- Bioinformatics analysis of high-throughput biological data, including proteomics, using our well-defined analysis pipelines
- Consulting services for custom analysis beyond our standard pipelines, including genome-wide association studies
- Grant writing assistance, including assistance fully developing the bioinformatics components of a grant, cost analysis, letters of support, and documenting the availability of tools and expertise to complete the research indicated
- Free training sessions in bioinformatics topics: visit the CRI Seminar Series to find out about upcoming classes and download materials from past sessions
The Bioinformatics Core’s work combines the use of powerful computing resources, advanced analytics tools, and a commitment to security to transform large amounts of raw data into meaningful results. We use the CRI’s high-performance computing cluster and large-scale storage resources, with which complex analytics can be executed in parallel or distributed environments to produce fast data processing rates, improving application performance and cost effectiveness. Through advanced high-throughput analytics solutions, we dig down to the root of each computational challenge and design the most direct path to a solution. All our work is protected with the CRI’s automated, resilient backup and security systems, ensuring data integrity and access controls that are aligned with standards required by HIPAA, FISMA, and other regulations.
LET’S GET STARTED
Planning an experiment? The Bioinformatics Core has created a guide to Bioinformatics Experimental Design to help you get the best results.
For each project request, the Core creates a proposal for the researcher that includes the scope of deliverables, a timeline for completion, and the estimated cost. The execution of the project is guided by frequent discussion between researchers and bioinformaticians, with progress updates provided regularly. Project results are delivered in the form of a written report.
- RNA-Seq: Raw Data QC, Filtering, Mapping, Data Summarization, Expression Quantification, Differentially Expressed Genes, Pathways, and Gene Ontology Analysis
- ChIP-Seq: Raw Data QC, Filtering, Mapping, Peak Calling, Peak Differential Analysis, Peak Related Genes Analysis, Gene Ontology Analysis, and Annotation
- Exome Sequencing: Raw Data QC, Pre-processing, Mapping with 3 different tools, Realignment and Quality Recalibration, Multiple Samples Variant Calling, Variant Annotation, Varian Comparison, Filtration, and Summarization
- Whole Genome Re-Sequencing (WGRS): Raw Data QC, Filtering, Mapping, Genotyping, SNP Detection, InDel Detection, SV (Somatic SV) Detection, CNV Analysis, and Annotation
- Consensus Genotyping Pipeline: Genotyping, SNP Detection and InDel Detection using three different methods (Samtools, GATK and Atlas-2), comparison of variant calls, list of consensus call variants, and list of method specific calls
- De-novo Assembly: Raw data QC, Merging, Clipping, Filtering, Contigs Assemble, Scaffold Assembly, Assemble Statistics, and Downstream Analysis
- Somatic Mutation Detection for Tumor/Normal Pairs: Raw Data QC, Pre-processing, Mapping with 2 different tools, Realignment and Quality Recalibration, Somatic Mutation Detection with 4 different tools, Variant Annotation, and Summarization
- Small RNA-Seq: Raw Data QC, Filtering, Mapping, Data Summarization, Quantification, Detection of Differentially Expressed miRNAs, Putative Gene Target Prediction, and Pathways Analysis
Illumina and Affymetrix Expression Arrays
- Filtering, Data Summarization and Normalization, Sample/Gene/Probe-based QC, Differentially Expressed Genes, Functional Annotation, and Pathway Enrichment Analysis
Affymetrix and Exiqon miRNA Arrays
- Filtering, Data Summarization and Normalization, Sample/Gene/Probe-based QC, Differentially Expressed miRNAs, Predict miRNA Targeted Genes, Functional Annotation, and Pathway Enrichment Analysis
- We provide bioinformatics analysis service for single-cell transcriptomic sequencing data generated by different technologies, including UMI-based Drop-seq and 10x Genomics Chromium, as well as non-UMI-based CEL-seq and Smart-seq. Our pipeline consists of (1) data de-multiplexing; (2) read alignment; (3) processing of cellular and molecular barcodes; (4) read count table; (5) quality control and normalization; (6) removal of debris, dead cells, and doublets; (7) detect batch effects; (8) clustering and identification of cell subsets; (9) cluster visualization using tSNE or UMAP; (10) marker gene identification; (11) differential gene expression analysis; (12) GO term and pathway analysis. Our customized pipeline can also perform single cell lineage analysis and other study-specific analyses upon request.
Proteomics Analysis Pipeline
- Raw MS data processing, deisotoping, data conversion, spectral filtering, spectral library creation, extracted ion chromatogram generation (MASIC), peptide and protein identification (X!Tandem, MaxQuant, Mascot, MSGF+), quantification (MaxQuant, Scaffold), targeted assay generation (Skyline), and dataset alignment and feature generation (MultiAlign)
- We provide bioinformatics analysis service for single-cell Mass Cytometry (CyTOF) data. Our pipeline consists of (1) pre-gating (removal of debris, dead cells, and doublets); (2) diagnostic analysis; (3) marker ranking; (4) clustering, identification, and annotation of cell subsets; (5) cluster visualization using tSNE or UMAP; (10) differential analysis, including differential cell population abundance, differential analysis of marker expression stratified by cell population, and differential analysis of the overall marker expression. Our customized pipeline can also be incorporated into other study-specific analyses upon request.
- Profiling of post-translational modifications (phosphorylation, glycosylation, etc.), statistical analysis for labeled and label-free proteomics, and pathway enrichment analysis (Ingenuity Pathway Analysis)
We also offer custom-made pipelines and expertise for types of analysis not listed above, including genome-wide association studies. Email us to get started!
TOOLS AND DATASETS
The Bioinformatics Core maintains the following catalogs of software tools, reference datasets, and databases for use by the BSD research community:
MEET THE BIOINFORMATICS CORE
Our team of bioinformaticians offer a diversity of experience and areas of expertise. Meet the team at the link below and learn more about the scientists you’ll be working with.
Pictured from left to right: Wen-Ching Chan, PhD; Wenjun Kang, MS; Yan Li, PhD; Jorge Andrade, PhD; Tzuni Garcia, PhD; Riyue Bao, PhD; Kyle Hernandez, PhD; Chunling Zhang, MS; Lei Huang, PhD.