Biology of Reproduction: Rhox8 Ablation in the Sertoli Cells Using a Tissue-Specific RNAi Approach Results in Impaired Male Fertility in Mice

July 1, 2015

Joshua P. Welborn, Matthew G. Davis, Steven D. Ebers, Genna R. Stodden, Kanako Hayashi, Joseph L. Cheatwood, Manjeet K. Rao, James A. MacLean, II Abstract The reproductive homeobox X-linked, Rhox, genes encode transcription factors that are selectively expressed in reproductive tissues. While there are 33 Rhox genes in mice, only Rhox and Rhox8 are expressed in Sertoli cells, suggesting that they may regulate the expression of somatic-cell gene products […]

BMC Genomics: Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes

June 11, 2015

Yu-Chiao Chiu, Chin-Ting Wu, Tzu-Hung Hsiao, Yi-Pin Lai, Chuhsing Kate Hsiao, Yidong Chen & Eric Y Chuang Abstract Background Gene regulation is dynamic across cellular conditions and disease subtypes. From the aspect of regulation under modulation, regulation strength between a pair of genes can be modulated by (dependent on) expression abundance of another gene (modulator gene). […]

BMC Genomics: Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads

June 11, 2015

Hung-I Harry Chen, Yuanhang Liu, Yi Zou, Zhao Lai, Devanand Sarkar, Yufei Huang & Yidong Chen Abstract Background RNA sequencing (RNA-seq) is a powerful tool for genome-wide expression profiling of biological samples with the advantage of high-throughput and high resolution. There are many existing algorithms nowadays for quantifying expression levels and detecting differential gene expression, but […]

Endocrine-Related Cancer: Integrity of the pheochromocytoma susceptibility TMEM127 gene in patients with pediatric malignancies

June 1, 2015

Authors: E E King 1 , Y Qin 1 , R A Toledo 1 , A Luo 1 , E Ball 1 , F R Faucz 1 , K A Janeway1 , C A Stratakis 1 , G E Tomlinson 1 , 1 , 1 , and P L M Dahia 1 , 1 , 1 Dear Editor, Germline mutations of the tumor suppressor gene TMEM127 occur in the neural-crest-derived tumors, pheochromocytomas, and paragangliomas (Qin et al. 2010, Yao et al. 2010, Neumann et al. 2011), and have also been detected in renal cell […]

RNA Biology: microRNA-449a functions as a tumor suppressor in neuroblastoma through inducing cell differentiation and cell cycle arrest

May 6, 2015

Zhenze ZhaoGreehey Children’s Cancer Research Institute; ,Xiuye Ma,Derek Sung,Monica Li,Adam Kosti,Gregory Lin,Yidong Chen,Alexander Pertsemlidis,Tzu-Hung Hsiao &Liqin Du Abstract microRNA-449a (miR-449a) has been identified to function as a tumor suppressor in several types of cancers. However, the role of miR-449a in neuroblastoma has not been intensively investigated. We recently found that the overexpression of miR-449a significantly induces […]

BMC Genomics: HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data

April 21, 2015

Xiaodong Cui, Jia Meng, Manjeet K Rao, Yidong Chen & Yufei Huang Abstract Background Methylated RNA Immunoprecipitation combined with RNA sequencing (MeRIP-seq) is revolutionizing the de novo study of RNA epigenomics at a higher resolution. However, this new technology poses unique bioinformatics problems that call for novel and sophisticated statistical computational solutions, aiming at identifying and […]

BMC Genomics: Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers

April 21, 2015

Yu-Chiao Chiu, Tzu-Hung Hsiao, Yidong Chen & Eric Y Chuang Abstract Background In addition to direct targeting and repressing mRNAs, recent studies reported that microRNAs (miRNAs) can bridge up an alternative layer of post-transcriptional gene regulatory networks. The competing endogenous RNA (ceRNA) regulation depicts the scenario where pairs of genes (ceRNAs) sharing, fully or partially, common […]

Fitoterapia: Jonquailine, a new pretazettine-type alkaloid isolated from Narcissus jonquilla quail, with activity against drug-resistant cancer

April 1, 2015

Marco Masi 1, Liliya V Frolova 2, Xiaojie Yu 3, Véronique Mathieu 4, Alessio Cimmino 1, Annelise De Carvalho 4, Robert Kiss 4, Snezna Rogelj 2, Alexander Pertsemlidis 3, Alexander Kornienko 5, Antonio Evidente 6 Abstract A new alkaloid, belonging to the pretazettine group of Amaryllidaceae alkaloids, was isolated from dried bulbs of Narcissus jonquilla quail and named jonquailine. Its structure, including the absolute configuration, was elucidated using various NMR, ECD, and ESI MS techniques. The […]

IEEE Xplore: MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data

March 2, 2015

Lin Zhang; Jia Meng; Manjeet K. Rao; Yidong Chen; Yufei Huang Abstract: N6-Methyladenosine (m6A) transcriptome methylation is an exciting new research area that just captures the attention of the research community. We present in this paper, MeTDiff, a novel computational tool for predicting differential m6A methylation sites from Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) data. Compared with the existing algorithm […]