Computational Biosciences

Oct 15, 2024 | cell.com | Katherine M. Sheu |Computational Biosciences |Alexander Hoffmann

Keywords inducible gene expression dynamics single cell trajectory ensembles information theory machine learning macrophage context dependence stimulus-response specificity gene expression trajectories Introduction Macrophages are immune sentinel cells that deploy their diverse functions in response to exposure to pathogens or activating stimuli.1,2 Immune response genes not only differ in the magnitudes of induction but also show distinctive temporal dynamics evident in the gene expression...

Nov 24, 2023 | academic.oup.com | Computational Biosciences

Clinical outcomes in bacterial bloodstream infections (BSI) are influenced by multiple factors, including bacterial species, host immunity, and antibiotic therapy. However, the mechanisms by which such factors influence outcomes and their potential biomarkers are poorly understood. We aimed to identify bacterial- and antibiotic-specific host transcriptional signatures in patients with bacterial BSI. RNA-Seq was performed on blood from patients with BSI due to prototypic Gram-negative vs.

Nov 24, 2023 | academic.oup.com | Computational Biosciences

Clinical outcomes in bacterial bloodstream infections (BSIs) are influenced by bacterial species, host immunity, and antibiotic therapy. The mechanisms by which such factors influence outcomes are poorly understood. We aimed to identify bacterial- and antibiotic-specific host transcriptional signatures in patients with bacterial BSI.

Oct 4, 2023 | academic.oup.com | Computational Biosciences |Xu Han |Foster City

As a data-driven method, SPA-STOCSY estimates all parameters from the input dataset. It first investigates the covariance pattern among datapoints and then calculates the optimal threshold with which to cluster datapoints belonging to the same structural unit, i.e., the metabolite. Generated clusters are then automatically linked to a metabolite library to identify candidates.

Aug 30, 2023 | cell.com | Yikai Luo |Computational Biosciences

Highlights Single-cell profiling technologies provide an unprecedented resolution in investigating the coordinated compositional and state alterations of immune and stromal components in response to cancer therapies on the tumor microenvironment, enabling a holistic and more nuanced understanding of treatment response and resistance.