Professor Ron Weiss

Lab Focus: Biological Engineering

Lab Website:

Project Name: Programmable Human Induced Pluripotent Stem Cells Using RNAi-based Logic Circuitry

Project Description: Human induced pluripotent stem cells (hiPSCs), reprogrammed from adult cells, allow the creation of unique new cells and tissues from patient-specific stem cells. These tissues are being used for research in drug development, disease models, and regenerative medicine. In the Weiss Lab, we work on engineering biological computation in hiPSCs that can control the way they form those new cells and tissues. This project involves both designing and implementing biological circuits encoded in the genome of human stem cells. The type of circuits used is based on RNA interference (RNAi), which can perform computer-like operations in human cells. This project will involve learning about CRISPR, genome engineering, biological circuit design, DNA cloning, and quantitative analysis of biological data.

Weiss Lab Mentors:

Sebastian Palacios – PhD Candidate (Research Areas: Electrical Engineering, Computer Science)

Jesse Tordoff – PhD Candidate (Research Areas: Stem Cell and Developmental Systems Biology, Synthetic Biology and Biological Design)

Professor Roger Kamm

Lab Focus: Biological Engineering

Lab Website:

Project Name: Understanding Immune Cell Migration in In Vitro Cancer Models

Project Description: Immunotherapy is the most recent breakthrough in cancer treatment. However, it is not successful in all patients. Biomarkers predicting response to therapy have not been established yet, so we are using in vitro systems to model interactions between cancer cells and immune cells. Two-dimensional and unique 3-dimensional microfluidic cell culture methods will be used to quantify migration of T cells toward several cancer cell lines. The student will be introduced to several techniques including microfluidic device fabrication, cell culture, immunostaining, and fluorescent microscopy.

Kamm Lab Mentors:

Cynthia Hajal – PhD Candidate (Research Areas:Vascular Models)

Sarah Shelton – PhD (Research Areas: Cancer Models)

Professor Mathias Kolle

Lab Focus: Mechanical Engineering

Lab Website:

Project Name: Designing and Creating a Video Game for Interacting with Microscopic Biological Systems in Real-Time

Project Description: This project is an open-ended exploration into designing and creating a video game for interacting with microscopic biological systems in real-time. It consists of four main tasks. The first task involves culturing living cells in the lab, most likely a simple single-celled model organism such as E. coli. The second task is taking measurements from the biological system and transmitting them to a computer using a variety of microscopy and image processing techniques. The third task is using a video game engine (e.g. Unity) or modding an existing game (e.g. Minecraft), to create a virtual environment where the biological system can be visualized and interacted with by the user. The fourth and final task is taking that user input and affecting the physical biological system in some way, such as triggering motion, gene expression, cell death, etc; the specific details of the interaction would be open for discussion. Some experience in coding could be beneficial, but is not required.

Kolle Laboratory Mentors:

Benjamin Miller – PhD Candidate

Anthony McDougal – PhD Candidate

Professor Asegun Henry

Lab Focus: Mechanical Engineering

Lab Website:

Project Name: Sonification of the Periodic Table

Project Description: Many of us know that we are surrounded by sound waves that travel in the air around us, but maybe only a few of us know that we are also surrounded by sound waves that travel inside the solid materials that we have around ourselves. In fact, all the jiggling of atoms in a solid material come together to make different tones and pitches of sounds in that solid structure. This is the reason that physicists, from old days, have used the term “phonon” (phon in Greek means sound) to describe all these atomic jigglings (vibrations) in the solid structure. Aside from the sound nature of these atomic vibrations, they play a huge role in determining many of the properties in solid materials. For instance, these sound waves can determine how strong a solid material is or how fast it can respond to a temperature change in its surroundings. Therefore, obtaining a deeper knowledge about these sound waves will help us better understand the properties that each solid material exhibits.

Henry Lab Mentors:

Kiarash Gordiz – PhD

Andrew Rohskopf – PhD Candidate

Professor Ming Guo 

Lab Focus: Mechanical Engineering

Lab Website:

Project Name: Tracking 4D spatial and temporal cell migration during tumorigenesis

Project Description: Within a multicellular tissue the precise control of physical characteristics of individual cells in space and time is critical for maintenance of mechanical integrity and biological function of tissues. Deviation from mechanical hemostasis is associated with diseases including aberrant wound repair, developmental abnormalities, and cancer. Recent advances in optical microscopy has enabled the real time imaging of every single cell in an entire tissue. We can thus watch how individual cells are migrating, and interacting with their peers. However, a major challenge nowadays is to track these cells with a computer program that allow us to, not only see them, but also obtain their migration trajectories and patterns in the 3D space. 

Thus, the overall objective of this project is to understand the 4D (spatial and temporal) organization and evolution of cells in a developing human breast cancer model. We have already obtained enormous amount of data via advanced optical imaging method, seeing through a micro-tumor cluster of hundreds of cells, and their spatiotemporal evolution over several days. The nuclei of individual cells are fluorescently labeled. We would like to develop a computer program to automatically identify single cells in 3D, and trace themover time.

Guo Lab Mentors:

Yu Long Han – PhD

Wenhui Tang – PhD Candidate

Professor Alex Shalek

Lab Focus: Biological Engineering

Lab Website:

Project Description: Single-cell RNA sequencing is a technique that scientists use to identify cell types in the body and understand how they work. For example, single-cell RNA sequencing can help define the molecular differences between a muscle cell and a skin cell. In the Shalek lab’s Summer 2020 project, we will use chemistry to invent more advanced methods for single-cell RNA sequencing.

Shalek Lab Mentors:

Samuel Jonathan Allon – PhD Candidate

Sarah Lynne Quinn – PhD Candidate

Andrew Warren Navia – PhD Candidate

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