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Centrosome loss results in an unstable genome and malignant prostate tumors.

Wang M, Nagle RB, Knudsen BS, Cress AE, Rogers GC.

Oncogene. 2019 Sep 2. doi: 10.1038/s41388-019-0995-z. [Epub ahead of print]


A Circulating Tumor Cell-RNA Assay for Assessment of Androgen Receptor Signaling Inhibitor Sensitivity in Metastatic Castration-Resistant Prostate Cancer.

Jan YJ, Yoon J, Chen JF, Teng PC, Yao N, Cheng S, Lozano A, Chu GCY, Chung H, Lu YT, Chen PJ, Wang JJ, Lee YT, Kim M, Zhu Y, Knudsen BS, Feng FY, Garraway IP, Gao AC, Chung LWK, Freeman MR, You S, Tseng HR, Posadas EM.

Theranostics. 2019 Apr 13;9(10):2812-2826. doi: 10.7150/thno.34485. eCollection 2019.


Integrin α6β4E variant is associated with actin and CD9 structures and modifies the biophysical properties of cell-cell and cell-extracellular matrix interactions.

Wang M, Hinton JP, Gard JMC, Garcia JGN, Knudsen BS, Nagle RB, Cress AE.

Mol Biol Cell. 2019 Mar 21;30(7):838-850. doi: 10.1091/mbc.E18-10-0652. Epub 2019 Mar 13.


Convolutional neural networks can accurately distinguish four histologic growth patterns of lung adenocarcinoma in digital slides.

Gertych A, Swiderska-Chadaj Z, Ma Z, Ing N, Markiewicz T, Cierniak S, Salemi H, Guzman S, Walts AE, Knudsen BS.

Sci Rep. 2019 Feb 6;9(1):1483. doi: 10.1038/s41598-018-37638-9.


A method of quantifying centrosomes at the single-cell level in human normal and cancer tissue.

Wang M, Knudsen BS, Nagle RB, Rogers GC, Cress AE.

Mol Biol Cell. 2019 Mar 21;30(7):811-819. doi: 10.1091/mbc.E18-10-0651. Epub 2019 Jan 30.


Spatial Mapping of Myeloid Cells and Macrophages by Multiplexed Tissue Staining.

Saylor J, Ma Z, Goodridge HS, Huang F, Cress AE, Pandol SJ, Shiao SL, Vidal AC, Wu L, Nickols NG, Gertych A, Knudsen BS.

Front Immunol. 2018 Dec 14;9:2925. doi: 10.3389/fimmu.2018.02925. eCollection 2018.


ONECUT2 is a targetable master regulator of lethal prostate cancer that suppresses the androgen axis.

Rotinen M, You S, Yang J, Coetzee SG, Reis-Sobreiro M, Huang WC, Huang F, Pan X, Yáñez A, Hazelett DJ, Chu CY, Steadman K, Morrissey CM, Nelson PS, Corey E, Chung LWK, Freedland SJ, Di Vizio D, Garraway IP, Murali R, Knudsen BS, Freeman MR.

Nat Med. 2018 Dec;24(12):1887-1898. doi: 10.1038/s41591-018-0241-1. Epub 2018 Nov 26.


Path R-CNN for Prostate Cancer Diagnosis and Gleason Grading of Histological Images.

Li W, Li J, Sarma KV, Ho KC, Shen S, Knudsen BS, Gertych A, Arnold CW.

IEEE Trans Med Imaging. 2019 Apr;38(4):945-954. doi: 10.1109/TMI.2018.2875868. Epub 2018 Oct 12.


Effect of Preanalytic Variables on an Automated PTEN Immunohistochemistry Assay for Prostate Cancer.

Guedes LB, Morais CL, Fedor H, Hicks J, Gurel B, Melamed J, Lee P, Gopalan A, Knudsen BS, True LD, Scher HI, Fine SW, Trock BJ, De Marzo AM, Lotan TL.

Arch Pathol Lab Med. 2019 Mar;143(3):338-348. doi: 10.5858/arpa.2018-0068-OA. Epub 2018 Oct 8.


An EM-based semi-supervised deep learning approach for semantic segmentation of histopathological images from radical prostatectomies.

Li J, Speier W, Ho KC, Sarma KV, Gertych A, Knudsen BS, Arnold CW.

