1. Computational Pathology: A Path Ahead.

    Archives of Pathology & Laboratory Medicine 140(1):41 (2016) PMID 26098131

    We define the scope and needs within the new discipline of computational pathology, a discipline critical to the future of both the practice of pathology and, more broadly, medical practice in general. To define the scope and needs of computational pathology. A meeting was convened in Boston, Ma...
  2. Supervised multi-view canonical correlation analysis (sMVCCA): integrating histologic and proteomic features for predicting recurrent prostate cancer.

    Medical Imaging, IEEE Transactions on 34(1):284 (2015) PMID 25203987

    In this work, we present a new methodology to facilitate prediction of recurrent prostate cancer (CaP) following radical prostatectomy (RP) via the integration of quantitative image features and protein expression in the excised prostate. Creating a fused predictor from high-dimensional data str...
  3. Computerized image analysis for identifying triple-negative breast cancers and differentiating them from other molecular subtypes of breast cancer on dynamic contrast-enhanced MR images: a feasibility study.

    Radiology 272(1):91 (2014) PMID 24620909 PMCID PMC4263619

    To determine the feasibility of using a computer-aided diagnosis (CAD) system to differentiate among triple-negative breast cancer, estrogen receptor (ER)-positive cancer, human epidermal growth factor receptor type 2 (HER2)-positive cancer, and benign fibroadenoma lesions on dynamic contrast ma...
  4. Co-occurring gland angularity in localized subgraphs: predicting biochemical recurrence in intermediate-risk prostate cancer patients.

    PLoS ONE 9(5):e97954 (2014) PMID 24875018 PMCID PMC4038543

    Quantitative histomorphometry (QH) refers to the application of advanced computational image analysis to reproducibly describe disease appearance on digitized histopathology images. QH thus could serve as an important complementary tool for pathologists in interrogating and interpreting cancer m...
  5. Histostitcher™: An informatics software platform for reconstructing whole-mount prostate histology using the extensible imaging platform framework.

    Journal of Pathology Informatics 5(1):8 (2014) PMID 24843820 PMCID PMC4023035

    Co-registration of ex-vivo histologic images with pre-operative imaging (e.g., magnetic resonance imaging [MRI]) can be used to align and map disease extent, and to identify quantitative imaging signatures. However, ex-vivo histology images are frequently sectioned into quarters prior to imaging...
  6. Immunohistochemical studies of metastatic germ-cell tumors in retroperitoneal dissection specimens: a sensitive and specific panel.

    International Journal of Surgical Pathology 21(4):342 (2013) PMID 23893437

    Germ-cell tumors (GCTs) are the most common malignancies in adolescent and young men. These tumors are highly treatable, even at an advanced stage; therefore, accurate diagnosis is imperative. In this study, we evaluated immunohistochemical stains for SALL4, NANOG, glypican-3 (GPC3), D2-40, and ...
  7. The tumor suppressor TERE1 (UBIAD1) prenyltransferase regulates the elevated cholesterol phenotype in castration resistant prostate cancer by controlling a program of ligand dependent SXR target genes.

    Oncotarget 4(7):1075 (2013) PMID 23919967 PMCID PMC3759667

    Castrate-Resistant Prostate Cancer (CRPC) is characterized by persistent androgen receptor-driven tumor growth in the apparent absence of systemic androgens. Current evidence suggests that CRPC cells can produce their own androgens from endogenous sterol precursors that act in an intracrine mann...
  8. Microsatellite instability and TARBP2 mutation study in upper urinary tract urothelial carcinoma.

    American Journal of Clinical Pathology 139(6):765 (2013) PMID 23690119

    Microsatellite instability (MSI) contributes to the tumorigenesis of upper urinary tract urothelial carcinomas (UUT-UCs). In this study, we first used MLH1 and MSH2 immunohistochemistry to identify patients with loss of expression of either or both of these proteins in 132 UUT-UCs. We found a to...
  9. Role of carbonic anhydrase IX, α-methylacyl coenzyme a racemase, cytokeratin 7, and galectin-3 in the evaluation of renal neoplasms: a tissue microarray immunohistochemical study.

    Annals of Diagnostic Pathology 17(1):58 (2013) PMID 22898056

    Kidney tumors of various types may behave differently and have different prognosis. Because of some overlapping morphological features and immunohistochemical staining pattern, they may pose diagnostic challenge. Therefore, it is necessary to explore additional immunohistochemical stains to help...
  10. Fluorescence in situ hybridization study of chromosome abnormalities of upper urinary tract urothelial carcinoma in paraffin-embedded tissue.

