Data-driven normalization strategies for high-throughput quantitative RT-PCR (2009)
Mar Jessica, Kimura Yasumasa, Schroder Kate, Irvine Katharine, Hayashizaki Yoshihide, Suzuki Harukazu, ...
Abstract Background High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to...
Boedigheimer Michael, Wolfinger Russell, Bass Michael, Bushel Pierre, Chou Jeff, Cooper Matthew, ...
Abstract Background The use of gene expression profiling in both clinical and laboratory settings would be enhanced by better characterization of variance due to individual, environmental, and...
Seeded Bayesian Networks: Constructing genetic networks from microarray data (2008)
Djebbari Amira, Quackenbush John
Abstract Background DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes...
Danley Patrick, Mullen Sean, Liu Fenglong, Nene Vishvanath, Quackenbush John, Shaw Kerry
Abstract Background As the developmental costs of genomic tools decline, genomic approaches to non-model systems are becoming more feasible. Many of these systems may lack advanced genetic tools but...
The molecular portraits of breast tumors are conserved across microarray platforms (2006)
Hu Zhiyuan, Fan Cheng, Oh Daniel, Marron JS, He Xiaping, Qaqish Bahjat, ...
Abstract Background Validation of a novel gene expression signature in independent data sets is a critical step in the development of a clinically useful test for cancer patient risk-stratification....
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. (2006)
Maeda Norihiro, Kasukawa Takeya, Oyama Rieko, Gough Julian, Frith Martin, Engström Pär G, ...
The international FANTOM consortium aims to produce a comprehensive picture of the mammalian transcriptome, based upon an extensive cDNA collection and functional annotation of full-length enriched...
Hu Valerie, Frank Bryan, Heine Shannon, Lee Norman, Quackenbush John
Abstract Background The autism spectrum encompasses a set of complex multigenic developmental disorders that severely impact the development of language, non-verbal communication, and social skills,...
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB (2006)
Rayner Tim, Rocca-Serra Philippe, Spellman Paul, Causton Helen, Farne Anna, Holloway Ele, ...
Abstract Background Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the...
A robust method for the amplification of RNA in the sense orientation (2005)
Marko Nicholas, Frank Bryan, Quackenbush John, Lee Norman
Abstract Background Small quantities of RNA (1–4 μg total RNA) available from biological samples frequently require a single round of amplification prior to analysis, but current...
The limits of log-ratios (2004)
Sharov Vasily, Kwong Ka, Frank Bryan, Chen Emily, Hasseman Jeremy, Gaspard Renee, ...
Abstract Background DNA microarray assays typically compare two biological samples and present the results of those comparisons gene-by-gene as the logarithm base two of the ratio of the measured...
Ghedin Elodie, Pumfery Anne, Yao Karen, Miller Naomi, Lacoste Vincent, ...
Abstract Background Since the discovery of human immunodeficiency virus (HIV-1) twenty years ago, AIDS has become one of the most studied diseases. A number of viruses have subsequently been...
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones (2004)
Imanishi Tadashi, Itoh Takeshi, Suzuki Yutaka, O'Donovan Claire, Fukuchi Satoshi, Koyanagi Kanako O, ...
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this...