View source for BioMicroCenter:Analysis

{{BioMicroCenter}}

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 [https://ki-sbc.mit.edu/dsmi 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 [https://mit.ilabsolutions.com/sc/3381/ki-genomics-core-mit-biomicro-center/ 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 [[BioMicroCenter:Pricing|Pricing page]].

== BIOINFORMATICS STAFF ==

[[User:Stuart S. Levine|Stuart Levine, PhD]] is the director of the BioMicro Center (slevine@mit.edu) and [https://scholar.google.com/citations?user=c3eio1wAAAAJ Google Scholar].

[https://ki.mit.edu/people/sbc-leadership/charlie-whittaker Charlie Whittaker, PhD] is the Facility Scientific Director (charliew@mit.edu) and [https://scholar.google.com/scholar?q=Charles+A+Whittaker+MIT+bioinformatics Google Scholar].

Vincent Butty, MD, PhD is a Bioinformatics Research Scientist (vbutty@mit.edu) and [https://scholar.google.com/citations?user=OiMbt6cAAAAJ Google Scholar].

Duan Ma, PhD is a Bioinformatics Research Scientist (duan@mit.edu) and [https://scholar.google.com/scholar?q=Duanduan+Ma+MIT+bioinformatics Google Scholar].

Yann Vanrobaeys, PhD is a Bioinformatics Research Scientist (yannvrb@mit.edu) and [https://scholar.google.ca/citations?user=JJPt-ZsAAAAJ Google Scholar].

Huiming Ding, PhD is a Bioinformatics Research Scientist (huiming@mit.edu) and [https://scholar.google.com/scholar?q=Huiming+Ding+MIT+bioinformatics Google Scholar].

== TRAINING ==
<!-- Link to BioinfoClasses page -->
Monthly training sessions are offered on a broad range of computational topics. Sessions are advertised by email; registration is through [https://mit.ilabsolutions.com/sc/3381/ki-genomics-core-mit-biomicro-center/ 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 [mailto:biomicro@mit.edu biomicro@mit.edu]. See [[BioMicroCenter:BioinfoClasses|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 [https://ki-sbc.mit.edu/acknowledge 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 [https://www.abrf.org/authorship-guidelines 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: [[BioMicroCenter:Servers|Research Computing page]]
* '''Data management''' — repository submission, FAIR compliance, and archiving: [[BioMicroCenter:DataManagement|Data Management page]]

[[Category:BioMicroCenter]]