High Throughput Sequencing Initiative (IHTSI) - Illinois Institute of Technology

About IHTSI

The High Throughput Sequencing Initiative (IHTSI) at the Institute for Food Safety and Health revolutionizes food safety research using cutting-edge next-generation sequencing technology. Our mission is to collaborate with FDA and IFSH scientists to improve food safety and quality through innovative genomic approaches.

We focus on analyzing major foodborne pathogens including Salmonella, Listeria, and E. coli, examining food environments from production to consumption. Our research encompasses microorganism identification, food spoilage detection, and provides crucial support to regulatory and health agencies.

The IHTSI laboratory primarily focuses on microbiological research and bioinformatics tool development, with special interest in applying AI and machine learning to solve biological problems using big data. We welcome external researchers interested in applying HTS technology and offer comprehensive laboratory and analytical services to the food industry.

Our Team

Dr. Behzad Imanian

Research Assistant Professor & Laboratory Director

Email: bimanian@iit.edu

Phone: 708-563-8171

Dr. Renmao "Tim" Tian

Research Scientist in Microbial Genomics

Email: rtian@iit.edu

Phone: 708-563-8169

Facilities & Services

Sequencing Equipment

Two Illumina MiSeq sequencers
Oxford Nanopore MinION sequencer
Bioinformatic facility with four high-performance computers
High-capacity backup system for data storage

Laboratory Services

DNA/RNA extraction, purification, and quantification
Library preparation
Whole genome sequencing
RNA sequencing
Metagenomics (16S rDNA and shotgun sequencing)

Analytical Services

Data storage and remote access
Sequence quality control
Sequence assembly and assessment
BLAST search
Sequence annotation
SNP analysis
Phylogenomic and phylogenetic analyses

Bioinformatics Tools

Visit our Galaxy server at hts.iit.edu/galaxy to access these tools

ASAP2 - Amplicon Data Analysis

Automatically analyze prokaryotic 16S rRNA gene amplicon sequencing data using QIIME 2 and other tools. This pipeline provides comprehensive analysis of microbial communities.

PlasmidHunter - Genomic Data Analysis

Predict the location (chromosome or plasmid) of contig sequences from input FASTA files using advanced machine learning algorithms for accurate genomic classification.

VBCG - Phylogenomic Analysis

Build phylogenomic trees based on 20 validated bacterial core genes (VBCG) with input of whole genome sequence FASTA files, providing high-resolution phylogenetic analysis.

Recent Publications

Tian, Renmao; Imanian Behzad; VBCG: 20 validated bacterial core genes for phylogenomic analysis with high fidelity and resolution (2023) Microbiome (11) 247 (IF: 15.3) GitHub Repository
Tian, Renmao; Zhou, Jizhong; Imanian, Behzad; PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning (2024) Briefings in Bioinformatics, Volume 25, Issue 4, bbae322 (IF: 9.5) https://doi.org/10.1093/bib/bbae322 GitHub Repository
Tian, R. Imanian, B. ASAP 2: A Pipeline and Web Server to Analyze Marker Gene Amplicon Sequencing Data Automatically and Consistently 2022 BMC Bioinformatics (23) 27 (IF: 3.1) GitHub Repository
Tian, Renmao; Ning, Daliang; He, Zhili; Zhang, Ping; Spencer, Sarah J; Gao, Shuhong; Shi, Weiling; Wu, Linwei; Zhang, Ya; Yang, Yunfeng; et al. Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity 2020 Microbiome (8) 44211 (IF: 15.3) High citations (200+) Featured by Berkeley Lab
Tian, Renmao, Melissa Widel, and Behzad Imanian. "The Light Chain Domain and Especially the C-Terminus of Receptor-Binding Domain of the Botulinum Neurotoxin (BoNT) Are the Hotspots for Amino Acid Variability and Toxin Type Diversity." Genes 13.10 (2022): 1915. (IF: 4.1)
Tian, R., Smith, T. J., Imanian, B., Williamson, C. H., Johnson, S. L., Daligault, H. E., & Schill, K. M. Integration of Complete Plasmids Containing Bont Genes into Chromosomes of Clostridium parabotulinum, Clostridium sporogenes, and Clostridium argentinense. 2021 Toxins, 13(7), 473. (IF: 5.1)

Events & Symposiums

2025 IFSH Annual Meeting

September 8-10, 2025

The 2025 IFSH Annual Meeting and Task Force Groups at the Crowne Plaza in Rosemont, IL. This year's topic: Wellness Through Food Safety & Health.

Bioinformatics Data Analysis Workshop

November 12, 2025

Specialized workshop on bioinformatics data analysis, focusing on Galaxy platform and our custom tools. Perfect for researchers and industry professionals.

7th IFSH High-Throughput Sequencing Symposium & Workshop

November 13-14, 2025

Join us for the latest advances in high-throughput sequencing technology and its applications in food safety research. Registration now open.

Historical HTS Symposiums

6th IFSH High-Throughput Sequencing Symposium

2023

Successfully conducted symposium focusing on advances in HTS technology applications in food safety research and industry implementation.

5th IFSH High-Throughput Sequencing Symposium (Virtual)

May 2022

Virtual symposium adapting to pandemic conditions while maintaining high-quality scientific exchange and networking opportunities.

High-Throughput Sequencing and Predictive Microbiology Webinar

2020

Specialized webinar exploring the intersection of HTS technology and predictive microbiology in food safety applications.

Whole Genome Sequencing Workshop

May 2019

Hands-on workshop providing practical training in whole genome sequencing techniques and data analysis methods.

Food Safety & High-Throughput Sequencing Symposium

May 2018

Landmark symposium establishing the foundation for ongoing collaboration between food safety researchers and HTS technology experts.

Earlier Symposiums

2017 & Earlier

Previous symposiums and workshops that built the foundation for the IHTSI, establishing industry partnerships and research collaborations.

Contact Us

Institute for Food Safety and Health

Illinois Institute of Technology

10 West 35th Street
Chicago, IL 60616

Phone: 312.567.3000

Website: hts.iit.edu

Galaxy Server: hts.iit.edu/galaxy

Industry Advisory Committee

We maintain an Industry Advisory Committee (IIAC) with 32 representatives from 19 food companies, trade unions, and associations, as well as an Industry-Governmental Agencies Council (IIGAC) with representatives from FDA, CDC, and USDA.