Research Paper
IEEE: Estimating Conditional Probabilities for the Detection of Unfavorable Copy Number Alterations in a Targeted Therapy
June 5, 2013
Fang-Han Hsu; Edward R. Dougherty; Yidong Chen; Erchin Serpedin Abstract: Emerging targeted therapies have shown benefits such as less toxicity and higher effectiveness in specific types of cancer treatment; however, the accessibility of these advantages may rely on the correct identification of suitable patients, which remains highly immature. We assume that copy number profiles, being accessible genomic data […]
Diabetes Journal: Enhanced NF-κB Activity Impairs Vascular Function Through PARP-1–, SP-1–, and COX-2–Dependent Mechanisms in Type 2 Diabetes
June 1, 2013
Modar Kassan1,2, Soo-Kyoung Choi1, Maria Galán1,2, Alexander Bishop3, Kazuo Umezawa4, Mohamed Trebak5, Souad Belmadani2⇑ , and Khalid Matrougui1,2⇑ Abstract Type 2 diabetes (T2D) is associated with vascular dysfunction. We hypothesized that increased nuclear factor-κB (NF-κB) signaling contributes to vascular dysfunction in T2D. We treated type 2 diabetic (db−/db−) and control (db−/db+) mice with two NF-κB inhibitors (6 mg/kg dehydroxymethylepoxyquinomicin twice a week […]
Cancer Epidemiology: Maternal pregnancy events and exposures and risk of hepatoblastoma: a Children’s Oncology Group (COG) study
June 1, 2013
Jessica R B Musselman 1, Michael K Georgieff, Julie A Ross, Gail E Tomlinson, James Feusner, Mark Krailo, Logan G Spector Abstract Background: Hepatoblastoma is a rare childhood liver cancer with an obscure etiology, however, it is potentially associated with selected pregnancy events and hepatoblastoma risk in offspring. Methods: Adjusted unconditional logistic regression estimated odds ratios (OR) and corresponding 95% confidence intervals (CI) for […]
PLOS One: CMS: A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers
April 22, 2013
Fei Gu ,Mark S. Doderer ,Yi-Wen Huang,Juan C. Roa,Paul J. Goodfellow,E. Lynette Kizer,Tim H. M. Huang ,Yidong Chen Abstract Background DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. […]
Proteomics Clinical Applications: Using proteomics to uncover extracellular matrix interactions during cardiac remodeling
March 23, 2013
Nicolle L. Patterson, Rugmani Padmanabhan Iyer, Lisandra E. de Castro Brás, Yaojun Li, Thomas G. Andrews, Gregory J. Aune, Richard A. Lange, Merry L. Lindsey Abstract The left ventricle (LV) responds to myocardial infarction with an orchestrated sequence of events that result in fundamental changes to both the structure and function of the myocardium. This collection of responses is termed LV […]
Advances in Bioinformatics: Computational and Statistical Approaches for Modeling of Proteomic and Genomic Networks
March 13, 2013
Mario Flores,1 Tzu-Hung Hsiao,2 Yu-Chiao Chiu,3 Eric Y. Chuang,3 Yufei Huang,1 and Yidong Chen2,4 Abstract Common microarray and next-generation sequencing data analysis concentrate on tumor subtype classification, marker detection, and transcriptional regulation discovery during biological processes by exploring the correlated gene expression patterns and their shared functions. Genetic regulatory network (GRN) based approaches have been employed in many large studies in […]
Cell: Jmjd3 Inhibits Reprogramming by Upregulating Expression of INK4a/Arf and Targeting PHF20 for Ubiquitination
February 28, 2013
WeiZhao1 QingtianLi1, StephenAyers2, YifengGu1, ZhongShi3, QingyuanZhu1, YidongChen4, Helen Y.Wang1, Rong-FuWang1 Summary Although somatic cell reprogramming to generate inducible pluripotent stem cells (iPSCs) is associated with profound epigenetic changes, the roles and mechanisms of epigenetic factors in this process remain poorly understood. Here, we identify Jmjd3 as a potent negative regulator of reprogramming. Jmjd3-deficient MEFs produced significantly more iPSC colonies than did wild-type […]
Translational Cancer Research: Utilizing signature-score to identify oncogenic pathways of cholangiocarcinoma
February 1, 2013
Tzu-Hung Hsiao, Hung-I Harry Chen, Jo-Yang Lu, Pei-Ying Lin, Charles Keller, Sarah Comerford, Gail E. Tomlinson, Yidong Chen Abstract Extracting maximal information from gene signature sets (GSSs) via microarray-based transcriptional profiling involves assigning function to up and down-regulated genes. Here we present a novel sample scoring method called Signature-score (S-score) which can be used to […]
PLOS One: Genomic Loss of Tumor Suppressor miRNA-204 Promotes Cancer Cell Migration and Invasion by Activating AKT/mTOR/Rac1 Signaling and Actin Reorganization
December 21, 2012
J. Saadi Imam, Jason R. Plyler , Hima Bansal , Suresh Prajapati , Sanjay Bansal, Jennifer Rebeles, Hung-I Harry Chen, Yao-Fu Chang, Subbarayalu Panneerdoss, Behyar Zoghi, Kalyan C. Buddavarapu, Russell Broaddus, Peter Hornsby, Gail Tomlinson, Jeffrey Dome, Ratna K. Vadlamudi, Alexander Pertsemlidis, Yidong Chen, Manjeet K. Rao Abstract Increasing evidence suggests that chromosomal regions containing microRNAs are functionally important […]
Pediatric Blood & Cancer: Children’s Oncology Group’s 2013 blueprint for research: rare tumors
December 19, 2012
Carlos Rodriguez-Galindo 1, Mark Krailo, Lindsay Frazier, Murali Chintagumpala, James Amatruda, Howard Katzenstein, Marcio Malogolowkin, Logan Spector, Farzana Pashankar, Rebecka Meyers, Gail Tomlinson, COG Rare Tumors Disease Committee Abstract In the US, approximately 2,000 children are diagnosed with rare cancers each year, with 5-year survival ranging from <20% for children with advanced carcinomas to >95% for children with intraocular retinoblastoma or localized germ cell tumors. During the […]