Professional Summary

Interdisciplinary researcher with Ph.D. in Microbial Genomics and extensive expertise in bioinformatics, genomics, and AI machine learning. Published 70+ papers in reputed journals with 4000+ total citations. Experienced in teaching microbiology at undergraduate and graduate levels, with extensive mentorship experience.


Academic Leadership: Academic Editor in Microorganisms journal and Research Topic Editor in Frontiers in Microbiology.

Research Highlights

🦠 Patescibacteria Research (2020)

Pioneered the "Less Is More" concept in genome simplification for evolutionary advancement. 300+ citations, featured by Berkeley National Lab. Published in top journal Microbiome (IF: 14).

🌊 Marine Sponge Microbiome (2014-2017)

First genomes of marine sponge-associated sulfur-oxidizing bacteria (SOB) and ammonia-oxidizing archaea (AOA). Nine influential papers inspired worldwide research on sponge symbiotic relationships.

🧬 VBCG (2023)

Identified 20 validated bacterial core genes for phylogenomic analysis from 30,500+ genomes. Superior resolution to traditional methods. Published in Microbiome (IF: 14).

🤖 PlasmidHunter (2024)

Developed the most accurate AI tool for bacterial plasmid prediction (97.6% accuracy) using novel features. Published in top bioinformatics journal.

Professional Experience

Research Scientist
High Throughput Sequencing Initiative, Illinois Institute of Technology
2019 – Present

Leading development of bioinformatics tools, pipelines and machine learning applications. Investigating bacterial pathogenesis for human diseases. Maintaining sequencing and bioinformatics facilities.


Key Projects:
  • Developed PlasmidHunter ML tool for plasmid prediction
  • Built Galaxy server (hts.iit.edu/galaxy) for genomic data analysis
  • Research on bacterial pathogens (C. botulinum, E. coli)
  • Grant applications for ML in bioinformatics and crop diseases
Postdoctoral Research Associate
Institute for Environmental Genomics, University of Oklahoma
2016 – 2019

Conducted bioinformatics analysis on genomes and metagenomes of environmental microbiomes. Developed automatic bioinformatics pipelines for amplicon, genome, and metagenome sequence data analysis.

Teaching Experience

Adjunct Professor of Microbiology
Roosevelt University
2023

Developed and delivered Microbiology (BIOL360/460A) and Microbiology Laboratory (BIOL360/460B) courses for undergraduate and graduate students. Student evaluation scores: 4.2 and 4.3 out of 5 respectively.

Grant Writing

Co-Principal Investigator
"Identifying Reservoirs of Microbial Pathogens in Illinois" - FDA GenomeTrakr Network
$550,000 • 2025-2030 • Under Review
Co-Principal Investigator
"FASS: Fast Alignment-free Sequence Search with ML" - NSF
$475,000 • 3 years • Under Review

Honors & Awards

Academic Editor - Microorganisms Journal (2022 - present)
Research Topic Editor - Frontiers in Microbiology (2024)
Guest Editor - Special Issue in Genes (2021)
Best Presenter - Environmental Sciences Program, HKUST (2014)

Selected Publications

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity
Microbiome, 8, 1-15 (2020)
300+ citations • Berkeley Lab featured
PlasmidHunter: Accurate and fast prediction of plasmid sequences using gene content profile and machine learning
Briefings in Bioinformatics, 25(4) (2024)
VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution
Microbiome, 11(247) (2023)
Effect of copper treatment on the composition and function of the bacterial community in the sponge Haliclona cymaeformis
MBio, 5(6) (2014)
Genomic analysis reveals versatile heterotrophic capacity of a potentially symbiotic sulfur-oxidizing bacterium in sponge
Environmental Microbiology, 16(11), 3548-3561 (2014)

See Google Scholar for complete publication list: 70+ publications, 4000+ citations, H-index 34