CV

Education and Training

Software Carpentry Instructor Certification, May - August 2016.
Certification to teach Software Carpentry workshops.  Certification included an intensive two-day workshop in pedagogy, an original contribution to the Software Carpentry teaching materials, and a teaching demonstration.

Kauffman Teaching Certificate Program, January - March 2015
The Kauffman Teaching Certificate Program was offered through the Massachusetts Institute of Technology Teaching and Learning Lab. Instruction and exercises totaled 5 hours per week; topics included backward design, reverse scaffolding, assessments and inclusive instruction.

An Introduction to Evidence-Based Undergraduate STEM Teaching, Fall 2014
This MOOC on teaching and learning was led by Centers for the Integration of Research, Teaching and Learning at Vanderbilt University and the University of Wisconsin--Madison. Instruction and exercises totaled 10 hours per week; topics included development of learning objectives, various assessment methods, and a significant exploration of active learning strategies (cooperative and peer learning, inquiry- and problem-based learning, flipped classrooms, etc.)  Completed with Statement of Accomplishment with Distinction.

University of Wisconsin-Madison, Madison, WI, 2004-2012
Doctorate, Cellular and Molecular Biology
Dissertation: Experimental and computational advances for studying the human genome with optical mapping.

Rice University, Houston, TX, 2000-2004
Bachelor of Arts, cum laude, Biochemistry / Computer Science
GPA (Major / Overall): 3.87 / 3.76


Professional Experience

Research Experience

Weiss Laboratory for Synthetic Biology, MIT, 2012-present
I developed genetic tools for synthetic intercellular communication in yeast and mammalian systems. These tools will allow us to both understand the operation of natural patterning and development, as well as construct and direct the patterning and cell fate of synthetic systems to create synthetic tissues and complex structures of differentiated mammalian cells.  I also developed experimental systems to test forward-design of synthetic pattern-forming gene circuits in mammalian tissue culture systems. I wrote modular, developer- and user-friendly software to analyze flow cytometry data. I served as a science communication resource, assisting other members of the laboratory in preparing manuscripts for publication.

Laboratory for Molecular and Computational Genomics, University of Wisconsin--Madison, 2004-2012
Characterization structural polymorphism in phenotypically normal humans using optical mapping. Structural polymorphism (large insertions, deletions, inversions) affects up to 30% of the human genome, but remains poorly characterized due to technological constraints. Optical mapping is a high-throughput method for creating single-molecule restriction maps that can analyze the structure of a genome at sub-kilobase resolution. I developed analytical methods to optimize optical mapping data quality and increase throughput. Then, I used these methods to collect, assemble and analyze optical maps for three lymphoblast-derived cell lines. I also developed optical map analysis software based on hidden Markov models, then deployed the software on a high-throughput computing cluster.

Janet Braam's Laboratory, Rice University, 2003-2004
Expression profiling and knock-out mutant characterization of calmodulin genes in Arabidopsis thalliana. Calcium is an important intracellular signal in all eukaryotes, and calmodulins interface calcium signaling with other signaling pathways in the cell. Interestingly, Arabidopsis has six calmodulins that share >98% sequence homology, suggesting that they might be differentially expressed. I fused the 6 calmodulin promoters (1-2 kb upstream of each gene) to the beta-glucuronidase reporter, created transgenic plants using Agrobacterium tumifaciens and demonstrated differential expression of the calmodulin genes. I also screened several insertional mutagenesis knock-out lines for increased sensitivity to various environmental stresses.

Michael Deem's Laboratory, Rice University, 2002-2003
Wrote software for Monte Carlo simulation of cyclic antimicrobial polypeptides. These polypeptides are key components of the innate immune system, and their constrained conformation makes ensemble Monte Carlo simulations particularly efficient. I implemented and evaluated a new energy model, ECEPP, in the peptide simulator that was being developed by the laboratory.

Human Genome Sequencing Center (HGSC), Baylor College of Medicine, Summer 2002
Wrote software supporting the HGSC's efforst to finish their part of the Human Genome Project. My tool ordered and oriented sequence contigs based on an Euler path built using paired-end sequencing data. It was widely used by the sequence finishing team, resulting in my inclusion on several publications from the HGSC.

Teaching Experience: Courses and Team Mentorship

MIT iGEM Team Lead Instructor, 2013-2017
iGEM is an international competition in synthetic biology where teams build new biological systems out of reusable parts, then present their work at the iGEM Jamboree held in Boston each fall. I have been the lead instructor since I arrived at MIT. Each year, I have supported a team of 10-12 undergraduates in learning about synthetic biology, choosing a project, developing a research plan, executing the research, and communicating their results. My goal is to structure this experience so that students who enter never having had a research experience leave as fully-functional junior scientists.

