The Bioinformatics Core supports biological research through collaboration, data analysis, and the development of computational workflows designed to meet the specific needs of each individual project. Our work spans the full breadth of modern biological inquiry—from experimental design through the interpretation and visualization of complex data—emphasizing reproducibility, coherence, and scientific rigor. 

We regularly assist researchers working with next-generation sequencing (NGS) data, encouraging early consultation to ensure experiments are structured with downstream analysis in mind. Our focus is on supporting the practical use of computational tools to extract meaningful biological insight. 

Services and Expertise

Sequencing Data Analysis | Processing and interpretation of NGS datasets, including quality control, genome mapping, variant calling, and de novo assembly

Omics and Metagenomics | Analysis of microbial communities and mixed datasets, with emphasis on the biological context and associated research questions

Phylogenetics and Population Structure | Inference of evolutionary relationships and population genetic structure, incorporating metadata and environmental variables

Workflow Design | Development of scalable, and reproducible pipelines tailored to specific project needs; support for cloud-based, highperformance computing environments (e.g., Google Cloud)

AI and Machine Learning | Development of bioinformatics workflows that integrate machine learning or artificial intelligence to enhance recognition, classification, and prediction in biological datasets

Data Visualization | Custom figures and interactive visual tools to enhance exploration and communication of results; implemented in R or Python

Computational Support and Infrastructure | Guidance on the use of high-performance computing and storage solutions in Google Cloud and NextFlow Tower; assistance with open-source tool installation and environment configuration

Training and Knowledge Sharing | Workshops, small group training, and community-building through monthly meetings 

Facilities and Resources

The Core operates with access to scalable compute environments, including Google Cloud resources configured specifically for research computing applications. We also support the use of an extensive library of open-source tools and maintain licenses for some commercial software such as Qiagen Genomics Workbench.

Custom solutions or pipelines can be deployed locally or across laboratory environments for east of use and long-term reproducibility.

Program Updates

Differentiated biofilms of M. abscessus

Wadsworth Center Launches Web Tool to Explore the Mycobacterium abscessus Pangenome

Scientists at the Wadsworth Center have developed a new online resource to help researchers better understand Mycobacterium abscessus (MABS), an opportunistic bacterial pathogen that can cause difficult-to-treat infections.  Drs. Anil Ojha and Pallavi Ghosh of the Division of Genetics, together with Dr. Pascal Lapierre of the Bioinformatics Core, created the MABS Pangenome Explorer, an interactive, web-based tool designed for rapid exploration of the M. abscessus pangenome (https://abscessus.wadsworth.org/)
Spencer Bruce, Ph.D.

Wadsworth Center Bioinformatics Software Management Featured on StaPH-B Call

Dr. Spencer Bruce, Director of the Bioinformatics Core at Wadsworth, recently presented during the February State Public Health Bioinformatics (StaPH-B) Monthly Call. StaPH-B is a bioinformatics consortium created by subject matter experts affiliated with the Association of Public Health Laboratories. The consortium represents bioinformaticians from across the United States and internationally who are focused on addressing common barriers to bioinformatics implementation in state and public health laboratories.
Chip used in sequencing at Wadsworth Center's Advanced Genomic Technologies Core

Publication Exemplifies the Cross-cutting Work of Wadsworth Center’s Public Health Laboratories and Cores

Some of the work of the cores, such as media preparation, is based on techniques that go back over a hundred years, even to the beginnings of what became the Wadsworth Center. Other Wadsworth Center cores perform high-quality antigen production, sophisticated image analysis and manipulation, and sequencing and bioinformatic analysis that may be completed in hours to days rather than weeks or months, often providing comprehensive assessment of a full bacterial genome.
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