Bioinformatics Unit
A team in the Biostatistics & Computational Biology Shared Resource

Mission

To deliver rigorous, reproducible and high-quality bioinformatics solutions through collaborative research that enables investigators to generate meaningful biological insights and advance cancer discovery.

Overview

The bioinformatics team, part of the UF Health Cancer Center Biostatistics & Computational Biology Shared Resource, provides comprehensive and collaborative support for cancer research across a spectrum of omics data analysis. Our core mission is to deliver rigorous, reproducible and high-quality bioinformatics solutions through collaborative research that enables investigators to generate meaningful biological insights and advance cancer discovery.

Our team specializes in the end-to-end analysis of raw high-throughput omics data, including genomics, transcriptomics, epigenomics, proteomics and single-cell sequencing, using robust, standardized workflows. By integrating advanced computational approaches and industry-standard best practices, we help transform complex datasets into interpretable findings that drive impactful research.

In addition to data analysis, we actively collaborate with scientists and investigators on experimental study design, development of custom analysis pipelines and Shiny tools, and the bioinformatics components of grant proposals and manuscripts. We ensure seamless coordination with sequencing facilities for efficient data transfers and deliver detailed, user-friendly reports to support scientific decision-making. We leverage the University of Florida’s HiPerGator high-performance computing system to efficiently process and analyze large-scale omics datasets.

Our team also contributes to the development of informatics infrastructure for secure data sharing, management and storage, enabling efficient handling of large-scale cancer omics datasets.

Our team also offers educational programs, including seminar series, journal clubs, workshops and walk-in clinics, to build bioinformatics capacity in the research community.

Through these efforts, the bioinformatics team serves as a trusted partner, enabling rigorous, innovative and reproducible research that accelerates progress in cancer science.

Common assays in bioinformatics research

The bioinformatics core analyzes a wide range of high-throughput data types, including:

Software and tools

Our bioinformatics team supports a wide range of analytical tools, with in-house and publicly available standardized tools and pipelines aligning with the ENCODE practices. Our pipelines are NextFlow-based, many of which are adapted from nf-core.

Additionally, we develop interactive in-house applications to enhance data interpretation and visualization, with current deployments focused on RNA-Seq analysis that provide users the freedom to explore the analyzed data by generating custom heatmaps, volcano plots, pathway analysis plots and dimensionality reduction plots.

We also offer custom workflows and modules tailored to diverse omics analyses.

Our team can also provide hosting for publicly available tools upon request. This is ideal for researchers facing computational constraints or privacy concerns.

Our team

Bioinformatics Unit Leader

Jason Brant, Ph.D.

Jason Brant, Ph.D., is an assistant professor in the Department of Biostatistics. His research interests are focused on the role of DNA methylation and chromatin structure in regulating gene expression and how perturbations in the epigenome can result in disease onset and progression.

BIOINFORMATICS ANALYST III

Heather Kates, Ph.D.

Heather Kates, Ph.D., is a bioinformatician who works to develop tools and strategies that bridge the gap between data and discovery in multi-omics biomedical research. She aims to design and execute thoughtful analyses using gold-standard methods while presenting findings in formats that are clear, interpretable and actionable for investigators.

BIOINFORMATICS ANALYST III

Kalyanee Shirlekar, M.S.

Kalyanee Shirlekar, M.S., is a bioinformatician who bridges the gap between data scientists and biologists. She enjoys analyzing and visualizing exciting data.

Consultation and contact

As part of the Biostatistics & Computational Biology Shared Resource, the bioinformatics team is also present at the weekly Biostatistics & Bioinformatics virtual walk-in clinic for consultation. Alternatively, if you would like to have a dedicated time slot for your project, our bioinformatics staff are available by appointment for personalized consultations. We are happy to support you with experimental design, selection of analytical approaches, software tools and troubleshooting during your data analysis journey.

We highly recommend engaging with our team early in your project planning phase. Early collaboration ensures robust experimental design and maximizes the success of downstream analyses.

Our team operates under a collaborative research model, where bioinformatics staff scientists are included as key personnel on grant proposals, with salary support provided through the funded project.

To learn more about our services, approach and how we can collaborate, we invite you to schedule a meeting with Jason Orr Brant, Ph.D., bioinformatics unit leader.