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, […]

Frontiers in Psychiatry: The CHRNA3 rs578776 Variant is Associated with an Intrinsic Reward Sensitivity Deficit in Smokers

September 23, 2013

Jason D Robinson 1, Francesco Versace, Cho Y Lam, Jennifer A Minnix, Jeffrey M Engelmann, Yong Cui, Maher Karam-Hage, Sanjay S Shete, Gail E Tomlinson, Tina T-L Chen, David W Wetter, Charles E Green, Paul M Cinciripini Abstract A compromised brain reward system has been postulated as a key feature of drug dependence. We examined whether several polymorphisms of genes found to regulate nicotinic acetylcholine receptor (nAChR) and […]