Somatic mutations affect key pathways in lung adenocarcinoma (2008)
Ding, Li, Getz, Gad, Wheeler, David A., Mardis, Elaine R., McLellan, Michael D., Cibulskis, Kristian, ...
Characterizing the cancer genome in lung adenocarcinoma (2007)
Weir, Barbara A., Woo, Michele S., Getz, Gad, Perner, Sven, Ding, Li, Beroukhim, Rameen, ...
Doubly Penalized Buckley-James Method for Survival Data with High-Dimensional Covariates (2006)
Wang, Sijian, Nan, Bin, Zhu, Ji, Beer, David G.
Recent interest in cancer research focuses on predicting patients' survival by investigating gene expression profiles based on microarray analysis. We propose a doubly penalized Buckley-James method...
Doubly Penalized Buckley-James Method for Survival Data with High-Dimensional Covariates (2006)
Wang, Sijian, Nan, Bin, Zhu, Ji, Beer, David G.
Recent interest in cancer research focuses on predicting patients' survival by investigating gene expression profiles based on microarray analysis. We propose a doubly penalized Buckley-James method...
Doubly Penalized Buckley-James Method for Survival Data with High-Dimensional Covariates (2006)
Wang, Sijian, Nan, Bin, Zhu, Ji, Beer, David G.
Recent interest in cancer research focuses on predicting patients' survival by investigating gene expression profiles based on microarray analysis. We propose a doubly penalized Buckley-James method...
Doubly Penalized Buckley-James Method for Survival Data with High-Dimensional Covariates (2006)
Wang, Sijian, Nan, Bin, Zhu, Ji, Beer, David G.
Recent interest in cancer research focuses on predicting patients' survival by investigating gene expression profiles based on microarray analysis. We propose a doubly penalized Buckley-James method...
Yoo, Chul, Zhao, Jia, Pal, Manoj, Hersberger, Katherine, Huber, Christian G., Simeone, Diane M., ...
A unique approach of automating the integration of monolithic capillary HPLC-based protein separation and on-plate digestion for subsequent MALDI-MS analysis has been developed. All liquid-handling...
Lin, Lin, Wang, Zhuwen, Prescott, Michael S., Van Dekken, Herman, Thomas, Dafydd G., Giordano, Thomas J., ...
Gene amplification is one of the mechanisms to activate oncogenes in many cancers, including esophageal adenocarcinoma (EA). In the present study, we used two-dimensional restriction landmark genome...
Chen, Guoan, Wang, Hong, Miller, Charles T., Thomas, Dafydd G., Gharib, Tarek G., Misek, David E., ...
The effects of selenium, an essential nutrient with anti-carcinogenic properties, are mediated by selenium-binding proteins. The protein expression status of human selenium-binding protein 1 (SBP1)...
Arlt, Martin F., Miller, Diane E., Beer, David G., Glover, Thomas W.
The common fragile site, FRA3B, has been shown to be a site of frequent homozygous deletions in some cancers, resulting in loss of expression of the associated FHIT gene. It has been proposed that...
Fang, Jianming M., Arlt, Martin F., Burgess, Ann C., Dagenais, Susan L., Beer, David G., Glover, Thomas W.
Common fragile sites have been proposed to play a mechanistic role in chromosome translocations and other rearrangements in cancer cells in vivo based on their behavior in vitro and their...
Compton, Keith R., Orringer, Mark B., Beer, David G.
Barrett's metaplasia consists of columnar epithelium that replaces the normal esophageal mucosa in patients with chronic gastroesophageal reflux. Because intestinal-type Barrett's metaplasia is the...
MacLennan, Allison J., Orringer, Mark B., Beer, David G.
Villin is an actin-binding cytoskeletal protein required for brush-border formation in the normal small intestinal and renal proximal tubule epithelium. Villin is a marker of cell differentiation in...
Petty, Elizabeth M., Kalikin, Linda M., Orringer, Mark B., Beer, David G.
The molecular genetic mechanisms underlying esophageal cancer are poorly understood. However, a novel gene that may be involved in esophageal carcinogenesis was recently localized by others to distal...
Wei, Ru-Qi, Lin, Hua, Chen, Gwo-Hsiao, Beer, David G., Kunkel, Steven L., Bolling, Steven F.
Tumor necrosis factor-[alpha] (TNF) is a multifunctional cytokine involved in the immunopathologic consequences of allograft rejection. We have previously demonstrated that anti-TNF antibody...
