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Items: 1 to 50 of 328

1.

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.

Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG, Ylstra B.

Genome Res. 2014 Dec;24(12):2022-32. doi: 10.1101/gr.175141.114. Epub 2014 Sep 18.

2.

Genomic profiling of isolated circulating tumor cells from metastatic breast cancer patients.

Magbanua MJ, Sosa EV, Roy R, Eisenbud LE, Scott JH, Olshen A, Pinkel D, Rugo HS, Park JW.

Cancer Res. 2013 Jan 1;73(1):30-40. doi: 10.1158/0008-5472.CAN-11-3017. Epub 2012 Nov 7.

3.

Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer.

Magbanua MJ, Sosa EV, Scott JH, Simko J, Collins C, Pinkel D, Ryan CJ, Park JW.

BMC Cancer. 2012 Feb 28;12:78. doi: 10.1186/1471-2407-12-78.

4.

Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis.

Bhattacharya A, Roy R, Snijders AM, Hamilton G, Paquette J, Tokuyasu T, Bengtsson H, Jordan RC, Olshen AB, Pinkel D, Schmidt BL, Albertson DG.

Clin Cancer Res. 2011 Nov 15;17(22):7024-34. doi: 10.1158/1078-0432.CCR-11-1944. Epub 2011 Nov 8.

5.

Response to letter by Pulsipher et al.

Pinkel D.

Leukemia. 2010 Aug;24(8):1532-3. doi: 10.1038/leu.2010.125. Epub 2010 Jun 10. No abstract available.

PMID:
20535154
6.

'Allogeneic marrow transplantation in children with acute leukemia: a practice whose time has gone': twenty years later.

Pinkel D.

Leukemia. 2009 Dec;23(12):2189-96. doi: 10.1038/leu.2009.132. Review. No abstract available.

PMID:
20016481
7.

Quantum dots-based reverse phase protein microarray.

Shingyoji M, Gerion D, Pinkel D, Gray JW, Chen F.

Talanta. 2005 Sep 15;67(3):472-8. doi: 10.1016/j.talanta.2005.06.064. Epub 2005 Aug 10.

PMID:
18970191
8.

High-efficiency microarray printer using fused-silica capillary tube printing pins.

Clark SM, Hamilton GE, Nordmeyer RA, Uber D, Cornell EW, Brown N, Segraves R, Davis R, Albertson DG, Pinkel D.

Anal Chem. 2008 Oct 1;80(19):7639-42. doi: 10.1021/ac8010395. Epub 2008 Sep 3.

PMID:
18763810
9.

Expanding the genetic spectrum of pigmentation.

Bastian BC, Pinkel D.

Pigment Cell Melanoma Res. 2008 Oct;21(5):507-8. doi: 10.1111/j.1755-148X.2008.00490.x. Epub 2007 Aug 20. No abstract available.

PMID:
18721233
10.

Improving melanoma classification by integrating genetic and morphologic features.

Viros A, Fridlyand J, Bauer J, Lasithiotakis K, Garbe C, Pinkel D, Bastian BC.

PLoS Med. 2008 Jun 3;5(6):e120. doi: 10.1371/journal.pmed.0050120.

11.

Comparative genomic hybridization.

DeVries S, Gray JW, Pinkel D, Waldman FM, Sudar D.

Curr Protoc Hum Genet. 2001 May;Chapter 4:Unit4.6. doi: 10.1002/0471142905.hg0406s06.

PMID:
18428281
12.

Distribution and significance of occult intraepidermal tumor cells surrounding primary melanoma.

North JP, Kageshita T, Pinkel D, LeBoit PE, Bastian BC.

J Invest Dermatol. 2008 Aug;128(8):2024-30. doi: 10.1038/jid.2008.41. Epub 2008 Mar 6.

13.

Roadmap for new opportunities in melanoma research.

Herlyn M, Halaban R, Ronai Z, Schuchter L, Berwick M, Pinkel D.

Semin Oncol. 2007 Dec;34(6):566-76.

PMID:
18083380
14.

