The 3I-UCGD Bioinformatics Core expansion offers immunology and microbiology-related bioinformatics services to all University of Utah investigators. We can perform, or expand on, most bioinformatic processing or analyses with domain expertise in immunology, microbial genomics and metagenomic approaches. We also offer consultation on experimental design and sequencing strategies, as well as reanalysis of publicly available data.
Major Analysis Types We Offer:
Genomics
- Alignment and variant calling for NGS datasets, including whole genome, whole exome, and panel sequences
- Joint genotyping of separate data sets and controls
- Whole genome bisulfite sequencing analysis
- Disease gene discovery in cohorts and families using VAAST, PHEVOR, VIQ, Slivar, and IOBIO
- Reference-free variant calling and investigation of de novovariants using RUFUS
- Structural variant calling and prioritization using Smoove and Manta
- Analysis of ChIP-Seq, ATAC-Seq, CUT&Tag data
- Taxonomical analysis
- Multiple sequence alignment and phylogenetic analysis
- Transcription factor motif enrichment analysis
- Genome assembly and annotation
- Validation of CRISPR modifications. WGS sequencing analysis to search for off target effects and identify structural complexity not identifiable using PCR.
- Project and data management through the Mosaic platform
Transcriptomics
- Analysis of RNA microarrays
- Analysis of RNA-Seq data (bulk, single-cell, long reads) at gene, transcript, and exon level
- Transcripts analysis from long RNA reads
- Identitication of splicing aberrations and outlier gene expression in patient RNA samples
- Correlation of gene expression to patients' survival
- Differential gene expression analysis
- Over-representation analysis and Gene Set Enrichement Analysis (standard and pre-ranked)
- Deconvolution of bulk RNA-Seq
- Single-cell datasets integration (e.g. from different publications)
- Identification and comparison of cell populations (both abundant and rare) in single-cell sequencing
- Trajectory and pseudo-time analysis of single-cell RNASeq data
- Comparisons of data across species
Metabolomics/Lipidomics
- Comparisons of individual metabolites or lipids across different conditions (univariate and multi-variate analyses)
- Differential abundance analysis of lipid classes
- Lipid ontology enrichment analysis
Image Analysis
- Analysis of fluorescent microscopy images (intensity measurements, segmentation, time-lapse analysis, etc.)
Machine Learning
- Machine learning and custom deep learning networks
- Analysis and integration of clinical and omics data for predictive and exploratory purposes
Custom Development
- Generation of parallelized and portable pipelines for any of the services described above
- Development of custom bioinformatics tools and analysis approaches
- Custom data visualizations
- Integration of complex omics datasets
Core Personnel
Directors
Carson Holt
Research Associates
Joselin Hernandez-Ruiz
