BMC Genomics: Robust inference of the context specific structure and temporal dynamics of gene regulatory network

December 1, 2010

Jia Meng, Mingzhu Lu, Yidong Chen, Shou-Jiang Gao & Yufei Huang Abstract Background The response of cells to changing endogenous or exogenous conditions is governed by intricate molecular interactions or regulatory networks. To lead to appropriate responses, the regulatory network should be 1) context-specific, i.e., its constituents and topology depend on the phenotypical and experimental context including tissue types and […]

BMC Genomics: A Bayesian approach for identifying miRNA targets by combining sequence prediction and gene expression profiling

December 1, 2010

Hui Liu, Dong Yue, Lin Zhang, Yidong Chen, Shou-Jiang Gao & Yufei Huang Abstract Background MicroRNAs (miRNAs) are single-stranded non-coding RNAs shown to plays important regulatory roles in a wide range of biological processes and diseases. The functions and regulatory mechanisms of most miRNAs are still poorly understood in part because of the difficulty in identifying the miRNA regulatory targets. To […]

Breast Cancer Research & Treatment: Germline mutations in PALB2 in African-American breast cancer cases

November 27, 2010

Yuan Chun Ding 1, Linda Steele, Li-Hao Chu, Karen Kelley, Helen Davis, Esther M John, Gail E Tomlinson, Susan L Neuhausen Abstract Breast cancer incidence is lower in African Americans than in Caucasian Americans. However, African-American women have higher breast cancer mortality rates and tend to be diagnosed with the earlier-onset disease. Identifying factors correlated to the racial/ethnic variation in the epidemiology of […]

Blood: Heat shock protein 90 regulates the expression of Wilms tumor 1 protein in myeloid leukemias

November 25, 2010

Hima Bansal 1, Sanjay Bansal, Manjeet Rao, Kevin P Foley, Jim Sang, David A Proia, Ronald K Blackman, Weiwen Ying, James Barsoum, Maria R Baer, Kevin Kelly, Ronan Swords, Gail E Tomlinson, Minoo Battiwalla, Francis J Giles, Kelvin P Lee, Swaminathan Padmanabhan Abstract The aberrant overexpression of Wilms tumor 1 (WT1) in myeloid leukemia plays an important role in blast cell survival and resistance to chemotherapy. High expression of WT1 is also […]

BMC Bioinformatics: Improving performance of mammalian microRNA target prediction

September 22, 2010

Hui Liu, Dong Yue, Yidong Chen, Shou-Jiang Gao & Yufei Huang Abstract Background MicroRNAs (miRNAs) are single-stranded non-coding RNAs known to regulate a wide range of cellular processes by silencing the gene expression at the protein and/or mRNA levels. Computational prediction of miRNA targets is essential for elucidating the detailed functions of miRNA. However, the prediction specificity and sensitivity of […]

Journal of Nucleic Acids: Mouse WRN Helicase Domain Is Not Required for Spontaneous Homologous Recombination-Mediated DNA Deletion

August 19, 2010

Adam D. Brown,1,2 Alison B. Claybon,1 and Alexander J. R. Bishop1,2 Abstract Werner syndrome is a rare disorder that manifests as premature aging and age-related diseases. WRN is the gene mutated in WS, and is one of five human RecQ helicase family members. WS cells exhibit genomic instability and altered proliferation, and in vitro studies suggest that WRN has a role in […]

Annals of Human Genetics: Power of Genetic Association Studies with Fixed and Random Genotype Frequencies

August 15, 2010

Julia Kozlitina Chao Xing Alexander Pertsemlidis William R. Schucany Summary When estimating the power of genetic association studies, the allele and genotype frequencies are often assumed to be known, and the numbers of individuals with each genotype are set equal to their expectations under Hardy‐Weinberg equilibrium. In fact, both allele and genotype frequencies are unknown […]

Nucleic Acids Research: PARP1 suppresses homologous recombination events in mice “in vivo”

July 21, 2010

Alison Claybon, Bijal Karia, Crystal Bruce, Alexander J. R. Bishop Abstract Recent studies suggest that PARP1 inhibitors, several of which are currently in a clinical trial, may selectively kill BRCA1/2 mutant cancer cells. It is thought that the success of this therapy is based on immitigable lethal DNA damage in the cancer cells resultant from the concurrent loss […]

Oncogene: MicroRNA-185 suppresses tumor growth and progression by targeting the Six1 oncogene in human cancers

July 5, 2010

J S Imam, K Buddavarapu, J S Lee-Chang, S Ganapathy, C Camosy, Y Chen & M K Rao Abstract Homeobox genes encode transcription factors that are essential for normal development and are often dysregulated in cancers. The molecular mechanisms that cause their misregulation in cancers are largely unknown. In this study, we investigate the mechanism by which the Six1 homeobox protein, which […]

BMC: MicroRNA expression distinguishes SCLC from NSCLC lung tumor cells and suggests a possible pathological relationship between SCLCs and NSCLCs

June 17, 2010

Liqin Du, Jeoffrey J Schageman, Irnov, Luc Girard, Scott M Hammond, John D Minna, Adi F Gazdar & Alexander Pertsemlidis Abstract Background Recent studies have shown that microRNAs (miRNAs) play roles in tumorigenesis and are reliable classifiers of certain cancer types and subtypes. However, the role of miRNAs in the pathogenesis and diagnosis of small cell […]