Comput Med Imaging Graph. 2018 Nov;69:125-133. doi: 10.1016/j.compmedimag.2018.08.003. Epub 2018 Sep 3.


Emerin Deregulation Links Nuclear Shape Instability to Metastatic Potential.

Reis-Sobreiro M, Chen JF, Novitskaya T, You S, Morley S, Steadman K, Gill NK, Eskaros A, Rotinen M, Chu CY, Chung LWK, Tanaka H, Yang W, Knudsen BS, Tseng HR, Rowat AC, Posadas EM, Zijlstra A, Di Vizio D, Freeman MR.

Cancer Res. 2018 Nov 1;78(21):6086-6097. doi: 10.1158/0008-5472.CAN-18-0608. Epub 2018 Aug 28.


A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors.

Alvarez MJ, Subramaniam PS, Tang LH, Grunn A, Aburi M, Rieckhof G, Komissarova EV, Hagan EA, Bodei L, Clemons PA, Dela Cruz FS, Dhall D, Diolaiti D, Fraker DA, Ghavami A, Kaemmerer D, Karan C, Kidd M, Kim KM, Kim HC, Kunju LP, Langel Ü, Li Z, Lee J, Li H, LiVolsi V, Pfragner R, Rainey AR, Realubit RB, Remotti H, Regberg J, Roses R, Rustgi A, Sepulveda AR, Serra S, Shi C, Yuan X, Barberis M, Bergamaschi R, Chinnaiyan AM, Detre T, Ezzat S, Frilling A, Hommann M, Jaeger D, Kim MK, Knudsen BS, Kung AL, Leahy E, Metz DC, Milsom JW, Park YS, Reidy-Lagunes D, Schreiber S, Washington K, Wiedenmann B, Modlin I, Califano A.

Nat Genet. 2018 Jul;50(7):979-989. doi: 10.1038/s41588-018-0138-4. Epub 2018 Jun 18.


A Multi-scale U-Net for Semantic Segmentation of Histological Images from Radical Prostatectomies.

Li J, Sarma KV, Chung Ho K, Gertych A, Knudsen BS, Arnold CW.

AMIA Annu Symp Proc. 2018 Apr 16;2017:1140-1148. eCollection 2017.


A Non-integrating Lentiviral Approach Overcomes Cas9-Induced Immune Rejection to Establish an Immunocompetent Metastatic Renal Cancer Model.

Hu J, Schokrpur S, Archang M, Hermann K, Sharrow AC, Khanna P, Novak J, Signoretti S, Bhatt RS, Knudsen BS, Xu H, Wu L.

Mol Ther Methods Clin Dev. 2018 Feb 23;9:203-210. doi: 10.1016/j.omtm.2018.02.009. eCollection 2018 Jun 15.


Novel Regulation of Integrin Trafficking by Rab11-FIP5 in Aggressive Prostate Cancer.

Das L, Gard JMC, Prekeris R, Nagle RB, Morrissey C, Knudsen BS, Miranti CK, Cress AE.

Mol Cancer Res. 2018 Aug;16(8):1319-1331. doi: 10.1158/1541-7786.MCR-17-0589. Epub 2018 May 14.


Regulation of inside-out β1-integrin activation by CDCP1.

Pollan SG, Huang F, Sperger JM, Lang JM, Morrissey C, Cress AE, Chu CY, Bhowmick NA, You S, Freeman MR, Spassov DS, Moasser MM, Carter WG, Satapathy SR, Shah K, Knudsen BS.

Oncogene. 2018 May;37(21):2817-2836. doi: 10.1038/s41388-018-0142-2. Epub 2018 Mar 7.


A novel machine learning approach reveals latent vascular phenotypes predictive of renal cancer outcome.

Ing N, Huang F, Conley A, You S, Ma Z, Klimov S, Ohe C, Yuan X, Amin MB, Figlin R, Gertych A, Knudsen BS.

Sci Rep. 2017 Oct 16;7(1):13190. doi: 10.1038/s41598-017-13196-4.


Data integration from pathology slides for quantitative imaging of multiple cell types within the tumor immune cell infiltrate.

Ma Z, Shiao SL, Yoshida EJ, Swartwood S, Huang F, Doche ME, Chung AP, Knudsen BS, Gertych A.

