Discover your pathway through engineering biology.
Participating
Mentors
Mentors' specific research areas span genetic circuits, cellular engineering, synthetic epigenetics, experimental evolution, immunotherapy, systems biology, stem cell engineering, regenerative medicine, optogenetics and neural control, antibiotic resistance, drug/gene delivery, and microbial communities.
The research focus areas for the STEM Pathways SURE Program include:
Gene Expression and Gene Circuits
Gene expression refers to the process by which information in a gene is used to synthesize a functional gene product, while gene circuits involve the intricate network of interactions between genes that regulate their expression in a coordinated manner.
Juan Fuxman Bass
Associate Professor
Biology
The Fuxman Bass Laboratory has developed and implemented experimental and computational tools to study gene regulation in a high-throughput manner, with a long-term goal of understanding the mechanisms by which immune genes are regulated during inflammatory processes.
Wilson Wong
Associate Professor
Biomedical Engineering
The overarching goal of Wilson Wong’s Laboratory is to develop ways to control mammalian cell functions through engineering, biological network design, molecular biology, and chemical biology in order to understand how complex mammalian systems function. The lab achieves this goal through receptor engineering, transcription and post-transcription regulation, and DNA-level control. The lab has developed orthogonal systems at each level, allowing them to regulate multiple genes and signaling independently.
Ahmad (Mo) Khalil
Professor
Biomedical Engineering
The Khalil Laboratory has recently developed new toolkits to engineer synthetic gene circuits in mammalian cells and demonstrated how they can be used to precisely control the activity and function of primary human T cells. Using these tools, the lab seeks to create artificial gene regulatory circuits that instruct mammalian cells to process input signals and convert them into desired transcriptional output responses in order to control cellular behavior for a wide variety of applications.
Zeba Wunderlich
Associate Professor
Biology and Biomedical Engineering
The Wunderlich Laboratory aims to determine how the structure of gene regulatory networks and their regulatory DNA is shaped by biological needs and evolutionary pressures. They use quantitative data and mathematical models to uncover how the architecture of gene regulatory networks shape early embryonic patterning and the innate immune response in Drosophila.
Trevor Siggers
Associate Professor
Biology
The Siggers Laboratory is developing and applying high-throughput biochemical approaches to characterize TF–COF networks in cells to examine how they coordinate gene expression and cellular responses. Part of this work involves designing synthetic COF proteins to probe mechanisms of TF–COF interactions, to examine mechanisms of regulatory specificity, and to design new tools for synthetic biology applications.
Transducing Cellular Information
The Dunlop Laboratory focuses on cell-to-cell variation in bacterial gene expression. Cell-to-cell heterogeneity can have broad-ranging effects: It can elevate antibiotic resistance in one microbe while other cells remain susceptible. In metabolic engineering contexts, it can decrease production within a subset of cells, impacting population-level yields. The Dunlop Lab uses a range of tools and approaches to study cellular heterogeneity including optogenetics, deep learning, feedback control, and synthetic biology.
Mary Dunlop
Associate Professor
BME, MCBB
The Teplensky Laboratory develops and uses nanotechnology to control immunological cell connectivity, processing, and communication. They combine techniques across chemistry, nanotechnology, engineering, immunology, and biomaterials to impact how we program the immune system for therapeutic benefit. They explore the structure–property relationships that kinetically and spatially position immune-relevant cargo and evaluate the impact of chemical parameters on interactions at the nano-immune interface.
Michelle Teplensky
Assistant Professor
BME and MSE
The Garcia-Marcos Laboratory is focused on intercellular communication mediated by G proteincoupled receptors (GPCRs) and heterotrimeric G proteins, which are widely utilized by eukaryotes to sense and response to very diverse stimuli, from chemicals to light and mechanical forces. They use a broad range of approaches to study GPCR–G protein signaling regulation, including engineering synthetic proteins that regulate G protein signaling in a spatiotemporally controllable manner and developing live-cell probes to measure G protein activity in cells with high fidelity.
Mikel Garcia-Marcos
Professor
Biochemistry, Cell Biology, Biology
The Younger Laboratory is focused on olfaction in mosquitoes. The Aedes aegypti olfactory system has significantly more olfactory receptors than expected (when compared to other organisms), and there are multiple chemosensory receptors co-expressed within individual olfactory sensory neurons. Their goal is to understand how this non-canonical olfactory system encodes odor, particularly human odor (as it is this scent that lures mosquitoes towards their human prey). To understand how odor is encoded in the mosquito brain, they study the receptors that detect odorants, the sensory neurons that house these receptors, and the neural circuits that encode odor.
Meg Younger
Assistant Professor
Biology and Biomedical Engineering
The Larkin Laboratory is interested in learning how microbes engage in multicellular behaviors and how those behaviors give them emergent benefits. For example, they investigate how cells within bacterial biofilms differentiate into extracellular matrix producers and how biofilm communities take advantage of matrix material properties such as osmotic absorption of beneficial resources. To study microbial multicellular systems, the lab uses time-lapse microscopy, microfluidics, and novel transistor arrays that enable non-optical imaging of microbial samples.
Joseph Larkin
Assistant Professor
Biology and Physics
Converting external signals into intracellular responses, enabling cells to interpret and appropriately respond to environmental cues.
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Biological constructs created in the laboratory through the manipulation of cells, biomaterials, and bioengineering techniques to mimic or replace natural tissues and organs for medical applications.
