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:
Joseph T Burke*, Samuel Z Chen*, Jacob D Krol*, Lo M Sosinski*, Faisal S Alquaddoomi, Vincent P Rubinetti, Evan P Brenner, Ethan P Wolfe, Shaddai Amolitos, Kellen M Reason, John B Johnson, Janani Ravi#.
[*Co-primary authors; listed alphabetically. #Corresponding author:]

Connectivity Scores for Drug Repurposing

Reconciling Multiple Connectivity Scores for Drug Repurposing
Kewalin Samart*, Phoebe Tuyishime*, Arjun Krishnan#, Janani Ravi#.
Brief. Bioinform. 2021 Nov 5;22(6):bbab161. doi:
PMID: 34013329; PMCID: PMC8597919.
[*Co-primary authors. #Corresponding authors:;]
Live doc:

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.
Helen C. Blaine*, Joseph T. Burke*, Janani Ravi#, Christina L. Stallings#
J. Bacteriology 2022 Aug 16;204(8):e0016322; doi:
PMID: 35880876; PMCID: PMC9380583.
[*Co-primary authors. #Corresponding authors:;]

Internalins in Listeria

Novel Internalin P homologs in Listeria ivanovii londoniensis and Listeria seeligeri.
Kayla N Conner*, Joseph T Burke*, Janani Ravi#, Jonathan W Hardy#
Microb. Genomics 2022 Jul;8(7); doi:
PMID: 35904424; PMCID: PMC9455699.
[*Co-primary authors. #Corresponding authors:;]

Bacterial phage defense

Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria.
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.
Nat. Microbiol. 2022 Aug;7(8):1210-1220; doi:
PMID: 35817890; PMCID: PMC9830645.
[*Co-primary authors. Corresponding author:]

Phage shock protein stress response system

Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History & Discovery of Novel Players.
Janani Ravi#, Vivek Anantharaman, Samuel Zorn Chen, Evan P Brenner, Pratik Datta, L Aravind#, Maria Laura Gennaro#.
bioRxiv 2020. doi:
[#Corresponding authors:;;]
Web-app: Web-app by JR and SZC.


Ten simple rules to host an inclusive conference.
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#.
PLoS Comput. Biol. 2022 Jul;18(7):e1010164. doi:
PMID: 35862309; PMCID: PMC9302732.
[*Co-primary authors. #Corresponding authors:;]