Computational Systems Biology of Infectious Diseases

We develop discovery platforms that enable experimental and computational biologists use our approaches to study the molecular basis of pathogenesis and intervention of infectious diseases.

We welcome collaborations: if you are interested in studying an infectious disease/pathogen using our platforms or if you would like to see your computational tool incorporated into our platforms, do get in touch.

Learn more about our group here.


Software & Methods

MolEvolvR | Connectivity Scores

MolEvolvR: A web-app for molecular evolution and phylogeny

MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny
bioRxiv 2022. doi: https://doi.org/10.1101/2022.02.18.461833.
Joseph T Burke*, Samuel Z Chen*, Lo M Sosinski*, John B Johnson, Janani Ravi#.
*Co-primary authors. #Corresponding author: janani@msu.edu
Web-app: jravilab.org/molevolvr

Connectivity Scores for Drug Repurposing

Reconciling Multiple Connectivity Scores for Drug Repurposing
Brief Bioinform. 2021 Nov 5;22(6):bbab161. doi: http://doi.org/10.1093/bib/bbab161. PMID: 34013329; PMCID: PMC8597919.
Kewalin Samart*, Phoebe Tuyishime*, Arjun Krishnan#, Janani Ravi#.
*Co-primary authors. #Corresponding authors: arjun@msu.edu; janani@msu.edu
Live doc: jravilab.github.io/connectivity_score_review


Data repos & Web-apps

Bacterial DciA | Listeria Internalins | Bacterial phage defense | Phage shock stress response

Bacterial DciA

DciA helicase operators exhibit diversity across bacterial phyla
bioRxiv 2022.01.24.477630; doi: https://doi.org/10.1101/2022.01.24.477630
Helen C. Blaine*, Joseph T. Burke*, Janani Ravi#, Christina L. Stallings#
*Co-primary authors. #Corresponding authors: stallings@wustl.edu; janani@msu.edu
Data: https://github.com/JRaviLab/dcia_evolution

Internalins in Listeria

Novel Internalin P homologs in Listeria ivanovii londoniensis and Listeria seeligeri.
bioRxiv 2022.01.19.476994; doi: https://doi.org/10.1101/2022.01.19.476994 (accepted at Microbial Genomics)
Kayla N Conner*, Joseph T Burke*, Janani Ravi#, Jonathan W Hardy#
*Co-primary authors. #Corresponding authors: hardyjon@msu.edu; janani@msu.edu
Data: https://github.com/JRaviLab/inlp_listeria

Bacterial phage defense

A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection
bioRxiv 2021.03.31.437871; doi: https://doi.org/10.1101/2021.03.31.437871 (accepted at Nature Microbiology)
Hsueh BY*, Severin GB*, Elg CA, Waldron EJ, Kant A, Wessel AJ, Dover JA, Rhoades CR, Ridenhour BJ, Parent KN, Neiditch MB, Ravi J, Top EM, and Waters CM.
*Co-primary authors. Corresponding author:
Data: https://github.com/JRaviLab/phage_defense_avcd

Phage shock protein stress response system

Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History & Discovery of Novel Players
bioRxiv 2020. doi: https://doi.org/10.1101/2020.09.24.301986
Janani Ravi#, Vivek Anantharaman, Samuel Zorn Chen, Pratik Datta, L Aravind#, Maria Laura Gennaro#.
#Corresponding authors: janani@msu.edu; aravind@nih.gov; marila.gennaro@rutgers.edu.
Web-app: jravilab.shinyapps.io/psp-evolution. Web-app by JR and SZC.


Other

Ten simple rules to host an inclusive conference.
2022 (accepted at PLoS Computational Biology)
Rocío Joo*#, Andrea Sánchez-Tapia*, Sara Mortara, Yanina B Saibene, Heather Turner, Dorothea H Peter, Natalia S Morandeira, Matthias Bannert, Batool Almazrouq, Elizabeth Hare, Laura Ación, Juan P Narváez-Gómez, Marcela A Córdoba, Federico Marini, Rita Giordano, Silvia Canelón, Anicet Ebou, Adithi Upadhya, Joselyn Chávez, Janani Ravi#.
*Co-primary authors. #Corresponding authors: rocio.joo@globalfishingwatch.org; janani@msu.edu
Repo: github.com/rociojoo/Ten-simple-rules-inclusive-conference.