Janani Ravi, PhD

Professional Titles

• Assistant Professor

Recognitions

• All-University Excellence in Diversity Award, Michigan State University (2020)
  for work as the founder and co-organizer of R-Ladies East Lansing

Research Interests

We develop general-purpose computational approaches that integrate large-scale heterogeneous public datasets that lead to the mechanistic understanding of microbial genotypes, phenotypes, and diseases. Specifically, we focus on two key questions: - How do we link microbial genotypes to phenotypic traits? We use a combination of protein sequence-structure-function relationships, comparative genomics, and machine learning to bridge the genotype-phenotype gap (e.g., phenotypes, antimicrobial resistance, host-specificity, microbial pathogenesis). - How do we delineate molecular mechanisms underlying host response to infection and discover host-directed therapeutics? We use comparative transcriptomics, disease-drug signatures, and machine learning to learn about host response and drug repurposing. Our methods are generally pathogen- and disease-agnostic. We also release open data/software and easy-to-use web applications for wide use by the biomedical community. I am also actively engaged in training, education, and outreach, and committed to creating and sustaining a diverse and inclusive ecosystem in data science and R for learners and professionals alike, focusing on increasing the participation of underrepresented minorities in data science and R programming. Towards this effort, I founded R-Ladies East Lansing and R-Ladies Aurora, and co-founded Women+ Data Science and AsiaR. I also co-chair the R/Bioconductor Community Advisory Board.

Publications

• Cantoria MJ^, Alizadeh E^, Ravi J, Varghese RP, Bunnag N, Pond KW, Kettenbach AN, Ahmed Y, Paek AL, Tyson JJ, Doubrovinski K, Lee E, Thorne CA. Feedback in the ß-catenin destruction complex imparts bistability and cellular memory. Proc Natl Acad Sci U S A. 2023 Jan 10;120(2):e2208787120. PubMed PMID: 36598937 [^Primary]
• Lensmire JM, Wischer MR, Kraemer-Zimpel C, Kies PJ, Sosinski L, Ensink E, Dodson JP, Shook JC, Delekta PC, Cooper CC, Havlichek DH Jr, Mulks MH, Lunt SY, Ravi J, Hammer ND. The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition. PLoS Genet. 2023 Jul;19(7):e1010834. PubMed PMID: 37418503
• Ravi J*, Samart K, Zwolak J. Modeling the START transition in the budding yeast cell cycle. 2023. bioRxiv. DOI: https://doi.org/10.1101/2023.11.05.564806 [*Corresponding]
• Krol JD^, Burke JT^, Chen SZ^, Sosinski L^, Alquaddoomi FS, Brenner EP, Wolfe EP, Rubinetti VP, Amolitos S, Reason KM, Johnston JB, Ravi J*. MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny. 2022 bioRxiv (updated 2023) DOI: https://doi.org/10.1101/2022.02.18.461833 [^Primary; *Corresponding]
• Conner KN^, Burke JT^, Ravi J*, Hardy JW*. Novel internalin P homologs in Listeria. Microb Genom. 2022 Jul;8(7). PubMed PMID: 35904424. [^Primary; *Corresponding]
• Blaine HC^, Burke JT^, Ravi J*, Stallings CL*. DciA Helicase Operators Exhibit Diversity across Bacterial Phyla. J Bacteriol. 2022 Aug 16;204(8):e0016322. PubMed PMID: 35880876 [^Primary; *Corresponding]
• Joo R^*, Sánchez-Tapia A^, Mortara S, Bellini Saibene Y, Turner H, Hug Peter D, Morandeira NS, Bannert M, Almazrouq B, Hare E, Ación L, Narváez-Gómez JP, Alfaro Córdoba M, Marini F, Giordano R, Canelón S, Ebou A, Upadhya AR, Chávez J, Ravi J*. Ten simple rules to host an inclusive conference. PLoS Comput Biol. 2022 Jul;18(7):e1010164. PubMed PMID: 35862309 [^Primary; *Corresponding]
• 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, Waters CM. Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nat Microbiol. 2022 Aug;7(8):1210-1220. PubMed PMID: 35817890 [^Primary]
• Samart K^, Tuyishime P^, Krishnan A*, Ravi J*. Reconciling multiple connectivity scores for drug repurposing. Brief Bioinform. 2021 Nov 5;22(6). PubMed PMID: 34013329. [^Co-primary; *Co-corresponding]
• Ravi J^*, Fioravanti A^*. S-layers: The Proteinaceous Multifunctional Armors of Gram-Positive Pathogens. Front Microbiol. 2021;12:663468. PubMed PMID: 33889148. [^Primary; *Corresponding]
• Lensmire JM, Dodson JP, Hsueh BY, Wischer MR, Delekta PC, Shook JC, Ottosen EN, Kies PJ, Ravi J, Hammer ND. The Staphylococcus aureus Cystine Transporters TcyABC and TcyP Facilitate Nutrient Sulfur Acquisition during Infection. Infect Immun. 2020 Feb 20;88(3). PubMed PMID: 31843961
• Ravi J*, Anantharaman V, Chen SZ, Brenner EP, Datta, P, Aravind L*, Gennaro ML*. Phage-shock-protein (PSP) Envelope Stress Response: Evolutionary History and Novel Players. 2020. bioRxiv (updated 2023) DOI: https://doi.org/10.1101/2020.09.24.301986 [*Corresponding]
• Ravi J, Anantharaman V, Aravind L, Gennaro ML. Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria. Antonie Van Leeuwenhoek. 2018 May;111(5):753-760. PubMed PMID: 29488183
• Datta P, Ravi J, Guerrini V, Chauhan R, Neiditch MB, Shell SS, Fortune SM, Hancioglu B, Igoshin OA, Gennaro ML. The Psp system of Mycobacterium tuberculosis integrates envelope stress-sensing and envelope-preserving functions. Mol Microbiol. 2015 Aug;97(3):408-22. PubMed PMID: 25899163
• Salamon H, Bruiners N, Lakehal K, Shi L, Ravi J, Yamaguchi KD, Pine R, Gennaro ML. Cutting edge: Vitamin D regulates lipid metabolism in Mycobacterium tuberculosis infection. J Immunol. 2014 Jul 1;193(1):30-34. PubMed PMID: 24899504

Professional Memberships

• International Society for Computational Biology, Member, Evolution and Comparative Genomics Co-Chair
• American Society for Microbiology, Member
• R-Ladies East Lansing, Founder, Co-organizer
• AsiaR, Co-Founder, Co-organizer
• Women+ Data Science, Co-founder, Co-organizer
• R/Bioconductor, Member, Community Advisory Board
• American Society for Human Genetics, Member

Practice Locations

Center Affiliations

• Center for Health Artificial Intelligence