We allow the teams to choose their own projects (within some constraints), and thus they have varied widely.  Projects have included:

  • 2013: Intercellular communication using small virus-like vesicles called exosomes. The students built and characterized several devices for producing exosomes, as well as a number of sending and receiving modules that could be useful to package up in these vesicles.
  • 2014: Molecular systems for sensing and treating beta-amyloid plaques associated with Alzheimers disease. Approaches included native receptors and engineered B-cell receptors for sensing beta amyloid aggregates, as well as characterization of proteases that could be used to reduce plaque formation.
  • 2015: A consolidated bioprocessing approach for turning cellulosic agricultural waste into biofuels. The team developed several new parts for Cytophaga hutchinsonii, a bacterium that is naturally cellulolytic, as well as E. coli parts for producing biofuels. Their goal was to grow the two bacteria simultaneously, with the C. hutchinsonii breaking the cellulose down into sugar that an engineered E. coli could use to produce biofuels.
  • 2016: Genetic devices for diagnosing endometriosis. Endometriosis is a disease of the female reproductive system where endometrial tissue grows elsewhere in a woman's body, causing severe chronic pain and fertility issues. The team developed several genetic sensors for hormone dysregulation, which is a common molecular phenotype of the disease; these sensors may some day be used to provide better diagnostics and treatments for this common gynepathology.
  • 2017: Programming alternative splicing for therapeutic and engineering applications. Most of the coding sequences in the human genome are alternatively spliced; that is, there are exons that are missing in some transcripts and present in others. A number of genetic diseases can be traced to changes in alternative splicing, and controlling the splicing of a synthetic RNA could be a powerful tool for novel synthetic gene networks.

SEED Academy Instructor, Spring 2017
In the spring of 2017, I taught a synthetic biology course at SEED Academy, a program organized by the MIT Office of Engineering Outreach Programs. The class met for 8 Saturdays and had 27 students on the roster. I designed and taught a course that allowed the students the freedom to choose an issue that they were interested in, design a biological system to address the problem, then build and test a part of that system. The course finished up with presentations to the students' families. This captured in an authentic way the design - build - test cycle of synthetic biology, with particular attention paid to problem-solving, social and ethical concerns and scientific communication.

Teaching Experience: Workshops and Outreach

Software Carpentry and Data Carpentry Workshops
I have co-taught three workshops with Software Carpentry and Data Carpentry. Topics covered included scientific computing and data analysis in R and Python; data management with an SQL database; and scripting with the UNIX shell bash. In each instance, I customized the material to the various audiences (microbiologists, immunologists and environmental biologists), and coordinated teaching plans with my co-instructors.

Quantitative Flow Cytometry, Apr-June 2017
I presented a pair of workshops for the Synthetic Biology Center on quantitative flow cytometry.  The first workshop covered experimental design and instrument setup considerations motivated by the physical and chemical processes involved in measuring fluorescence.  The second workshop introduced the software package I've authored, Cytoflow, to support quantitative analysis of flow cytometry data.

Mammalian Synthetic Biology and iGEM, October 2016
I presented a workshop at the 2016 iGEM International Jamboree on mammalian synthetic biology projects and iGEM.  We discussed the state of the art in mammalian gene circuits, then spent over an hour discussing barriers to entry: a lack of parts, resources, and knowledge, as well as opportunities for decreasing these barriers.

Sanford Middle School, Minneapolis Public Schools, January 2016
I was invited by a friend who teaches at a middle school in Minneapolis to share some of my science with her coworkers' classes. We developed a set of learning goals ("Learn how a scientist approaches real world problems", etc), and then I led five separate classes in discussions about malaria, mosquitos, gene drives and the practice of responsible science.

Building with Biology, July 2015
The Boston Museum of Science led a multi-site project with the aim of engaging the public with the science of synthetic biology.  As a participating scientist, I received training in public engagement and then led several activities exploring advances in synthetic biology and their broader societal context.

Mammalian Synthetic Biology and iGEM, September 2015
Alongside Deepak Mishra, I presented a workshop at the 2015 iGEM International Jamboree on mammalian synthetic biology projects and iGEM.  We discussed the state of the art in assembling synthetic mammalian gene circuits, the potential that mammalian synthetic biology has to address problems inaccessible in projects in more traditional chassis (yeast and E. coli), and the barriers to entry to doing mammalian synthetic biology, in general and with regards to iGEM in particular.  We then led an extended discussion about these topics and collated some proposed improvements for presentation to iGEM Headquarters.

