compbio-bioinfo

Using computational appraches to understand host-pathogen biology

Resources

Posts and updates on useful academic blogs & resources!

Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria

Evolution and Conservation of the Psp Envelope Stress-Response System

Microbial Mechanosensing: Phage Shock Protein Response System in Gram-positive Bacteria

Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis

Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Here we reconstruct the complete sigma factor regulatory network of the human pathogen …

Host-responses to infection

Characterizing host response to infection and host-directed interventions

Studying lipid metabolism deregulation in TB

Summary We also studied host responses to M. tuberculosis infection using computational approaches: characterizing the transcriptional response in infected macrophages under various small molecule perturbations using RNA-Seq analysis; understanding the dysregulation of lipid metabolism in M. tuberculosis-infected macrophages using dynamic Bayesian model and statistical analyses of heterogeneous single-cell populations. Collaborators Rutgers University Marila Gennaro Sanjay Tyagi Eduardo Sontag (now in North Eastern) Tulane University Deepak Kaushal Knowledge Synthesis Hugh Salamon

Stochastic nature of adipogenic and inflammatory responses in tuberculous macrophages

The Psp system of Mycobacterium tuberculosis integrates envelope stress-sensing and envelope-preserving functions

The bacterial envelope integrates essential stress-sensing and adaptive functions; thus, envelope-preserving functions are important for survival. In Gram-negative bacteria, envelope integrity during stress is maintained by the multi-gene Psp …