Now showing items 1-20 of 20

    • Chromosomal copy number alterations for associations of ductal carcinoma in situ with invasive breast cancer 

      Afghahi, Anosheh; Forgó, Erna; Mitani, Aya A.; Desai, Manisha; Varma, Sushama; Seto, Tina; Rigdon, Joseph; Jensen, Kristin C.; Troxell, Megan L.; Gomez, Scarlett Lin; Das, Amar K.; Beck, Andrew H.; Kurian, Allison W.; West, Robert B. (BioMed Central, 2015)
      Introduction: Screening mammography has contributed to a significant increase in the diagnosis of ductal carcinoma in situ (DCIS), raising concerns about overdiagnosis and overtreatment. Building on prior observations from ...
    • Comparative Gene Expression Profiling of Benign and Malignant Lesions Reveals Candidate Therapeutic Compounds for Leiomyosarcoma 

      Edris, Badreddin; Fletcher, Jonathan A.; West, Robert B.; van de Rijn, Matt; Beck, Andrew H. (Hindawi Publishing Corporation, 2012)
      Leiomyosarcoma (LMS) is a malignant, soft-tissue tumor for which few effective therapies exist. Previously, we showed that there are three molecular subtypes of LMS. Here, we analyzed genes differentially expressed in each ...
    • Computational Pathology to Discriminate Benign from Malignant Intraductal Proliferations of the Breast 

      Dong, Fei; Irshad, Humayun; Oh, Eun-Yeong; Lerwill, Melinda F.; Brachtel, Elena F.; Jones, Nicholas C.; Knoblauch, Nicholas W.; Montaser-Kouhsari, Laleh; Johnson, Nicole B.; Rao, Luigi K. F.; Faulkner-Jones, Beverly; Wilbur, David C.; Schnitt, Stuart J.; Beck, Andrew H. (Public Library of Science, 2014)
      The categorization of intraductal proliferative lesions of the breast based on routine light microscopic examination of histopathologic sections is in many cases challenging, even for experienced pathologists. The development ...
    • Digital Quantification of Gene Expression in Sequential Breast Cancer Biopsies Reveals Activation of an Immune Response 

      Jeselsohn, Rinath M.; Werner, Lillian; Regan, Meredith M.; Fatima, Aquila; Gilmore, Lauren; Collins, Laura C.; Beck, Andrew H.; Bailey, Shannon T.; He, Housheng Hansen; Buchwalter, Gilles; Brown, Myles; Iglehart, J. Dirk; Richardson, Andrea; Come, Steven E. (Public Library of Science, 2013)
      Advancements in molecular biology have unveiled multiple breast cancer promoting pathways and potential therapeutic targets. Large randomized clinical trials remain the ultimate means of validating therapeutic efficacy, ...
    • EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes 

      Nabavi, Sheida; Schmolze, Daniel; Maitituoheti, Mayinuer; Malladi, Sadhika; Beck, Andrew H. (Oxford University Press, 2015)
      Motivation: A major goal of biomedical research is to identify molecular features associated with a biological or clinical class of interest. Differential expression analysis has long been used for this purpose; however, ...
    • Estrogen receptor negative/progesterone receptor positive breast cancer is not a reproducible subtype 

      Hefti, Marco M; Hu, Rong; Knoblauch, Nicholas W; Collins, Laura C; Haibe-Kains, Benjamin; Tamimi, Rulla M; Beck, Andrew H (BioMed Central, 2013)
      Introduction: Estrogen receptor (ER) and progesterone receptor (PR) testing are performed in the evaluation of breast cancer. While the clinical utility of ER as a predictive biomarker to identify patients likely to benefit ...
    • Expression of estrogen receptor, progesterone receptor, and Ki67 in normal breast tissue in relation to subsequent risk of breast cancer 