    American Journal of Clinical Pathology 138(3):382 (2012) PMID 22912355

    Urothelial carcinomas arising from the upper urinary tract (renal pelvis and ureter) are rare and few molecular genetic studies of these tumors have been conducted to date. We investigated hyperploidy at chromosomes 3, 7, and 17 using a multitarget fluorescence in situ hybridization system to id...
  11. Accumulation of intrahepatic islet amyloid in a nonhuman primate transplant model.

    Endocrinology 153(4):1673 (2012) PMID 22355065 PMCID PMC3320262

    Islet amyloid is hypothesized to play a role in nonimmunologic transplanted islet graft loss. We performed a quantitative histologic analysis of liver biopsies from intrahepatic islet grafts transplanted in streptozotocin-induced diabetic cynomolgus macaques. Seven animals treated with antithymo...
  12. p53 in pure epithelioid PEComa: an immunohistochemistry study and gene mutation analysis.

    International Journal of Surgical Pathology 20(2):115 (2012) PMID 22459898

    Pure epithelioid PEComa (PEP; so-called epithelioid angiomyolipoma) is rare and is more often associated with aggressive behaviors. The pathogenesis of PEP has been poorly understood. The authors studied p53 expression and gene mutation in PEPs by immunohistochemistry, single-strand conformation...
  13. The use of immunohistochemical expression of SF-1 and EMA in distinguishing adrenocortical tumors from renal neoplasms.

    Applied Immunohistochemistry 20(2):141 (2012) PMID 22553814

    Steroidogenic factor -1 (SF-1) is an orphan member of the nuclear hormone receptor superfamily, and is considered to play an important role in the differentiation of steroidogenic tissues. In this study, we compared the immunohistochemical stains of SF-1 and epithelial membrane antigen (EMA) in ...
  14. Integration of architectural and cytologic driven image algorithms for prostate adenocarcinoma identification.

    Analytical Cellular Pathology 35(4):251 (2012) PMID 22425661 PMCID PMC4605585

    The advent of digital slides offers new opportunities within the practice of pathology such as the use of image analysis techniques to facilitate computer aided diagnosis (CAD) solutions. Use of CAD holds promise to enable new levels of decision support and allow for additional layers of quality...
  15. Repeat prostate biopsy and the incremental risk of clinically insignificant prostate cancer.

    Urology 77(3):548 (2011) PMID 21215436

    To determine the incremental risk of diagnosis of clinically insignificant prostate cancer with serial prostate biopsies. We reviewed our institutional radical prostatectomy (RP) database comprising 2411 consecutive patients undergoing RP. We then stratified patients by the prostate biopsy on wh...
  16. Supervised regularized canonical correlation analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery.

    BMC Bioinformatics 12:483 (2011) PMID 22182303 PMCID PMC3267835

    Multimodal data, especially imaging and non-imaging data, is being routinely acquired in the context of disease diagnostics; however, computational challenges have limited the ability to quantitatively integrate imaging and non-imaging data channels with different dimensionalities and scales. To...
  17. Clear cell papillary renal cell carcinoma in the bilateral native kidneys after 2 years of renal transplantation: report of a case and review of the literature.

    Case Reports in Transplantation 2011:387645 (2011) PMID 23198258 PMCID PMC3504274

    Renal transplantation increases the probability of malignant tumors by about 2-4-fold overall with a much higher rate for renal epithelial malignancy. Renal tumors in renal transplant recipients are commonly conventional clear cell or papillary renal cell carcinoma. Clear cell papillary renal ce...
  18. HistoStitcher(©): an interactive program for accurate and rapid reconstruction of digitized whole histological sections from tissue fragments.

    Computerized Medical Imaging and Graphics 35(7-8):557 (2011) PMID 21397459 PMCID PMC3118267

    We present an interactive program called HistoStitcher(©) for accurate and rapid reassembly of histology fragments into a pseudo-whole digitized histological section. HistoStitcher(©) provides both an intuitive graphical interface to assist the operator in performing the stitch of adjacent histo...
  19. Supervised regularized canonical correlation analysis: integrating histologic and proteomic data for predicting biochemical failures.

    International Conference of the IEEE Engineerin... 2011:6434 (2011) PMID 22255811

    Multimodal data, especially imaging and non-imaging data, is being routinely acquired in the context of disease diagnostics; however computational challenges have limited the ability to quantitatively integrate imaging and non-imaging data channels with different dimensionalities for making diag...
  20. Image microarrays (IMA): Digital pathology's missing tool.

    Journal of Pathology Informatics 2:47 (2011) PMID 22200030 PMCID PMC3237063

    The increasing availability of whole slide imaging (WSI) data sets (digital slides) from glass slides offers new opportunities for the development of computer-aided diagnostic (CAD) algorithms. With the all-digital pathology workflow that these data sets will enable in the near future, literally...