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Items: 44

1.

Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations.

Fischer CG, Beleva Guthrie V, Braxton AM, Zheng L, Wang P, Song Q, Griffin JF, Chianchiano PE, Hosoda W, Niknafs N, Springer S, Dal Molin M, Masica D, Scharpf RB, Thompson ED, He J, Wolfgang CL, Hruban RH, Roberts NJ, Lennon AM, Jiao Y, Karchin R, Wood LD.

Gastroenterology. 2019 Oct;157(4):1123-1137.e22. doi: 10.1053/j.gastro.2019.06.001. Epub 2019 Jun 5.

PMID:
31175866
2.

Genome-wide cell-free DNA fragmentation in patients with cancer.

Cristiano S, Leal A, Phallen J, Fiksel J, Adleff V, Bruhm DC, Jensen SØ, Medina JE, Hruban C, White JR, Palsgrove DN, Niknafs N, Anagnostou V, Forde P, Naidoo J, Marrone K, Brahmer J, Woodward BD, Husain H, van Rooijen KL, Ørntoft MW, Madsen AH, van de Velde CJH, Verheij M, Cats A, Punt CJA, Vink GR, van Grieken NCT, Koopman M, Fijneman RJA, Johansen JS, Nielsen HJ, Meijer GA, Andersen CL, Scharpf RB, Velculescu VE.

Nature. 2019 Jun;570(7761):385-389. doi: 10.1038/s41586-019-1272-6. Epub 2019 May 29.

3.

Early Noninvasive Detection of Response to Targeted Therapy in Non-Small Cell Lung Cancer.

Phallen J, Leal A, Woodward BD, Forde PM, Naidoo J, Marrone KA, Brahmer JR, Fiksel J, Medina JE, Cristiano S, Palsgrove DN, Gocke CD, Bruhm DC, Keshavarzian P, Adleff V, Weihe E, Anagnostou V, Scharpf RB, Velculescu VE, Husain H.

Cancer Res. 2019 Mar 15;79(6):1204-1213. doi: 10.1158/0008-5472.CAN-18-1082. Epub 2018 Dec 20.

4.

Dynamics of Tumor and Immune Responses during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.

Anagnostou V, Forde PM, White JR, Niknafs N, Hruban C, Naidoo J, Marrone K, Sivakumar IKA, Bruhm DC, Rosner S, Phallen J, Leal A, Adleff V, Smith KN, Cottrell TR, Rhymee L, Palsgrove DN, Hann CL, Levy B, Feliciano J, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Isbell JM, Sauter JL, Taube J, Scharpf RB, Karchin R, Pardoll DM, Chaft JE, Hellmann MD, Brahmer JR, Velculescu VE.

Cancer Res. 2019 Mar 15;79(6):1214-1225. doi: 10.1158/0008-5472.CAN-18-1127. Epub 2018 Dec 12.

5.

Detection of rare disease variants in extended pedigrees using RVS.

Sherman T, Fu J, Scharpf RB, Bureau A, Ruczinski I.

Bioinformatics. 2019 Jul 15;35(14):2509-2511. doi: 10.1093/bioinformatics/bty976.

6.

Integrated Genomic, Epigenomic, and Expression Analyses of Ovarian Cancer Cell Lines.

Papp E, Hallberg D, Konecny GE, Bruhm DC, Adleff V, Noë M, Kagiampakis I, Palsgrove D, Conklin D, Kinose Y, White JR, Press MF, Drapkin R, Easwaran H, Baylin SB, Slamon D, Velculescu VE, Scharpf RB.

Cell Rep. 2018 Nov 27;25(9):2617-2633. doi: 10.1016/j.celrep.2018.10.096.

7.

Detection of de novo copy number deletions from targeted sequencing of trios.

Fu JM, Leslie EJ, Scott AF, Murray JC, Marazita ML, Beaty TH, Scharpf RB, Ruczinski I.

Bioinformatics. 2019 Feb 15;35(4):571-578. doi: 10.1093/bioinformatics/bty677.

8.

Neoadjuvant PD-1 Blockade in Resectable Lung Cancer.

Forde PM, Chaft JE, Smith KN, Anagnostou V, Cottrell TR, Hellmann MD, Zahurak M, Yang SC, Jones DR, Broderick S, Battafarano RJ, Velez MJ, Rekhtman N, Olah Z, Naidoo J, Marrone KA, Verde F, Guo H, Zhang J, Caushi JX, Chan HY, Sidhom JW, Scharpf RB, White J, Gabrielson E, Wang H, Rosner GL, Rusch V, Wolchok JD, Merghoub T, Taube JM, Velculescu VE, Topalian SL, Brahmer JR, Pardoll DM.