Diagn Pathol. 2017 Sep 18;12(1):69. doi: 10.1186/s13000-017-0658-8.


Impact of carbohydrate restriction in the context of obesity on prostate tumor growth in the Hi-Myc transgenic mouse model.

Allott EH, Macias E, Sanders S, Knudsen BS, Thomas GV, Hursting SD, Freedland SJ.

Prostate Cancer Prostatic Dis. 2017 Jun;20(2):165-171. doi: 10.1038/pcan.2016.73. Epub 2017 Feb 28.


Impact of treatment on progression to castration-resistance, metastases, and death in men with localized high-grade prostate cancer.

Miller ET, Chamie K, Kwan L, Lewis MS, Knudsen BS, Garraway IP.

Cancer Med. 2017 Jan;6(1):163-172. doi: 10.1002/cam4.981. Epub 2016 Dec 20.


High-throughput sequencing of two populations of extracellular vesicles provides an mRNA signature that can be detected in the circulation of breast cancer patients.

Conley A, Minciacchi VR, Lee DH, Knudsen BS, Karlan BY, Citrigno L, Viglietto G, Tewari M, Freeman MR, Demichelis F, Di Vizio D.

RNA Biol. 2017 Mar 4;14(3):305-316. doi: 10.1080/15476286.2016.1259061. Epub 2016 Nov 18.


Quantitative imaging for development of companion diagnostics to drugs targeting HGF/MET.

Huang F, Ma Z, Pollan S, Yuan X, Swartwood S, Gertych A, Rodriguez M, Mallick J, Bhele S, Guindi M, Dhall D, Walts AE, Bose S, de Peralta Venturina M, Marchevsky AM, Luthringer DJ, Feller SM, Berman B, Freeman MR, Alvord WG, Vande Woude G, Amin MB, Knudsen BS.

J Pathol Clin Res. 2016 Jul 1;2(4):210-222. eCollection 2016 Oct.


The Cohesive Metastasis Phenotype in Human Prostate Cancer.

Harryman WL, Hinton JP, Rubenstein CP, Singh P, Nagle RB, Parker SJ, Knudsen BS, Cress AE.

Biochim Biophys Acta. 2016 Dec;1866(2):221-231. doi: 10.1016/j.bbcan.2016.09.005. Epub 2016 Sep 24. Review.


Keratin 13 Is Enriched in Prostate Tubule-Initiating Cells and May Identify Primary Prostate Tumors that Metastasize to the Bone.

Liu S, Cadaneanu RM, Zhang B, Huo L, Lai K, Li X, Galet C, Grogan TR, Elashoff D, Freedland SJ, Rettig M, Aronson WJ, Knudsen BS, Lewis MS, Garraway IP.

PLoS One. 2016 Oct 6;11(10):e0163232. doi: 10.1371/journal.pone.0163232. eCollection 2016.


A basal cell defect promotes budding of prostatic intraepithelial neoplasia.

Wang M, Nagle RB, Knudsen BS, Rogers GC, Cress AE.

J Cell Sci. 2017 Jan 1;130(1):104-110. doi: 10.1242/jcs.188177. Epub 2016 Sep 8.


Characterization of Laminin Binding Integrin Internalization in Prostate Cancer Cells.

Das L, Anderson TA, Gard JM, Sroka IC, Strautman SR, Nagle RB, Morrissey C, Knudsen BS, Cress AE.

J Cell Biochem. 2017 May;118(5):1038-1049. doi: 10.1002/jcb.25673. Epub 2017 Jan 5.


Integrated Classification of Prostate Cancer Reveals a Novel Luminal Subtype with Poor Outcome.

You S, Knudsen BS, Erho N, Alshalalfa M, Takhar M, Al-Deen Ashab H, Davicioni E, Karnes RJ, Klein EA, Den RB, Ross AE, Schaeffer EM, Garraway IP, Kim J, Freeman MR.

Cancer Res. 2016 Sep 1;76(17):4948-58. doi: 10.1158/0008-5472.CAN-16-0902. Epub 2016 Jun 14.


PTEN loss and chromosome 8 alterations in Gleason grade 3 prostate cancer cores predicts the presence of un-sampled grade 4 tumor: implications for active surveillance.

