Computational Systems Biology of Infectious Diseases

We develop computational approaches to study the molecular basis of pathogenesis and intervention of infectious diseases.

Our research involves developing computational approaches that can leverage large-scale genomic data to gain actionable insights into infectious disease biology. Specifically, we focus on three key areas:

i) unraveling molecular mechanisms common between non-infectious and infectious diseases, to guide targeted drug repurposing, ii) identifying genomic signatures, functions, and mechanisms relevant to host-pathogen interactions, to enable understanding and guide diagnosis, and iii) developing tools and resources for seamlessly relating sequence, structure, and function of genes/proteins in poorly characterized pathogens.

Keywords

Super powers!

Computational Biology

Pathogenomics & Molecular Evolution

Drug-repurposing

Data Analysis & Viz

Education

Diversity

Lab News

2021 Manuscripts

Accepted manuscripts and submitted preprints! Jan 2021

Samart K, Tuyishime P, et al., Now accepted in Briefings in Bioinformatics! (2021) | Live doc | GitHub.
Ravi J^p,c, Fioravanti A^p,c. S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens. Frontiers in Microbiology. 2021. DOI
Severin GB^p, Hsueh BY^p, Elg CA, Dover JA, Rhoades CR, Wessel AJ, Ridenhour BJ, Top EM, Ravi J, Parent KN, and Waters CM. A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection. 2021 bioRxiv [in preparation for Cell]
^pco-primary authors; ^cco-corresponding authors.

More $$ for the group!

2021 grants! Jan 2021 – Mar 2023

(PI) Awarded the Endowed Research, Sheila McMonagle Fund from the College of Veterinary Medicine, MSU for the molecular evolution project!
(PI) Received grant support from the NSF-funded BEACON Center for ML-based feature detection and comparative pathogenomics.
(co-I) Received a grant from Spectrum Health and MSU Alliance for a COVID-19 project!
(subaward) Received NIH NIAID grant subaward to study molecular pathogenesis in Staphylococci using computational approaches

First manuscripts submitted from JRaviLab!

2020 Preprints! Sep 2020

Two preprints submitted to arXiv and bioRxiv in Sep ‘20! Another manuscript under review in Scientific Reports w/ collaborator, Dr. Sreevatsan!

Samart K^p, Tuyishime P^p, Krishnan A^c, Ravi J^c. Reconciling multiple connectivity scores for drug repurposing. arXiv 2020 | Live doc | GitHub.
^pco-primary authors; ^cco-corresponding authors.
Ravi J^c, Anantharaman V, Chen SZ, Datta, P, Aravind L^c, Gennaro ML^c. Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History & Discovery of Novel Players. bioRxiv 2020 | Webapp.
^cco-corresponding authors.

Students’ Accomplishments

2020 Spring, Summer, Fall! Mar 2020 – Oct 2020

Karn & Sam received Honorable mention for their posters at ISMB 2020 (by International Society for Computational Biology)!
Karn & Sam were nominated for the NSF-funded REU-ACRES program from ICER, MSU! Karn also gets accepted into the AdvanceU internship program at MSU!
Phil received the NIH NHLBI-funded BRUSH scholarship from the College of Veterinary Medicine!
Kewalin received the MSU College of Natural Sciences, Scholarship to work with us this Spring!
Lauryn joined us from Hampton University, Virginia starting Jul ‘20 (as part of NSURP, BIPOC research program for microbiologists).
[Outgoing] Phoebe received the Mastercard foundation scholarship to work back home in Rwanda from Oct ‘20.
[Outgoing] Lauren got accepted into the MSU post-baccalaureate program to start working with Dr. Rob Quinn (BMB, MSU) from Sep ‘20.

Phoebe gets her admits!

2020-Fall | Grad school awaits! Feb 2020

Phoebe gets her first admits rolling in from Purdue University & UC Davis, and an interview with the University of British Columbia!

Janani & Camille win the Excellence in Diversity Award!

MSU Feb 2020

Janani & Camille win the All-University Excellence in Diversity Award for founding R-Ladies East Lansing! The MSU President & Provost granted the award during the EIDA ceremony!

2019 Grants

Michigan State University Jan 2020

Received the Launch Award from MSU’s Diversity Research Network for the drug-repurposing project!

Awarded the Endowed Research, Harvey J Fiege Fund from the College of Veterinary Medicine, MSU for the molecular evolution project!

Janani Ravi

Asst. Professor

Michigan State University

Founder

R-Ladies East Lansing

Women+ Data Science

PI

I am a computational biologist at the Dept. of Pathobiology and Diagnostic Investigation, Michigan State University. I work on protein sequence-structure-function relationships, comparative genomics, and drug repurposing as they relate to infectious diseases.

I also teach data analysis and visualization and /Python programming to diverse groups in non-traditional settings. As part of this effort, I founded R-Ladies East Lansing and Women+ Data Science, through which we host our meetups & webinars!

Interests

Computational biology
Molecular evolution and phylogeny
Comparative genomics
Drug repurposing
R for biological data science
R-Ladies East Lansing
Women+ Data Science
Other Interests & Experience

Education

PhD in Genetics, Bioinformatics and Computational Biology, 2011

Virginia Tech | Blacksburg, VA
BTech in Biotechnology, 2006

Anna University | Chennai, India