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 […]

SA Express-News: Childhood cancer survivor active in Obama’s ‘precision medicine’ effort

February 9, 2015

S.A. scientist also a cancer survivor As a childhood cancer survivor, San Antonio pediatric oncologist Greg Aune understood the excitement felt by cancer patients and their families when President Barack Obama announced his “precision medicine” initiative nearly two weeks ago. The groundbreaking initiative — for which Obama has requested an initial $215 million in his […]

International Journal of Molecular Sciences (MDPI): Potential Relationship between Inadequate Response to DNA Damage and Development of Myelodysplastic Syndrome

January 5, 2015

Ting Zhou 1,2,Peishuai Chen 1,3,Jian Gu 3,Alexander J. R. Bishop 1,2,4,5,Linda M. Scott 6,Paul Hasty 4,5,7 and Vivienne I. Rebel 1,2,4,5,* Abstract Hematopoietic stem cells (HSCs) are responsible for the continuous regeneration of all types of blood cells, including themselves. To ensure the functional and genomic integrity of blood tissue, a network of regulatory pathways tightly controls the proliferative status of HSCs. […]

Journal of Biological Chemistry: Hormone-induced and DNA Demethylation-induced Relief of a Tissue-specific and Developmentally Regulated Block in Transcriptional Elongation*

December 19, 2014

Abstract Genome-wide studies have revealed that genes commonly have a high density of RNA polymerase II just downstream of the transcription start site. This has raised the possibility that genes are commonly regulated by transcriptional elongation, but this remains largely untested in vivo, particularly in vertebrates. Here, we show that the proximal promoter from the Rhox5 homeobox […]

American Journal of Physiology – Heart & Circulatory Physiology: The tell-tale heart: molecular and cellular responses to childhood anthracycline exposure

November 15, 2014

Merry L. Lindsey, Richard A. Lange, Helen Parsons, Thomas Andrews, and Gregory J. Aune Abstract Since the modern era of cancer chemotherapy that began in the mid-1940s, survival rates for children afflicted with cancer have steadily improved from 10% to current rates that approach 80% (60). Unfortunately, many long-term survivors of pediatric cancer develop chemotherapy-related health effects; 25% are […]