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 […]

BMC Genomics: A Bayesian decision fusion approach for microRNA target prediction

December 17, 2012

Dong Yue, Maozu Guo, Yidong Chen & Yufei Huang Abstract MicroRNAs (miRNAs) are 19-25 nucleotides non-coding RNAs known to have important post-transcriptional regulatory functions. The computational target prediction algorithm is vital to effective experimental testing. However, since different existing algorithms rely on different features and classifiers, there is a poor agreement among the results of different algorithms. To benefit […]

BMC Genomics: Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer

October 26, 2012

Fang-Han Hsu, Erchin Serpedin, Tzu-Hung Hsiao, Alexander JR Bishop, Edward R Dougherty & Yidong Chen Abstract Background Despite initial response in adjuvant chemotherapy, ovarian cancer patients treated with the combination of paclitaxel and carboplatin frequently suffer from recurrence after a few cycles of treatment, and the underlying mechanisms causing the chemoresistance remain unclear. Recently, The Cancer Genome Atlas (TCGA) research network […]

BMC Genomics: Pathway Distiller – multisource biological pathway consolidation

October 26, 2012

Mark S Doderer, Zachry Anguiano, Uthra Suresh, Ravi Dashnamoorthy, Alexander JR Bishop & Yidong Chen  Abstract Background One method to understand and evaluate an experiment that produces a large set of genes, such as a gene expression microarray analysis, is to identify overrepresentation or enrichment for biological pathways. Because pathways are able to functionally describe the set of genes, much effort […]