Mahacek, Michael L., Beer, David G., Frank, Thomas S., Ethier, Stephen P.
We recently described culture conditions that allow proliferation of metastatic human breast cancer cells from biopsy specimens of certain patient samples. These conditions resulted in the...
A novel amplicon at 8p22–23 results in overexpression of cathepsin B in esophageal adenocarcinoma
Hughes, Steven J., Glover, Thomas W., Zhu, Xiao-Xiang, Kuick, Rork, Thoraval, Didier, Orringer, Mark B., ...
Cathepsin B (CTSB) is overexpressed in tumors of the lung, prostate, colon, breast, and stomach. However, evidence of primary genomic alterations in the CTSB gene during tumor initiation or...
Brichory, Franck M., Misek, David E., Yim, Anne-Marie, Krause, Melissa C., Giordano, Thomas J., Beer, David G., ...
The identification of circulating tumor antigens or their related autoantibodies provides a means for early cancer diagnosis as well as leads for therapy. The purpose of this study was to identify...
Protein profiles associated with survival in lung adenocarcinoma
Chen, Guoan, Gharib, Tarek G, Wang, Hong, Huang, Chiang-Ching, Kuick, Rork, Thomas, Dafydd G., ...
Morphologic assessment of lung tumors is informative but insufficient to adequately predict patient outcome. We previously identified transcriptional profiles that predict patient survival, and here...
Chen, Guoan, Bhojani, Mahaveer S., Heaford, Andrew C., Chang, Daniel C., Laxman, Bharathi, Thomas, Dafydd G., ...
In an effort to identify a clinical biomarker for lung cancer, we used cDNA microarray and 2D protein analyses to demonstrate that increased Fas-associated death domain (FADD) mRNA and protein were...
Cytochromes P450 are Expressed in Proliferating Cells in Barrett's Metaplasia
Hughes, Steven J, Morse, Mark A, Weghorst, Christopher M, Kim, Hyesook, Watkins, Paul B, Guengerich, F Peter, ...
The expression of cytochromes P450 (CYP) in Barrett's esophagus and esophageal squamous mucosa was investigated. Esophagectomy specimens from 23 patients were examined for CYP expression of CYP1A2,...
Lin, Jules, Raoof, Duna A, Thomas, Dafydd G, Greenson, Joel K, Giordano, Thomas J, Robinson, Gregory S, ...
The L-type amino acid transporter-1 (LAT-1) has been associated with tumor growth. Using cDNA microarrays, overexpression of LAT-1 was found in 87.5% (7/8) of esophageal adenocarcinomas relative to...
Aggarwal, Sanjeev, Taneja, Neelam, Lin, Lin, Orringer, Mark B, Rehemtulla, Alnawaz, Beer, David G
The prolonged use of nonsteroidal anti-inflammatory drugs (NSAIDs) has been shown to exert a chemopreventive effect in esophageal and other gastrointestinal tumors. The precise mechanism by which...
Gharib, Tarek G., Chen, Guoan, Wang, Hong, Huang, Chiang-Ching, Prescott, Michael S., Shedden, Kerby, ...
Cytokeratins (CK) are intermediate filaments whose expression is often altered in epithelial cancer. Systematic identification of lung adenocarcinoma proteins using two-dimensional polyacrylamide gel...
A novel amplicon at 8p22–23 results in overexpression of cathepsin B in esophageal adenocarcinoma
Hughes, Steven J., Glover, Thomas W., Zhu, Xiao-Xiang, Kuick, Rork, Thoraval, Didier, Orringer, Mark B., ...
Cathepsin B (CTSB) is overexpressed in tumors of the lung, prostate, colon, breast, and stomach. However, evidence of primary genomic alterations in the CTSB gene during tumor initiation or...
Brichory, Franck M., Misek, David E., Yim, Anne-Marie, Krause, Melissa C., Giordano, Thomas J., Beer, David G., ...
The identification of circulating tumor antigens or their related autoantibodies provides a means for early cancer diagnosis as well as leads for therapy. The purpose of this study was to identify...
Protein profiles associated with survival in lung adenocarcinoma
Chen, Guoan, Gharib, Tarek G, Wang, Hong, Huang, Chiang-Ching, Kuick, Rork, Thomas, Dafydd G., ...
