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

Computational biology | Bioinformatics | Molecular evolution & phylogeny | Comparative pathogenomics | Molecular drug/vaccine discovery | Data analysis & visualization

Super powers!

Computational Biology

Pathogenomics & Molecular Evolution

Drug-repurposing

Data Analysis & Viz

Education

Diversity

Lab News

2021 Manuscripts

  • Samart K, Tuyishime P, et al., Now accepted in Briefings in Bioinformatics! (2021) | Live doc | GitHub.
  • Ravi Jp,c, Fioravanti Ap,c. S-layers: the proteinaceous multifunctional armours of Gram-positive pathogens. Frontiers in Microbiology. 2021. DOI
  • Severin GBp, Hsueh BYp, 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!

  • (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!

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

  • Samart Kp, Tuyishime Pp, Krishnan Ac, Ravi Jc. Reconciling multiple connectivity scores for drug repurposing. arXiv 2020 | Live doc | GitHub.
    pco-primary authors; cco-corresponding authors.
  • Ravi Jc, Anantharaman V, Chen SZ, Datta, P, Aravind Lc, Gennaro MLc. Phage-shock-protein (Psp) Envelope Stress Response: Evolutionary History & Discovery of Novel Players. bioRxiv 2020 | Webapp.
    cco-corresponding authors.

Students’ Accomplishments

  • 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!

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!

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

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!

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

Education

  • PhD in Genetics, Bioinformatics and Computational Biology, 2011

    Virginia Tech | Blacksburg, VA

  • BTech in Biotechnology, 2006

    Anna University | Chennai, India

Meet the Team

Students

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Samuel Chen

Undergraduate Researcher

Data Science, Web-apps, R-pkgs, Molecular Evolution

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Kewalin Samart

Undergraduate Researcher

Drug-repurposing, Computational Math

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Elliot Majlessi

Undergraduate Researcher

sRNA discovery, Infectious Diseases, Biochemistry

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Joseph Burke

Undergraduate Researcher

Computational Biology, Biochemistry

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Karn Jongnarangsin

Undergraduate Researcher

Computer Science, Data Science, Object Oriented Programming, Web Development, Comparative Pathogenomics

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Larissa Ford

Undergraduate Researcher

Molecular Evolution, Molecular Biology, Biochemistry

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Mary Zhang

Undergraduate Researcher

Molecular Evolution, Molecular Biology, Synthetic Biology

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Philip Calhoun

Undergraduate Researcher

sRNA discovery, Infectious diseases, Human biology

Visitors

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Vignesh Sridhar

Graduate Researcher

Data Science, Machine Learning

Alumni

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Phoebe Tuyishime

Post-baccalaureate Researcher

Drug-repurposing, Infectious Diseases, Public Health, Nutrition

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Lauren Sosinski

Post-baccalaureate Researcher

Computational Biology, Molecular Evolution, Biochemistry

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Lauryn Brooks

Undergraduate Researcher

Comparative Pathogenomics, Biochemistry

Projects

.js-id-ongoing

Computational evolutionary approaches

Integrating molecular evolution and comparative genomics to achieve comprehensive, multiscale characterization of bacterial proteins …

sRNA discovery

Discovering unique pathogenic sRNA in infected hosts

Bacterial Stress Response

Studying stress response systems using molecular evolution and phylogenetics.

R & R-Ladies East Lansing

Posts, news, & material pertaining to R & R-Ladies East Lansing

Host-responses to infection

Characterizing host response to infection and host-directed interventions

Dynamical Systems & Modeling

Mathematical modeling of pathways involved in cell cycle regulation and differentiation

Recent & Upcoming Talks

Recent Posts

2019: RLEL Upcoming Events

What’s in store for 2019: workshops, conference, bookclubs & more!

2018: Year in Books | Goodreads

My Year in Books: 2018!

R-Ladies East Lansing: 2018, Year in Review

Some accomplishments from 2018 & announcements for 2019!

Contact