Bioinformatics Expertise Invested in your Research

UFHCC BCB-SR Bioinformatics Team

Meet Your Bioinformatics Team

• 3 bioinformaticians with complementary skills
• 30+ years combined experience
• Integrated approach collaborate with one, benefit from all

Emphasize team’s diverse skills: computational biology, stats, cancer genomics.
- Stress 20+ years of collective omics experience.
- Highlight collaboration: “Work with one, get all of us.”

Our Collaboration Model

Not a service core we’re partners • Key personnel on grants • Funded through your research • Invested in your success

Strengthening Your Grant Applications

NIH expects plans for:
• Code & software
• Data management & sharing
• Computational resources

If your project includes high-dimensional data, an expert bioinformatician makes the proposal stronger.

• Assays chosen with clear rationale
• Experimental design avoids QC pitfalls
• Named personnel to analyze data
• Code & software packages specified
• Compute & storage resources identified
• Results visualization approach defined

NIH increasingly emphasizes robust data management and data analysis plans •• We help you craft compelling data management and sharing plans, justify your analytical approaches, and budget appropriately for computational resources

Experience = Robust, Reproducible Analyses

• Hundreds of datasets analyzed
  
• Every major omics assay
  
• Problems solved before they derail your project
  

newbie chaos vs. our organized expertise.
- Highlight hundreds of datasets analyzed, omics assay experience.
- Mention tools (GitHub, READMEs, reports) for transparency.
- End strong: we save time and deliver insights

Bioinformatics Project Lifecycle

Proposal & Funding

• Assist in grant writing
• Experimental design planning and choosing the protocol

Data Generation & Delivery

• Coordination with the sequencing core
• Data storage on HiPerGator

Data Pre-Processing

• Rigorous quality control
• Troubleshooting at multiple levels
• MultiQC reports

Primary and Secondary Analysis

• Use of scalable best-practice pipelines
• Downstream analysis: differential analysis, pathway analysis, tool building etc.
• Access to in-house tools

Reports Delivery

• Automated project tracking
• Traceable and extensive reports

Publication & Data Management

• Transfer of analysis files
• Generation of publication quality images
• Uploading files to SRA

• People familiar with software development know about the Software Development Life Cycle (SDLC).
  Similarly, for a bioinformatics project, this is how a typical lifecycle looks with us.

• Project Proposal: We often get involved early, helping collaborators with grant writing (e.g., NIH) and advising on study design, feasibility, and data requirements.

• Data Generation & Delivery: We coordinate with sequencing cores to ensure smooth and well-documented data transfer. Raw FASTQ files are stored on HiPerGator, and we also help set up dedicated PI resources or temporary BCBSR resources.

• QC & Pre-processing: Once data are in hand, we perform QC, processing, and analysis using best-practice pipelines (often ENCODE-based). QC reports summarize results, but a “perfect” QC is rare — troubleshooting may involve revisiting tapestation results, over-digestion, high PCR cycles, or small insert sizes.

• Analysis & Interpretation: We then carry out primary and secondary analyses, working closely with collaborators to ensure findings are biologically meaningful and aligned with their goals.

• Reporting & Outputs: Throughout, collaborators expect transparent communication, reproducible workflows, and clear reports/visualizations. We often assist in manuscript preparation and grant support to help translate analyses into impactful scientific outputs.
  

Our Deep Experience Across Cancer Omics

Full list of assays we have experience with: RNA-seq, ATAC-seq, CUT&RUN Methyl-Seq (EM-Seq, RRBS, WGBS)
MAPit/NOMe-Seq Single-cell approaches, spatial transcriptomics CRISPR screens, AI-driven rare disease research

This isn’t just familiarity we understand the unique analytical challenges, optimal parameters, and common pitfalls for each platform.

Experienced Quality Control Saves Time + Improves Results

Catch critical issues early:

• Failed library prep detection
• Contamination identification
• Sequencing quality issues

• QC is the foundation of any bioinformatics project — it helps us spot technical problems before they impact results.
• Example 1: The Picard insert size plot showed a very narrow distribution with a shift toward small fragments.
  This flagged over-digestion or library prep issues, which would have biased downstream mapping and peak calling
• Example 2: A PCA revealed strong batch effects — samples clustering by sequencing batch rather than biological condition.
  Without QC, this artifact could easily be mistaken for a biological signal.
  
• These checks save time, prevent misinterpretation, and ensure our analyses reflect true biology rather than technical noise.
  

Analysis That Answers Your Questions

• Common tools provide simple analysis
• Standard approaches may throw away information or lead to false positives
• We can fit mixed models that match the design and interpret the results

Proven Track Record of Success

Research outcomes supported by BCB-SR Bioinformatics

• Project completion: Most funded projects progress to manuscripts or other outputs.
  
• Sustained collaboration: Ongoing partnerships with investigators across disciplines.

Scaling expertise across the cancer center

Our collaborative insights become accessible tools:

Comprehensive documentation

Specialized applications

Hands-on Training

Explore Our Resources

Last slide before Demos: Our expertise doesn’t just benefit direct collaborators—we’ve built comprehensive resources that support the entire cancer center community. Our Documentation Hub provides dynamic best practices that evolve with the field. We create interactive reports that transform standard pipeline outputs into comprehensive, explorable documents. Our custom applications like DECODeR, HeatPath, and ClusterPicker address specific bottlenecks we see repeatedly. These tools democratize sophisticated analysis while maintaining analytical rigor.

Advancing Cancer Center Research with Experienced Bioinformatics

Complete research lifecycle support

Experimental design → Publication

Sustainable tools & documentation

Emerging methodologies integration

Works in progress:

Hands-on training in Spring 2026

Multi-omics integration in DECODeR

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Contact and Work With Us

Ready to elevate your research?
Bioinforamtics Unit webpage → UF Health Cancer Center

Bioinformatics Hub → immediate resources

UF Health channels → request consultation

email us:
UFHCC BCB-SR      Jason Orr Brant
Heather Kates        Kalyanee Shirlekar

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Discussion and Questions

Let’s discuss your research challenges

Analytical bottlenecks limiting progress?

How could interactive tools accelerate discoveries?

What collaborations might amplify impact?

Your turn: Questions about integrating rigorous bioinformatics?

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