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 […]

Echocardiography: Cardiac Assessment in Pediatric Mice: Strain Analysis as a Diagnostic Measurement

June 7, 2013

Thomas G. Andrews, M.Sc.,* Merry L. Lindsey, PhD,† Richard A. Lange, MD, M.B.A,‡ and Gregory J. Aune, MD, PhD§ Echocardiography is a robust tool for assessing cardiac function in both humans and laboratory animals. Conventional echocardiographic measurements, including chamber dimensions, wall thickness, and ejection fraction are routinely obtained to assess cardiac function in mice. Recently, […]

Translational Cancer Research: Utilizing signature-score to identify oncogenic pathways of cholangiocarcinoma

February 1, 2013

Tzu-Hung Hsiao, Hung-I Harry Chen, Jo-Yang Lu, Pei-Ying Lin, Charles Keller, Sarah Comerford, Gail E. Tomlinson, Yidong Chen Abstract Extracting maximal information from gene signature sets (GSSs) via microarray-based transcriptional profiling involves assigning function to up and down-regulated genes. Here we present a novel sample scoring method called Signature-score (S-score) which can be used to […]

Journal of Clinical Investigation: ZEB1 drives prometastatic actin cytoskeletal remodeling by downregulating miR-34a expression

August 1, 2012

Young-Ho Ahn,1 Don L. Gibbons,1,2 Deepavali Chakravarti,3 Chad J. Creighton,4 Zain H. Rizvi,1 Henry P. Adams,5 Alexander Pertsemlidis,6 Philip A. Gregory,7,8 Josephine A. Wright,7,8 Gregory J. Goodall,7,8,9 Elsa R. Flores,3 and Jonathan M. Kurie1 Abstract Metastatic cancer is extremely difficult to treat, and the presence of metastases greatly reduces a cancer patient’s likelihood of long-term survival. The ZEB1 transcriptional repressor promotes metastasis through downregulation of microRNAs (miRs) […]

Pediatric Blood & Cancer: Genetics and epigenetics of hepatoblastoma

July 13, 2012

Gail E Tomlinson 1, Roland Kappler Abstract A number of unique genetic features are observed in hepatoblastoma that has provided insights into the origins of hepatoblastoma. Hallmark cytogenetic changes in hepatoblastoma include the acquisition of additional copies of whole chromosomes and a recurring unbalanced translocation involving 1q. Genetic syndromes are associated with approximately 15% of hepatoblastoma and […]

Biotechniques: Isolation of Sertoli, Leydig, and spermatogenic cells from the mouse testis

November 5, 2011

Yao-Fu Chang 1, Jennifer S Lee-Chang, Subbarayalu Panneerdoss, James A MacLean 2nd, Manjeet K Rao Abstract A thorough understanding of the events during mammalian spermatogenesis requires studying specific molecular signatures of individual testicular cell populations as well as their interaction in co-cultures. However, most purification techniques to isolate specific testicular cell populations are time-consuming, require large numbers of animals, and/or […]

Molecular Profiling: Genome-Wide Methylation Profiling in Archival Formalin-Fixed Paraffin-Embedded Tissue Samples

October 21, 2011

J. Keith Killian, Robert L. Walker, Sven Bilke, Yidong Chen, Sean Davis, Robert Cornelison, William I. Smith, Paul S. Meltzer Abstract New technologies allow for the genome-scale measurement of DNA methylation. In an effort to increase the clinical utility of DNA methylation as a biomarker, we have adapted a commercial bisulfite epigenotype assay for genome-wide methylation profiling in archival formalin-fixed paraffin-embedded pathology specimens. This […]