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Genomic analysis of benign prostatic hyperplasia implicates cellular re-landscaping in disease pathogenesis.

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.

JCI Insight. 2019 May 16;5. pii: 129749. doi: 10.1172/jci.insight.129749.


Most canine ameloblastomas harbor HRAS mutations, providing a novel large-animal model of RAS-driven cancer.

Saffari PS, Vapniarsky N, Pollack AS, Gong X, Vennam S, Pollack AJ, Verstraete FJM, West RB, Arzi B, Pollack JR.

Oncogenesis. 2019 Feb 11;8(2):11. doi: 10.1038/s41389-019-0119-1.


The HTN3-MSANTD3 Fusion Gene Defines a Subset of Acinic Cell Carcinoma of the Salivary Gland.

Andreasen S, Varma S, Barasch N, Thompson LDR, Miettinen M, Rooper L, Stelow EB, Agander TK, Seethala RR, Chiosea SI, Homøe P, Wessel I, Larsen SR, Erentaite D, Bishop JA, Ulhøi BP, Kiss K, Melchior LC, Pollack JR, West RB.

Am J Surg Pathol. 2019 Apr;43(4):489-496. doi: 10.1097/PAS.0000000000001200.


SWI/SNF aberrations sensitize pancreatic cancer cells to DNA crosslinking agents.

Davidson J, Shen Z, Gong X, Pollack JR.

Oncotarget. 2017 Aug 8;9(11):9608-9617. doi: 10.18632/oncotarget.20033. eCollection 2018 Feb 9.


XPNPEP3 is a novel transcriptional target of canonical Wnt/β-catenin signaling.

Kumar R, Kotapalli V, Naz A, Gowrishankar S, Rao S, Pollack JR, Bashyam MD.

Genes Chromosomes Cancer. 2018 Jun;57(6):304-310. doi: 10.1002/gcc.22531. Epub 2018 Feb 22.


Genes co-amplified with ERBB2 or MET as novel potential cancer-promoting genes in gastric cancer.

Kwon MJ, Kim RN, Song K, Jeon S, Jeong HM, Kim JS, Han J, Hong S, Oh E, Choi JS, An J, Pollack JR, Choi YL, Park CK, Shin YK.

Oncotarget. 2017 Sep 21;8(54):92209-92226. doi: 10.18632/oncotarget.21150. eCollection 2017 Nov 3.


Ca2+/nuclear factor of activated T cells signaling is enriched in early-onset rectal tumors devoid of canonical Wnt activation.

Kumar R, Raman R, Kotapalli V, Gowrishankar S, Pyne S, Pollack JR, Bashyam MD.

J Mol Med (Berl). 2018 Feb;96(2):135-146. doi: 10.1007/s00109-017-1607-4. Epub 2017 Nov 9.


Novel lincRNA SLINKY is a prognostic biomarker in kidney cancer.

Gong X, Siprashvili Z, Eminaga O, Shen Z, Sato Y, Kume H, Homma Y, Ogawa S, Khavari PA, Pollack JR, Brooks JD.

Oncotarget. 2017 Mar 21;8(12):18657-18669. doi: 10.18632/oncotarget.15703.


Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma.

Barasch N, Gong X, Kwei KA, Varma S, Biscocho J, Qu K, Xiao N, Lipsick JS, Pelham RJ, West RB, Pollack JR.

PLoS One. 2017 Feb 17;12(2):e0171265. doi: 10.1371/journal.pone.0171265. eCollection 2017.


BRAF inhibitor therapy of primary ameloblastoma.

Tan S, Pollack JR, Kaplan MJ, Colevas AD, West RB.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2016 Oct;122(4):518-9. doi: 10.1016/j.oooo.2016.05.017. Epub 2016 Jul 5. No abstract available.


Loss of Expression of AZGP1 Is Associated With Worse Clinical Outcomes in a Multi-Institutional Radical Prostatectomy Cohort.

Brooks JD, Wei W, Pollack JR, West RB, Shin JH, Sunwoo JB, Hawley SJ, Auman H, Newcomb LF, Simko J, Hurtado-Coll A, Troyer DA, Carroll PR, Gleave ME, Lin DW, Nelson PS, Thompson IM, True LD, McKenney JK, Feng Z, Fazli L.

