Forsyth Research Cores: Animal | Bioinformatics | Histology | Imaging | Microbiome | MicroCT | Multiplex

Mission Statement

High-throughput, next generation sequencing (NGS) technology has transformed today's biological research in many areas including genomics, transcriptomics and microbiomics. A variety of NGS sequencing methods are available to satisfy a wide range of research requirements such as read length, accuracy, speed, and cost. Accompanying the advent of NGS is the generation of large amount of data. In this biological big data era, biologists are facing new challenges for data analysis management and interpretation. Traditional bioinformatics software tools that run on a personal computer often are crippled by the sheer size of the NGS sequencing data. High-performance computational resource with multiple central processing units (CPUs), ample amount of memory, and storage space with fast I/O (input/output, read/write) speed, are no longer luxurious but necessary for doing research. Parallelly emerged in recent years in the field of computer and information technology (IT) is the cloud computing technology - a computational model that enables ubiquitous access to shared pools of computational resources such as networks, servers, storage, applications and services. Cloud computing has gained a strong foothold in both industry and science in the past decade and has risen to tackle the big data challenge. The goal of Forsyth Bioinformatics Core is to help researchers meet this challenge and provide assistance in big data analysis.

Who We Are

The Forsyth Bioinformatics Core was established alongside the Human Oral Microbiome Database (HOMD) since 2006. Led by Dr. Tsute (George) Chen, a human oral microbiome data analysis expert, the core has been developing bioinformatics tools to analyze the NGS data for research community in the oral/dental and nasal study fields. The core houses an array of high-performance multi-CPU computers with high memory that can analyze NGS data.

Two of our flagship NGS bioinformatics analysis pipelines are:

1.Species-level classification and profiling of 16S rRNA marker gene amplicon sequences
  Click to view pipeline flowchart
2.Organismic and functional profiling of meta-genomic and meta-transcriptomic NGS data
  Click to view pipeline flowchart

The key feature of our pipelines is the use of the HOMD curated 16S rRNA genes and whole genome reference sequences. Thus the results are tailored to, but not limited to, oral and nasal microbiological and clinical research fields. Please follow this link to the publications involving these pipelines. Check out some of the results using these two pipelines here.

We also provide consultation and analytical services in oral microbiomics, genomics, taxonomy, phylogenetics and all next generation sequence (NGS) data analysis. The services are provided to both internal and external researchers including the Harvard CATALYST community, for funded projects and funding applications requiring preliminary bioinfromatics analysis or method writing.

Core Services

Next generation sequencing (NGS) data analysis Microbiome profiling from 16S rRNA gene NGS data
Genomic sequencing raw reads assembly and annotation RNAseq read mapping, transcriptome profiling and gene expression analysis
Metagenomic NGS sequence analysis Metatranscriptomic NGS sequence Aanalysis
Grant writing and preliminary data analysis Consultation on bioinformatics data analysis

Service Inquiry and Request

We charge the service by hourly rate, by project, or by percent effort for a funded grant.
To request or inquire our services, please contact core director Dr. Tsute (George) Chen (Email:

Forsyth Bioinformatics Core Publicatons

A list of publications that the core coauthored is available here

Databases and Research Projects Supported by the Forsyth Bioinformatics Core

eHOMD: The Expanded Human Oral Microbiome Database BROP: The Bioinformatics Resource for Oral Pathogens
HOMIM: The Human Oral Microbe Identification Microarray Data Analysis HOMINGS: Human Oral Microbe Identification using Next Generation Sequencing
FOMC: Forsyth Oral Microbiome Core: MTD: Microbial Transcriptome Database
ORALGEN Database Archive PGGP: Porphyromonas gingivalis Genome Project

Software Tools Used by the Core

phyloseq: Explore microbiome profiles using R
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Page last updated: December 10, 2020 21:13:04