Selected Publications:


Bergamaschi A, Kim Y, Kwei K, Choi Y, Bocanegra M, Langerod A, Han W, Noh D-Y, Huntsman D, Jeffrey S, Borresen-Dale A, Pollack J.
CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer. Mol Oncol.  2:327-39.?
Mol Oncol.. 2008 2:327-39.
PubMed Mol Oncol  


Horlings HM, Bergamaschi A, Nordgard SH, Kim YH, Han W, Noh DY, Salari K, Joosse SA, Reyal F, Lingjaerde OC, Kristensen VN, Borresen-Dale AL, Pollack J, van de Vijver MJ.
ESR1 gene amplification in breast cancer: a common phenomenon?
Nat Genet. 2008 Jul;40(7):807-8.
PubMed Nat Genet  


Kwei KA, Bashyam MD, Kao J, Ratheesh R, Reddy EC, Kim YH, Montgomery K, Giacomini CP, Choi YL, Chatterjee S, Karikari CA, Salari K, Wang P, Hernandez-Boussard T, Swarnalata G, van de Rijn M, Maitra A, Pollack JR.
Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer.
PLoS Genet. 2008 May 23;4(5):e1000081.
PubMed PLoS Genet  


Thompson M, Lapointe J, Choi YL, Ong DE, Higgins JP, Brooks JD, Pollack JR..
Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.
Prostate. 2008 Aug 1;68(11):1248-56.
PubMed Prostate  


Bullinger L, Döhner K, Kranz R, Stirner C, Fröhling S, Scholl C, Kim YH, Schlenk RF, Tibshirani R, Döhner H, Pollack JR.
An FLT3 gene-expression signature predicts clinical outcome in normal karyotype AML.
Blood. 2008 May 1;111(9):4490-5.
PubMed Blood  


Kwei KA, Kim YH, Girard L, Kao J, Pacyna-Gengelbach M, Lee J, Choi Y , Sato M, Wang P, Hernandez-Boussard T, Gazdar AF, Petersen I, Minna JD, Pollack JR.
Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer.
Oncogene. 2008 Jun 5;27(25):3635-40.
PubMed Oncogene  


Lapointe J, Li C, Giacomini CLapointe J, Malhotra S, Higgins JP, Bair E, Thompson M, Salari K, Giacomini CP, Ferrari M, Montgomery K, Tibshirani R, van de Rijn M, Brooks JD, Pollack JR.
hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature.
Am J Surg Pathol. 2008 Feb;32(2):205-209..
PubMed Am J Surg Pathol  


Lapointe J, Li C, Giacomini CP, Salari K, Huang S, Wang P, Ferrari M, Hernandez-Boussard T, Brooks JD, Pollack JR.
Genomic profiling reveals alternative genetic pathways of prostate tumorigenesis.
Cancer Res. 2007 Sep 15;67(18):8504-10.
PubMed Cancer Res  


Dumas L, Kim Y, Karimpour-Fard A, Cox M, Hopkins J, Pollack J, Sikela J.
Gene copy number variation spanning 60 million years of human and primate evolution.
Genome Res. 2007 Sep;17(9):1266-77.
PubMed Genome Res  


Pollack JR. Pollack JR.
A perspective on DNA microarrays in pathology research and practice.
Am J Pathol. 2007 Aug;171(2):375-85.
PubMed Am J Pathol  


Bullinger L, Rücker FG, Kurz S, Du J, Scholl C, Sander S, Corbacioglu A, Lottaz C, Krauter J, Fröhling S, Ganser A, Schlenk RF, Döhner K, Pollack JR, Döhner H.
Gene-expression profiling identifies distinct subclasses of core binding factor acute myeloid leukemia.
Blood. 2007 Aug 15;110(4):1291-300.
PubMed Blood  


Lapointe J, Kim YH, Miller MA, Li C, Kaygusuz G, van de Rijn M, Huntsman DG, Brooks JD, Pollack JR.
A variant TMPRSS2 isoform and ERG fusion product in prostate cancer with implications for molecular diagnosis.
Mod Pathol. 2007 Apr;20(4):467-73.
PubMed Mod Pathol


Pollack JR.
Chromosome instability leaves its mark.
Nat Genet. 2006 Sep;38(9):973-4.
PubMed Nat Genet   PDF


Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, Lonning PE, Tibshirani R, Borresen-Dale AL, Pollack JR.
Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer.
Genes Chromosomes Cancer. 2006 Nov;45(11):1033-40.
PubMed Genes Chromosomes Cancer   PDF


Kao J, Pollack JR.
RNA interference-based functional dissection of the 17q12 amplicon in breast cancer reveals contribution of coamplified genes.
Genes Chromosomes Cancer. 2006 Aug;45(8):761-9.
PubMed Genes Chromosomes Cancer   PDF


