Harvard Chan Bioinformatics Core
The Harvard Chan Bioinformatics Core in the Department of Biostatistics provides a single point of contact for Harvard researchers seeking bioinformatics analysis services, training and platform development. Specializing in applications of high-throughput sequencing analysis, core staff aid researchers with the management, integration, and contextual analysis of biological data, supporting the advancement of research and ultimately, aiming to improve human health.
401 Park Drive
Level 3 East
Boston, MA 02215
Consulting and Analysis
The HBC is a fee-for-service bioinformatics core offering expert support in high-throughput sequence analysis. Our team can assist with every stage of your project – from data retrieval, management, and storage to quality control, analysis, and preparation of results for publications or grant applications. We follow community best practices and re-use public workflows and tools wherever possible, while also tailoring or developing custom methods when your project requires it.
We encourage you to contact us during the planning stage of your analysis. Our staff can provide guidance on power calculations, experimental design, and cost-effective sequencing strategies—helping you set your project up for success while minimizing unnecessary expenses.
- Single-cell and single-nuclei RNA-seq (CITE-seq, TCR/BCR, TEA-seq, 10X Multiome, custom)
- Bulk RNA-seq (quantification, splicing, and de novo transcriptome analysis)
- Small RNA-seq (i.e. miRNA analysis)
- Spatial profiling (Visium, Visium HD, Xenium, GeoMX, CosMX, MERSCOPE, STOmics Stereo-seq, Slide-seq)
- ChIP-seq, CUT&RUN, CUT&Tag and ATAC-seq
- DNA methylation (bisulfite sequencing and DNA methylation arrays)
- Variant analysis (whole genome, exome, variant calling and prioritization)
- Genome assembly (reference guided and de novo)
- Multimodal data integration
- Custom analysis
We can provide a path from genes to function by delivering extensive functional annotation, prioritizing new markers and developing testable hypotheses for future experiments. We test for functional information using different gene set enrichment approaches (using Gene Ontology, pathway databases as well as curated and generic gene sets), provide context by integrating your data with public resources such as GEO and TCGA, and explore the biological interaction space in co-expression and high-throughput interaction data sets using network analysis techniques.
We encourage you to talk to us early; we often cannot save a poorly designed experiment, but we can help you design a successful experiment. Initial consults are free, and we are committed to helping you determine the optimal experimental design given your budget. We discuss sample size, number of replicates, sources of batch effects, sequencing depth, and overall impressions of the experiment from a bioinformatics perspective.
We can support grant proposals and review manuscripts on short notice. The Core’s team has extensive experience in providing standard descriptions and implementing best practices in data management, quality control, and data dissemination to the scientific community that fulfill NIH and NSF requirements and simplify the process of publishing your manuscript. We are available to help you with your data submission to standardized databases such as the Gene Expression Omnibus and the Sequence Read Archive.
Pricing
The initial consultation is free of charge. During this meeting, our bioinformaticians will work with you to determine the project specifications and create a time estimate and set of deliverables.
Rates for FY26 are as follows:
| Internal (HCSPH, HMS, HSDM, FAS) | $180/hour |
| Harvard-affiliated hospitals and external academic institutions | $193/hour |
| Industry | $265/hour |
The rate covers computing time, basic data storage costs, and other technical expenses. Person time is billed in minimum 15 minute increments, and includes communications and meetings in addition to time spent performing analyses. Industry rates are negotiable depending on volume.
For more information, email us at bioinformatics@hsph.harvard.edu.