Prostate. 2016 Nov;76(15):1409-19. doi: 10.1002/pros.23225. Epub 2016 Jun 21.


BRAF inhibitor treatment of primary BRAF-mutant ameloblastoma with pathologic assessment of response.

Tan S, Pollack JR, Kaplan MJ, Colevas AD, West RB.

Oral Surg Oral Med Oral Pathol Oral Radiol. 2016 Jul;122(1):e5-7. doi: 10.1016/j.oooo.2015.12.016. Epub 2016 Feb 23.


Integrative Genomics Implicates EGFR as a Downstream Mediator in NKX2-1 Amplified Non-Small Cell Lung Cancer.

Clarke N, Biscocho J, Kwei KA, Davidson JM, Sridhar S, Gong X, Pollack JR.

PLoS One. 2015 Nov 10;10(11):e0142061. doi: 10.1371/journal.pone.0142061. eCollection 2015.


Ameloblastoma: a clinical review and trends in management.

McClary AC, West RB, McClary AC, Pollack JR, Fischbein NJ, Holsinger CF, Sunwoo J, Colevas AD, Sirjani D.

Eur Arch Otorhinolaryngol. 2016 Jul;273(7):1649-61. doi: 10.1007/s00405-015-3631-8. Epub 2015 Apr 30. Review.


SIRT7 inactivation reverses metastatic phenotypes in epithelial and mesenchymal tumors.

Malik S, Villanova L, Tanaka S, Aonuma M, Roy N, Berber E, Pollack JR, Michishita-Kioi E, Chua KF.

Sci Rep. 2015 Apr 29;5:9841. doi: 10.1038/srep09841.


Identification of recurrent SMO and BRAF mutations in ameloblastomas.

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.

Nat Genet. 2014 Jul;46(7):722-5. doi: 10.1038/ng.2986. Epub 2014 May 25. Erratum in: Nat Genet. 2015 Jan;47(1):97.


Integrative genomic and functional profiling of the pancreatic cancer genome.

Shain AH, Salari K, Giacomini CP, Pollack JR.

BMC Genomics. 2013 Sep 16;14:624. doi: 10.1186/1471-2164-14-624.


Integrative bioinformatics links HNF1B with clear cell carcinoma and tumor-associated thrombosis.

Cuff J, Salari K, Clarke N, Esheba GE, Forster AD, Huang S, West RB, Higgins JP, Longacre TA, Pollack JR.

PLoS One. 2013 Sep 9;8(9):e74562. doi: 10.1371/journal.pone.0074562. eCollection 2013.


ARID1B, a member of the human SWI/SNF chromatin remodeling complex, exhibits tumour-suppressor activities in pancreatic cancer cell lines.

Khursheed M, Kolla JN, Kotapalli V, Gupta N, Gowrishankar S, Uppin SG, Sastry RA, Koganti S, Sundaram C, Pollack JR, Bashyam MD.

Br J Cancer. 2013 May 28;108(10):2056-62. doi: 10.1038/bjc.2013.200. Epub 2013 May 9.


Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types.

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.

PLoS Genet. 2013 Apr;9(4):e1003464. doi: 10.1371/journal.pgen.1003464. Epub 2013 Apr 25.


The spectrum of SWI/SNF mutations, ubiquitous in human cancers.

Shain AH, Pollack JR.

PLoS One. 2013;8(1):e55119. doi: 10.1371/journal.pone.0055119. Epub 2013 Jan 23.


CDX2 is an amplified lineage-survival oncogene in colorectal cancer.

Salari K, Spulak ME, Cuff J, Forster AD, Giacomini CP, Huang S, Ko ME, Lin AY, van de Rijn M, Pollack JR.

Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):E3196-205. doi: 10.1073/pnas.1206004109. Epub 2012 Oct 29.


Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers.

Brunner AL, Beck AH, Edris B, Sweeney RT, Zhu SX, Li R, Montgomery K, Varma S, Gilks T, Guo X, Foley JW, Witten DM, Giacomini CP, Flynn RA, Pollack JR, Tibshirani R, Chang HY, van de Rijn M, West RB.