      Oh, Hannah; Eliassen, A Heather; Wang, Molin; Smith-Warner, Stephanie A; Beck, Andrew H; Schnitt, Stuart J; Collins, Laura C; Connolly, James L; Montaser-Kouhsari, Laleh; Polyak, Kornelia; Tamimi, Rulla M (2016)
      Although expression of estrogen receptor (ER), progesterone receptor (PR), and cell proliferation marker Ki67 serve as predictive and prognostic factors in breast cancers, little is known about their roles in normal breast ...
    • Extensive rewiring of epithelial-stromal co-expression networks in breast cancer 

      Oh, Eun-Yeong; Christensen, Stephen M; Ghanta, Sindhu; Jeong, Jong Cheol; Bucur, Octavian; Glass, Benjamin; Montaser-Kouhsari, Laleh; Knoblauch, Nicholas W; Bertos, Nicholas; Saleh, Sadiq MI; Haibe-Kains, Benjamin; Park, Morag; Beck, Andrew H (BioMed Central, 2015)
      Background: Epithelial-stromal crosstalk plays a critical role in invasive breast cancer pathogenesis; however, little is known on a systems level about how epithelial-stromal interactions evolve during carcinogenesis. ...
    • Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk 

      Lindström, Sara; Thompson, Deborah J.; Paterson, Andrew D.; Li, Jingmei; Gierach, Gretchen L.; Scott, Christopher; Stone, Jennifer; Douglas, Julie A.; dos-Santos-Silva, Isabel; Fernandez-Navarro, Pablo; Verghase, Jajini; Smith, Paula; Brown, Judith; Luben, Robert; Wareham, Nicholas J.; Loos, Ruth J.F.; Heit, John A.; Pankratz, V. Shane; Norman, Aaron; Goode, Ellen L.; Cunningham, Julie M.; deAndrade, Mariza; Vierkant, Robert A.; Czene, Kamila; Fasching, Peter A.; Baglietto, Laura; Southey, Melissa C.; Giles, Graham G.; Shah, Kaanan P.; Chan, Heang-Ping; Helvie, Mark A.; Beck, Andrew H.; Knoblauch, Nicholas W.; Hazra, Aditi; Hunter, David J.; Kraft, Peter; Pollan, Marina; Figueroa, Jonine D.; Couch, Fergus J.; Hopper, John L.; Hall, Per; Easton, Douglas F.; Boyd, Norman F.; Vachon, Celine M.; Tamimi, Rulla M. (2015)
      Mammographic density reflects the amount of stromal and epithelial tissues in relation to adipose tissue in the breast and is a strong risk factor for breast cancer. Here we report the results from meta-analysis of genome-wide ...
    • Image-guided Coring for Large-scale Studies in Molecular Pathology 

      Montaser-Kouhsari, Laleh; Knoblauch, Nicholas W.; Oh, Eun-Yeong; Baker, Gabrielle; Christensen, Stephen; Hazra, Aditi; Tamimi, Rulla M.; Beck, Andrew H. (Lippincott Williams & Wilkins, 2016)
      Sampling of formalin-fixed paraffin-embedded (FFPE) tissue blocks is a critical initial step in molecular pathology. Image-guided coring (IGC) is a new method for using digital pathology images to guide tissue block coring ...
    • Importance of collection in gene set enrichment analysis of drug response in cancer cell lines 

      Bateman, Alain R.; El-Hachem, Nehme; Beck, Andrew H.; Aerts, Hugo J. W. L.; Haibe-Kains, Benjamin (Nature Publishing Group, 2014)
      Gene set enrichment analysis (GSEA) associates gene sets and phenotypes, its use is predicated on the choice of a pre-defined collection of sets. The defacto standard implementation of GSEA provides seven collections yet ...
    • Mammographic density and risk of breast cancer by age and tumor characteristics 

      Bertrand, Kimberly A; Tamimi, Rulla M; Scott, Christopher G; Jensen, Matthew R; Pankratz, V Shane; Visscher, Daniel; Norman, Aaron; Couch, Fergus; Shepherd, John; Fan, Bo; Chen, Yunn-Yi; Ma, Lin; Beck, Andrew H; Cummings, Steven R; Kerlikowske, Karla; Vachon, Celine M (BioMed Central, 2013)
      Introduction: Understanding whether mammographic density (MD) is associated with all breast tumor subtypes and whether the strength of association varies by age is important for utilizing MD in risk models. Methods: Data ...
    • Open Access to Large Scale Datasets Is Needed to Translate Knowledge of Cancer Heterogeneity into Better Patient Outcomes 

