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MOTIVATION Time series expression experiments are used to study a wide range of biological systems. More than 80% of all time series expression datasets are short (8 time points or fewer). These datasets present unique challenges. On account of the large number of genes profiled (often tens of thousands) and the small number of time points many patterns are(More)
The innate immune response is the first line of host defense against infections. This system employs a number of different types of cells, which in turn activate different sets of genes. Microarray studies of human and mouse cells infected with various pathogens identified hundreds of differentially expressed genes. However, combining these datasets to(More)
Viral and bacterial infections of the lower respiratory tract are major causes of morbidity and mortality worldwide. Alveolar macrophages line the alveolar spaces and are the first cells of the immune system to respond to invading pathogens. To determine the similarities and differences between the responses of mice and macaques to invading pathogens we(More)
Vaccination is a proven strategy to mitigate morbidity and mortality of infectious diseases. The methodology of identifying and testing new vaccine candidates could be improved with rational design and in vitro testing prior to animal experimentation. The tularemia vaccine, Francisella tularensis live vaccine strain (LVS), does not elicit complete(More)
The Gene Ontology (GO) is extensively used to analyze all types of high-throughput experiments. However, researchers still face several challenges when using GO and other functional annotation databases. One problem is the large number of multiple hypotheses that are being tested for each study. In addition, categories often overlap with both direct(More)
BACKGROUND After infecting a mammalian host, the facultative intracellular bacterium, Francisella tularensis, encounters an elevated environmental temperature. We hypothesized that this temperature change may regulate genes essential for infection. RESULTS Microarray analysis of F. tularensis LVS shifted from 26 degrees C (environmental) to 37 degrees C(More)
Mycobacterium tuberculosis is an intracellular pathogen that persists within macrophages and remains a considerable global threat to human health. The purpose of this study was to investigate how interleukin (IL)-12 and IL-27 regulate human macrophage interactions with M. tuberculosis. Quantitative measurement of transcripts showed that IL-12 or M.(More)
OxyR is a conserved bacterial transcription factor with a regulatory role in oxidative stress response. From a genetic screen for genes that modulate biofilm formation in the opportunistic pathogen Serratia marcescens, mutations in an oxyR homolog and predicted fimbria structural genes were identified. S. marcescens oxyR mutants were severely impaired in(More)
Twenty-one patients were studied in whom ventricular preexcitation (VP) had been recorded in the past and had later disappeared, indicating antegrade block in the accessory pathway (AP), either spontaneously (10 patients) or under the effect of chronic treatment with amiodarone (11 patients). VP reappeared in nine cases during vagal stimulation, and in five(More)