Computational Biology and Bioinformatics Services and Consultation
- Consulting for the study design, including the selection of appropriate technologies and experimental parameters
- Grant proposal and manuscript preparation support
- Analysis of next generation sequencing data, including RNA-sequencing, ChIP-sequencing, whole exome-sequencing, ATAC-sequencing, whole genome re-sequencing, and long-read sequencing (e.g., Oxford Nanopore)
- Analysis of single-cell sequencing, spatial transcriptomics, TCR/BCR repertoire profiling, and targeted gene panels
- Various downstream and systems-level analyses of results from sequencing and microarray data
- Analysis of nCounter NanoString data
- Analysis of genomic editing (e.g., shRNA and CRISPR/Cas9 screening) data
Single-cell RNA-seq (scRNA-seq) data analysis services
- Basic scRNA-seq data analyses, including quality control, alignment, trimming, assembly, differentiation expression, and clustering
- Advanced scRNA-seq data analyses, including cell trajectory analysis, cell type prediction, and co-regulated gene module identification
- Interpretation of results
- Integrative analysis of single-cell multi-omics data
Spatial transcriptomics data analysis services
- Basic spatial transcriptomics data analyses, including quality control, tissue architecture identification, spatial variable gene identification, and differential expression analysis
- Advanced spatial transcriptomics data analyses, including deconvolution and cell-cell communication analyses
- Interpretation of results
- Integrative analysis of spatial multi-omics data
Immune profiling
- CyToF data analysis
- Analysis of immunome flow panels
Metabolomics data analysis
- LC-MS data preprocessing, including quality control assessment of raw chromatograms, peak calling, retention time alignment, and preliminary identification using MS2 data, if available
- Interpretation of liquid-chromatography untargeted metabolomics datasets, which include relative abundances of a broad spectrum of polar and non-polar small molecules (< 1500 Daltons)
- Statistical analysis to identify biologically relevant metabolites
- Pathway enrichment analysis of relevant metabolites
Proteomics data analysis
- Protein/peptide identification and quantification from label-free and label-based tandem mass spectrometry data
- Post-translational modification analysis (PTM), such as phosphorylation
- Downstream bioinformatics analysis, such as differential expression analysis, pathway analysis, functional enrichment analysis, and network analysis, involving finding pivotal proteins in the networks
Metagenomic and metatranscriptomics services
- Metagenomic data analysis, including species/strain composition profiling, taxonomic analysis, abundance analysis, phylogenetic analysis, and whole-genome shotgun analysis
- Metatranscriptomic data analysis, including functional profiling, expression activity analysis,16S ribosomal RNA analysis, and whole-transcriptome shotgun analysis
Public domain and commercial data source mining services
- Obtaining multiple data sources, including dbGaP, GEO, ENCODE, TCGA, ICGC, GTEx, and ORIEN Avatar
- Implementing integrative analyses of these datasets in concert with locally generated data
Data management and sharing services
- Big data transfer
- Data storage management
- Data/code submission to repositories
- Data management and sharing policy development, along with relevant cost estimation
Analysis workflow development and standardization
- Reviewing best practices
- Defining standard operating procedures
- Adopting standard data analysis protocols
Novel bioinformatics tool development
- Custom software engineering when existing tools do not meet investigators’ needs
- Development of novel computational methods for genomic data analysis and integration
- Development of R and Python packages
Cloud computing and web development
- Development and management of interactive and dynamic web interfaces
- Development and management of cloud infrastructures
Training and Workshops
BISR faculty and staff organize short 1-2 day workshops and seminars focused on bioinformatics data analysis. The workshops cover various areas of bioinformatics and contain hands-on activities to help CCC researchers understand the process of data analysis and the interpretation of the results.
| BISR Hourly Rates | PerUnitPrice |
|---|---|
| Junior Staff (Bioinformatics Analyst 1 - 2) | $72.00 |
| Mid to Senior Staff (Bioinformatics Analyst 3 - 4) | $102.00 |
| Senior Staff (Bioinformatics Analyst 5 / Research Scientist) | $116.00 |
| Faculty | $160.00 |