gene expression data.

Cope L, Zhong X, Garrett E, Parmigiani G.

Stat Appl Genet Mol Biol. 2004;3:Article29. Epub 2004 Oct 31.PMID: 16646808 [PubMed]Related articlesFree article

BayesMendel: an R environment for Mendelian risk prediction.

Chen S, Wang W, Broman KW, Katki HA, Parmigiani G.

Stat Appl Genet Mol Biol. 2004;3:Article21. Epub 2004 Sep 17.PMID: 16646800 [PubMed]Related articlesFree article