Research Paper
BMC Genomics: Education, collaboration, and innovation: intelligent biology and medicine in the era of big data
June 11, 2015
Jianhua Ruan, Victor Jin, Yufei Huang, Hua Xu, Jeremy S Edwards, Yidong Chen & Zhongming Zhao Abstract Here we present a summary of the 2014 International Conference on Intelligent Biology and Medicine (ICIBM 2014) and the editorial report of the supplement to BMC Genomics and BMC Systems Biology that includes 20 research articles selected from ICIBM […]
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 […]
Familial Cancers: Mutations of HNRNPA0 and WIF1 predispose members of a large family to multiple cancers
February 26, 2015
Chongjuan Wei 1, Bo Peng, Younghun Han, Wei V Chen, Joshua Rother, Gail E Tomlinson, C Richard Boland, Damien Chaussabel, Marsha L Frazier, Christopher I Amos Erratum in Erratum to: Mutations of HNRNPA0 and WIF1 predispose members of a large family to multiple cancers. Wei C, Peng B, Han Y, Chen WV, Rother J, Tomlinson GE, Richard Boland C, Chaussabel D, Frazier ML, Amos CI.Fam […]
Genes & Cancer: Microarray profile of human kidney from diabetes, renal cell carcinoma and renal cell carcinoma with diabetes
February 14, 2015
Adam Kosti2, Hung-I Harry Chen4, Sumathy Mohan3, Sitai Liang2, Yidong Chen4,5, and Samy L. Habib1,2 ABSTRACT A recent study from our laboratory showed that patients with diabetes are at a higher risk of developing kidney cancer. In the current study, we have screened the whole human DNA genome from healthy control, patients with diabetes or renal […]