Genome Biol. 2012 Aug 28;13(8):R75. doi: 10.1186/gb-2012-13-8-r75.


EGFRvIII gene rearrangement is an early event in glioblastoma tumorigenesis and expression defines a hierarchy modulated by epigenetic mechanisms.

Del Vecchio CA, Giacomini CP, Vogel H, Jensen KC, Florio T, Merlo A, Pollack JR, Wong AJ.

Oncogene. 2013 May 23;32(21):2670-81. doi: 10.1038/onc.2012.280. Epub 2012 Jul 16.


Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer.

Shain AH, Giacomini CP, Matsukuma K, Karikari CA, Bashyam MD, Hidalgo M, Maitra A, Pollack JR.

Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):E252-9. doi: 10.1073/pnas.1114817109. Epub 2012 Jan 10.


Recurrent deletion of CHD1 in prostate cancer with relevance to cell invasiveness.

Huang S, Gulzar ZG, Salari K, Lapointe J, Brooks JD, Pollack JR.

Oncogene. 2012 Sep 13;31(37):4164-70. doi: 10.1038/onc.2011.590. Epub 2011 Dec 19.


SMURF1 amplification promotes invasiveness in pancreatic cancer.

Kwei KA, Shain AH, Bair R, Montgomery K, Karikari CA, van de Rijn M, Hidalgo M, Maitra A, Bashyam MD, Pollack JR.

PLoS One. 2011;6(8):e23924. doi: 10.1371/journal.pone.0023924. Epub 2011 Aug 22.


A fused lasso latent feature model for analyzing multi-sample aCGH data.

Nowak G, Hastie T, Pollack JR, Tibshirani R.

Biostatistics. 2011 Oct;12(4):776-91. doi: 10.1093/biostatistics/kxr012. Epub 2011 Jun 3.


A tri-marker proliferation index predicts biochemical recurrence after surgery for prostate cancer.

Malhotra S, Lapointe J, Salari K, Higgins JP, Ferrari M, Montgomery K, van de Rijn M, Brooks JD, Pollack JR.

PLoS One. 2011;6(5):e20293. doi: 10.1371/journal.pone.0020293. Epub 2011 May 23.


Comparative profiling of primary colorectal carcinomas and liver metastases identifies LEF1 as a prognostic biomarker.

Lin AY, Chua MS, Choi YL, Yeh W, Kim YH, Azzi R, Adams GA, Sainani K, van de Rijn M, So SK, Pollack JR.

PLoS One. 2011 Feb 24;6(2):e16636. doi: 10.1371/journal.pone.0016636.


Steroid receptor coactivator-3 expression in lung cancer and its role in the regulation of cancer cell survival and proliferation.

Cai D, Shames DS, Raso MG, Xie Y, Kim YH, Pollack JR, Girard L, Sullivan JP, Gao B, Peyton M, Nanjundan M, Byers L, Heymach J, Mills G, Gazdar AF, Wistuba I, Kodadek T, Minna JD.

Cancer Res. 2010 Aug 15;70(16):6477-85. doi: 10.1158/0008-5472.CAN-10-0005. Epub 2010 Jul 27.


Development of an orthotopic model of invasive pancreatic cancer in an immunocompetent murine host.

Tseng WW, Winer D, Kenkel JA, Choi O, Shain AH, Pollack JR, French R, Lowy AM, Engleman EG.

Clin Cancer Res. 2010 Jul 15;16(14):3684-95. doi: 10.1158/1078-0432.CCR-09-2384. Epub 2010 Jun 9.


Genomic instability in breast cancer: pathogenesis and clinical implications.

Kwei KA, Kung Y, Salari K, Holcomb IN, Pollack JR.

Mol Oncol. 2010 Jun;4(3):255-66. doi: 10.1016/j.molonc.2010.04.001. Epub 2010 Apr 9. Review.


LYN is a mediator of epithelial-mesenchymal transition and a target of dasatinib in breast cancer.

Choi YL, Bocanegra M, Kwon MJ, Shin YK, Nam SJ, Yang JH, Kao J, Godwin AK, Pollack JR.

Cancer Res. 2010 Mar 15;70(6):2296-306. doi: 10.1158/0008-5472.CAN-09-3141. Epub 2010 Mar 9.