      Beck, Andrew H. (Public Library of Science, 2015)
      In this guest editorial, Andrew Beck discusses the importance of open access to big data for translating knowledge of cancer heterogeneity into better outcomes for cancer patients.
    • Postmenopausal mammographic breast density and subsequent breast cancer risk according to selected tissue markers 

      Yaghjyan, Lusine; Pettersson, Andreas; Colditz, Graham A; Collins, Laura C; Schnitt, Stuart J; Beck, Andrew H; Rosner, Bernard; Vachon, Celine; Tamimi, Rulla M (Nature Publishing Group, 2015)
      Background: This study aimed to determine if associations of pre-diagnostic percent breast density, absolute dense area, and non-dense area with subsequent breast cancer risk differ by the tumour's molecular marker status. ...
    • Precision Cancer Diagnostics: Tracking Genomic Evolution in Clinical Trials 

      Beca, Francisco; Beck, Andrew H. (Public Library of Science, 2016)
      In a Perspective, Francisco Beca and Andrew Beck discuss Charles Swanton and colleagues' accompanying Research Article on somatic mutations in patients with inflammatory breast cancer treated in a Phase II clinical trial.
    • Progress in Medicine: Experts Take Stock 

      Beck, Andrew; Birney, Ewan; Graeber, Manuel; Tumwine, James; Hay, Phillipa; Ahn, Hyeong Sik; Patel, Anushka; du Cros, Philipp; von Seidlein, Lorenz; Wareham, Nick; Low, Nicola (Public Library of Science, 2015)
      In the year-end editorial, the PLOS Medicine editors ask 11 researchers and clinicians about the most relevant challenges, promising research, and important initiatives in their fields as we head into 2016.
    • The Reprogramming of Tumor Stroma by HSF1 Is a Potent Enabler of Malignancy 

      Scherz-Shouval, Ruth; Santagata, Sandro; Mendillo, Marc L.; Sholl, Lynette Marie; Ben-Aharon, Irit; Beck, Andrew H; Dias-Santagata, Dora; Koeva, Martina; Stemmer, Salomon M.; Whitesell, Luke; Lindquist, Susan (Elsevier BV, 2014)
      Stromal cells within the tumor microenvironment are essential for tumor progression and metastasis. Surprisingly little is known about the factors that drive the transcriptional reprogramming of stromal cells within tumors. ...
    • Significance Analysis of Prognostic Signatures 

      Beck, Andrew H; Knoblauch, Nicholas W.; Hefti, Marco; Kaplan, Jennifer; Schnitt, Stuart Jay; Culhane, Aedin; Schroeder, Markus S.; Risch, Thomas; Quackenbush, John; Haibe-Kains, Benjamin (Public Library of Science (PLoS), 2013)
      A major goal in translational cancer research is to identify biological signatures driving cancer progression and metastasis. A common technique applied in genomics research is to cluster patients using gene expression ...
    • Systematic Analysis of Sex-Linked Molecular Alterations and Therapies in Cancer 

      Ma, Jonathan; Malladi, Sadhika; Beck, Andrew H (Nature Publishing Group, 2016)
      Though patient sex influences response to cancer treatments, little is known of the molecular causes, and cancer therapies are generally given irrespective of patient sex. We assessed transcriptomic differences in tumors ...
    • Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers 

      Brunner, Alayne L; Beck, Andrew H; Edris, Badreddin; Sweeney, Robert T; Zhu, Shirley X; Li, Rui; Montgomery, Kelli; Varma, Sushama; Gilks, Thea; Guo, Xiangqian; Foley, Joseph W; Witten, Daniela M; Giacomini, Craig P; Flynn, Ryan A; Pollack, Jonathan R; Tibshirani, Robert; Chang, Howard Y; van de Rijn, Matt; West, Robert B (BioMed Central, 2012)
      Background: Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied ...