Computational evolutionary approaches

Oct 10, 2020 Research

Summary

We are developing an integrated computational evolutionary framework that will bring together: 1) molecular evolution and phylogeny; and 2) comparative genomics/pangenomics to study any pathogen-group or protein family, and discover distinctive protein/genomic features relevant to biological comparisons of interest (such as identifying diagnostic or candidate vaccine targets in emerging, poorly characterized pathogens).

Team

Students

Current

  • Joe Burke
  • Elliot Majlessi
  • Vignesh Sridhar
  • Ethan Wolfe

Alumni

  • Samuel Chen
  • Lo Sosinski
  • Karn Jongnarangsin
  • Lauryn Brooks

Collaborators

  • Neal Hammer, MSU (Staphylococci)
  • Srinand Sreevatsan, Robert Abramovitch, and Andrew Olive (MSU), Christina Stallings, WUSTL (Mycobacteria)
  • Antonella Fioravanti, VUB Brussels (B. anthracis)
  • Chris Waters, MSU (Vibrio)
  • Jonathan Hardy, MSU (Listeria)
  • Stephanie Shames, KSU (Legionella)
  • Priya Shah, UCD (Flaviviruses)
  • Sean Crosson, MSU (Brucella, Caulobacter)
molecular-evolution phylogeny comparative-genomics pangenomics pathogenic-features tree-of-life mycobacteria staphylococci banthracis brucella vibrio listeria ongoing compbio-bioinfo
Avatar
Janani Ravi
Assistant Professor

My research interests include computational pathogenomics and host-directed drug-repurposing.

Related

Publications

Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria

Preprint PDF Dataset Project DOI

DciA Helicase Operators Exhibit Diversity across Bacterial Phyla

Despite the fundamental importance of DNA replication for life, this process remains understudied in bacteria outside Escherichia coli …
Preprint PDF Dataset Project DOI

Novel Internalin P homologs in Listeria ivanovii londoniensis and Listeria seeligeri

The intracellular bacterial pathogen Listeria monocytogenes can breach protective barriers in the pregnant host, allowing the …
Preprint PDF Dataset Project DOI

MolEvolvR: a web-app for characterizing proteins using molecular evolution and phylogeny

Studying proteins through the lens of evolution can help identify conserved features and lineage-specific variants, and potentially, …
Preprint PDF Project DOI Webapp

S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens

Project DOI

The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition

Sulfur is an indispensable element for proliferation of bacterial pathogens. Prior studies indicated that the human pathogen, …
Preprint PDF Project DOI

Discovery of a predominant and distinct lineage of Mycobacterium tuberculosis in Brazilian indigenous population

After nearly a century of vaccination and six decades of drug therapy, tuberculosis (TB) kills more people annually than any other …
PDF Project DOI PubMed

Talks

MolEvolvR BTS: When and how to build a web-app and software package?

We recently developed a web application, MolEvolvR, to characterize proteins using molecular evolution and phylogeny. This session will …

May 15, 2023 1:00 PM — 5:00 PM Virtual (Montreal, Canada
Code Project

Cross-database integration using evolution and machine learning to identify multiscale molecular building blocks for antibiotic resistance

Jul 14, 2022 1:45 PM — 2:05 PM Virtual (Wisconsin, MI, USA)
Project

Computational approaches to study molecular pathogenesis and intervention of infectious diseases

Nov 22, 2021 8:00 PM — 9:00 PM Virtual (Colorado)
Project Project Project Slides Video

MolEvolvR: A webapp for characterizing proteins using molecular evolution and phylogeny

Studying how bacterial pathogenic proteins evolve can help identify lineage-specific and pathogen-specific signatures and variants, and …
Jul 27, 2021 8:00 PM — 9:00 PM Virtual (Global)
Project Slides Video

MolEvolvR: Web-app and R-package for characterizing proteins using molecular evolution and phylogeny

Molecular evolution and phylogeny can provide key insights into pathogenic protein families. Studying how these proteins evolve across …
Jul 9, 2021 8:00 PM — 9:00 PM Virtual (Global)
Project Project Project Slides Video

Using a computational molecular evolution and phylogeny to study pathogenic proteins

Background: Studying bacterial physiology, adaptation, and pathogenicity through the lens of evolution requires delineating the …
May 13, 2021 8:00 PM — 9:00 PM Virtual
Project Project Slides

MolEvolvR: a web-app for molecular evolution and phylogeny

We will discuss the alpha version of their new easy-to-use interactive webapp: MolEvolvR, for characterizing proteins using molecular …

Mar 26, 2021 8:00 PM — 9:00 PM Virtual
Project Slides Video

Computational evolutionary approaches for understanding pathogen proteins and genomes

Aug 13, 2020 4:15 PM — Aug 13, 2019 4:30 PM Virtual
Project

Computational evolutionary approaches to characterize bacterial proteins

Jul 14, 2020 3:00 AM — 3:30 AM Virtual
Project