Regularized Multivariate Regression for Identifying Master Predictors with Application to Integrative Genomics Study of Breast Cancer.

Peng J, Zhu J, Bergamaschi A, Han W, Noh DY, Pollack JR, Wang P.

Ann Appl Stat. 2010 Mar;4(1):53-77.


KIT mutations confer a distinct gene expression signature in core binding factor leukaemia.

Lück SC, Russ AC, Du J, Gaidzik V, Schlenk RF, Pollack JR, Döhner K, Döhner H, Bullinger L.

Br J Haematol. 2010 Mar;148(6):925-37. doi: 10.1111/j.1365-2141.2009.08035.x. Epub 2010 Jan 8.


DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data.

Salari K, Tibshirani R, Pollack JR.

Bioinformatics. 2010 Feb 1;26(3):414-6. doi: 10.1093/bioinformatics/btp702. Epub 2009 Dec 22.


Genomic and functional analysis identifies CRKL as an oncogene amplified in lung cancer.

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.

Oncogene. 2010 Mar 11;29(10):1421-30. doi: 10.1038/onc.2009.437. Epub 2009 Dec 7.


Focal amplification and oncogene dependency of GAB2 in breast cancer.

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.

Oncogene. 2010 Feb 4;29(5):774-9. doi: 10.1038/onc.2009.364. Epub 2009 Nov 2.


Molecular profiling of breast cancer cell lines defines relevant tumor models and provides a resource for cancer gene discovery.

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.

PLoS One. 2009 Jul 3;4(7):e6146. doi: 10.1371/journal.pone.0006146.


Integration of diverse microarray data types.

Salari K, Pollack JR.

Methods Mol Biol. 2009;556:205-16. doi: 10.1007/978-1-60327-192-9_15.


Comparative genomic hybridization on spotted oligonucleotide microarrays.

Kim YH, Pollack JR.

Methods Mol Biol. 2009;556:21-32. doi: 10.1007/978-1-60327-192-9_3.


DNA microarray technology. Introduction.

Pollack JR.

Methods Mol Biol. 2009;556:1-6. doi: 10.1007/978-1-60327-192-9_1.


CAMK1D amplification implicated in epithelial-mesenchymal transition in basal-like breast cancer.

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.

Mol Oncol. 2008 Dec;2(4):327-39. doi: 10.1016/j.molonc.2008.09.004. Epub 2008 Oct 2.


MYC stimulates EZH2 expression by repression of its negative regulator miR-26a.

Sander S, Bullinger L, Klapproth K, Fiedler K, Kestler HA, Barth TF, Möller P, Stilgenbauer S, Pollack JR, Wirth T.

Blood. 2008 Nov 15;112(10):4202-12. doi: 10.1182/blood-2008-03-147645. Epub 2008 Aug 19.


Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer.

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.

PLoS Genet. 2008 May 23;4(5):e1000081. doi: 10.1371/journal.pgen.1000081.


Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

Thompson M, Lapointe J, Choi YL, Ong DE, Higgins JP, Brooks JD, Pollack JR.

Prostate. 2008 Aug 1;68(11):1248-56. doi: 10.1002/pros.20792.


An FLT3 gene-expression signature predicts clinical outcome in normal karyotype AML.

Bullinger L, Döhner K, Kranz R, Stirner C, Fröhling S, Scholl C, Kim YH, Schlenk RF, Tibshirani R, Döhner H, Pollack JR.

Blood. 2008 May 1;111(9):4490-5. doi: 10.1182/blood-2007-09-115055. Epub 2008 Feb 28.


hCAP-D3 expression marks a prostate cancer subtype with favorable clinical behavior and androgen signaling signature.

Lapointe 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.

Am J Surg Pathol. 2008 Feb;32(2):205-9. doi: 10.1097/PAS.0b013e318124a865.


Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer.

Kwei KA, Kim YH, Girard L, Kao J, Pacyna-Gengelbach M, Salari K, Lee J, Choi YL, Sato M, Wang P, Hernandez-Boussard T, Gazdar AF, Petersen I, Minna JD, Pollack JR.

Oncogene. 2008 Jun 5;27(25):3635-40. doi: 10.1038/sj.onc.1211012. Epub 2008 Jan 21.

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