We received two Colorado Program for Musculoskeletal Research (CPMR) / Department of Biomedical Informatics (DBMI) dyad pilot grants.

• With Dr. Honey Hendesi on studying how the effect of intermittent fasting on the gut microbiome impacts bone health and fracture healing
• With Dr. Reed Ayers on studying metallosis — how bacteria (and hosts) break down metal implants (that supposedly can’t be corroded!)

See Associated news article

Our project on developing novel data science technologies to study antimicrobial resistance is officially now funded by NIH NIAID! If you are interested in bridging microbial genotypes to phenotypes, esp. in the context of AMR, come join us!

Now looking for postdocs: check out CU ad here.

Exciting times as we welcome new people to our group:

• 2023-06: Evalyn Resnick, undergraduate researcher (planning to attend Simpson College starting in the Fall of 2023; Biology major – pre-medicine/pre-veterinary track)
• 2023-06: Kritika Verma, undergraduate researcher (pursuing Bachelor of Technology, Cluster Innovation Centre at University of Delhi)
• 2023-06: Sana Paktinyar, undergraduate researcher (pursuing BS in Bimolecular Chemical Engineering, Pre-Med Track at California Institute of Technology)
• 2023-06: Vy ‘Andy’ Tran, undergraduate researcher (pursuing BS in Physics at University of Colorado Boulder)
• 2022-11: Jake Krol, postbac, Informational Science Professional (BS, Computational Neuroscience from MSU)
• 2023-02: Karla Vela Lopez, graduate researcher (pursuing MS in Biomedical Sciences and Biotechnology, CU Anschutz)
• 2023-02: Jill Bilodeaux, graduate rotation student from Microbiology
• 2023-03: Kewalin Samart & Keenan Manpearl, two graduate pseudo-rotation students from Computational Biosciences
• 2023-05: Evan Brenner, postdoc (PhD, Comparative Medicine and Integrative Biology, MSU)

• Joshua M. Lensmire, Michael R. Wischer, Cristina Kraemer-Zimpel, Paige J. Kies, Lo Sosinski, Elliot Ensink, Jack P. Dodson, John C. Shook, Phillip C. Delekta, Christopher C. Cooper, Daniel H. Havlichek Jr., Martha H. Mulks,Sophia Y. Lunt, Janani Ravi, Neal D. Hammer. The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition. PLoS Genetics . 2023. DOI.

• (co-PI) Notice of Award for NIH NIAID Data Science R21 on “Mechanism-guided drug repurposing for host-directed therapy of infectious diseases using interpretable and integrative ML” | co-PI: Arjun Krishnan

• Ethan receives a summer research scholarship from the MSU College of Natural Science, and presents at his first international meeting!
• [Outgoing] Kewalin graduated from MSU with the McCartney Math Award for outstanding graduating Math majors. She will be joining the University of Colorado, Anschutz Medical Campus, Computational Biosciences graduate program this Fall (joining us back in Aug @CU!). She also received grad admits at MSU (BMS, CMSE), and Penn State, along with the College of Engineering Distinguished Scholarship at MSU, the Rasmussen Doctoral Recruitment Award at MSU.
• [Outgoing] Joseph Burke graduated from MSU with an outstanding student award from the Dept of Microbiology and Molecular Genetics, and three co-primary author publications under his belt. He’s now a software engineer at CRISPR Therapeutics.
• [Outgoing] Elliot Majlessi graduated from MSU and is taking a gap year to apply to Medical School!
• [Outgoing] Mary Zhang graduated from Carleton College to join med school at the National University of Singapore, Fall of ‘22!

• Burke JT^p, Chen SZ^p, Sosinski LM^p, Johnston JB, Ravi J^c. MolEvolvR: A webapp for characterizing proteins using molecular evolution and phylogeny. bioRxiv 2022. Webapp
• Joo R^p,c, Sánchez-Tapia A^p, Mortara S, Saibene YB, et al., Ravi J^c. Ten simple rules to host an inclusive conference. PLoS Computational Biology. 2022. DOI GitHub
• Conner KN^p, Burke JT^p, Ravi J^c, Hardy JW^c. Novel Internalin P homologs in Listeria ivanovii londoniensis and Listeria seeligeri. Microbial Genomics. 2022. DOI GitHub
• Blaine HC^p, Burke JT^p, Ravi J^c, Stallings CL^c. DciA helicase operators exhibit diversity across bacterial phyla. Journal of Bacteriology. 2022. DOI GitHub
• Cantoria MJ^p, Alizadeh E^p, Ravi J, et al., Feedback in the β-catenin destruction complex imparts bistability and cellular memory. bioRxiv 2022.
• [update] Hsueh BY^p, Severin GB^p, et al., now at Nature Microbiology (2022)! DOI
  ^pco-primary authors; ^cco-corresponding authors. In bold, members of JRaviLab.

• [update] Samart K^p, Tuyishime P^p, Krishnan A^c, Ravi J^c published in Briefings in Bioinformatics (2021)! DOI | 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
• Hsueh BY^p, Severin GB^p, et al., A Broadly Conserved Deoxycytidine Deaminase Protects Bacteria from Phage Infection. bioRxiv 2021.
• Lensmire JM, et al., Ravi J, Hammer ND. The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition. bioRxiv 2021.
• [update] Hadi SA^p, Kolte IV^p, Brenner EP^p, et al., Ravi J, Sreevatsan S, Basta PC. Identification of a predominant genotype of Mycobacterium tuberculosis in Brazilian indigenous population. Scientific Reports. 2021;11(1):1224. DOI
  ^pco-primary authors; ^cco-corresponding authors. In bold, members of JRaviLab.

• (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

• Kewalin, Sam, Vignesh, Elliot, and Joe present at their first (inter)national meetings!
• Kewalin received several research scholarships for 2021, including the Engineering Summer Undergraduate Research Experience (EnSURE), MSU; College of Natural Science scholarships for Spring and Fall.
• Ethan Wolfe and Amy Tonielli join the group! They received Professorial Assistantships from the Honors College, MSU (given to the Top200 students).
• Elliot received the NIH R25-funded BRUSH summer scholarship.
• [Outgoing] Sam Chen graduated as one of 38 students across MSU with a 4.0 GPA. He’s now a software engineer at Amazon Inc.
• [Outgoing] Phil Calhoun graduated with Honors and joined the MSU College of Human Medicine.

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.
• 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.
  ^pco-primary authors; ^cco-corresponding authors. In bold, members of JRaviLab.

• Karn and Sam received Honorable mention for their posters at ISMB 2020 (by International Society for Computational Biology)!
• Karn and 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 Science, 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). Now a PREP student at the University of Pennsylvania.
• [Outgoing] Phoebe received the Mastercard foundation scholarship to work back home in Rwanda from Oct ‘20; University of British Columbia, Fall ‘21. She also gets grad admits from Purdue University and UC Davis!
• [Outgoing] Lo got accepted into the MSU post-baccalaureate program to start working with Dr. Rob Quinn (BMB, MSU) from Sep ‘20. Lo is now pursuing their PhD at Michigan State University.