PLOS One: ATR Suppresses Endogenous DNA Damage and Allows Completion of Homologous Recombination Repair

March 27, 2014

Adam D. Brown, Brian W. Sager, Aparna Gorthi, Sonal S. Tonapi, Eric J. Brown, Alexander J. R. Bishop  Abstract DNA replication fork stalling or collapse that arises from endogenous damage poses a serious threat to genome stability, but cells invoke an intricate signaling cascade referred to as the DNA damage response (DDR) to prevent such […]

Europe PMCP: Negative elongation factor controls energy homeostasis in cardiomyocytes. (Aune & Chen)

March 19, 2014

Abstract Negative elongation factor (NELF) is known to enforce promoter-proximal pausing of RNA polymerase II (Pol II), a pervasive phenomenon observed across multicellular genomes. However, the physiological impact of NELF on tissue homeostasis remains unclear. Here, we show that whole-body conditional deletion of the B subunit of NELF (NELF-B) in adult mice results in cardiomyopathy […]

Bioinformatics: A novel significance score for gene selection and ranking

March 15, 2014

Yufei Xiao, Tzu-Hung Hsiao, Uthra Suresh, Hung-I Harry Chen, Xiaowu Wu, Steven E. Wolf, Yidong Chen Abstract Motivation: When identifying differentially expressed (DE) genes from high-throughput gene expression measurements, we would like to take both statistical significance (such as P-value) and biological relevance (such as fold change) into consideration. In gene set enrichment analysis (GSEA), a score that can combine fold-change and P-value […]

Oncotarget: A high-content morphological screen identifies novel microRNAs that regulate neuroblastoma cell differentiation

February 28, 2014

Zhenze Zhao1, Xiuye Ma1, Tzu-Hung Hsiao1, Gregory Lin1, Adam Kosti1, Xiaojie Yu2, Uthra Suresh1, Yidong Chen1,3, Gail E. Tomlinson1,4, Alexander Pertsemlidis1,4,5, Liqin Du1,5 ABSTRACT Neuroblastoma, the most common extracranial solid tumor of childhood, arises from neural crest cell precursors that fail to differentiate. Inducing cell differentiation is an important therapeutic strategy for neuroblastoma. We developed […]

PLOS One: Mice Fed Rapamycin Have an Increase in Lifespan Associated with Major Changes in the Liver Transcriptome

January 14, 2014

Wilson C. Fok, Yidong Chen, Alex Bokov, Yiqiang Zhang, Adam B. Salmon, Vivian Diaz, Martin Javors, William H. Wood 3rd, Yongqing Zhang, Kevin G. Becker, Viviana I. Pérez, Arlan Richardson  Abstract Rapamycin was found to increase (11% to 16%) the lifespan of male and female C57BL/6J mice most likely by reducing the increase in the hazard […]

Molecular Ecology Resources: Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives

January 1, 2014

Kathryn A Hodgins 1, Zhao Lai, Luiz O Oliveira, David W Still, Moira Scascitelli, Michael S Barker, Nolan C Kane, Hannes Dempewolf, Alex Kozik, Richard V Kesseli, John M Burke, Richard W Michelmore, Loren H Rieseberg Abstract Although the Compositae harbors only two major food crops, sunflower, and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here, we […]

Molecular Oncology: PELP1 oncogenic functions involve alternative splicing via PRMT6

December 30, 2013

Monica Mann, Yi Zou, Yidong Chen, Darrell Brann, Ratna Vadlamudi Abstract Proline‐, glutamic acid‐, and leucine‐rich protein 1 (PELP1) is a proto‐oncogene that functions as a coactivator of the estrogen receptor and is an independent prognostic predictor of shorter survival of breast cancer patients. The dysregulation of PELP1 in breast cancer has been implicated in oncogenesis, metastasis, and […]

Aging Cell: Combined treatment of rapamycin and dietary restriction has a larger effect on the transcriptome and metabolome of liver

December 13, 2013

Wilson C. Fok  Alex Bokov Jonathan Gelfond Zhen Yu Yiqiang Zhang Mark Doderer Yidong Chen Martin Javors William H. Wood III Yongqing Zhang Kevin G. Becker Arlan Richardson Viviana I. Pérez Summary Rapamycin (Rapa) and dietary restriction (DR) have consistently been shown to increase lifespan. To investigate whether Rapa and DR affect similar pathways in mice, we compared the effects of feeding mice ad libitum (AL), Rapa, DR, [...]

BMC Systems Biology: BRCA-Monet: a breast cancer specific drug treatment mode-of-action network for treatment effective prediction using large scale microarray database

December 9, 2013

Chifeng Ma, Hung-I Harry Chen, Mario Flores, Yufei Huang & Yidong Chen Abstract Background Connectivity map (cMap) is a recently developed dataset and algorithm for uncovering and understanding the treatment effect of small molecules on different cancer cell lines. It is widely used but there are still remaining challenges for accurate predictions. Method Here, we propose BRCA-MoNet, a network of […]

Journal of Biological Chemistry: The RHOX Homeodomain Proteins Regulate the Expression of Insulin and Other Metabolic Regulators in the Testis*

November 29, 2013

James A. MacLean II‡,§, Zhiying Hu§, Joshua P. Welborn‡, Hye-Won Song§,¶,‖, Manjeet K. Rao§,**, Chad M. Wayne§,‡‡ and Miles F. Wilkinson§,¶,‖1 Abstract Defects in cellular metabolism have been widely implicated in causing male infertility, but there has been little progress in understanding the underlying mechanism. Here we report that several key metabolism genes are regulated in […]