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 […]

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 […]