About CCBR
The CCR Collaborative Bioinformatics Resource (CCBR) is a centralized bioinformatics group embedded within the Center for Cancer Research (CCR) at NCI. CCBR was established to provide CCR investigators with access to sophisticated bioinformatics expertise they may not have within their own laboratory groups.
CCBR is staffed by a multidisciplinary team of bioinformaticians, computational biologists, and data scientists with expertise in next-generation sequencing data analysis, statistical genomics, and software development.
Organizational Structure
CCBR is part of the Office of Science and Technology Resources (OSTR) within CCR and coordinates with:
- Frederick Sequencing and Genomics Core (FSGC): Generates raw sequencing data for many CCBR-supported projects and coordinates sample submission and library preparation.
- NIH Biowulf HPC: High-performance computing cluster where CCBR pipelines are executed at scale.
- NIDAP: Cloud-based platform hosting CCBR workflows, interactive visualizations, and collaborative analysis tools.
- BTEP: Bioinformatics Training and Education Program providing training resources to CCR scientists.
Collaborative Support Model
CCBR provides bioinformatics support at no cost through a collaborative, effort-based model. CCBR bioinformaticians are assigned to projects as scientific collaborators.
- CCBR staff contribute intellectual input and are eligible for co-authorship on resulting publications
- Projects are accepted based on scientific fit, feasibility, and available CCBR capacity
- Investigators are expected to engage early and provide the information needed to enable efficient completion
- Support is available to all CCR principal investigators working on high-throughput sequencing projects
Scientific & Computational Expertise
CCBR provides collaborative expertise across a broad range of genomics, transcriptomics, epigenomics, and computational analysis areas. Our support spans both domain-specific analysis and the computational methods needed to generate interpretable, reproducible results.
Scientific Expertise
DNA Sequencing & Variant Analysis
- Whole-genome sequencing (WGS), whole-exome sequencing (WES), and targeted DNA sequencing
- Somatic and germline variant analysis
- Structural variant detection and copy-number analysis
Single-Cell, Spatial & Multiome
- scRNA-seq, scATAC-seq, integrated multiome, and spatial transcriptomics
- Clustering, annotation, trajectory analysis, accessibility analysis, and tissue-context interpretation
Immunogenomics & Functional Genomics
- TCR/BCR repertoire analysis and broader immunogenomic interpretation
- CRISPR screen analysis
- Perturbation-based functional genomics
Long-Read Sequencing
- PacBio and Oxford Nanopore workflows for genome and transcriptome profiling
Transcriptomics & Gene Expression
- Bulk RNA-seq, small RNA-seq, circRNA-seq, EV-seq, and microarray
- Allele-specific expression, QC, alignment, quantification, differential expression, pathway analysis, and visualization
Epigenomics, Chromatin & 3D Genome
- ChIP-seq, ATAC-seq, CUT&RUN, DNA methylation analysis, chromatin-state profiling, and Hi-C-related assays
Microbiome, Public Data & Specialized Analyses
- Metagenomics, microbiome profiling, public data mining, cross-study integration, and external dataset reanalysis
- Proteomics, metabolomics, survival analysis, and other specialized collaborative analyses
Collaborative Research Support
- Grant bioinformatics plans, methods writing, figure preparation, and reviewer-response support
Computational Expertise
Statistical & Analytical Methods
- Statistical modeling
- Experimental design consultation
- Differential analysis
- Pathway interpretation and quantitative result synthesis
Workflow Engineering & Reproducibility
- Pipeline development and automation using Snakemake and Nextflow
- Containerized and reproducible execution on NIH Biowulf
Data Integration and Machine Learning
- Integrative multi-omics analysis across modalities
- Machine learning for genomic data
- Cross-platform integration and biological interpretation
Visualization & Reporting
- Interactive visualization using Shiny, Plotly, and custom tools
- Publication-ready figures, reporting, and result communication
Data Handling
CCBR manages data across the full sequencing-to-results pipeline. Understanding data flow helps investigators plan projects effectively and ensures security and integrity throughout.
Sequencing Data Flow
CCR Sequencing Facility (FSGC)
Researchers consult with the FSGC team for sequencing. On the NAS form, specify “CCBR” as the Bioinformatics contact. Samples are submitted for library preparation and sequencing. FSGC bioinformatics team coordinates with CCBR on data handoff logistics.
Globus Transfer
Raw FASTQ files are transferred securely to investigators and CCBR via Globus, NIH’s high-performance data transfer platform.
NIH Biowulf HPC
Data are staged on Biowulf, where CCBR executes validated, version-controlled pipelines at scale.
Analysis & Quality Control
CCBR pipelines produce quality-controlled outputs: count matrices, alignment files, QC reports, and interactive visualizations.
Results Delivery
Final results returned via AMP workspace or shared on NIDAP for interactive exploration and collaboration.
Data Security & Compliance
All data handled by CCBR are managed in compliance with NIH data security policies. Protected human subjects data are handled through approved secure computing environments. CCBR does not retain investigator data beyond the active project period without explicit agreement.
NIDAP Integration
Routine bulk RNA-seq and single-cell RNA-seq workflows are also available through NIDAP, enabling secure browser-based access to workflows, collaborative data sharing & interactive result exploration.
Office Hours & Locations
Weekly office hours give CCR scientists an opportunity to discuss bioinformatics-related questions with CCBR bioinformaticians. You may attend virtually or in person.
VIRTUAL / IN-PERSON OFFICE HOURS
| Day | Time | Format | Location / Access |
|---|---|---|---|
| Thursday | 3:00 – 5:00 PM | Virtual / In-person | Bethesda: Bldg 37, Rm 3041 Join via Webex |
| Tuesday | 11:00 AM – 1:00 PM | In-Person | Frederick: Bldg 1043, Rm 13 |
In-Person Visits
Drop in during the scheduled Bethesda or Frederick office hours listed above. No advance appointment is required for in-person attendance during the posted session times.
VIRTUAL / IN-PERSON OFFICE HOURS
Use the Webex meeting link in the schedule above to join Thursday virtual office hours. To arrange a separate virtual meeting, email nciccbr@mail.nih.gov.
CCR Collaborative Bioinformatics Resource (CCBR)
Building 37, Room 3041 · National Cancer Institute, NIH
9000 Rockville Pike, Bethesda, MD 20892 · nciccbr@mail.nih.gov
Primary Points of Contact
For project consultations
Maggie Cam, Head CCBR, CCR, NCI (maggie.cam@nih.gov)
Parthav Jailwala, Bioinformatics Manager, CCBR, ABCS, FNLCR (parthav.jailwala@nih.gov)
For technical assistance on CCBR Pipelines
Vishal Koparde, Technical Lead, CCBR, ABCS, FNLCR (vishal.koparde@nih.gov)
For training related inquiries
Amy Stonelake, BTEP Program Manager, ABCS, FNLCR (NCI-BTEP@mail.nih.gov)
General Contact
| Contact Type | Details |
|---|---|
| General CCBR inquiries | nciccbr@mail.nih.gov |
| Office hours | See Office Hours & Directions |
| Project requests | CCBR Project Request Form |