Bioinformatics: Exome-based analysis for RNA epigenome sequencing data

June 15, 2013

Jia Meng, Xiaodong Cui, Manjeet K. Rao, Yidong Chen, Yufei Huang Abstract Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques. Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data […]

Echocardiography: Cardiac Assessment in Pediatric Mice: Strain Analysis as a Diagnostic Measurement

June 7, 2013

Thomas G. Andrews, M.Sc.,* Merry L. Lindsey, PhD,† Richard A. Lange, MD, M.B.A,‡ and Gregory J. Aune, MD, PhD§ Echocardiography is a robust tool for assessing cardiac function in both humans and laboratory animals. Conventional echocardiographic measurements, including chamber dimensions, wall thickness, and ejection fraction are routinely obtained to assess cardiac function in mice. Recently, […]

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. […]

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 […]