Selected Publications

Pollack AJ, Gong X, Pollack JR.
A common phytoene synthase mutation underlies white petal varieties of the California poppy.
Sci Rep. 2019 Aug 12;9(1):11615.

Middleton LW, Shen Z, Varma S, Pollack AS, Gong X, Zhu S, Zhu C, Foley JW, Vennam S, Sweeney RT, Tu K, Biscocho J, Eminaga O, Nolley R, Tibshirani R, Brooks JD*, West RB*, Pollack JR*.
Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis.
JCI Insight. 2019 May 16;5. pii: 129749.

Saffari PS, Vapniarsky N*, Pollack AS, Gong X, Vennam S, Pollack AJ, Verstraete FJM, West RB*, Arzi B, Pollack JR*.
Most canine ameloblastomas harbor HRAS mutations, providing a novel large-animal model of RAS-driven cancer.
Oncogenesis. 2019 Feb 11;8(2):11.

Davidson J, Shen Z, Gong X, Pollack JR.
SWI/SNF aberrations sensitize pancreatic cancer cells to DNA crosslinking agents.
Oncotarget. 2017 Aug 8;9(11):9608-9617.

Gong X, Shen Z, Sato Y, Kume H, Homma Y, Ogawa S, Pollack JR*, Brooks JD*.
The novel lincRNA SLINKY is a prognostic biomarker in clear cell renal cell carcinoma.
Oncotarget. 2017 Mar 21;8(12):18657-18669

Barasch N, Gong X, Kwei KA, Varma S, Biscocho J, Qu K, Xiao N, Lipsick JS, Pelham RJ, West RB*, Pollack JR*.
Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma.
PLoS One. 2017 Feb 17;12(2):e0171265.

Clarke N, Biscocho J, Kwei KA, Davidson JM, Sridhar S, Gong X, Pollack JR.
Integrative genomics implicates EGFR as a downstream mediator in NKX2-1 amplified non-small cell lung cancer.
PLoS One. 2015 Nov 10;10(11):e0142061

Sweeney RT#, McClary AC#, Myers BR#, Biscocho J#, Neahring L, Kwei KA, Qu K, Gong X, Ng T, Jones CD, Varma S, Odegaard JI, Sugiyama T, Koyota S, Rubin BP, Troxell ML, Pelham RJ, Zehnder JL, Beachy PA*, Pollack JR*, West RB*.
Identification of recurrent SMO and BRAF mutations in ameloblastoma
Nat Genet. 2014 Jul;46(7):722-5.

Shain AH, Salari K, Giacomini CP, Pollack JR.
Integrative genomic and functional profiling of the pancreatic cancer genome.
BMC Genomics. 2013 Sep 16;14(1):624.

Cuff J, Salari K, Clarke N, Esheba GE, Forster AD, Huang S, West RB, Higgins JP, Longacre TA, Pollack JR.
Integrative bioinformatics links HNF1B with clear cell carcinoma and tumor-associated thrombosis.
PLoS One. 2013 Sep 9;8(9):e74562.

Giacomini CP, Sun S, Varma S, Shain AH, Giacomini MM, Balagtas J, Sweeney RT, Lai E, Del Vecchio CA, Forster AD, Clarke N, Montgomery KD, Zhu S, Wong AJ, van de Rijn M, West RB, Pollack JR.
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types.
PLoS Genet. 2013 Apr;9(4):e1003464.

Shain AH, Pollack JR.
The spectrum of SWI/SNF mutations, ubiquitous in human cancers.
PLoS One. 2013;8(1):e55119.

Salari K, Spulak ME, Cuff J, Forster AD, Giacomini CP, Huang S, Ko M, Lin AY, van de Rijn M, Pollack JR.
CDX2 is an amplified lineage-survival oncogene in colorectal cancer.
Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):E3196-205.

Shain AH, Giacomini CP, Matsukuma K, Karikari CA, Bashyam MD, Hidalgo M, Maitra A, Pollack JR.
Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer.
Proc Natl Acad Sci USA. 2012 Jan 31;109(5):E252-9.

Huang S, Gulzar ZG, Salari K, Lapointe J, Brooks JD, Pollack JR.
Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness.
Oncogene. 2012 Sep 13;31(37):4164-70.

Kwei KA, Shain AH, Bair R, Montgomery K, Karikari CA, van de Rijn M, Hidalgo M, Maitra A, Bashyam MD, Pollack JR.
SMURF1 amplification promotes invasiveness in pancreatic cancer.
PLoS One. 2011;6(8):e23924..

Malhotra S#, Lapointe J#, Salari K, Higgins JP, Ferrari M, Montgomery K, van de Rijn M, Brooks JD*, Pollack JR*.
A tri-marker proliferation index predicts biochemical recurrence after surgery for prostate cancers.
PLoS One. 2011;6(5):e20293.

Lin AY, Chua MS, Choi YL, Yeh W, Kim YH, Azzi R, Adams GA, Sainani K, van de Rijn M, So SK, Pollack JR.
Comparative profiling of primary colorectal carcinomas and liver metastases identifies LEF1 as a prognostic biomarker.
PLoS One. 2011 Feb 24;6(2):e16636.

Kwei KA, Kung Y, Salari K, Holcomb IN, Pollack JR.
Genomic instability in breast cancer: Pathogenesis and clinical implications.
Mol Oncol. 2010 Jun;4(3):255-66.

Choi YL#, Bocanegra M#, Kwon MJ, Shin YK, Nam SJ, Yang JH, Kao J, Godwin AK, Pollack JR.
LYN is a mediator of epithelial-mesenchymal transition and a target of dasatinib in breast cancer.
Cancer Res. 2010 Mar 15;70(6):2296-306.

Salari K, Tibshirani R, Pollack JR.
DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. 
Bioinformatics. 2010 Feb 1;26(3):414-6.

Kim YH, Kwei KA, Girard L, Salari K, Kao J, Pacyna-Gengelbach M, Wang P, Hernandez-Boussard T, Gazdar AF, Petersen I, Minna JD, Pollack JR.
Genomic and functional analysis identifies CRKL as an oncogene amplified in lung cancer. 
Oncogene. 2010 Mar 11;29(10):1421-30.

Bocanegra M, Bergamaschi A, Kim YH, Miller MA, Rajput AB, Kao J, Langerød A, Han W, Noh DY, Jeffrey SS, Huntsman DG, Børresen-Dale AL, Pollack JR.
Focal amplification and oncogene dependency of GAB2 in breast cancer.
Oncogene. 2010 Feb 4;29(5):774-9.

Kao J#, Salari K#, Bocanegra M, Choi YL, Girard L, Gandhi J, Kwei KA, Hernandez-Boussard T, Wang P, Gazdar AF, Minna JD, Pollack JR.
Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery. 
PLoS One. 2009 Jul 3;4(7):e6146.

Bergamaschi A, Kim YH, Kwei KA, La Choi Y, Bocanegra M, Langerød A, Han W, Noh DY, Huntsman DG, Jeffrey SS, Børresen-Dale AL, Pollack JR.
CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer. 
Mol Oncol. 2008 Dec;2(4):327-39.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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 USA2004 Jan 20; 101(3): 811-16.

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

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

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.

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.

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

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.

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.