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Search: authors:"Timothy E. Sweeney"

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Methods to increase reproducibility in differential gene expression via meta-analysis

Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by...

Unique transcriptomic response to sepsis is observed among patients of different age groups

authors of the public datasets used here. Author Contributions Conceptualization: Timothy E. Sweeney, Purvesh Khatri, Lyle L. Moldawer, James L. Wynn. Data curation: Steven L. Raymond, MarÂõa Cecilia ... LoÂpez, Timothy E. Sweeney. Formal analysis: Steven L. Raymond, MarÂõa Cecilia LoÂpez, James L. Wynn. Funding acquisition: Shawn D. Larson, Philip A. Efron, Timothy E. Sweeney, Purvesh Khatri, Lyle L

Combined Mapping of Multiple clUsteriNg ALgorithms (COMMUNAL): A Robust Method for Selection of Cluster Number, K

States.Timothy E. Sweeney & Olivier GevaertDepartment of Statistics, Stanford University, Stanford, CA 94305, United States.Albert C. Chen AuthorsSearch for Timothy E. Sweeney in:Nature Research journals • PubMed ... declare no competing financial interests. Corresponding authors Correspondence to Timothy E. Sweeney or Olivier Gevaert. Supplementary information PDF files1.Supplemental Figures and Tables Rights

A community approach to mortality prediction in sepsis via gene expression analysis

Improved risk stratification and prognosis prediction in sepsis is a critical unmet need. Clinical severity scores and available assays such as blood lactate reflect global illness severity with suboptimal performance, and do not specifically reveal the underlying dysregulation of sepsis. Here, we present prognostic models for 30-day mortality generated independently by three...

Differential Regulation of the PGC Family of Genes in a Mouse Model of Staphylococcus aureus Sepsis

The PGC family of transcriptional co-activators (PGC-1α [Ppargc1a], PGC-1β [Ppargc1b], and PRC [Pprc]) coordinates the upregulation of mitochondrial biogenesis, and Ppargc1a is known to be activated in response to mitochondrial damage in sepsis. Therefore, we postulated that the PGC family is regulated by the innate immune system. We investigated whether mitochondrial biogenesis...

A Toll-Like Receptor 2 Pathway Regulates the Ppargc1a/b Metabolic Co-Activators in Mice with Staphylococcal aureus Sepsis

Activation of the host antibacterial defenses by the toll-like receptors (TLR) also selectively activates energy-sensing and metabolic pathways, but the mechanisms are poorly understood. This includes the metabolic and mitochondrial biogenesis master co-activators, Ppargc1a (PGC-1α) and Ppargc1b (PGC-1β) in Staphylococcus aureus (S. aureus) sepsis. The expression of these genes...