BioMicroCenter:Analysis
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The MIT BioMicro Center bioinformatics group provides data analysis support for members of the Departments of Biology and Biological Engineering. This is the same team and resource that serves Koch Institute members under the name Data Science & Multimodal Integration (DSMI) — access, staff, and capabilities are identical regardless of which department you belong to.
BIOINFORMATICS SERVICES
The BioMicro Center offers project-based bioinformatics collaboration. Staff work directly with researchers to plan and execute analyses, document their work to support manuscript preparation, and check in regularly to keep projects on track. Projects may be paused at any time by the researcher.
To start a project, submit a request through iLabs with a brief description of your experiment. A staff member will contact you to arrange a free initial consultation.
Methods
The informatics team works across a broad range of genomic and multi-omic methods. The following is a sampling of areas in which the group has active experience:
- Transcriptomics (bulk RNA-Seq, single-cell RNA-Seq, spatial transcriptomics)
- Regulatory genomics (ChIP-Seq, ATAC-Seq, CUT&RUN, Hi-C)
- Variant analysis (SNP calling, copy number variation, whole-genome sequencing)
- Metagenomics
- Functional analyses (gene set enrichment, pathway analysis, WGCNA)
- Machine learning, deep learning, and generative AI applications
- Custom analysis pipelines and manuscript data portals
Pricing
Bioinformatics support is available either hourly or as a fractional FTE. Labs that purchase a fractional FTE receive priority access; one unit equals 10% of an FTE, approximately 4 hours per week, measured quarterly. Full pricing is on the Pricing page.
BIOINFORMATICS STAFF
Stuart Levine, PhD is the director of the BioMicro Center (slevine@mit.edu) and Google Scholar.
Charlie Whittaker, PhD is the Facility Scientific Director (charliew@mit.edu) and Google Scholar.
Vincent Butty, MD, PhD is a Bioinformatics Research Scientist (vbutty@mit.edu) and Google Scholar.
Duan Ma, PhD is a Bioinformatics Research Scientist (duan@mit.edu) and Google Scholar.
Yann Vanrobaeys, PhD is a Bioinformatics Research Scientist (yannvrb@mit.edu) and Google Scholar.
Huiming Ding, PhD is a Bioinformatics Research Scientist (huiming@mit.edu) and Google Scholar.
TRAINING
Monthly training sessions are offered on a broad range of computational topics. Sessions are advertised by email; registration is through iLabs. Topics include UNIX and cluster usage, R and Python, RNA-Seq and scRNA-Seq analysis, FAIR data principles, and machine learning. Custom sessions for individuals or small groups can be arranged by contacting biomicro@mit.edu. See the Classes page for the current schedule.
ACKNOWLEDGMENT AND AUTHORSHIP
It is important to acknowledge use of the BioMicro Center in your publications. Suggested language is available on the Koch Institute acknowledgment page.
When a member of the Core has contributed significantly to a project, we ask that you consider making them a co-author. BioMicro Center staff are valued scientists and their contributions deserve recognition like any other co-author. For guidelines on including Core Facility personnel as co-authors, please see the recommendations of the Association of Biomolecular Resource Facilities (ABRF).
OTHER SERVICES
- Research computing — storage (BMC-LAB), the LURIA compute cluster, and Project AMON at MGHPCC: Research Computing page
- Data management — repository submission, FAIR compliance, and archiving: Data Management page