CCR Collaborative Bioinformatics Resource

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

The CCR Collaborative Bioinformatics Resource (CCBR) continues to serve as a vital hub for CCR investigators seeking expert bioinformatics support. Since its establishment in 2011, CCBR has grown into an integrated ecosystem that simplifies access to computational expertise, fosters collaboration, and advances the scientific goals of the NCI intramural research community. CCBR's bioinformatics ecosystem is built on close partnerships across CCR and beyond-uniting core services, embedded bioinformaticians, informatics trainers, and scientific collaborators. These relationships enhance CCBR's ability to deliver scalable, reproducible, and customized support through centralized infrastructure and strategic coordination. In addition to providing collaborative expertise, the resource also includes dedicated personnel for training CCR scientists to learn programming and scientific data analysis through the Bioinformatics Training and Education Program (BTEP) that has helped accelerate data interpretation and discovery. CCBR's work centered on four interconnected pillars: [I] Hands-on Bioinformatics Support - Supporting a broad range of next-generation sequencing (NGS) and computational biology projects. The group supported 83 collaborative projects, including 53 new submissions from CCR investigators and co-authored 11 peer-reviewed publications, contributing significantly to cancer genomics. Highlighted collaborations included: 1) Tumor Antigen Escape Study: Conducted data analysis for a study on caIL-12 therapy, identifying mechanisms of immune escape in solid tumors (Zhang et al., J Immunother Cancer, 2024). 2) Kaposi's Sarcoma Gene Regulation: Discovered that ORF57 binds and stabilizes FOS RNA during KSHV infection, leading to oncogenic gene expression (Majerciak et al., mBio, 2025). 3) tRNA Acetylation and Translation: Analyzed how loss of tRNA acetylation affects ribosome activity and translation, revealing insights into eIF2alpha phosphorylation and therapeutic implications (Gamage et al., Sci Adv, 2025). 4) Circular RNA in Herpesviruses: Developed the CHARLIE pipeline to identify circRNA variants across lytic and latent infection phases (Dremel et al., EMBO J, 2025). 5) GVHD Biomarker Discovery: Used the LOGAN pipeline to analyze WGS data and identify inflammation-linked somatic variants in GVHD patients (Schulz et al., Bone Marrow Transplant, 2025). 6) COVID-19 Vaccine Study: Performed immune profiling for the DNA/LION SARS-CoV-2 vaccine, demonstrating durable humoral and cellular immunity over 2 years (Karaliota et al., iScience, 2025). 7) Liquid Biopsy Innovation: Collaborated on the first liquid biopsy assay for detecting HLA-I loss of heterozygosity, aiding resistance prediction to PD-1 and adoptive T cell therapies. This led to patent filings and the launch of Sesh Inc., with plans for clinical assay development and collaborations across NIH, academia, and industry. 8) Exon-Level Expression Profiling: Created a workflow for exon-specific gene expression analysis with Dr. Rosa Nguyen, based on CSEMiner, contributing to a novel CAR-T immunotherapy patent. [II] Automated Pipeline Development: Created and maintained scalable and reproducible NGS analysis workflows. Achievements included successful adoption of the NIH LabArchives Electronic Lab Notebook (ELN) for compliant data management. CCBR modernized its infrastructure by migrating from Snakemake to the cloud-optimized Nextflow framework. This included creation of 100+ Docker containers, runtime optimization of pipelines, documentation improvements and standardized configurations. Novel and updated pipelines included ASPEN v1.0.2 (ATAC-seq; Enhanced analysis steps, improved documentation), CHARLIE v0.11 (circRNA; Eliminated Biowulf dependency; improved memory handling), CARLISLE v2.6 (CutandRun; New visualizations; optional steps for flexible use), CHAMPAGNE v0.4 (ChIP-seq; Enhanced handling of shared inputs and multi-sample workflows), CRISPIN v1.0 (CRISPR-seq; Automatic job statistics and clearer documentation), ESCAPE v1.2 (EV-seq; Mitochondrial biotype support and custom genome compatibility), RENEE v2.6 (RNA-seq; GUI interface; expanded genome support), XAVIER v3.1 (Exome-seq; Integrated genome settings; reduced footprint; UI improvements), LOGAN v0.2 (WGS; New variant callers (Deepsomatic, GRIDSS); MHC LOH reporting via LOHHLA/MHC Hammer) and ccbrpipeliner v7 (Improved reliability and reproducibility across pipelines). [III] User-Centered Tools - Designing intuitive, UI-based workflows on the NIH Integrated Data Analysis Platform (NIDAP). Achievements included updated release of user-friendly workflows for Bulk RNA-seq, Single-cell RNA-seq, NanoString Digital Spatial Profiling and 10x Visium spatial transcriptomics. [IV] Training and Education - Delivering instruction via the Bioinformatics Training and Education Program (BTEP website), including office hours, workshops, and self-paced learning. Over the reporting period, the BTEP team successfully delivered 73 online offerings, which included classes, events, and training sessions. These covered a broad spectrum of topics such as programming (Unix, R, Python), artificial intelligence, and specialized seminar series including our Distinguished Speakers Series, AI Seminar Series, and Single Cell Seminar Series. Additionally, monthly coding clubs provided ongoing learning opportunities. The curriculum spanned various domains, including statistics, cloud computing resources, omics research, software tools, databases, and high-performance computing (HPC). Content was designed to accommodate beginner, intermediate, and advanced learners, depending on subject complexity and instructional approach. To further support foundational learning, BTEP hosted 10 in-person, small-group (1-10 participants) help sessions tied to the Unix and Python classes, as well as the Bioinformatics for Beginners course. These sessions provided individualized guidance, helping newcomers gain confidence and align with the pace of their respective courses. Collectively, both online and in-person training sessions reached an estimated 2,500 learners across the NIH. In addition to training delivery, BTEP coordinates monthly NIH-wide meetings for data science and bioinformatics educators. These gatherings focus on educational strategy, available resources, and Institute-specific initiatives, offering a valuable forum for sharing best practices and enhancing collaboration among trainers. BTEP also distributes a monthly BTEP Bulletin to our NCI/CCR audience. This newsletter features announcements about upcoming trainings, highlights of online learning programs and BTEP resources, and includes a featured topic of interest tailored to our learner community. The BTEP website serves as a vital hub for documentation, tutorials and video recordings of informatics events, drawing a vast audience from within and outside the NIH. The BTEP website was visited by over 80,000 visitors this year with over 200,000 page views. CCBR and BTEP continue to serve as a catalyst for computational innovation and training within CCR and NIH, bridging data science with biological insight to accelerate discovery and translational impact.