John Quackenbush

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White1, J. Li1, W. Liang1, N. Bhagabati1, J. Braisted1, M. Klapa1, T. Currier1, M. Thiagarajan1, A. Sturn1, M. Snuffin2, A. Rezantsev2, D. Popov2, A. Ryltsov2, E. Kostukovich2, I. Borisovsky2, Z. Liu3, A. Vinsavich3, V. Trush3, and J. Quackenbush1,4 1The Institute for Genomic Research, Rockville, MD, 2DataNaut, Bethesda, MD, 3Syntek Systems, Bethesda, MD,(More)
UNLABELLED PURPOSE To improve on current standards for breast cancer prognosis and prediction of chemotherapy benefit by developing a risk model that incorporates the gene expression-based "intrinsic" subtypes luminal A, luminal B, HER2-enriched, and basal-like. METHODS A 50-gene subtype predictor was developed using microarray and quantitative reverse(More)
TGICL is a pipeline for analysis of large Expressed Sequence Tags (EST) and mRNA databases in which the sequences are first clustered based on pairwise sequence similarity, and then assembled by individual clusters (optionally with quality values) to produce longer, more complete consensus sequences. The system can run on multi-CPU architectures including(More)
This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and(More)
Helicobacter pylori, strain 26695, has a circular genome of 1,667,867 base pairs and 1,590 predicted coding sequences. Sequence analysis indicates that H. pylori has well-developed systems for motility, for scavenging iron, and for DNA restriction and modification. Many putative adhesins, lipoproteins and other outer membrane proteins were identified,(More)
Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment(More)
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. However, validation is often unconvincing because the size of the test set is typically small. To overcome this problem we used publicly available breast cancer gene expression(More)
A versatile, platform independent and easy to use Java suite for large-scale gene expression analysis was developed. Genesis integrates various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means,(More)
Underlying every microarray experiment is an experimental question that one would like to address. Finding a useful and satisfactory answer relies on careful experimental design and the use of a variety of data-mining tools to explore the relationships between genes or reveal patterns of expression. While other sections of this issue deal with these lofty(More)
Powerful specialized software is essential for managing, quantifying, and ultimately deriving scientific insight from results of a microarray experiment. We have developed a suite of software applications, known as TM4, to support such gene expression studies. The suite consists of open-source tools for data management and reporting, image analysis,(More)