Kim YH, Girard L, Giacomini CP, Wang P, Hernandez-Boussard T, Tibshirani R, Minna JD, Pollack JR.
Combined microarray analysis of small cell lung cancer reveals altered apoptotic balance and distinct expression signatures of MYC family gene amplification.
Oncogene. 2006 Jan 5;25(1):130-8.
PubMed Oncogene   PDF


Giacomini CP, Leung SY, Chen X, Yuen ST, Kim YH, Bair E, Pollack JR.
A gene-expression signature of genetic instability in colon cancer.
Cancer Res. 2005 Oct 15;65(20):9200-5.
PubMed Cancer Research   PDF


Kim H, Lapointe J, Kaygusuz G, Ong DE, Li C, van de Rijn M, Brooks JD, Pollack JR.
The retinoic acid synthesis gene ALDH1a2 is a candidate tumor suppressor in prostate cancer.
Cancer Res. 2005 Sep 15;65(18):8118-24.
PubMed Cancer Research PDF


Bashyam MD, Bair R, Kim YH, Wang P, Hernandez-Boussard T, Karikari CA, Tibshirani R, Maitra A, Pollack JR.
Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer.
Neoplasia. 2005 Jun;7(6):556-62.
PubMed Neoplasia


Bullinger L, Döhner H, Pollack JR.
Genomics in myeloid leukemias: an array of possibilities.
Rev Clin Exp Hematol. 2005 Jun 1;9(1):E2.
PubMed    


Sander S, Bullinger L, Karlsson A, Giuriato S, Hernandez-Boussard T, Felsher DW, Pollack JR.
Comparative genomic hybridization on mouse cDNA microarrays and its application to a murine lymphoma model.
Oncogene. 2005 Sep 8;24(40):6101-7.
PubMed Oncogene   PDF


Shyamsundar R, Kim YH, Higgins JP, Montgomery K, Jorden M, Sethuraman A, van de Rijn M, Botstein D, Brown PO, Pollack JR.
A DNA microarray survey of gene expression in normal human tissues.
Genome Biol. 2005;6(3):R22.
PubMed Genome Biol Web Supplement PDF


Wang P, Kim Y, Pollack J, Narasimhan B, Tibshirani R.
A method for calling gains and losses in array CGH data.
Biostatistics. 2005 Jan;6(1):45-58.
PubMed     PDF


Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, Karimpour-Fard A, Glueck D, McGavran L, Berry R, Pollack J, Sikela JM.
Lineage-specific gene duplication and loss in human and great ape evolution.
PLoS Biol. 2004 Jul;2(7):E207.
PubMed PLoS Biol   PDF


Bullinger L, Döhner K, Bair E, Fröhling S, Schlenk RF, Tibshirani R, Dohner H, Pollack JR.
Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia.
N Engl J Med. 2004 Apr 15;350(16):1605-16.
PubMed NEJM   PDF


Lapointe J, Li C, Higgins JP, van de Rijn M, Bair E, Montgomery K, Ferrari M, Egevad L, Rayford W, Bergerheim U, Ekman P, DeMarzo AM, Tibshirani R, Botstein D, Brown PO, Brooks JD, Pollack JR.
Gene expression profiling identifies clinically relevant subtypes of prostate cancer.
Proc Natl Acad Sci USA. 2004 Jan 20; 101(3): 811-16.
PubMed PNAS Web Supplement PDF


Pollack JR.
Parallel analysis of gene copy number and expression using cDNA microarrays.
Methods Mol Biol. 2003;224:89-97.
PubMed Methods Mol Biol


Pollack JR, Iyer VR.
Characterizing the physical genome.
Nat Genet. 2002 Dec; 32(Suppl 2):515-21.
PubMed Nature Genetics PDF


Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO.
Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.
Proc Natl Acad Sci USA. 2002 Oct 1; 99(20): 12963-8.
PubMed PNAS Web Supplement PDF


Pollack JR.
Comparative genomic hybridization using cDNA microarrays.
in DNA Microarrays: A Molecular Cloning Manual, ed. D. Bowtell and J. Sambrook, Cold Spring Harbor Press. 2002, Section 6.1:363-9.
  CSHLP
 


Pollack JR, van de Rijn M, Botstein D.
Challenges in developing a molecular characterization of cancer.
Semin Oncol. 2002 Jun; 29(3): 280-5.
PubMed Semin Oncol


Perou CM, Sorlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D.
Molecular portraits of human breast tumours.
Nature. 2000 Aug 17; 406(6797): 747-52.
PubMed Nature Web Supplement PDF


Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO.
Genome-wide analysis of DNA copy-number changes using cDNA microarrays.
Nat Genet. 1999 Sep; 23(1): 41-6.
PubMed Nature Genetics Web Supplement PDF