Analytical description of mutational effects in competing asexual populations.

Pinkel D.

Genetics. 2007 Dec;177(4):2135-49. Epub 2007 Oct 18.

15.

Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy.

Mefford HC, Clauin S, Sharp AJ, Moller RS, Ullmann R, Kapur R, Pinkel D, Cooper GM, Ventura M, Ropers HH, Tommerup N, Eichler EE, Bellanne-Chantelot C.

Am J Hum Genet. 2007 Nov;81(5):1057-69. Epub 2007 Sep 26.

16.

Absence of PDGFRA mutations in primary melanoma.

Curtin JA, Pinkel D, Bastian BC.

J Invest Dermatol. 2008 Feb;128(2):488-9. Epub 2007 Aug 30. No abstract available.

17.

Novel risk stratification of patients with neuroblastoma by genomic signature, which is independent of molecular signature.

Tomioka N, Oba S, Ohira M, Misra A, Fridlyand J, Ishii S, Nakamura Y, Isogai E, Hirata T, Yoshida Y, Todo S, Kaneko Y, Albertson DG, Pinkel D, Feuerstein BG, Nakagawara A.

Oncogene. 2008 Jan 17;27(4):441-9. Epub 2007 Jul 16.

PMID:
17637744
18.

Genome position and gene amplification.

Gajduskova P, Snijders AM, Kwek S, Roydasgupta R, Fridlyand J, Tokuyasu T, Pinkel D, Albertson DG.

Genome Biol. 2007;8(6):R120.

19.

Detection of single clone deletions using array CGH: identification of submicroscopic deletions in the 22q11.2 deletion syndrome as a model system.

Tokuyasu TA, Cotter PD, Segraves R, Harris J, Elder ME, Gonzales M, Pinkel D, Albertson DG, Rauen KA.

Am J Med Genet A. 2007 May 1;143A(9):925-32.

PMID:
17394204
20.

Deletion of chromosome 11q predicts response to anthracycline-based chemotherapy in early breast cancer.

Climent J, Dimitrow P, Fridlyand J, Palacios J, Siebert R, Albertson DG, Gray JW, Pinkel D, Lluch A, Martinez-Climent JA.

Cancer Res. 2007 Jan 15;67(2):818-26.

21.

Genomic and transcriptional aberrations linked to breast cancer pathophysiologies.

Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW.

Cancer Cell. 2006 Dec;10(6):529-41.

22.

A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.

Neve RM, Chin K, Fridlyand J, Yeh J, Baehner FL, Fevr T, Clark L, Bayani N, Coppe JP, Tong F, Speed T, Spellman PT, DeVries S, Lapuk A, Wang NJ, Kuo WL, Stilwell JL, Pinkel D, Albertson DG, Waldman FM, McCormick F, Dickson RB, Johnson MD, Lippman M, Ethier S, Gazdar A, Gray JW.

Cancer Cell. 2006 Dec;10(6):515-27.

23.

Regional copy number-independent deregulation of transcription in cancer.

Stransky N, Vallot C, Reyal F, Bernard-Pierrot I, de Medina SG, Segraves R, de Rycke Y, Elvin P, Cassidy A, Spraggon C, Graham A, Southgate J, Asselain B, Allory Y, Abbou CC, Albertson DG, Thiery JP, Chopin DK, Pinkel D, Radvanyi F.

Nat Genet. 2006 Dec;38(12):1386-96. Epub 2006 Nov 12. Erratum in: Nat Genet. 2008 Mar;40(3):373.

PMID:
17099711
24.

Chromosomal aberrations in angioimmunoblastic T-cell lymphoma and peripheral T-cell lymphoma unspecified: A matrix-based CGH approach.

Thorns C, Bastian B, Pinkel D, Roydasgupta R, Fridlyand J, Merz H, Krokowski M, Bernd HW, Feller AC.

Genes Chromosomes Cancer. 2007 Jan;46(1):37-44.

PMID:
17044049
25.

Homozygous deletions localize novel tumor suppressor genes in B-cell lymphomas.