Trock BJ, Fedor H, Gurel B, Jenkins RB, Knudsen BS, Fine SW, Said JW, Carter HB, Lotan TL, De Marzo AM.

Mod Pathol. 2016 Jul;29(7):764-71. doi: 10.1038/modpathol.2016.63. Epub 2016 Apr 15.


Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens.

Knudsen BS, Kim HL, Erho N, Shin H, Alshalalfa M, Lam LLC, Tenggara I, Chadwich K, Van Der Kwast T, Fleshner N, Davicioni E, Carroll PR, Cooperberg MR, Chan JM, Simko JP.

J Mol Diagn. 2016 May;18(3):395-406. doi: 10.1016/j.jmoldx.2015.12.006. Epub 2016 Mar 3.


Neoadjuvant dasatinib for muscle-invasive bladder cancer with tissue analysis of biologic activity.

Hahn NM, Knudsen BS, Daneshmand S, Koch MO, Bihrle R, Foster RS, Gardner TA, Cheng L, Liu Z, Breen T, Fleming MT, Lance R, Corless CL, Alva AS, Shen SS, Huang F, Gertych A, Gallick GE, Mallick J, Ryan C, Galsky MD, Lerner SP, Posadas EM, Sonpavde G.

Urol Oncol. 2016 Jan;34(1):4.e11-7. doi: 10.1016/j.urolonc.2015.08.005. Epub 2015 Sep 9.


Machine learning approaches to analyze histological images of tissues from radical prostatectomies.

Gertych A, Ing N, Ma Z, Fuchs TJ, Salman S, Mohanty S, Bhele S, Velásquez-Vacca A, Amin MB, Knudsen BS.

Comput Med Imaging Graph. 2015 Dec;46 Pt 2:197-208. doi: 10.1016/j.compmedimag.2015.08.002. Epub 2015 Aug 20.


Docetaxel-induced polyploidization may underlie chemoresistance and disease relapse.

Ogden A, Rida PC, Knudsen BS, Kucuk O, Aneja R.

Cancer Lett. 2015 Oct 28;367(2):89-92. doi: 10.1016/j.canlet.2015.06.025. Epub 2015 Jul 13. Review.


Regulation of microtubule dynamics by DIAPH3 influences amoeboid tumor cell mechanics and sensitivity to taxanes.

Morley S, You S, Pollan S, Choi J, Zhou B, Hager MH, Steadman K, Spinelli C, Rajendran K, Gertych A, Kim J, Adam RM, Yang W, Krishnan R, Knudsen BS, Di Vizio D, Freeman MR.

Sci Rep. 2015 Jul 16;5:12136. doi: 10.1038/srep12136.


Rapid 3-D delineation of cell nuclei for high-content screening platforms.

Gertych A, Ma Z, Tajbakhsh J, Velásquez-Vacca A, Knudsen BS.

Comput Biol Med. 2016 Feb 1;69:328-38. doi: 10.1016/j.compbiomed.2015.04.025. Epub 2015 Apr 25.


Hypoxia after transarterial chemoembolization may trigger a progenitor cell phenotype in hepatocellular carcinoma.

Lai JP, Conley A, Knudsen BS, Guindi M.

Histopathology. 2015 Oct;67(4):442-50. doi: 10.1111/his.12623. Epub 2015 Apr 20.


Effects of tissue decalcification on the quantification of breast cancer biomarkers by digital image analysis.

Gertych A, Mohan S, Maclary S, Mohanty S, Wawrowsky K, Mirocha J, Balzer B, Knudsen BS.

Diagn Pathol. 2014 Nov 25;9:213. doi: 10.1186/s13000-014-0213-9.


Computerized delineation of nuclei in liquid-based pap smears stained with immunohistochemical biomarkers.

Qin Y, Walts AE, Knudsen BS, Gertych A.

Cytometry B Clin Cytom. 2015 Mar;88(2):110-9. doi: 10.1002/cyto.b.21193. Epub 2014 Oct 3.


Circulating microRNA profiling identifies a subset of metastatic prostate cancer patients with evidence of cancer-associated hypoxia.

Cheng HH, Mitchell PS, Kroh EM, Dowell AE, Chéry L, Siddiqui J, Nelson PS, Vessella RL, Knudsen BS, Chinnaiyan AM, Pienta KJ, Morrissey C, Tewari M.

