Publications

For our latest publications, see our Google Scholar Page

  • Patel PG, Selvarajah S, Guérard KP, Bartlett JMS, Lapointe J, Berman DM, Okello JBA, Park PC (2017) Reliability and performance of commercial RNA and DNA extraction kits for FFPE tissue cores. PLoS ONE, 12(6): e0179732. 10.1371/journal.pone.0179732.  Online
  • Patel PG, Selvarajah S, Boursalie S, How N, Ejdelman J, Guérard KP, Bartlett JMS, Lapointe J, Park PC, Okello JBA, Berman DM (2016) Preparation of Formalin-Fixed Paraffin-Embedded Tissue Cores for Optimized Extraction of RNA and DNA. J Vis Exp, 114: 54299. doi:10.3791/54299.  Online
  • Carvalho FLF, Marchionni L, Gupta A, Kummangal BA, Schaeffer EM, Ross AE, Berman DM (2015), HES6 promotes prostate cancer aggressiveness independently of Notch signalling. J Cell Mol Med, 19: 1624–1636. doi: 10.1111/jcmm.12537. Online
  • Blume-Jensen P, Berman DM, Rimm DL, Shipitsin M, Putzi M, Nifong TP, Small C, Choudhury S, Capela T, Coupal L, Ernst C, Hurley A, Kaprelyants A, Chang H, Giladi E, Nardone J, Dunyak J, Loda M, Klein EA, Magi-Galluzzi C, Latour M, Epstein JI, Kantoff P, Saad F (2015) Development and Clinical Validation of an In Situ Biopsy-Based Multimarker Assay for Risk Stratification in Prostate Cancer. Clin Cancer Res, 21: 2591-2600.
  • Berman DM, Kawashima A, Peng Y, Mackillop WJ, Siemens DR, Booth CM (2014) Reporting trends and prognostic significance of lymphovascular invasion in muscle-invasive urothelial carcinoma: A population-based study. Int J Urol, 22: 163170. doi: 10.1111/iju.12611. Online
  • Wang DH, Tiwari A, Kim ME, Clemons NJ, Regmi NL, Hodges WA, Berman DM, Montgomery EA, Watkins DN, Zhang X, Zhang Q, Jie C, Spechler SJ, Souza RF (2014) Hedgehog signaling regulates FOXA2 in esophageal embryogenesis and Barrett’s metaplasia. J Clin Invest, 124(9): 3767-80. doi: 10.1172/JCI66603. Online
  • Booth CM, Siemens DR, Wei X, Peng Y, Berman DM, Mackillop WJ (2014) Pathologic Factors Associated with Survival Benefit From Adjuvant Chemotherapy: A Population-Based Study of Bladder Cancer. BJU Int, 116(3): 373-81. doi: 10.1111/bju.12913. Online
  • Bellmunt J, Selvarajah S, Rodig S, Salido M, de Muga S, Costa I, Bellosillo B, Werner L, Mullane S, Fay AP, O’Brien R, Barretina J, Minoche AE, Signoretti S, Montagut C, Himmelbauer H, Berman DM, Kantoff P, Choueiri TK, Rosenberg JE (2014) Identification of ALK gene alterations in urothelial carcinoma. PLoS ONE 9(8): e103325. doi: 10.1371/journal.pone.0103325. Online
  • Shipitsin M, Small C, Giladi E, Siddiqui S, Choudhury S, Hussain S, Huang YE, Chang H, Rimm DL,Berman DM, Nifong TP, Blume-Jensen P (2014) Automated quantitative multiplex immunofluorescence in situ imaging identifies phospho-S6 and phospho-PRAS40 as predictive protein biomarkers for prostate cancer lethality. Proteome Sci, 12: 40. doi: 10.1186/1477-5956-12-40. Online
  • Shipitsin M, Small C, Choudhury S, Giladi E, Friedlander S, Nardone J, Hussain S, Hurley AD, Ernst C, Huang YE, Chang H, Nifong TP, Rimm DL, Dunyak J, Loda M, Berman DM, Blume-Jensen P (2014) Identification of proteomic biomarkers predicting prostate cancer aggressiveness and lethality despite biopsy-sampling error. Br J Cancer, 111: 1201-1212. doi:10.1038/bjc.2014.396. Online
  • Lotan TL, Carvalho FL, Peskoe SB, Hicks JL, Good J, Fedor HL, Humphreys E, Han M, Platz EA, Squire JA, De Marzo AM, Berman DM (2014) PTEN loss is associated with upgrading of prostate cancer from biopsy to radical prostatectomy. Mod Pathol, 28(1): 128-137. doi: 10.1038/modpathol.2014.85. Online
  • Carvalho FLF, Simons BW, Eberhart CG and Berman DM (2014), Notch signaling in prostate cancer: A moving target. Prostate, 74: 933–945. doi: 10.1002/pros.22811. Online
  • Booth CM, Siemens DR, Li G, Peng Y, Tannock IF, Kong W, Berman DM, and Mackillop, WJ (2014) Peri-Operative Chemotherapy for Muscle-Invasive Bladder Cancer: A Population-Based Outcomes Study. Cancer, 120(11): 1630-8. doi: 10.1002/cncr.28510. Online.