Morphologic assessment of lung tumors is informative but insufficient to adequately predict patient outcome. We previously identified transcriptional profiles that predict patient survival, and here...
Chen, Guoan, Bhojani, Mahaveer S., Heaford, Andrew C., Chang, Daniel C., Laxman, Bharathi, Thomas, Dafydd G., ...
In an effort to identify a clinical biomarker for lung cancer, we used cDNA microarray and 2D protein analyses to demonstrate that increased Fas-associated death domain (FADD) mRNA and protein were...
Cytochromes P450 are Expressed in Proliferating Cells in Barrett's Metaplasia
Hughes, Steven J, Morse, Mark A, Weghorst, Christopher M, Kim, Hyesook, Watkins, Paul B, Guengerich, F Peter, ...
The expression of cytochromes P450 (CYP) in Barrett's esophagus and esophageal squamous mucosa was investigated. Esophagectomy specimens from 23 patients were examined for CYP expression of CYP1A2,...
Lin, Jules, Raoof, Duna A, Thomas, Dafydd G, Greenson, Joel K, Giordano, Thomas J, Robinson, Gregory S, ...
The L-type amino acid transporter-1 (LAT-1) has been associated with tumor growth. Using cDNA microarrays, overexpression of LAT-1 was found in 87.5% (7/8) of esophageal adenocarcinomas relative to...
Aggarwal, Sanjeev, Taneja, Neelam, Lin, Lin, Orringer, Mark B, Rehemtulla, Alnawaz, Beer, David G
The prolonged use of nonsteroidal anti-inflammatory drugs (NSAIDs) has been shown to exert a chemopreventive effect in esophageal and other gastrointestinal tumors. The precise mechanism by which...
Gharib, Tarek G., Chen, Guoan, Wang, Hong, Huang, Chiang-Ching, Prescott, Michael S., Shedden, Kerby, ...
Cytokeratins (CK) are intermediate filaments whose expression is often altered in epithelial cancer. Systematic identification of lung adenocarcinoma proteins using two-dimensional polyacrylamide gel...
Lin, Jules, Raoof, Duna A, Wang, Zhuwen, Lin, Mu-Yen, Thomas, Dafydd G, Greenson, Joel K, ...
Ubiquitin-dependent proteolysis of cyclins plays a critical role in cell cycle progression and tumorigenesis. We examined the expression of ubiquitin-conjugating enzyme E2C (UBE2C) during progression...
Giordano, Thomas J., Shedden, Kerby A., Schwartz, Donald R., Kuick, Rork, Taylor, Jeremy M. G., Lee, Nana, ...
Molecular classification of tumors based on their gene expression profiles promises to significantly refine diagnosis and management of cancer patients. The establishment of organ-specific gene...
Amplification and Overexpression of the L-MYC Proto-Oncogene in Ovarian Carcinomas
Wu, Rong, Lin, Lin, Beer, David G., Ellenson, Lora H., Lamb, Barbara J., Rouillard, Jean-Marie, ...
Gene amplification is an important mechanism of oncogene activation in various human cancers, including ovarian carcinomas (OvCas). We used restriction landmark genomic scanning (RLGS) to detect...
Shedden, Kerby A., Taylor, Jeremy M. G., Giordano, Thomas J., Kuick, Rork, Misek, David E., Rennert, Gad, ...
Recent studies suggest accurate prediction of tissue of origin for human cancers can be achieved by applying sophisticated statistical learning procedures to gene expression data obtained from DNA...
Diversity of the Angiogenic Phenotype in Non–Small Cell Lung Cancer
McClelland, Marc R., Carskadon, Shannon L., Zhao, Liujian, White, Eric S., Beer, David G., Orringer, Mark B., ...
Angiogenesis is crucial for tumor biology. There are many mechanisms by which tumors induce angiogenesis. We hypothesize that each individual tumor develops a unique mechanism to induce angiogenesis,...
EML4-ALK Fusion Lung Cancer: A Rare Acquired Event
Perner, Sven, Wagner, Patrick L, Demichelis, Francesca, Mehra, Rohit, LaFargue, Christopher J, Moss, Benjamin J, ...
A recurrent gene fusion between EML4 and ALK in 6.7% of non-small cell lung cancers (NSCLCs) and NKX2-1 (TTF1, TITF1) high-level amplifications in 12% of adenocarcinomas of the lung were...