Projects & Collaborators

Bioinformatics Projects and Collaborators

We offer services in various bioinformatics areas. Below are some of our main projects with brief explanations:

Standard Service for all Cancer Center Researchers

Collaborator(s): ♦ Dr. Francois Spitz’s Lab (3 Projects) ♦ UCCCC Dr. Odunsi’s Lab (6 Projects) – Dr. Sean Kraus, Dr. Khaled Alharshawi

This service offers:

- Quality Control (QC) and Preprocessing: We ensure data quality and prepare raw RNA-seq data for analysis
- Differential Expression Analysis: We identify genes that are expressed at different levels across conditions or treatments
- Pathway Enrichment Analysis: We determine biological pathways significantly affected by gene expression changes
- Alternative Splicing Analysis: We investigate variations in splicing patterns that may affect gene function

Collaborator(s): ♦ UCCCC

This project emphasizes:

- Cell Clustering and Annotation: We group similar cells and label them based on gene expression profiles
- Trajectory Analysis: We map the developmental pathways of cells over time
- Cell-Type Identification: We classify cells into distinct types based on their gene expression
- Gene Regulatory Networks: We analyze interactions between genes that regulate cellular functions
- Cellular Heterogeneity Analysis: We examine the diversity of cell populations within a sample

Collaborator(s): ♦ UCCCC – Dr. Sean Kraus

Core elements include:

- Variant Calling and Annotation: We identify genetic variants and provide functional annotations
- Genome Assembly: We construct complete genomes from sequenced DNA fragments
- Structural Variant Analysis: We investigate larger genomic alterations, such as deletions and duplications
- Copy Number Variation: We assess variations in the number of copies of genes
- Comparative Genomics: We compare genomes from different species to identify evolutionary relationships

Collaborator(s): ♦ UCCCC

This area explores:

- SNP/IDEL Calling: We detect single nucleotide polymorphisms (SNPs) and insertion/deletion (IDEL) variants
- Variant Interpretation: We evaluate the potential impact of identified variants on health and disease
- Clinical Significance Analysis: We assess the relevance of variants in a clinical context for patient diagnosis or treatment

Collaborator(s): ♦ UCCCC – Dr. Odunsi

This study encompasses:

- Mutation Impact Prediction: We evaluate how mutations affect protein function and potential immunogenicity
- Epitope Prediction: We identify peptide sequences recognized by the immune system
- Immunogenicity Scoring: We assess the likelihood that a peptide will trigger an immune response
- Peptide Binding Prediction: We predict how well peptides bind to HLA molecules
- Vaccine Candidate Selection: We identify promising candidates for therapeutic vaccines based on neoantigens

Collaborator(s): ♦ Dr. Francois Spitz

This analysis entails:

- Peak Calling and Annotation: We identify regions of open chromatin where gene regulation occurs
- Motif Analysis. We search for DNA sequences recognized by transcription factors
- Nucleosome Positioning: We determine the location of nucleosomes to understand chromatin structure
- Regulatory Element Identification: We identify elements that control gene expression
- Integration with RNA-seq: We combine ATAC-seq data with RNA-seq to correlate chromatin accessibility with gene expression

– In progress with Google

– In progress (60% complete)

– In collaboration with Dr. Francois Spitz

– In collaboration with UCCCC, CRI, 5-10 African countries

– In progress (50% complete)