  • Riester M, Werner L, Bellmunt J, Selvarajah S, Guancial E, Weir B, Stack E, Park R, O’Brien R, Schultz F, Choueiri T, Signoretti S, Lloreta J, Marchionni L, Gallardo E, Rojo F, Garcia D, Chekaluk Y, Kwiatkowski K, Bochner B, Hahn W, Ligon A, Barletta J, Loda M, Berman DM, Kantoff P, Michor F, and Rosenberg JE (2014) Integrative analysis of 1q23.3 copy number gain in metastatic urothelial carcinoma. Clin Cancer Res, 20(70): 1873-83. doi: 10.1158/1078-0432.CCR-13-0759. Online.
  • Berman DM and Epstein JI (2014) When is prostate cancer really cancer? Urol Clin North Am, 41(2): 339-46. doi:10.1016/j.ucl.2014.01.006. Online.
  • Guancial EA, Bellmunt J, Roseberg JE, and Berman DM (2014) The Evolving Understanding of MicroRNA in Bladder Cancer. Urol Oncol , 32(1): 41.e31–40. Online
  • Toivanen R, Frydenberg M, Murphy D, Pedersen J, Ryan R, Pook D, Berman DM, Australian Prostate Cancer BioResource, Taylor RA, and Risbridger GP (2013) A pre-clinical xenograft model identifies castration-tolerant cancer repopulating cells in localized prostate tumors. Sci Transl Med, 5(187): 187ra12. doi:10.1126/scitranslmed.3005688. Online
  • Carvalho LF, Simons BW, Antonarakis ES, Rasheed Z, Douglas N, Villegas D, Matsui W, and Berman DM (2013) Tumorigenic potential of circulating prostate tumor cells. Oncotarget, 4: 413-21. PubMed
  • Simons BW, Hurley PJ, Huang Z, Ross AE, Miller R, Marchionni L, Berman DM, Schaeffer EM (2012) Wnt signaling though beta-catenin is required for prostate lineage specification. Dev Biol, 371: 246-55. PubMed
  • Hurley PJ, Marchionni L, Simons BW, Ross AE, Peskoe, SB, Miller, RM, Erho NG, Vergara IS, Ghadessi M, Huang Z, Gurel B, Park B, Davicioni E, Jenkins RB, Platz EA, Berman DM, and Schaeffer EM (2012) Secreted protein, acidic and rich in cysteine-like 1 (SPARCL1) is down regulated in aggressive prostate cancers and is prognostic for poor clinical outcome. Proc Natl Acad Sci U S A, 109: 14977-82. PubMed
  • Huang Z, Hurley PJ, Simons BW, Marchionni L, Berman DM, Ross AE, Schaeffer EM (2012) Sox9 is required for prostate development and prostate cancer initiation. Oncotarget, 3(6): 651-63. PubMed
  • Berman DM, Bosenberg M, Orwant RL, Thurberg BL, Draetta G, Fletcher CD, and Loda M (2012) Investigative Pathology: Leading the Post-Genomic Revolution. Lab Invest, 92: 4-8. PubMed
  • Ghosh S, Lau H, Simons BW, Powell JD, Meyers DJ, De Marzo AM, Berman DM, Lotan TL (2011) PI3K/mTOR signaling regulates prostatic branching morphogenesis. Dev Biol, 360: 329-42. PubMed
  • Toivanen R, Berman DM, Wang H, Pedersen J, Frydenberg P, Meeker AK, Ellem SJ, Risbridger GP and Taylor RA (2011) A bioassay to identify primary human prostate cancer repopulating cells. Stem Cells, 29: 1310. PubMed
  • Ling S, Chang X, Schultz L, Lee TK, Chaux A, Marchionni L, Netto GJ, Sidransky D, and Berman DM (2011). An EGFR-ERK1/2-Sox9 signaling cascade links urothelial development and regeneration to cancer. Cancer Res, 71: 3812. PubMed
  • Ross AE, Marchionni L, Vuica-Ross M, Cheadle C, Fan J, Berman DM, Schaeffer EM (2011) Gene expression pathways of high grade localized prostate cancer. Prostate, 71(14): 1568–1577. PubMed
