Research Paper

Genes & Development: Lineage of origin in rhabdomyosarcoma informs pharmacological response

June 3, 2014

Jinu Abraham1, Yaiza Nuñez-Álvarez2, Simone Hettmer3,4, Elvira Carrió2, Hung-I Harry Chen5, Koichi Nishijo5, Elaine T. Huang1, Suresh I. Prajapati5, Robert L. Walker6, Sean Davis6, Jennifer Rebeles5, Hunter Wiebush5, Amanda T. McCleish5, Sheila T. Hampton5, Christopher R.R. Bjornson7, Andrew S. Brack7, Amy J. Wagers3, Thomas A. Rando7, Mario R. Capecchi8, Frank C. Marini9, Benjamin R. Ehler10, Lee Ann Zarzabal10, Martin W. Goros10, Joel E. Michalek10, Paul S. Meltzer6, David M. Langenau11, Robin D. LeGallo12, Atiya Mansoor13, Yidong Chen5,10, Mònica Suelves2, Brian P. Rubin14 and Charles Keller1,15 Abstract Lineage […]

Cell Reports: Negative Elongation Factor Controls Energy Homeostasis in Cardiomyocytes

April 17, 2014

HaihuiPan1 KunhuaQin1 ZhanyongGuo23 YonggangMa4CraigApril7 XiaoliGao5T homas G.Andrews2 AlexBokov3 JianhuaZhang4 YidongChen23 Susan T.Weintraub5 Jian-BingFan7 DegengWang 23YanfenHu1 Gregory J.Aune26 Merry L.Lindsey4 RongLi1 Summary 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 […]

Breast Cancer Research & Treatment: Long-term risk of medical conditions associated with breast cancer treatment

April 3, 2014

Deirdre A Hill 1, Nora K Horick, Claudine Isaacs, Susan M Domchek, Gail E Tomlinson, Jan T Lowery, Anita Y Kinney, Jonathan S Berg, Karen L Edwards, Patricia G Moorman, Sharon E Plon, Louise C Strong, Argyrois Ziogas, Constance A Griffin, Carol H Kasten, Dianne M Finkelstein Abstract Early and late effects of cancer treatment are of increasing concern with growing survivor populations, but relevant data are sparse. We sought to […]

Cancer Prevention Research: Pubertal Bisphenol A Exposure Alters Murine Mammary Stem Cell Function Leading to Early Neoplasia in Regenerated Glands

April 1, 2014

Danhan Wang, Hui Gao, Abhik Bandyopadhyay, Anqi Wu, I-Tien Yeh, Yidong Chen, Yi Zou, Changjiang Huang, Christi A. Walter, Qiaoxiang Dong, and Lu-Zhe Sun Abstract Perinatal exposure to bisphenol A (BPA) has been shown to cause aberrant mammary gland morphogenesis and mammary neoplastic transformation. Yet, the underlying mechanism is poorly understood. We tested the hypothesis that mammary glands exposed to BPA during a susceptible window may lead to its susceptibility to tumorigenesis through a stem cell-mediated mechanism. […]

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 […]