Invited speaker on DNA assembly technologies, iGEM Headquarters, May 2015
I spoke about the current state-of-the-art for assembling mammalian gene circuits to members of iGEM Headquarters, who were looking to update the iGEM "biobrick" assembly standards to match the current state-of-the-art.

Microscopy 101, Synthetic Biology Center Technical Seminar Series, April 2015
Led a workshop on light microscopy, covering transmitted light microscopy, fluorescence light microscopy, and advanced techniques such as confocal and superresolution microscopy.  Estimated attendance was 60 people.

How to Make a Scientist, Whitehead Seminar Series for Highschool Teachers, November 2014
I was invited to share my experience mentoring the MIT iGEM team with an auditorium full of highschool teachers participating in the Whitehead Institute's seminar series for highschool teachers.  I spoke about iGEM in general, my motivations for how I structure the iGEM experience, and the lessons that I think are transferable from iGEM to a highschool science experience.

Service: Committees and Working Groups

Synthetic Biology Standards Consortium, Flow Cytometry Working Group
I helped develop a pair of white papers describing (a) best practices for quantitative flow cytometry and (b) a sample workflow that conforms to these best practices. The CytoFlow project (described above) includes a reference implementation of the data processing components required for the the workflow described in (b).

iGEM Technology Committee
I participated in the iGEM Foundation's Technology Committee, tasked with keeping iGEM abreast of best technological practice in synthetic biology, including methods for assembling DNA and software for assisting in synthetic gene circuit design.


Publications and Presentations

Jacob Beal, Nicholas Delateur, Brian Teague, et al. Toward Quantitative Comparison of Fluorescent Protein Expression Levels via Fluorescent Beads. International Workshop on Biological Design Automation, 2017.

Cytoflow: Software for Quantitative Flow Cytometry. The Fourth Mammalian Synthetic Biology Workshop, Boston University, February 2017.

Teague, B., Guye, P., Weiss, R.  Synthetic MorphogenesisCold Spring Harbor Perspectives in Biology 2016, DOI:10.1101/cshperspect.a023929.

Teague, B and Weiss, R. Synthetic communities, the sum of parts. SCIENCE 349:6251. 2015.

Teague, B et al. Intercellular Signalling in Yeast: Quorum Sensing and Spatial Patterning. Keystone Symposium on Precision Genome Engineering and Synthetic Biology, January 2015.

Zhou, S. et al. Optical Mapping and Nanocoding Systems Potentiate Genome Assembly and Discover Structural Variants. International Plant and Animal Genome Conference XXII 2014.

Teague, B. et al. High-resolution human genome structure by single molecule analysis. Proc Natl Acad Sci USA 107:10848. 2010.

Antonacci, F. et al. A large and complex structural polymorphism at 16p12.1 underlies microdeletion disease risk. Nature Genetics 42:745. 2010.

Church, DM. et al. Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biology 7:e1000112. 2009.

Kidd, JM. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453:56. 2008.

Teague, B. et al. Structural Polymorphism Discovery Using Optical Mapping - Intelligent Systems for Molecular Biology, July 2008

Scherer, SE. et al. The finished DNA sequence of human chromosome 12. Nature 440:346. 2006.

Ross, MT. et al. The DNA sequence of the human X chromosome. Nature 434:325. 2005.

Goldstein, S., Cook, A., Teague, B., et al.: Validation of mammalian genome sequence using optical maps. The Biology of Genomes. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. 2005.

Research and Teaching Interests

I'm fascinated by emergent behavior in biological systems -- how do cells work together to accomplish what a single cell couldn't do alone?  The foundations of these behaviors are communication and specialization. I'm interested in building synthetic systems where cells communicate and specialize, with the dual goals of understanding natural biological systems and engineering synthetic systems to accomplish useful goals. Applications include understanding and engineering synthetic microbial communities for biomanufacturing, as well as biomedical topics such as biofilms and synthetic tissues.

I'm also interested in the way software can enable the process of biological discovery. This has taken several forms, from the application of machine learning and statistical analysis methods to large data sets, to tools to enable quantitative and reproducible analysis of experimental data, to laboratory information and workflow management systems to improve laboratory throughput and enable better engineering of biological systems.

Finally, I see teaching and research as integral to one another. Research provides an authentic setting in which to learn knowledge and practice skills that transfer to careers both within and outside of the research enterprise. New researchers bring new insights, talents and passions to the research process which keeps it vibrant and adaptive. I am interested in developing methods to support new learners' entre into research, enabling them to rapidly become productive researchers while building on and contributing to the work being done in the lab.

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