  • Ohm JE, Mali P, Van Neste L, Berman DM, Liang L, Pandiyan K, Briggs KJ, Zhang W, Argani P, Simons B, Yu W, Matsui W, Van Criekinge W, Rassool FV, Zambidis E, Schuebel KE, Cope L, Yen J, Mohammad HP, Cheng L, Baylin SB (2010) Cancer-related epigenome changes associated with reprogramming to induced pluripotent stem cells. Cancer Res, 70: 7662. PubMed
  • Rasheed Z, Yang J, Wang Q, Kowalski J, Freed I, Murter C, Hong SM, Koorstra JB, Rajeshkumar NV,  He X, Goggins M, Iacobuzio-Donahue C, Berman DM, Laheru D, Jimeno A, Hidalgo M, Maitra A, and Matsui W (2010) Prognostic significance of tumorigenic cells with mesenchymal features in pancreatic adenocarcinoma. J Natl Cancer Inst, 102:340. doi: 10.1093/jnci/djp535. PubMed
  • Altiok S, Mezzadra H, Jagannath S, Tsottles N, Rudek MA, Abdallah N, Berman D, Forastiere A, Gibson MK (2010) A novel pharmacodynamic approach to assess and predict tumor response to the epidermal growth factor receptor inhibitor gefitinib in patients with esophageal cancer. Int J Oncol, 36:19. PubMed
  • Brandt WD, Matsui W, Rosenberg JE, He X, Ling S, Schaeffer EM, and Berman DM (2009) Urothelial carcinoma: Stem cells on the edge. Cancer Metastasis Rev, 28(3-4): 291-304. doi: 10.1007/s10555-009-9187-6. PubMed
  • Xiaobing He, Luigi Marchionni, Donna E. Hansel, Wayne Yu, Akshay Sood, Jie Yang, Giovanni Parmigiani, William Matsui, DM Berman (2009) Differentiation of a Highly Tumorigenic Basal Cell Compartment in Urothelial Carcinoma. Stem Cells, 27: 1487-95. doi: 10.1002/stem.92. PubMed
  • Schaeffer EM, Marchionni L, Huang Z, Simons B, Blackman A, Yu W, Parmigiani G, Berman DM (2008) Androgen-induced programs for prostate epithelial growth and invasion arise in embryogenesis and are reactivated in cancer. Oncogene, 27: 7180-91. PubMed
  • Kleeberger W, Bova GS, Nielsen ME, Herawi M, Chuang AY, Epstein JI, Berman DM (2007) Roles for the stem cell associated intermediate filament nestin in prostate cancer migration and metastasis. Cancer Res, 67:9199-206. PubMed
  • Zahurak M, Parmigiani G, Yu W, Scharpf RB, Berman D, Schaeffer E, Shabbeer S, Cope L (2007) Pre-processing Agilent microarray data. BMC Bioinf, 8: 142. PubMed
  • Duelli DM, Padilla-Nash HM, Berman D, Murphy KM, Ried TM, Lazebnik YA (2007) A virus causes cancer by inducing massive chromosomal instability through cell fusion. Curr Biol, 17(5): 431-7. PubMed
  • Ohm JE, McGarvey KM, Yu X, Cheng L, Schuebel KE, Cope L, Mohammad HP, Chen W, Daniel VC, Yu W, Berman DM, Jenuwein T, Pruitt K, Sharkis SJ, Watkins DN, Herman JG, Baylin SB (2007) A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing. Nat Genet, 39: 237-42. PubMed
  • Parwani AV, Berman DM, Burger PC, and Ali SZ (2004) Gliosarcoma: Cytopathologic characteristics on fine-needle aspiration (FNA) and Intraoperative touch imprint. Diagn Cytopathol, 30 (2): 77-81. PubMed
  • Berman DM, Desai N, Wang X, Karhadkar SS, Reynon M, Abate-Shen C, Beachy PA, and Shen MM (2004) Roles for Hedgehog signaling in androgen production and prostate ductal morphogenesis. Dev Biol, 7: 387-398. PubMed