Publications

Cristina Penaranda, Evan Brenner, Anne Clatworthy, Lisa Cosimi, Janani Ravi, Deborah Hung (2026). Genomic comparison and phenotypic characterization of Pseudomonas aeruginosa isolates across environmental and diverse clinical isolation sites. mSystems.

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Evan Brenner, Charmie Vang, Connah Johnson, Janani Ravi (2025). Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence. bioRxiv.

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Abhirupa Ghosh, Evan Brenner, Charmie Vang, Ethan Wolfe, Emily Boyer, Raymond L Lesiyon, Keenan Manpearl, Vignesh Sridhar, Joseph Burke, Jacob Krol, Jill Bilodeaux, Janani Ravi (2025). From sequence to signature: Uncovering multiscale AMR features across bacterial pathogens with supervised machine learning. bioRxiv.

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Kewalin Samart, Ling Thang, Landon Buskirk, Amy Tonielli, Arjun Krishnan, Janani Ravi (2025). Integrative transcriptome-based drug repurposing in tuberculosis. bioRxiv.

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Abhirupa Ghosh, Charmie Vang, Evan Brenner, Janani Ravi (2025). Unlocking antimicrobial resistance with multiomics and machine learning. Trends in Micro.

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Evan Brenner, Abhirupa Ghosh, Ethan Wolfe, Emily Boyer, Charmie Vang, Raymond L Lesiyon, David Mayer, Janani Ravi (2025). amR: an R package suite to predict antimicrobial resistance in bacterial pathogens.

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Janani Ravi, Kewalin Samart, Jason Zwolak (2024). Modeling the START transition in the budding yeast cell cycle. PLoS Comp Biol.

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Janani Ravi, Vivek Anantharaman, Samuel Chen, Evan Brenner, Pratik Datta, L Aravind, Maria Gennaro (2024). The phage shock protein (PSP) envelope stress response: discovery of novel partners and evolutionary history. mSystems.

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Joshua Lensmire, Michael Wischer, Lo Sosinski, Elliot Ensink, Jack Dodson, John Shook, Phillip Delekta, Christopher Cooper, Daniel Havlichek Jr, Martha Mulks, Sophia Lunt, Janani Ravi, Neal Hammer (2023). The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition. PLoS Genetics.

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Mary Cantoria, Elaheh Alizadeh, Janani Ravi, Nawat Bunnag, Arminja Kettenbach, Yashi Ahmed, Andrew Paek, John Tyson, Konstantin Doubrovinski, Ethan Lee, Curtis Thorne (2023). Feedback in the β-catenin destruction complex imparts bistability and cellular memory. PNAS.

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Brian Hsueh, Geoffrey Severin, Clinton Elg, Evan Waldron, Abhiruchi Kant, Alex Wessel, John Dover, Christopher Rhoades, Benjamin Ridenhour, Kristin Parent, Matthew Neiditch, Janani Ravi, Eva Top, Chris Waters (2022). Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria. Nat Micro.

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Rocio Joo, Andrea Sanchez-Tapia, Sara Mortara, Yanina Bellini Saibene, Heather Turner, Dorothea Hug Peter, Natalia Soledad Morandeira, Matthias Bannert, Batool Almazrouq, Elizabeth Hare, Laura Acion, Juan Pablo Narvaez-Gomez, Marcela Alfaro Cordoba, Federico Marini, Rita Giordano, Silvia Canelon, Anicet Ebou, Adithi Upadhya, Joselyn Chavez, Janani Ravi (2022). Ten simple rules to host an inclusive conference. PLoS CompBio.

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Helen Blaine, Joseph Burke, Janani Ravi, Christina Stallings (2022). DciA Helicase Operators Exhibit Diversity across Bacterial Phyla. J Bac.

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Kayla Conner, Joseph Burke, Janani Ravi, Jonathan Hardy (2022). Novel Internalin P homologs in Listeria ivanovii londoniensis and Listeria seeligeri. Micro Genom.

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Faisal Alquaddoomi, Joseph Burke, Lo Sosinski, David Mayer, Evan Brenner, Samuel Chen, Jacob Krol, Ethan Wolfe, Vince Rubinetti, Shaddai Amolitos, Kellen Reason, John Johnston, Janani Ravi (2022). MolEvolvR: a web-app for characterizing proteins using molecular evolution and phylogeny. bioRxiv.

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Kewalin Samart, Phoebe Tuyishime, Arjun Krishnan, Janani Ravi (2021). Reconciling Multiple Connectivity Scores for Drug Repurposing. Brief Bioinform.

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Janani Ravi, Antonella Fioravanti (2021). S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens. Front Micro.

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Syeda Anum Hadi, Ida V Kolte, Evan P Brenner, EAT Cunha, V Simonsen, L Ferrazoli, DAM Villela, RS Santos, Janani Ravi, Srinand Sreevatsan, Paulo C Basta (2021). Discovery of a predominant and distinct lineage of Mycobacterium tuberculosis in Brazilian indigenous population. Scientific Reports.

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Joshua Lensmire, Jack Dodson, Brian Hsueh, Michael Wischer, Phillip Delekta, John Shook, Elizabeth Ottosen, Paige Kies, Janani Ravi, Neal Hammer (2019). The Staphylococcus aureus cystine transporters, TcyABC and TcyP, facilitate nutrient sulfur acquisition during infection. IAI.

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Janani Ravi, Vivek Anantharaman, L Aravind, Maria L Gennaro (2018). Variations on a theme: evolution of the phage-shock-protein system in Actinobacteria. Anto.

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Rinki Chauhan, Janani Ravi, Pratik Datta, Tian Chen, Dirk Schnappinger, Kevin Bassler, Gabor Balázsi, Maria Gennaro (2016). Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis. Nat Comm.

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Pratik Datta, Janani Ravi, Valentina Guerrini, Rinki Chauhan, Matthew Neiditch, Scarlet Shell, Sarah Fortune, Baris Hancioglu, Oleg Igoshin, Maria Gennaro (2015). The Psp system of Mycobacterium tuberculosis integrates envelope stress-sensing and envelope-preserving functions. Mol Micro.

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Hugh Salamon, Natalie Bruiners, Karim Lakehal, Lanbo Shi, Janani Ravi, Ken D Yamaguchi, Richard Pine, Maria L Gennaro (2014). Cutting edge: Vitamin D regulates lipid metabolism in Mycobacterium tuberculosis infection. J Imm.

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