Mestre-Escorihuela C, Rubio-Moscardo F, Richter JA, Siebert R, Climent J, Fresquet V, Beltran E, Agirre X, Marugan I, Marín M, Rosenwald A, Sugimoto KJ, Wheat LM, Karran EL, García JF, Sanchez L, Prosper F, Staudt LM, Pinkel D, Dyer MJ, Martinez-Climent JA.

Blood. 2007 Jan 1;109(1):271-80. Epub 2006 Sep 7.

26.

Somatic activation of KIT in distinct subtypes of melanoma.

Curtin JA, Busam K, Pinkel D, Bastian BC.

J Clin Oncol. 2006 Sep 10;24(26):4340-6. Epub 2006 Aug 14.

PMID:
16908931
27.

Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome.

Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA, Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA, Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, Eis PS, Schwartz S, Knight SJ, Eichler EE.

Nat Genet. 2006 Sep;38(9):1038-42. Epub 2006 Aug 13.

PMID:
16906162
28.

Congenital melanocytic nevi frequently harbor NRAS mutations but no BRAF mutations.

Bauer J, Curtin JA, Pinkel D, Bastian BC.

J Invest Dermatol. 2007 Jan;127(1):179-82. Epub 2006 Aug 3.

29.

Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genome.

Locke DP, Sharp AJ, McCarroll SA, McGrath SD, Newman TL, Cheng Z, Schwartz S, Albertson DG, Pinkel D, Altshuler DM, Eichler EE.

Am J Hum Genet. 2006 Aug;79(2):275-90. Epub 2006 Jun 15.

30.

MC1R germline variants confer risk for BRAF-mutant melanoma.

Landi MT, Bauer J, Pfeiffer RM, Elder DE, Hulley B, Minghetti P, Calista D, Kanetsky PA, Pinkel D, Bastian BC.

Science. 2006 Jul 28;313(5786):521-2. Epub 2006 Jun 29.

31.

A large field CCD system for quantitative imaging of microarrays.

Hamilton G, Brown N, Oseroff V, Huey B, Segraves R, Sudar D, Kumler J, Albertson D, Pinkel D.

Nucleic Acids Res. 2006 May 2;34(8):e58.

32.

Breast tumor copy number aberration phenotypes and genomic instability.

Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG.

BMC Cancer. 2006 Apr 18;6:96.

33.

PI3-kinase subunits are infrequent somatic targets in melanoma.

Curtin JA, Stark MS, Pinkel D, Hayward NK, Bastian BC.

J Invest Dermatol. 2006 Jul;126(7):1660-3. Epub 2006 Apr 13. No abstract available.

34.

Genomic analysis of tumors by array comparative genomic hybridization: more is better.

Albertson DG, Snijders AM, Fridlyand J, Jordan R, Pinkel D, Schmidt BL.

Cancer Res. 2006 Apr 1;66(7):3955-6; author reply 3956. No abstract available.

35.

Clinical cytogenetics and molecular cytogenetics.

Li M, Pinkel D.

J Zhejiang Univ Sci B. 2006 Feb;7(2):162-3.

36.

Duplication of distal 20q: clinical, cytogenetic and array CGH. Characterization of a new case.

Iglesias A, Rauen KA, Albertson DG, Pinkel D, Cotter PD.

Clin Dysmorphol. 2006 Jan;15(1):19-23.

PMID:
16317302
37.

Distinct sets of genetic alterations in melanoma.

Curtin JA, Fridlyand J, Kageshita T, Patel HN, Busam KJ, Kutzner H, Cho KH, Aiba S, Bröcker EB, LeBoit PE, Pinkel D, Bastian BC.

N Engl J Med. 2005 Nov 17;353(20):2135-47.

38.

Genomic microarray analysis identifies candidate loci in patients with corpus callosum anomalies.

Sherr EH, Owen R, Albertson DG, Pinkel D, Cotter PD, Slavotinek AM, Hetts SW, Jeremy RJ, Schilmoeller G, Schilmoeller K, Wakahiro M, Barkovich AJ.