N Engl J Med. 2018 May 24;378(21):1976-1986. doi: 10.1056/NEJMoa1716078. Epub 2018 Apr 16. Erratum in: N Engl J Med. 2018 Nov 29;379(22):2185.

9.

GATA3 frameshift mutation promotes tumor growth in human luminal breast cancer cells and induces transcriptional changes seen in primary GATA3 mutant breast cancers.

Gustin JP, Miller J, Farag M, Rosen DM, Thomas M, Scharpf RB, Lauring J.

Oncotarget. 2017 Oct 20;8(61):103415-103427. doi: 10.18632/oncotarget.21910. eCollection 2017 Nov 28.

10.

High grade serous ovarian carcinomas originate in the fallopian tube.

Labidi-Galy SI, Papp E, Hallberg D, Niknafs N, Adleff V, Noe M, Bhattacharya R, Novak M, Jones S, Phallen J, Hruban CA, Hirsch MS, Lin DI, Schwartz L, Maire CL, Tille JC, Bowden M, Ayhan A, Wood LD, Scharpf RB, Kurman R, Wang TL, Shih IM, Karchin R, Drapkin R, Velculescu VE.

Nat Commun. 2017 Oct 23;8(1):1093. doi: 10.1038/s41467-017-00962-1.

11.

Direct detection of early-stage cancers using circulating tumor DNA.

Phallen J, Sausen M, Adleff V, Leal A, Hruban C, White J, Anagnostou V, Fiksel J, Cristiano S, Papp E, Speir S, Reinert T, Orntoft MW, Woodward BD, Murphy D, Parpart-Li S, Riley D, Nesselbush M, Sengamalay N, Georgiadis A, Li QK, Madsen MR, Mortensen FV, Huiskens J, Punt C, van Grieken N, Fijneman R, Meijer G, Husain H, Scharpf RB, Diaz LA Jr, Jones S, Angiuoli S, Ørntoft T, Nielsen HJ, Andersen CL, Velculescu VE.

Sci Transl Med. 2017 Aug 16;9(403). pii: eaan2415. doi: 10.1126/scitranslmed.aan2415.

12.

Genome-Wide Association of Copy Number Polymorphisms and Kidney Function.

Li M, Carey J, Cristiano S, Susztak K, Coresh J, Boerwinkle E, Kao WH, Beaty TH, Köttgen A, Scharpf RB.

PLoS One. 2017 Jan 30;12(1):e0170815. doi: 10.1371/journal.pone.0170815. eCollection 2017.

13.

Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non-Small Cell Lung Cancer.

Anagnostou V, Smith KN, Forde PM, Niknafs N, Bhattacharya R, White J, Zhang T, Adleff V, Phallen J, Wali N, Hruban C, Guthrie VB, Rodgers K, Naidoo J, Kang H, Sharfman W, Georgiades C, Verde F, Illei P, Li QK, Gabrielson E, Brock MV, Zahnow CA, Baylin SB, Scharpf RB, Brahmer JR, Karchin R, Pardoll DM, Velculescu VE.

Cancer Discov. 2017 Mar;7(3):264-276. doi: 10.1158/2159-8290.CD-16-0828. Epub 2016 Dec 28.

14.

Whole exome association of rare deletions in multiplex oral cleft families.

Fu J, Beaty TH, Scott AF, Hetmanski J, Parker MM, Wilson JE, Marazita ML, Mangold E, Albacha-Hejazi H, Murray JC, Bureau A, Carey J, Cristiano S, Ruczinski I, Scharpf RB.

Genet Epidemiol. 2017 Jan;41(1):61-69. doi: 10.1002/gepi.22010. Epub 2016 Dec 1.

15.

Hemizygous Deletion on Chromosome 3p26.1 Is Associated with Heavy Smoking among African American Subjects in the COPDGene Study.

Begum F, Ruczinski I, Hokanson JE, Lutz SM, Parker MM, Cho MH, Hetmanski JB, Scharpf RB, Crapo JD, Silverman EK, Beaty TH.

PLoS One. 2016 Oct 6;11(10):e0164134. doi: 10.1371/journal.pone.0164134. eCollection 2016.

16.

Identifying a Deletion Affecting Total Lung Capacity Among Subjects in the COPDGene Study Cohort.

Begum F, Ruczinski I, Li S, Silverman EK, Cho MH, Lynch DA, Curran-Everett D, Crapo J, Scharpf RB, Parker MM, Hetmanski JB, Beaty TH.

Genet Epidemiol. 2016 Jan;40(1):81-8. doi: 10.1002/gepi.21943. Epub 2015 Dec 7.

17.

NDRG1 links p53 with proliferation-mediated centrosome homeostasis and genome stability.