Engineered Tissues and Organs
Christopher Chen
Professor
Biomedical Engineering
The Chen Laboratory builds organ-on-chip models to study 1) how cells use forces to organize into tissues; 2) how damage, repair, and regeneration occur in disease settings. They have developed culture systems that mimic heart tissue, perfused vascular beds, and wound repair, and are interested in developing tools to better manipulate and measure how cells are communicating and behaving in these systems.
Emma Lejeune
Assistant Professor
Mechanical Engineering
The research goal of the Lejeune Laboratory is to leverage the state-of-the-art in computational mechanics and image analysis to investigate multiscale emergent behavior in biological and biologically inspired systems. They develop opensource image analysis software to analyze microscopy data on the cell and tissue scale, integrate data-driven and physics based computational models, and predict the behavior of highly heterogeneous soft tissue using machine learning approaches.
Elise Morgan
Professor
ME, MSE, BME
The Morgan Laboratory uses bone healing as a model system to understand the mechanical cues experienced by cells in the injury environment and to learn how these cells sense and process these mechanical inputs to rebuild the individual tissues and the entire organ. They use a variety of in vivo and in vitro systems to study, model, and manipulate mechanical inputs to cells. Beyond the general goal of accelerating bone repair, the lab seeks to enable therapies that address slower rates of repair with aging.
Associate Professor
Biomedical Engineering
Alexander Green
The Green Laboratory applies engineering principles and computational design to devise RNA-based devices for diagnostic assays and synthetic biology applications . One of their main interests is to use machine learning approaches to generate new RNA sensors that activate translation in response to pathogen RNAs in low-cost, paper-based diagnostics. Existing design tools for these sensors rely solely on RNA thermodynamic models, which fail to consider the impact of ribosomal interactions, codon usage, and folding kinetics on RNA sensor function.
Professor
Biomedical and Materials Science Engineering
Joyce Wong
The Joyce Wong Laboratory develops biomaterial-based systems for the early detection and treatment of disease. An understanding of how physicochemical properties of this interface impacts cell and tissue behavior enables technology development for theranostic and tissue engineering applications. Projects include molecularly targeted nanoparticle and microparticle contrast agent synthesis and characterization and interactions with physiologically relevant tissue systems. Students will gain skills in materials design and synthesis, and characterization of the cell–biomaterial interface.
Assistant Professor
Biomedical Engineering
Liangliang Hao
The Hao Laboratory develops molecular and cellular tools to precisely track and control disease biology in intact organisms. The specific research interests include non-invasive disease detection and treatment monitoring at the pointof- care, tissue-specific transcriptome engineering, and multimodal systemic imaging. Research opportunities in this laboratory include the engineering of a family of microenvironment-triggered, tissue-specific non-viral nucleic acid delivery vehicles to realize the potential of precision RNA therapeutics.
Assistant Professor
Biomedical Engineering and Electrical Engineering
Rabia Yazicigil Kirby
The Yazicigil Laboratory develops Cyber-Secure Biological Systems (CSBS) that augment genetically engineered biological systems with secure custom-designed wireless electronics for biological sensing applications. The engineered living organisms achieve high specificity and sensitivity in harsh environments, while CMOS electronics provide reliable operation, real-time feedback, and communication abilities. These hybrid bio-electronic systems represent a critical technology to help address societal challenges in healthcare (e.g., disease monitoring, and disease biomarker discovery), environmental monitoring (i.e., water and soil quality), and sustainable manufacturing.
Assistant Professor
Biomedical Engineering
Miguel Jimenez
el Microbial Integration Group combines genetically engineered microbial cells into devices to make biochemical sensors and actuators that can be incorporated into consumer electronics. The group studies how to maintain microbial cells alive and functional with limited resources and despite environmental variation. They are developing self-contained microbioreactors by combining microfluidics and degradable nutrient matrices. Additionally, they are developing high throughput approaches to characterize, model and improve genetic circuit design in cells exposed to non-model environments (i.e., soil).
Biological Sensors
Devices that detect and measure specific biological signals, such as biomolecules or physiological changes, providing valuable information for applications in medical diagnostics and environmental monitoring
Design, Build, Test Automation
Douglas Densmore
Transducing Cellular Information
Professor
ECE, BME, MSE
The CIDAR Laboratory focuses on the development of tools for the specification, design, assembly, and test of synthetic biological systems. Their approach draws upon their experience with embedded system-level design and electronic design automation. Extracting concepts and methodologies from these fields, they aim to raise the level of abstraction in synthetic biology by employing standardized biological part-based designs that leverage domain-specific languages, constraint-based genetic circuit composition, visual editing environments, microfluidics, and automated DNA assembly. They will offer undergraduate opportunities in microfluidic design and fabrication, as well as designing algorithms and programming languages for synthetic biology.
Ahmad (Mo) Khalil
Transducing Cellular Information
Professor
Biomedical Engineering
The Khalil Laboratory has developed eVOLVER, which is an open-source, highly customizable continuous culture and evolution platform that enables the automated growth of hundreds of microbial populations in individually customized culture conditions over long experimental timescales. eVOLVER has also been used to generate novel genome editing agents [43, 44] and answer fundamental questions in microbial ecology, such as how environmental perturbations influence microbial communities. They are now using eVOLVER for long-term experimental evolution experiments in a broad range of other subject areas.
The use of advanced technologies and robotic systems to streamline and optimize various processes within the field of biotechnology, such as genetic engineering, drug discovery, and laboratory workflows.