Neurology. 2005 Nov 8;65(9):1496-8.

PMID:
16275846
39.

Ring chromosome 15: characterization by array CGH.

Glass IA, Rauen KA, Chen E, Parkes J, Alberston DG, Pinkel D, Cotter PD.

Hum Genet. 2006 Jan;118(5):611-7. Epub 2005 Nov 3.

PMID:
16267671
40.

Interstitial deletion of chromosome 12q: genotype-phenotype correlation of two patients utilizing array comparative genomic hybridization.

Klein OD, Cotter PD, Schmidt AM, Bick DP, Tidyman WE, Albertson DG, Pinkel D, Rauen KA.

Am J Med Genet A. 2005 Nov 1;138(4):349-54.

PMID:
16200635
41.

Fryns syndrome phenotype caused by chromosome microdeletions at 15q26.2 and 8p23.1.

Slavotinek A, Lee SS, Davis R, Shrit A, Leppig KA, Rhim J, Jasnosz K, Albertson D, Pinkel D.

J Med Genet. 2005 Sep;42(9):730-6.

42.

Comparative genomic hybridization.

Pinkel D, Albertson DG.

Annu Rev Genomics Hum Genet. 2005;6:331-54. Review.

PMID:
16124865
43.

Characterization of 8p21.3 chromosomal deletions in B-cell lymphoma: TRAIL-R1 and TRAIL-R2 as candidate dosage-dependent tumor suppressor genes.

Rubio-Moscardo F, Blesa D, Mestre C, Siebert R, Balasas T, Benito A, Rosenwald A, Climent J, Martinez JI, Schilhabel M, Karran EL, Gesk S, Esteller M, deLeeuw R, Staudt LM, Fernandez-Luna JL, Pinkel D, Dyer MJ, Martinez-Climent JA.

Blood. 2005 Nov 1;106(9):3214-22. Epub 2005 Jul 28.

44.

Array comparative genomic hybridization and its applications in cancer.

Pinkel D, Albertson DG.

Nat Genet. 2005 Jun;37 Suppl:S11-7. Review.

PMID:
15920524
45.

Segmental duplications and copy-number variation in the human genome.

Sharp AJ, Locke DP, McGrath SD, Cheng Z, Bailey JA, Vallente RU, Pertz LM, Clark RA, Schwartz S, Segraves R, Oseroff VV, Albertson DG, Pinkel D, Eichler EE.

Am J Hum Genet. 2005 Jul;77(1):78-88. Epub 2005 May 25.

46.

Fine-scale structural variation of the human genome.

Tuzun E, Sharp AJ, Bailey JA, Kaul R, Morrison VA, Pertz LM, Haugen E, Hayden H, Albertson D, Pinkel D, Olson MV, Eichler EE.

Nat Genet. 2005 Jul;37(7):727-32. Epub 2005 May 15.

PMID:
15895083
47.

Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3.

Ching TT, Maunakea AK, Jun P, Hong C, Zardo G, Pinkel D, Albertson DG, Fridlyand J, Mao JH, Shchors K, Weiss WA, Costello JF.

Nat Genet. 2005 Jun;37(6):645-51. Epub 2005 May 15.

PMID:
15895082
48.

Xq chromosome duplication in males: clinical, cytogenetic and array CGH characterization of a new case and review.

Cheng SF, Rauen KA, Pinkel D, Albertson DG, Cotter PD.

Am J Med Genet A. 2005 Jun 15;135(3):308-13. Review.

PMID:
15887264
49.

Array comparative genomic hybridization identifies genetic subgroups in grade 4 human astrocytoma.

Misra A, Pellarin M, Nigro J, Smirnov I, Moore D, Lamborn KR, Pinkel D, Albertson DG, Feuerstein BG.

Clin Cancer Res. 2005 Apr 15;11(8):2907-18.

50.

Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma.

Snijders AM, Schmidt BL, Fridlyand J, Dekker N, Pinkel D, Jordan RC, Albertson DG.

Oncogene. 2005 Jun 16;24(26):4232-42.

PMID:
15824737

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