Croessmann S, Wong HY, Zabransky DJ, Chu D, Mendonca J, Sharma A, Mohseni M, Rosen DM, Scharpf RB, Cidado J, Cochran RL, Parsons HA, Dalton WB, Erlanger B, Button B, Cravero K, Kyker-Snowman K, Beaver JA, Kachhap S, Hurley PJ, Lauring J, Park BH.

Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):11583-8. doi: 10.1073/pnas.1503683112. Epub 2015 Aug 31.

18.

A genome-wide study of inherited deletions identified two regions associated with nonsyndromic isolated oral clefts.

Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I.

Birth Defects Res A Clin Mol Teratol. 2015 Apr;103(4):276-83. doi: 10.1002/bdra.23362. Epub 2015 Mar 16.

19.

Detecting disease variants in case-parent trio studies using the bioconductor software package trio.

Schwender H, Li Q, Neumann C, Taub MA, Younkin SG, Berger P, Scharpf RB, Beaty TH, Ruczinski I.

Genet Epidemiol. 2014 Sep;38(6):516-22. doi: 10.1002/gepi.21836. Epub 2014 Jul 21.

20.

Copy number polymorphisms near SLC2A9 are associated with serum uric acid concentrations.

Scharpf RB, Mireles L, Yang Q, Köttgen A, Ruczinski I, Susztak K, Halper-Stromberg E, Tin A, Cristiano S, Chakravarti A, Boerwinkle E, Fox CS, Coresh J, Linda Kao WH.

BMC Genet. 2014 Jul 9;15:81. doi: 10.1186/1471-2156-15-81.

21.

Characterization of the genomic architecture and mutational spectrum of a small cell prostate carcinoma.

Scott AF, Mohr DW, Ling H, Scharpf RB, Zhang P, Liptak GS.

Genes (Basel). 2014 May 12;5(2):366-84. doi: 10.3390/genes5020366.

22.

A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk.

Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I.

BMC Genet. 2014 Feb 14;15:24. doi: 10.1186/1471-2156-15-24.

23.

Fast detection of de novo copy number variants from SNP arrays for case-parent trios.

Scharpf RB, Beaty TH, Schwender H, Younkin SG, Scott AF, Ruczinski I.

BMC Bioinformatics. 2012 Dec 12;13:330. doi: 10.1186/1471-2105-13-330.

24.

Detectable clonal mosaicism from birth to old age and its relationship to cancer.

Laurie CC, Laurie CA, Rice K, Doheny KF, Zelnick LR, McHugh CP, Ling H, Hetrick KN, Pugh EW, Amos C, Wei Q, Wang LE, Lee JE, Barnes KC, Hansel NN, Mathias R, Daley D, Beaty TH, Scott AF, Ruczinski I, Scharpf RB, Bierut LJ, Hartz SM, Landi MT, Freedman ND, Goldin LR, Ginsburg D, Li J, Desch KC, Strom SS, Blot WJ, Signorello LB, Ingles SA, Chanock SJ, Berndt SI, Le Marchand L, Henderson BE, Monroe KR, Heit JA, de Andrade M, Armasu SM, Regnier C, Lowe WL, Hayes MG, Marazita ML, Feingold E, Murray JC, Melbye M, Feenstra B, Kang JH, Wiggs JL, Jarvik GP, McDavid AN, Seshan VE, Mirel DB, Crenshaw A, Sharopova N, Wise A, Shen J, Crosslin DR, Levine DM, Zheng X, Udren JI, Bennett S, Nelson SC, Gogarten SM, Conomos MP, Heagerty P, Manolio T, Pasquale LR, Haiman CA, Caporaso N, Weir BS.

Nat Genet. 2012 May 6;44(6):642-50. doi: 10.1038/ng.2271.

25.

Using the R Package crlmm for Genotyping and Copy Number Estimation.

Scharpf RB, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I.

J Stat Softw. 2011 May 1;40(12):1-32.

26.

Cross-platform Comparison of Two Pancreatic Cancer Phenotypes.

Scharpf RB, Iacobuzio-Donahue CA, Cope L, Ruczinski I, Garrett-Mayer E, Lakkur S, Campagna D, Parmigiani G.

Cancer Inform. 2010 Nov 1;9:257-64. doi: 10.4137/CIN.S5755.

27.

Tackling the widespread and critical impact of batch effects in high-throughput data.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA.

Nat Rev Genet. 2010 Oct;11(10):733-9. doi: 10.1038/nrg2825. Epub 2010 Sep 14. Review.

28.

A multilevel model to address batch effects in copy number estimation using SNP arrays.

Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA.

Biostatistics. 2011 Jan;12(1):33-50. doi: 10.1093/biostatistics/kxq043. Epub 2010 Jul 12.

29.

R classes and methods for SNP array data.

Scharpf RB, Ruczinski I.

Methods Mol Biol. 2010;593:67-79. doi: 10.1007/978-1-60327-194-3_4.

