BioMicroCenter:AboutBMC
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About the MIT BioMicro Center
The MIT BioMicro Center is a genomics and bioinformatics core at MIT, built around a simple idea: that the best science happens when expert staff and cutting-edge technology work together with researchers as true collaborators. Since 2000, we have supported work across the full breadth of modern genomics, spanning sample preparation, single-cell and spatial transcriptomics, library preparation, short- and long-read sequencing, epigenomics, and bioinformatics, for labs across Biology, Biological Engineering, the Koch Institute, and beyond.
What We Do
The Center offers end-to-end support across the major domains of contemporary genomics:
- Sample Preparation & QC — Nucleic acid extraction, fragment analysis, qPCR quantification, and oligonucleotide synthesis
- Single-Cell & Spatial Genomics — 10X Chromium (3′ RNA, 5′ RNA, ATAC, Multiome), 10X Visium HD, and Element AVITI24 in situ sequencing
- Library Preparation — Standard and high-throughput methods for DNA and RNA, including automated miniaturized protocols that reduce reagent costs by up to six-fold
- Sequencing — High-, mid-, and low-yield short-read platforms (NovaSeqX*, AVITI24, Singular G4, MiSeq i100) plus long-read (ONT PromethION, PacBio Revio*)
* through collaboration with other shared resources
- Data Management & Bioinformatics — Dedicated data storage and delivery infrastructure, a 58-node Linux cluster, analysis pipelines for standard and custom genomics workflows, and consulting from PhD-level informatics scientists. Data is allocated by lab and accessible across platforms, with backend connections to sequencing instruments for direct delivery.
Both assisted services and walkup access are available depending on the application. All scheduling and recharge is handled through iLabs.
Our Staff
The BioMicro Center is staffed by approximately 12 full-time research scientists and technicians. The wet-lab team includes specialists in library preparation, sequencing, automation, single-cell and spatial methods, and quality control, with several staff holding advanced degrees and research backgrounds in genomics. The informatics team includes PhD-level bioinformatics scientists with expertise spanning RNAseq, epigenomics, single-cell analysis, and long-read data, as well as research computing specialists who work closely with labs on data management — from experimental design and data organization through deposition, sharing, and compliance with NIH open access requirements. The Center administers dedicated storage and delivery infrastructure and takes an active role in helping researchers meet FAIR data principles and funder mandates, not just in providing the data itself. All staff are cross-trained across methodologies, available for consultation at any stage of a project, and regularly contribute to methods development and peer-reviewed publications alongside MIT researchers. The Center conducts multiple hands-on training sessions each week to support independent instrument use.
The Center is directed by Dr. Stuart Levine. See the full staff directory.
Recent Collaboration Highlights
- Yilmaz / Jacks laboratories — RNAseq, CUT&RUN, ATACseq, and single-cell analysis identifying SOX17 as a key driver of immune evasion in colorectal cancer. Nature (PMID: 38418875)
- Sanchez-Rivera laboratory — High-throughput pegRNA library screening for p53 variants using Illumina and Singular G4 sequencing. Nature Biotechnology (PMID: 38472508)
- Henry / Griffith laboratories — Visium HD spatial transcriptomics to study ferroptosis in the uterine lining. Manuscript in preparation.
- White / Cima laboratories — Multi-omic extraction from single GBM biopsies for the BreakThrough Cancer Team Lab. Nature Communications (PMID: 40295505)
Affiliations & Governance
The BioMicro Center is a joint endeavor of the Department of Biology, the Department of Biological Engineering, the Koch Institute for Integrative Cancer Research (Integrated Genomics and Bioinformatics Core, IGB), and the MIT Center for Environmental Health Sciences (CEHS). Operational direction is set by an Executive Committee composed of the heads of each supporting unit, currently Amy Keating (Biology), Peter Dedon (Biological Engineering), and Stefani Spranger (Koch Institute). The Center is also guided by a Scientific Advisory Committee of nine MIT faculty, three from each sponsoring department, which meets twice yearly to help set technical priorities and ensure the Center remains responsive to the needs of the research community.
Contact
Building 68, Room 322 (main lab)
Building 76 (informatics & research computing)
biomicro@mit.edu
617-715-4533
NIH Acknowledgment Requirements
Researchers from the Koch Institute must include the following acknowledgment language in any publication or presentation based on work performed in the core:
- KI labs: This work was funded by the National Cancer Institute of the NIH under award P30-CA14051.