PLoS One. 2013 Jul 30;8(7):e69239. doi: 10.1371/journal.pone.0069239. Print 2013.


Tumour cell survival mechanisms in lethal metastatic prostate cancer differ between bone and soft tissue metastases.

Akfirat C, Zhang X, Ventura A, Berel D, Colangelo ME, Miranti CK, Krajewska M, Reed JC, Higano CS, True LD, Vessella RL, Morrissey C, Knudsen BS.

J Pathol. 2013 Jul;230(3):291-7. doi: 10.1002/path.4180.


Statistical Methods for Tissue Array Images - Algorithmic Scoring and Co-training.

Yan D, Wang P, Knudsen BS, Linden M, Randolph TW.

Ann Appl Stat. 2012 Sep;6(3):1280-1305.


Investigation of the relationship between prostate cancer and MSMB and NCOA4 genetic variants and protein expression.

FitzGerald LM, Zhang X, Kolb S, Kwon EM, Liew YC, Hurtado-Coll A, Knudsen BS, Ostrander EA, Stanford JL.

Hum Mutat. 2013 Jan;34(1):149-56. doi: 10.1002/humu.22176. Epub 2012 Oct 4.


Metastatic progression of prostate cancer and e-cadherin regulation by zeb1 and SRC family kinases.

Putzke AP, Ventura AP, Bailey AM, Akture C, Opoku-Ansah J, Celiktaş M, Hwang MS, Darling DS, Coleman IM, Nelson PS, Nguyen HM, Corey E, Tewari M, Morrissey C, Vessella RL, Knudsen BS.

Am J Pathol. 2011 Jul;179(1):400-10. doi: 10.1016/j.ajpath.2011.03.028. Epub 2011 May 4.


Mechanisms of prostate cancer initiation and progression.

Knudsen BS, Vasioukhin V.

Adv Cancer Res. 2010;109:1-50. doi: 10.1016/B978-0-12-380890-5.00001-6. Review.


Differential gene expression in benign prostate epithelium of men with and without prostate cancer: evidence for a prostate cancer field effect.

Risk MC, Knudsen BS, Coleman I, Dumpit RF, Kristal AR, LeMeur N, Gentleman RC, True LD, Nelson PS, Lin DW.

Clin Cancer Res. 2010 Nov 15;16(22):5414-23. doi: 10.1158/1078-0432.CCR-10-0272. Epub 2010 Oct 8.


Activation of the MEK-S6 pathway in high-grade ovarian cancers.

Ventura AP, Radhakrishnan S, Green A, Rajaram SK, Allen AN, O'Briant K, Schummer M, Karlan B, Urban N, Tewari M, Drescher C, Knudsen BS.

Appl Immunohistochem Mol Morphol. 2010 Dec;18(6):499-508. doi: 10.1097/PAI.0b013e3181e53e1c.


DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines.

Houshdaran S, Hawley S, Palmer C, Campan M, Olsen MN, Ventura AP, Knudsen BS, Drescher CW, Urban ND, Brown PO, Laird PW.

PLoS One. 2010 Feb 22;5(2):e9359. doi: 10.1371/journal.pone.0009359.


Regulation of miR-200 family microRNAs and ZEB transcription factors in ovarian cancer: evidence supporting a mesothelial-to-epithelial transition.

Bendoraite A, Knouf EC, Garg KS, Parkin RK, Kroh EM, O'Briant KC, Ventura AP, Godwin AK, Karlan BY, Drescher CW, Urban N, Knudsen BS, Tewari M.

Gynecol Oncol. 2010 Jan;116(1):117-25. doi: 10.1016/j.ygyno.2009.08.009. Epub 2009 Oct 24.


Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries.

Wyman SK, Parkin RK, Mitchell PS, Fritz BR, O'Briant K, Godwin AK, Urban N, Drescher CW, Knudsen BS, Tewari M.

PLoS One. 2009;4(4):e5311. doi: 10.1371/journal.pone.0005311. Epub 2009 Apr 23.


Spectral analysis of multiplex Raman probe signatures.

Lutz BR, Dentinger CE, Nguyen LN, Sun L, Zhang J, Allen AN, Chan S, Knudsen BS.

ACS Nano. 2008 Nov 25;2(11):2306-14. doi: 10.1021/nn800243g.

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