30.

Rejoinder.

Scharpf RB, Tjelmeland H, Parmigiani G, Nobel AB.

J Am Stat Assoc. 2009 Dec;104(488):1318-1323. No abstract available.

31.

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.

32.

Multiple loci associated with indices of renal function and chronic kidney disease.

Köttgen A, Glazer NL, Dehghan A, Hwang SJ, Katz R, Li M, Yang Q, Gudnason V, Launer LJ, Harris TB, Smith AV, Arking DE, Astor BC, Boerwinkle E, Ehret GB, Ruczinski I, Scharpf RB, Chen YD, de Boer IH, Haritunians T, Lumley T, Sarnak M, Siscovick D, Benjamin EJ, Levy D, Upadhyay A, Aulchenko YS, Hofman A, Rivadeneira F, Uitterlinden AG, van Duijn CM, Chasman DI, Paré G, Ridker PM, Kao WH, Witteman JC, Coresh J, Shlipak MG, Fox CS.

Nat Genet. 2009 Jun;41(6):712-7. doi: 10.1038/ng.377. Epub 2009 May 10.

33.

Genome-wide association study of blood pressure and hypertension.

Levy D, Ehret GB, Rice K, Verwoert GC, Launer LJ, Dehghan A, Glazer NL, Morrison AC, Johnson AD, Aspelund T, Aulchenko Y, Lumley T, Köttgen A, Vasan RS, Rivadeneira F, Eiriksdottir G, Guo X, Arking DE, Mitchell GF, Mattace-Raso FU, Smith AV, Taylor K, Scharpf RB, Hwang SJ, Sijbrands EJ, Bis J, Harris TB, Ganesh SK, O'Donnell CJ, Hofman A, Rotter JI, Coresh J, Benjamin EJ, Uitterlinden AG, Heiss G, Fox CS, Witteman JC, Boerwinkle E, Wang TJ, Gudnason V, Larson MG, Chakravarti A, Psaty BM, van Duijn CM.

Nat Genet. 2009 Jun;41(6):677-87. doi: 10.1038/ng.384. Epub 2009 May 10.

34.

A Bayesian model for cross-study differential gene expression.

Scharpf RB, Tjelmeland H, Parmigiani G, Nobel AB.

J Am Stat Assoc. 2009;104(488):1295-1310.

35.

Likelihood estimation of conjugacy relationships in linear models with applications to high-throughput genomics.

Caffo BS, Liu D, Scharpf RB, Parmigiani G.

Int J Biostat. 2009 May 29;5(1):Article 18. doi: 10.2202/1557-4679.1129.

36.

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.

37.

SNPchip: R classes and methods for SNP array data.

Scharpf RB, Ting JC, Pevsner J, Ruczinski I.

Bioinformatics. 2007 Mar 1;23(5):627-8. Epub 2007 Jan 4.

PMID:
17204461
38.

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
39.

Regulation of platelet granule exocytosis by S-nitrosylation.

Morrell CN, Matsushita K, Chiles K, Scharpf RB, Yamakuchi M, Mason RJ, Bergmeier W, Mankowski JL, Baldwin WM 3rd, Faraday N, Lowenstein CJ.

Proc Natl Acad Sci U S A. 2005 Mar 8;102(10):3782-7. Epub 2005 Feb 28.

40.

Platelet gene polymorphisms and cardiac risk assessment in vascular surgical patients.

Faraday N, Martinez EA, Scharpf RB, Kasch-Semenza L, Dorman T, Pronovost PJ, Perler B, Gerstenblith G, Bray PF, Fleisher LA.

Anesthesiology. 2004 Dec;101(6):1291-7.

PMID:
15564935
41.

Utility of whole blood hemostatometry using the clot signature analyzer for assessment of hemostasis in cardiac surgery.

Faraday N, Guallar E, Sera VA, Bolton ED, Scharpf RB, Cartarius AM, Emery K, Concord J, Kickler TS.

Anesthesiology. 2002 May;96(5):1115-22.

PMID:
11981151
42.

Leukocytes can enhance platelet-mediated aggregation and thromboxane release via interaction of P-selectin glycoprotein ligand 1 with P-selectin.

Faraday N, Scharpf RB, Dodd-o JM, Martinez EA, Rosenfeld BA, Dorman T.

Anesthesiology. 2001 Jan;94(1):145-51.

PMID:
11135734
43.

It's a knockout!

Anagnostopoulos AV, Scharpf RB.

Trends Genet. 1998 Feb;14(2):82. No abstract available.

PMID:
9520603
44.

It's a knockout!

Anagnostopoulos AV, Scharpf RB.

Trends Genet. 1997 Dec;13(12):499-500. No abstract available.

PMID:
9433143

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