Research Paper
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 […]
Skeletal Muscle: Rb1 loss modifies but does not initiate alveolar rhabdomyosarcoma
November 25, 2013
Ken Kikuchi, Eri Taniguchi, Hung-I Harry Chen, Matthew N Svalina, Jinu Abraham, Elaine T Huang, Koichi Nishijo, Sean Davis, Christopher Louden, Lee Ann Zarzabal, Olivia Recht, Ayeza Bajwa, Noah Berlow, Mònica Suelves, Sherrie L Perkins, Paul S Meltzer, Atiya Mansoor, Joel E Michalek, Yidong Chen, Brian P Rubin & Charles Keller Abstract Background Alveolar rhabdomyosarcoma (aRMS) is a myogenic childhood sarcoma frequently associated with a translocation-mediated fusion gene, Pax3: Foxo1a. Methods We investigated the complementary role of Rb1 loss […]
Proteome Science: Fully automated protein complex prediction based on topological similarity and community structure
November 7, 2013
Chengwei Lei, Saleh Tamim, Alexander JR Bishop & Jianhua Ruan Abstract To understand the function of protein complexes and their association with biological processes, a lot of studies have been done towards analyzing the protein-protein interaction (PPI) networks. However, the advancement in high-throughput technology has resulted in a humongous amount of data for analysis. Moreover, a […]
DNA Repair: Induction of homologous recombination following in utero exposure to DNA-damaging agents
November 1, 2013
Bijal Kariaab, Jo Ann Martinez, Alexander J.R.Bishop Abstract Much of our understanding of homologous recombination, as well as the development of the working models for these processes, has been derived from extensive work in model organisms, such as yeast and fruit flies, and mammalian systems by studying the repair of induced double-strand breaks or repair […]
EURASIP Journal on Bioinformatics and Systems Biology: Identification of genomic functional hotspots with copy number alteration in liver cancer
October 25, 2013
Tzu-Hung Hsiao, Hung-I Harry Chen, Stephanie Roessler, Xin Wei Wang & Yidong Chen Abstract Copy number alterations (CNAs) can be observed in most cancer patients. Several oncogenes and tumor suppressor genes with CNAs have been identified in different kinds of tumors. However, the systematic survey of CNA-affected functions is still lack. By employing systems biology approaches, instead of examining individual […]
Cancer Epidemiology Biomarkers & Preventinon: Parental tobacco and alcohol use and risk of hepatoblastoma in offspring: a report from the children’s oncology group
October 15, 2013
Kimberly J Johnson 1, Katherine S Williams, Julie A Ross, Mark D Krailo, Gail E Tomlinson, Marcio H Malogolowkin, James H Feusner, Logan G Spector Abstract Background: Hepatoblastoma is a rare pediatric liver tumor that has significantly increased in incidence over the last several decades. The International Agency for Research on Cancer (IARC) recently classified hepatoblastoma as tobacco-related cancer. Parental alcohol use has shown […]
Taylor Francis: A high-throughput screen identifies miRNA inhibitors regulating lung cancer cell survival and response to paclitaxel
September 30, 2013
Liqin Du, Robert Borkowski, Zhenze Zhao, Xiuye Ma, Xiaojie Yu, Xian-Jin Xie &Alexander Pertsemlidis microRNAs (miRNAs) are small RNAs endogenously expressed in multiple organisms that regulate gene expression largely by decreasing levels of target messenger RNAs (mRNAs). Over the past few years, numerous studies have demonstrated critical roles for miRNAs in the pathogenesis of many cancers, […]